(Former Name, Former Address and Former Fiscal Year, if Changed Since Last Report)

~~As of October 22, 2020, the registrant had 61,044,688 shares of common stock issued and outstanding.~~

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. ~~YES~~Yes ☑ NONo ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). ~~YES~~Yes ☑ NONo ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). ~~YES~~Yes ☐ NONo ☑

As of July 28, 2021, the registrant had 67,836,060 shares of common stock issued and outstanding.

This Quarterly Report on Form 10-Q (the Quarterly Report) contains forward-looking statements that involve risks and uncertainties. We make such forward-looking statements pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995 and other federal securities laws. All statements other than statements of historical facts contained in this Quarterly Report are forward-looking statements. In some cases, you can identify forward-looking statements by words such as “anticipate,” “believe,” “contemplate,” “continue,” “could,” “estimate,” “expect,” “forecast,” “intend,” “may,” “plan,” “potential,” “predict,” “project,” “seek,” “should,” “target,” “will,” “would,” or the negative of these words, or other comparable terminology. These forward-looking statements include, but are not limited to, statements about:

Any forward-looking statements in this Quarterly Report reflect our current views with respect to future events or to our future financial performance and involve known and unknown risks, uncertainties, and other factors that may cause our actual results, performance, or achievements to be materially different from any future results, performance, or achievements expressed or implied by these forward-looking statements. Factors that may cause actual results to differ materially from current expectations include, among other things, those discussed under Part II, Item 1A. Risk Factors and ~~discussed~~ elsewhere in this Quarterly Report. Given these uncertainties, you should not place undue reliance on these forward-looking statements. Except as required by law, we assume no obligation to update or revise these forward-looking statements for any reason, even if new information becomes available in the future.

This Quarterly Report also contains estimates, projections, and other information concerning our industry, our business, and the markets for certain diseases, including data regarding the estimated size of those markets, and the incidence and prevalence of certain medical conditions. Information that is based on estimates, forecasts, projections, market research, or similar methodologies is inherently subject to uncertainties and actual events or circumstances may differ materially from events and circumstances reflected in this information. Unless otherwise expressly stated, we obtained this industry, business, market, and other data from reports, research surveys, studies, and similar data prepared by market research firms and other third parties, industry, medical and general publications, government data, and similar sources.

	September 30,			December 31,			June 30,			December 31,
	2020			2019			2021			2020
Assets
Current assets:
Cash and cash equivalents	$	197,486		$	433,584		$	290,875		$	713,526
Short-term investments		568,034			321,646
Marketable debt securities								554,881			488,007
Accounts receivable, net		27,762			32,844			24,720			23,093
Inventory		14,457			11,546			15,083			13,048
Prepaid expenses and other current assets		64,264			51,397			63,933			57,630
Total current assets		872,003			851,017			949,492			1,295,304
Property and equipment, net		48,773			44,348
Investments in equity securities		129,320			27,752
Long-term investments		—			5,174
Property, plant, and equipment, net								104,568			73,515
Equity investments								103,710			155,375
Marketable debt securities								128,031			10,506
Right-of-use assets		37,597			30,328			38,619			40,524
Intangible assets, net		131,194			129,000			130,950			131,113
Goodwill		44,406			44,406			44,406			44,406
Other assets		5,092			3,471			12,668			8,812
Total assets	$	1,268,385		$	1,135,496		$	1,512,444		$	1,759,555

Liabilities and Stockholders’ Equity
Current liabilities:
Accounts payable	$	10,850		$	12,871		$	21,790		$	12,923
Accrued liabilities		79,653			83,194			91,060			108,491
Contract liabilities, net		102,898			—
Short-term lease liabilities		7,785			7,235
Contract liabilities								3,912			59,219
Lease liabilities								10,305			8,976
Total current liabilities		201,186			103,300			127,067			189,609
Long-term lease liabilities		36,668			29,757
Contract liabilities								—			7,349
Lease liabilities								35,861			39,251
Deferred tax liabilities		33,306			33,306			33,306			33,306
Liability related to the sale of future royalties		331,034			315,369			344,039			335,665
Total liabilities		602,194			481,732			540,273			605,180
Stockholders’ equity:
Preferred stock — 25,000,000 shares authorized; nil outstanding as of September 30, 2020 and December 31, 2019		—			—
Common stock — 250,000,000 shares authorized; 60,815,690 and 57,838,220 shares issued and outstanding as of September 30, 2020 and December 31, 2019, respectively		61			58
Preferred stock — 25,000,000 shares authorized; nil outstanding as of June 30, 2021 and December 31, 2020								—			—
Common stock — 250,000,000 shares authorized; 67,764,950 and 66,818,520 shares issued and outstanding as of June 30, 2021 and December 31, 2020, respectively								68			67
Additional paid-in capital		2,260,682			2,086,863			2,850,016			2,773,195
Accumulated other comprehensive income (loss)		1,013			(147	)
Accumulated other comprehensive income								232			689
Accumulated deficit		(1,595,565	)		(1,433,010	)		(1,878,145	)		(1,619,576	)
Total stockholders’ equity		666,191			653,764			972,171			1,154,375
Total liabilities and stockholders’ equity	$	1,268,385		$	1,135,496		$	1,512,444		$	1,759,555

	Three Months Ended September 30,						Nine Months Ended September 30,						Three Months Ended June 30,						Six Months Ended June 30,
	2020			2019			2020			2019			2021			2020			2021			2020
Revenues:
Collaboration and license	$	66,924		$	21,585		$	144,300		$	55,070		$	63,940		$	50,161		$	142,950		$	77,376
Product sales		11,215			4,215			25,760			13,051			18,346			8,066			34,859			14,545
Non-cash collaboration royalty revenue		3,331			—			9,428			—			4,689			3,482			8,561			6,097
Total revenues		81,470			25,800			179,488			68,121			86,975			61,709			186,370			98,018
Operating expenses:
Cost of sales		2,348			2,683			648			3,901			3,136			1,803			8,324			(1,700	)
Research and development		87,314			100,144			280,984			274,294			113,205			80,709			260,723			193,670
Selling, general and administrative		42,123			41,006			131,891			119,647			53,410			42,252			106,668			89,768
Total operating expenses		131,785			143,833			413,523			397,842			169,751			124,764			375,715			281,738
Loss from operations		(50,315	)		(118,033	)		(234,035	)		(329,721	)		(82,776	)		(63,055	)		(189,345	)		(183,720	)
Interest income		1,338			3,319			6,054			10,468			441			1,797			1,080			4,716
Change in fair value of investments in equity securities		(11,520	)		2,166			91,348			11,994
Change in fair value of equity investments														(31,046	)		95,200			(51,665	)		102,868
Non-cash interest expense on liability related to the sale of future royalties		(8,582	)		—			(25,093	)		—			(8,517	)		(8,429	)		(16,935	)		(16,511	)
Other income (expense)		547			(153	)		308			(941	)		(67	)		217			(862	)		(239	)
Loss before income taxes		(68,532	)		(112,701	)		(161,418	)		(308,200	)
Income (loss) before income taxes														(121,965	)		25,730			(257,727	)		(92,886	)
Provision for income taxes		(313	)		(293	)		(1,137	)		(722	)		(463	)		(415	)		(842	)		(824	)
Net loss	$	(68,845	)	$	(112,994	)	$	(162,555	)	$	(308,922	)
Net loss per share, basic and diluted	$	(1.13	)	$	(1.96	)	$	(2.73	)	$	(5.50	)
Weighted-average shares used in computing net loss per share, basic and diluted		60,687,177			57,707,694			59,564,163			56,161,996
Net income (loss)													$	(122,428	)	$	25,315		$	(258,569	)	$	(93,710	)
Net income (loss) per share:
Basic													$	(1.81	)	$	0.42		$	(3.84	)	$	(1.59	)
Diluted													$	(1.81	)	$	0.41		$	(3.84	)	$	(1.59	)
Weighted-average shares used in computing net income (loss) per share:
Basic														67,607,752			59,995,617			67,356,443			58,996,278
Diluted														67,607,752			61,146,231			67,356,443			58,996,278

Three Months Ended September 30,

Nine Months Ended September 30,

2020

2019

2020

2019

Net loss
$
(68,845
)

$
(112,994
)

$
(162,555
)

$
(308,922
)
Other comprehensive income:

Foreign currency translation adjustments

374

(234
)

414

(79
)
Unrealized gain (loss) on available-for-sale securities

(645
)

(92
)

746

641

Other comprehensive income (loss)

(271
)

(326
)

1,160

562

Total comprehensive loss
$
(69,116
)

$
(113,320
)

$
(161,395
)

$
(308,360
)

	Three Months Ended June 30,					Six Months Ended June 30,
	2021			2020		2021			2020
Net income (loss)	$	(122,428	)	$	25,315	$	(258,569	)	$	(93,710	)
Other comprehensive income (loss):
Foreign currency translation adjustments		103			89		(182	)		40
Unrealized gain (loss) on available-for-sale securities		73			2,740		(275	)		1,391
Other comprehensive income (loss):		176			2,829		(457	)		1,431
Total comprehensive income (loss)	$	(122,252	)	$	28,144	$	(259,026	)	$	(92,279	)

Common Stock

Additional
Paid-In

Accumulated
Other
Comprehensive

Accumulated

Total
Stockholders'

Shares

Amount

Capital

Income (Loss)

Deficit

Equity

Balance as of June 30, 2020

60,413,756

$
60

$
2,220,963

$
1,284

$
(1,526,720
)

$
695,587

Employee stock-based compensation

—

—

20,527

—

—

20,527

Issuance of common stock under equity
plan awards, net of tax

401,934

1

19,192

—

—

19,193

Other comprehensive loss

—

—

—

(271
)

—

(271
)

Net loss

—

—

—

—

(68,845
)

(68,845
)

Balance as of September 30, 2020

60,815,690

$
61

$
2,260,682

$
1,013

$
(1,595,565
)

$
666,191

	Common Stock				Additional Paid-In		Accumulated Other Comprehensive		Accumulated			Total Stockholders'
	Shares		Amount		Capital		Income (Loss)		Deficit			Equity
Balance as of March 31, 2021		67,439,477	$	67	$	2,810,176	$	56	$	(1,755,717	)	$	1,054,582
Stock-based compensation		—		—		27,099		—		—			27,099
Issuance of common stock under equity plan awards, net of tax		325,473		1		12,741		—		—			12,742
Other comprehensive income		—		—		—		176		—			176
Net loss		—		—		—		—		(122,428	)		(122,428	)
Balance as of June 30, 2021		67,764,950	$	68	$	2,850,016	$	232	$	(1,878,145	)	$	972,171

Common Stock

Additional
Paid-In

Accumulated
Other
Comprehensive

Accumulated

Total
Stockholders'

Shares

Amount

Capital

Income (Loss)

Deficit

Equity

Balance as of December 31, 2019

57,838,220

$
58

$
2,086,863

$
(147
)

$
(1,433,010
)

$
653,764

       Issuance of common stock in connection
          with license agreement, net of issuance
          costs

1,243,913

1

55,267

—

—

55,268

Issuance of common stock in connection with
    at-the-market offering, net of issuance costs

283,333

—

20,391

—

—

20,391

Employee stock-based compensation

—

—

63,112

—

—

63,112

Issuance of common stock upon exercise of
    warrants and under equity plan awards, net
    of tax

1,450,224

2

35,049

—

—

35,051

Other comprehensive income

—

—

—

1,160

—

1,160

Net loss

—

—

—

—

(162,555
)

(162,555
)

Balance as of September 30, 2020

60,815,690

$
61

$
2,260,682

$
1,013

$
(1,595,565
)

$
666,191

	Common Stock				Additional Paid-In		Accumulated Other Comprehensive			Accumulated			Total Stockholders'
	Shares		Amount		Capital		Income (Loss)			Deficit			Equity
Balance as of December 31, 2020		66,818,520	$	67	$	2,773,195	$	689		$	(1,619,576	)	$	1,154,375
Stock-based compensation		—		—		51,319		—			—			51,319
Issuance of common stock under equity plan awards, net of tax		946,430		1		25,502		—			—			25,503
Other comprehensive loss		—		—		—		(457	)		—			(457	)
Net loss		—		—		—		—			(258,569	)		(258,569	)
Balance as of June 30, 2021		67,764,950	$	68	$	2,850,016	$	232		$	(1,878,145	)	$	972,171

Common Stock

Additional
Paid-In

Accumulated
Other
Comprehensive

Accumulated

Total
Stockholders'

Shares

Amount

Capital

Income (Loss)

Deficit

Equity

Balance as of June 30, 2019

57,665,375

$
58

$
2,045,685

$
255

$
(1,226,211
)

$
819,787

Employee stock-based compensation

—

—

19,894

—

—

19,894

Issuance of common stock under equity plan
awards, net of tax

84,515

—

904

—

—

904

Other comprehensive loss

—

—

—

(326
)

—

(326
)

Net loss

—

—

—

—

(112,994
)

(112,994
)

Balance as of September 30, 2019

57,749,890

$
58

$
2,066,483

$
(71
)

$
(1,339,205
)

$
727,265

	Common Stock				Additional Paid-In		Accumulated Other Comprehensive			Accumulated			Total Stockholders'
	Shares		Amount		Capital		Income (Loss)			Deficit			Equity
Balance as of March 31, 2020		59,488,873	$	59	$	2,162,667	$	(1,545	)	$	(1,552,035	)	$	609,146
Issuance of common stock in connection with at-the-market offering, net of issuance costs		283,333		—		20,391		—			—			20,391
Stock-based compensation		—		—		22,428		—			—			22,428
Issuance of common stock under equity plan awards, net of tax		641,550		1		15,477		—			—			15,478
Other comprehensive income		—		—		—		2,829			—			2,829
Net income		—		—		—		—			25,315			25,315
Balance as of June 30, 2020		60,413,756	$	60	$	2,220,963	$	1,284		$	(1,526,720	)	$	695,587

Common Stock

Additional
Paid-In

Accumulated
Other
Comprehensive

Accumulated

Total
Stockholders'

Shares

Amount

Capital

Income (Loss)

Deficit

Equity

Balance as of December 31, 2018

50,860,588

$
51

$
1,639,773

$
(633
)

$
(1,030,283
)

$
608,908

Issuance of common stock in connection with
    underwritten public offering, net of
    issuance costs

5,833,333

6

330,409

—

—

330,415

Issuance of common stock in connection with
    at-the-market offering, net of issuance costs

468,685

—

24,828

—

—

24,828

Employee stock-based compensation

—

—

62,854

—

—

62,854

Issuance of common stock under equity plan
    awards, net of tax

587,284

1

8,619

—

—

8,620

Other comprehensive income

—

—

—

562

—

562

Net loss

—

—

—

—

(308,922
)

(308,922
)

Balance as of September 30, 2019

57,749,890

$
58

$
2,066,483

$
(71
)

$
(1,339,205
)

$
727,265

	Common Stock				Additional Paid-In		Accumulated Other Comprehensive			Accumulated			Total Stockholders'
	Shares		Amount		Capital		Income (Loss)			Deficit			Equity
Balance as of December 31, 2019		57,838,220	$	58	$	2,086,863	$	(147	)	$	(1,433,010	)	$	653,764
Issuance of common stock in connection with license agreement, net of issuance costs		1,243,913		1		55,267		—			—			55,268
Issuance of common stock in connection with at-the-market offering, net of issuance costs		283,333		—		20,391		—			—			20,391
Stock-based compensation		—		—		42,585		—			—			42,585
Issuance of common stock upon exercise of warrants and under equity plan awards, net of tax		1,048,290		1		15,857		—			—			15,858
Other comprehensive income		—		—		—		1,431			—			1,431
Net loss		—		—		—		—			(93,710	)		(93,710	)
Balance as of June 30, 2020		60,413,756	$	60	$	2,220,963	$	1,284		$	(1,526,720	)	$	695,587

	Nine Months Ended September 30,						Six Months Ended June 30,
	2020			2019			2021			2020
Operating activities:
Net loss	$	(162,555	)	$	(308,922	)	$	(258,569	)	$	(93,710	)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation		62,897			62,335			51,345			42,558
Amortization of premium (discount) on investment securities, net		217			(4,931	)
Amortization of premium (discount) on marketable debt securities, net								2,511			(149	)
Depreciation and amortization		9,128			6,370			6,488			6,036
Foreign currency remeasurement loss		167			925
Change in fair value of investments in equity securities		(91,348	)		(11,994	)
Change in fair value of equity investments								51,665			(102,868	)
Non-cash collaboration royalty revenue		(9,428	)		—			(8,561	)		(6,097	)
Non-cash interest expense on liability related to the sale of future royalties		25,093			—			16,935			16,511
Other		(28	)		220			511			(14	)
Changes in operating assets and liabilities:
Accounts receivable		5,126			(10,402	)		(1,669	)		9,482
Inventory		(2,635	)		(6,604	)		(2,174	)		521
Prepaid expenses and other assets		(12,461	)		(5,874	)		(9,002	)		(6,136	)
Right-of-use assets		(7,261	)		(15,581	)
Accounts payable, accrued, and other liabilities		2,822			4,043			(11,526	)		(8,833	)
Contract liabilities, net		102,898			—
Lease liabilities		7,600			17,071
Contract liabilities								(62,656	)		134,898
Net cash used in operating activities		(69,768	)		(273,344	)		(224,702	)		(7,801	)
Investing activities:
Purchase of property and equipment		(21,959	)		(13,332	)
Purchase of investments		(648,524	)		(610,267	)
Purchase of investments in equity securities		(10,220	)		(14,339	)
Purchase of convertible notes receivable		(1,880	)		—
Proceeds from the sale of investments		40,390			35,100
Proceeds from maturities of investments		367,446			522,533
Payment for intangible assets		(2,275	)		—
Purchase of property, plant, and equipment								(36,485	)		(18,179	)
Purchase of marketable debt securities								(664,347	)		(456,331	)
Purchase of equity investments								—			(9,600	)
Proceeds from sale of marketable debt securities								70,548			28,850
Proceeds from maturities of marketable debt securities								406,614			273,996
Net cash used in investing activities		(277,022	)		(80,305	)		(223,670	)		(181,264	)
Financing activities:
Proceeds from the issuance of common stock in connection with the license agreement, net		55,268			—			—			55,268
Proceeds from the issuance of common stock in connection with underwritten public offerings, net		—			330,415
Proceeds from the issuance of common stock in connection with at-the-market offering, net		20,391			24,828			—			20,391
Proceeds from the issuance of common stock from exercise of warrants and equity plan awards, net		35,051			8,620			25,503			15,858
Principal repayments of financing leases		(149	)		—
Other								(226	)		(91	)
Net cash provided by financing activities		110,561			363,863			25,277			91,426
Effect of exchange rate changes on cash		239			(502	)		(323	)		(198	)
Net increase (decrease) in cash, cash equivalents and restricted cash		(235,990	)		9,712
Net decrease in cash, cash equivalents and restricted cash								(423,418	)		(97,837	)
Cash, cash equivalents and restricted cash at beginning of period		436,244			115,525			726,294			436,244
Cash, cash equivalents and restricted cash at end of period	$	200,254		$	125,237		$	302,876		$	338,407

Supplemental disclosures of non-cash information:
Acquired lease liabilities arising from obtaining right-of-use assets	$	13,195		$	21,515		$	2,301		$	10,403

Ultragenyx Pharmaceutical Inc. (the Company) is a biopharmaceutical company incorporated in California on April 22, 2010. The Company subsequently reincorporated in the state of Delaware in June 2011.

The Company is focused on the identification, acquisition, development, and commercialization of novel products for the treatment of serious rare and ultra-rare genetic diseases. The Company operates as 1 reportable segment. The Company has ~~four~~three commercially approved ~~therapies. Crysvita~~®products. Crysvita® (burosumab) is approved in the United States by the U.S. Food and Drug Administration (FDA) and in Canada for the treatment of X-linked hypophosphatemia (XLH) in adult and pediatric patients one year of age and older, and ~~has received~~is approved in the European ~~conditional marketing authorization~~Union (EU) and the United Kingdom, for the treatment of XLH with radiographic evidence of bone disease in children one year of age and older, ~~and adolescents with growing skeletons. In October 2020, this authorization was expanded to include older~~ adolescents, and adults. In Brazil, Colombia, and Mexico, Crysvita is approved for treatment of XLH in adult and pediatric patients one year of age and older. Crysvita ~~was~~is also approved in the United States by the FDA ~~on June 18, 2020~~ for the treatment of ~~FGF23-related~~fibroblast growth factor 23 (FGF23)-related hypophosphatemia in tumor-induced osteomalacia (TIO), associated with phosphaturic mesenchymal tumors that cannot be curatively resected or localized in adults and pediatric patients 2 years of age and older.

The Company has also received FDA approval for ~~Mepsevii™~~Mepsevii® (vestronidase alfa), the first medicine approved for the treatment of children and adults with mucopolysaccharidosis VII (MPS VII), also known as Sly syndrome. In the European Union and the United Kingdom, Mepsevii is approved under exceptional circumstances for patients of all ages for the treatment of non-neurological manifestations of MPS VII. In Brazil, Mepsevii is approved for the treatment of MPS VII for patients of all ages.

Dojolvi®, formerly known as UX007, ~~was~~is approved ~~by FDA on June 30, 2020~~in the United States and Canada for the treatment of pediatric and adult patients severely affected by long-chain fatty acid oxidation disorders (LC-FAOD).

In addition to the approved ~~treatments,~~products, the Company has ~~two~~the following ongoing clinical development programs. DTX301 is an adeno-associated virus 8 (AAV8) gene therapy product candidate in development for the treatment of patients with ornithine transcarbamylase (OTC) deficiency, the most common urea cycle disorder; and DTX401 is an AAV8 gene therapy product candidate for the treatment of patients with glycogen storage disease type Ia (GSDIa). The Company operates as 1 reportable segment.programs:

The Company has sustained operating losses and expects such annual losses to continue over the next several years. The Company’s ultimate success depends on the outcome of its research and development and commercialization activities, for which it expects to incur additional losses in the future. Management recognizes that the Company will ~~likely~~ need to raise additional capital to fully implement its business plans. Through ~~September~~June 30, ~~2020,~~2021, the Company has relied primarily on ~~the proceeds~~its sale of equity securities, its revenues from ~~equity offerings and~~commercial products, its sale of future royalties, and strategic collaboration arrangements, to finance its operations.

The Company will likely raise additional capital through the issuance of equity, borrowings, or strategic alliances with partner companies. However, if such financing is not available at adequate levels, the Company would need to reevaluate its operating plans.

The accompanying unaudited Condensed Consolidated Financial Statements include the accounts of the Company and its wholly-owned subsidiaries and have been prepared in accordance with U.S. generally accepted accounting principles (GAAP) for interim financial information and in accordance with the instructions to Form 10-Q and Rule 10-01 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. The unaudited interim consolidated financial statements have been prepared on the same basis as the annual financial statements. In the opinion of management, the accompanying unaudited Condensed Consolidated financial Statements reflect all adjustments (consisting only of normal recurring adjustments) considered necessary for a fair presentation. These financial statements should be read in conjunction with the audited financial statements and notes thereto for the preceding fiscal year contained in the Company’s Annual Report on Form 10-K filed on February ~~14, 2020~~12, 2021 with the United States Securities and Exchange Commission (SEC).

The results of operations for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020~~2021 are not necessarily indicative of the results to be expected for the year ending December 31, ~~2020.~~2021. The Condensed Consolidated Balance Sheet as of December 31, ~~2019~~2020 has been derived from audited financial statements at that date, but does not include all of the information required by GAAP for complete financial statements.

The accompanying consolidated financial statements have been prepared in accordance with GAAP. The preparation of the consolidated financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent liabilities and the reported amounts of expenses in the consolidated financial statements and the accompanying notes. On an ongoing basis, management evaluates its estimates, including those related to clinical trial accruals, fair value of assets and liabilities, income taxes, stock-based compensation, and the liability related to the sale of future royalties. Management bases its estimates on historical experience and on various other market-specific and relevant assumptions that management believes to be reasonable under the circumstances. Actual results could differ from those estimates.

Restricted cash primarily consists of money market accounts used as collateral for the Company’s obligations under its facility ~~leases.~~leases and the gene therapy building construction project. The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheets that sum to the total of the same such amounts shown in the consolidated statement of cash flows (in thousands):

	September 30,				June 30,
	2020		2019		2021		2020
Cash and cash equivalents	$	197,486	$	122,577	$	290,875	$	335,639
Restricted cash included in prepaid expenses and other current assets		847		161		10,000		847
Restricted cash included in other assets		1,921		2,499		2,001		1,921
Total cash, cash equivalents, and restricted cash shown in the statements of cash flows	$	200,254	$	125,237	$	302,876	$	338,407

~~Effective January 1, 2020, the~~The Company ~~adopted Accounting Standards Update (ASU) 2016-13, Financial Instruments — Credit Losses,~~ ~~(Topic 326): Measurement of Credit Losses on Financial Instruments,~~ ~~which changed the impairment model for most financial assets~~is exposed to credit losses primarily through receivables from customers and ~~certain other instruments.~~collaborators and through its available-for-sale debt securities. For trade receivables and other instruments, the Company uses a new forward-looking expected loss model that generally results in the earlier recognition of allowances for losses. For available-for-sale debt securities with unrealized losses, the losses are recognized as allowances rather than as reductions in the amortized cost of the securities.

~~The Company is exposed to credit losses primarily through receivables from customers and collaborators and through its available-for-sale debt securities.~~ The Company’s expected loss allowance methodology for the receivables is developed using historical collection experience, current and future economic market conditions, a review of the current aging status and financial condition of the entities. Specific allowance amounts are established to record the appropriate allowance for customers that have a higher probability of default. Balances are written off when determined to be uncollectible. The Company’s expected loss allowance methodology for the debt securities is developed by reviewing the extent of the unrealized loss, the size, term, geographical location, and industry of the issuer, the issuers’ credit ratings and any changes in those ratings, as well as reviewing current and future economic market conditions and the issuers’ current status and financial condition. The Company considered the current and expected future economic and market conditions surrounding the novel coronavirus (COVID-19) pandemic and determined that the estimate of credit losses was not significantly impacted. ~~The adoption of ASU 2016-13 did not have a material impact on the Condensed Consolidated Financial Statements and related disclosures and there~~There was no material allowance recorded for losses on receivables and available-for-sale debt securities which were attributable to credit risk for the three and ~~nine~~six months ended ~~September~~June 30, 2021 and 2020.

The Company has certain license and collaboration agreements that are within the scope of Accounting Standards Codification (ASC) 808, Collaborative Agreements, which provides guidance on the presentation and disclosure of collaborative arrangements. Generally, the classification of the transactions under the collaborative arrangements is determined based on the nature of contractual terms of the arrangement, along with the nature of the operations of the participants. The Company records its share of collaboration revenue, net of transfer pricing related to net sales in the period in which such sales occur, if the Company is considered as an agent in the arrangement. The Company is considered an agent when the collaboration partner controls the product before transfer to the customers and has the ability to direct the use of and obtain substantially all of the remaining benefits from the product. Funding received related to research and development services and commercialization costs is generally classified as a reduction of research and development expenses and selling, general and administrative expenses, respectively, in the consolidated statement of operations, because the provision of such services for collaborative partners are not considered to be part of the Company’s ongoing major or central operations.

~~The~~ ~~Company~~ also records royalty revenues under certain of the Company’s license or collaboration agreements in exchange for license of intellectual property. If the Company does not have any future performance obligations for these license or collaboration agreements, royalty revenue is recorded as the underlying sales occur.

In order to record collaboration revenue, the Company utilizes certain information from its collaboration partners, including revenue from the sale of the product, associated reserves on revenue, and costs incurred for development and sales activities. For the periods covered in the financial statements presented, there have been no material changes to prior period estimates of revenues and expenses.

The Company sold the right to receive certain royalty payments from net sales of Crysvita to RPI Finance Trust (RPI), an affiliate of Royalty Pharma, as further described in Note 7. The Company records the royalty revenue from the net sales of Crysvita in the applicable European territories on a prospective basis as non-cash royalty revenue in the Consolidated Statements of Operations over the term of the arrangement.

The terms of the Company’s collaboration and license agreements may contain multiple performance obligations, which may include licenses and research and development activities. The Company evaluates these agreements under ASC 606, Revenue from Contracts with Customers (ASC 606), to determine the distinct performance obligations. The Company analogizes to ASC 606 for the accounting for distinct performance obligations for which there is a customer relationship. Prior to recognizing revenue, the Company makes estimates of the transaction price, including variable consideration that is subject to a constraint. Amounts of variable consideration are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur and when the uncertainty associated with the variable consideration is subsequently resolved. Total consideration may include nonrefundable upfront license fees, payments for research and development activities, reimbursement of certain third-party costs, payments based upon the achievement of specified milestones, and royalty payments based on product sales derived from the collaboration.

If there are multiple distinct performance obligations, the Company allocates the transaction price to each distinct performance obligation based on its relative standalone selling price. The standalone selling price is generally determined based on the prices charged to customers or using expected cost-plus margin. The Company estimates the efforts needed to complete the performance obligations and recognizes revenue by measuring the progress towards complete satisfaction of the performance obligations using input measures.

The Company sells its approved products through a limited number of distributors. Under ASC 606, revenue from product sales is recognized at the point in time when the delivery is made and when title and risk of loss transfers to these distributors. The Company also recognizes revenue from sales of certain products on a “named patient” basis, which are allowed in certain countries prior to the commercial approval of the product. Prior to recognizing revenue, the Company makes estimates of the transaction price, including any variable consideration that is subject to a constraint. Amounts of variable consideration are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur and when the uncertainty associated with the variable consideration is subsequently resolved. Product sales are recorded net of estimated government-mandated rebates and chargebacks, estimated product returns, and other deductions.

Provisions for returns and other adjustments are provided for in the period the related revenue is recorded, as estimated by management. These reserves are based on estimates of the amounts earned or to be claimed on the related sales and are reviewed periodically and adjusted as necessary. The Company’s estimates of government mandated rebates, chargebacks, estimated product returns, and other deductions depends on the identification of key customer contract terms and conditions, as well as estimates of sales volumes to different classes of payors. If actual results vary, the Company may need to adjust these estimates, which could have an effect on earnings in the period of the adjustment.

Effective January 1, 2020, the Company sold the right to receive certain royalty payments from net sales of Crysvita to RPI Finance Trust (RPI), an affiliate of Royalty Pharma, as further described in Note 7. The Company records the royalty revenue from the net sales of Crysvita in the applicable European territories on a prospective basis as non-cash royalty revenue in the Consolidated Statements of Operations over the term of the arrangement.

Financial assets and liabilities are recorded at fair value. The carrying amount of certain financial instruments, including cash and cash equivalents, accounts receivable, accounts payable and accrued liabilities approximate fair value due to their relatively short maturities. Assets and liabilities recorded at fair value on a recurring basis in the balance sheets are categorized based upon the level of judgment associated with the inputs used to measure their fair values. Fair value is defined as the exchange price that would be received for an asset or an exit price that would be paid to transfer a liability in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. The authoritative guidance on fair value measurements establishes a three-tier fair value hierarchy for disclosure of fair value measurements as follows:

Level 1—Inputs are unadjusted, quoted prices in active markets for identical assets or liabilities at the measurement date;

Level 2—Inputs are observable, unadjusted quoted prices in active markets for similar assets or liabilities, unadjusted quoted prices for identical or similar assets or liabilities in markets that are not active, or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the related assets or liabilities; and

Level 3—Unobservable inputs that are significant to the measurement of the fair value of the assets or liabilities that are supported by little or no market data.

10The Company determines the fair value of its equity investments in Arcturus Therapeutics Holdings Inc. (Arcturus) and Solid Biosciences Inc. (Solid) by using the quoted market prices, which are Level 1 fair value measurements.

The following tables set forth the fair value of the Company’s financial assets remeasured on a recurring basis based on the three-tier fair value hierarchy (in thousands):

	September 30, 2020								June 30, 2021
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Money market funds	$	135,764	$	—	$	—	$	135,764	$	206,674	$	—	$	—	$	206,674
Repurchase agreements		—		33,000		—		33,000
Time deposits		—		10,000		—		10,000
Certificate of deposits and time deposits										—		17,501		—		17,501
Corporate bonds		—		193,677		—		193,677		—		237,296		—		237,296
Commercial paper		—		102,891		—		102,891		—		341,522		—		341,522
Asset-backed securities		—		8,715		—		8,715		—		55,020		—		55,020
U.S. Government Treasury and agency securities		214,923		47,827		—		262,750		12,500		42,109		—		54,609
Investment in Arcturus common stock		128,700		—		—		128,700
Debt securities in government-sponsored entities										—		28,751		—		28,751
Investments in Arcturus and Solid common stock										103,091		—		—		103,091
Total	$	479,387	$	396,110	$	—	$	875,497	$	322,265	$	722,199	$	—	$	1,044,464

	December 31, 2019								December 31, 2020
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Money market funds	$	293,309	$	—	$	—	$	293,309	$	598,392	$	—	$	—	$	598,392
Repurchase agreements		—		100,000		—		100,000
Time deposits		—		10,000		—		10,000		—		10,000		—		10,000
Corporate bonds		—		77,026		—		77,026		—		193,802		—		193,802
Commercial paper		—		80,119		—		80,119		—		173,859		—		173,859
Asset-backed securities		—		30,406		—		30,406		—		11,225		—		11,225
U.S. Government Treasury and agency securities		96,329		53,979		—		150,308		167,967		17,661		—		185,628
Investment in Arcturus equity securities		26,088		—		1,664		27,752
Investments in Arcturus and Solid common stock										154,756		—		—		154,756
Total	$	415,726	$	351,530	$	1,664	$	768,920	$	921,115	$	406,547	$	—	$	1,327,662

The Company determined the fair value of the Arcturus Therapeutics Holdings Inc. (Arcturus) common stock by using the quoted market price on September 30, 2020, which is a Level 1 fair value measurement. See Note 6 for additional details on the Arcturus transaction.

In July 2020, the Company invested $2.5 million in ~~DiaCarta Ltd. (DiaCarta),~~ a private diagnostic company, in the form of a convertible promissory note that matures in two years, if not converted earlier. The Company was also issued a warrant to purchase up to $1.0 million of ~~DiaCarta~~the entity’s preferred stock. The fair value of the warrant to purchase shares of ~~DiaCarta~~the entity was based on unobservable inputs that are significant to the measurement of the fair value of the asset and is supported by little or no market data; accordingly, the warrant is considered a Level 3 financial asset and is remeasured on a nonrecurring basis. The Company measured the fair value of the warrant by applying the Black-Scholes option pricing method and utilizing the following inputs: stock price, strike price, volatility, risk-free interest rate, and expected term. The Company ~~will recognize~~recognizes the interest income on the convertible promissory note based on the effective interest rate method over the life of the note. As of ~~September~~June 30, ~~2020,~~2021, the balance of the convertible promissory note was ~~$2.0~~$2.2 million, including ~~$0.1~~$0.4 million in interest receivable, and was recorded in other assets, and the allocated fair value of the warrant was $0.6 million and was recorded in ~~investments~~equity investments.

In December 2020, the Company invested $1.4 million in ~~equity securities.~~Mazi Therapeutics, Inc. (Mazi), a private pharmaceutical company founded by a current employee of the Company, in the form of a convertible promissory note that matures in two years, if not converted earlier. As of June 30, 2021, the balance of the convertible promissory note was $1.4 million.

The fair values of cash equivalents and investments classified as available-for-sale securities consisted of the following (in thousands):

	September 30, 2020										June 30, 2021
				Gross Unrealized										Gross Unrealized
		Amortized Cost		Gains		Losses			Estimated Fair Value			Amortized Cost		Gains		Losses			Estimated Fair Value
Money market funds		$	135,764	$	—	$	—		$	135,764		$	206,674	$	—	$	—		$	206,674
Repurchase agreements			33,000		—		—			33,000
Time deposits			10,000		—		—			10,000
Certificate of deposits and time deposits													17,501		—		—			17,501
Corporate bonds			192,943		741		(7	)		193,677			237,310		45		(59	)		237,296
Commercial paper			102,890		1		—			102,891			341,522		—		—			341,522
Asset-backed securities			8,712		3		—			8,715			55,015		11		(6	)		55,020
U.S. Government Treasury and agency securities			262,583		167		—			262,750			54,605		7		(3	)		54,609
Debt securities in government-sponsored entities													28,761		4		(14	)		28,751
Total		$	745,892	$	912	$	(7	)	$	746,797		$	941,388	$	67	$	(82	)	$	941,373

	December 31, 2019										December 31, 2020
				Gross Unrealized										Gross Unrealized
		Amortized Cost		Gains		Losses			Estimated Fair Value			Amortized Cost		Gains		Losses			Estimated Fair Value
Money market funds		$	293,309	$	—	$	—		$	293,309		$	598,392	$	—	$	—		$	598,392
Repurchase agreements			100,000		—		—			100,000
Time deposits			10,000		—		—			10,000			10,000		—		—			10,000
Corporate bonds			77,022		17		(13	)		77,026			193,610		209		(17	)		193,802
Commercial paper			80,119		—		—			80,119			173,859		—		—			173,859
Asset-backed securities			30,375		31		—			30,406			11,224		1		—			11,225
U.S. Government Treasury and agency securities			150,184		124		—			150,308			185,561		67		—			185,628
Total		$	741,009	$	172	$	(13	)	$	741,168		$	1,172,646	$	277	$	(17	)	$	1,172,906

At ~~September~~June 30, ~~2020,~~2021, the remaining contractual maturities of available-for-sale securities were less than ~~one year.~~five years. There have been 0 significant realized gains or losses on available-for-sale securities for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020~~2021 and ~~2019.~~2020. All marketable securities with unrealized losses at ~~September~~June 30, ~~2020~~2021 have been in a loss position for less than twelve ~~months.~~months and were temporary in nature. ~~Based on~~We do not intend to sell the ~~Company’s application of its expected loss allowance methodology, it is probable~~investments that ~~the principal and interest will be collected~~are in ~~accordance with the contractual terms, and that the~~an unrealized loss ~~on these securities were not attributable to credit risk.~~position before recovery of their amortized cost basis.

	September 30,		December 31,		June 30,		December 31,
	2020		2019		2021		2020
Work-in-process	$	10,211	$	8,191	$	9,457	$	7,184
Finished goods		4,246		3,355		5,626		5,864
Total inventory	$	14,457	$	11,546	$	15,083	$	13,048

	September 30,		December 31,		June 30,		December 31,
	2020		2019		2021		2020
Research, clinical study, and manufacturing expenses	$	20,486	$	22,894	$	22,551	$	25,875
Payroll and related expenses		43,008		41,324		41,545		58,176
Other		16,159		18,976		26,964		24,440
Total accrued liabilities	$	79,653	$	83,194	$	91,060	$	108,491

	Three Months Ended September 30,				Nine Months Ended September 30,				Three Months Ended June 30,				Six Months Ended June 30,
	2020		2019		2020		2019		2021		2020		2021		2020
Collaboration and license revenue:
Crysvita collaboration revenue in profit- share territory	$	34,058	$	19,534	$	91,079	$	48,721	$	41,756	$	29,806	$	78,016	$	57,021
Crysvita royalty revenue in European territory		—		1,950		1,498		5,896		228		1,498		228		1,498
Daiichi Sankyo		32,866		—		51,723		—		21,956		18,857		64,706		18,857
Bayer		—		101		—		453
Total collaboration and license revenue		66,924		21,585		144,300		55,070		63,940		50,161		142,950		77,376
Product sales:
Crysvita		3,277		1,140		7,436		2,734		2,900		2,549		8,772		4,159
Mepsevii		4,076		2,361		11,686		8,274		5,399		4,185		9,006		7,610
Dojolvi		3,862		714		6,638		2,043		10,047		1,332		17,081		2,776
Total product sales		11,215		4,215		25,760		13,051		18,346		8,066		34,859		14,545
Crysvita non-cash collaboration royalty revenue		3,331		—		9,428		—		4,689		3,482		8,561		6,097
Total revenues	$	81,470	$	25,800	$	179,488	$	68,121	$	86,975	$	61,709	$	186,370	$	98,018

The following table disaggregates total revenues based on geographic location (in thousands):

	Three Months Ended September 30,				Nine Months Ended September 30,				Three Months Ended June 30,				Six Months Ended June 30,
	2020		2019		2020		2019		2021		2020		2021		2020
North America	$	72,651	$	21,700	$	154,939	$	56,318	$	75,567	$	51,931	$	163,309	$	82,288
Europe		5,002		2,790		15,707		8,522		6,700		6,548		12,337		10,705
All other		3,817		1,310		8,842		3,281
Latin America										4,708		3,230		10,724		5,025
Total revenues	$	81,470	$	25,800	$	179,488	$	68,121	$	86,975	$	61,709	$	186,370	$	98,018

The following table presents changes in the contract ~~assets (liabilities)~~liabilities (in thousands):

	Nine Months Ended September 30,						Six Months Ended June 30,
	2020			2019			2021			2020
Balance of contract assets at beginning of period	$	—		$	2,979
Balance of contract liabilities at beginning of period							$	66,568		$	—
Additions		(154,621	)		452			2,050			153,755
Deductions		51,723			(3,447	)		(64,706	)		(18,857	)
Balance of contract liabilities at end of period, net	$	(102,898	)	$	(16	)
Balance of contract liabilities at end of period							$	3,912		$	134,898

See Note 6 for additional details on contract ~~assets (liabilities)~~liabilities activities.

The Company’s largest accounts receivable balance accounted for ~~83%~~58% and ~~87%~~71% of the total accounts receivable balance as of ~~September~~June 30, ~~2020~~2021 and December 31, ~~2019,~~2020, respectively, and was due from a collaboration partner.

In August 2013, the Company entered into a collaboration and license agreement with Kyowa Kirin Co., Ltd. (KKC, or formerly Kyowa Hakko Kirin Co., Ltd. or KHK). Under the terms of this collaboration and license agreement, as amended, the Company and KKC collaborate on the development and commercialization of Crysvita in the field of orphan diseases in the United States and Canada, or the profit-share territory, and in the European Union, United Kingdom, and Switzerland, or the European territory, and the Company has the right to develop and commercialize such products in the field of orphan diseases in Mexico and Central and South America, or Latin America. In May 2017, the Company entered into an agreement with a wholly-owned subsidiary of KKC pursuant to which it was granted the right to commercialize Crysvita in Turkey.

In the field of orphan diseases, and except for ongoing studies being conducted by KKC, the Company is the lead party for development activities in the profit-share territory and in the European territory until the applicable transition ~~date; the Company is~~

~~also the lead party for core development activities conducted in Japan and Korea, for which the core development plan is limited to clinical trials mutually agreed to by the Company and KKC.~~date. The Company shares the costs for development activities in the profit-share territory and the European territory conducted pursuant to the

development plan before the applicable transition date equally with KKC. ~~KKC is responsible for 100% of the costs for development activities in Japan and Korea.~~ In April 2023, which is the transition date for the profit-share ~~territory, and on the applicable transition date for the European~~ territory, KKC will become the lead party and be responsible for the costs of the development activities. However, the Company will continue to share the costs of the studies commenced prior to the applicable transition date equally with KKC. Crysvita was approved in the European Union and United Kingdom in February 2018 and was approved by the FDA in April 2018.

The collaboration and license agreements are within the scope of ASC 808, which provides guidance on the presentation and disclosure of collaborative arrangements.

The Company and KKC share commercial responsibilities and profits in the profit-share territory until April 2023. Under the collaboration agreement, KKC manufactures and supplies Crysvita for commercial use in the profit-share territory and charges the Company the transfer price of 35% of net sales through December 31, 2022, and 30% thereafter. The remaining profit or loss after supply costs from commercializing products in the profit-share territory are shared between the Company and KKC on a 50/50 basis until April 2023. Thereafter, the Company will be entitled to receive a tiered double-digit revenue share in the mid-to-high 20% range.

As KKC is the principal in the sale transaction with the customer, the Company recognizes a pro-rata share of collaboration revenue, net of transfer pricing, in the period the sale occurs. The Company concluded that its portion of KKC’s sales in the profit-share territory is analogous to a royalty and therefore recorded its share as collaboration revenue, similar to a royalty.

KKC has the commercial responsibility for Crysvita in the European territory. In December 2019, the Company sold its right to receive royalty payments based on sales in the European territory to Royalty Pharma, effective January 1, 2020, as further described in Note 7. Prior to the Company’s sale of the royalty, the Company received a royalty of up to 10% on net sales in the European territory, which was recognized as the underlying sales occur. Beginning in 2020, the Company ~~records~~recorded the royalty revenue as non-cash royalty revenues. During the ~~nine~~three months ended ~~September~~June 30, 2021 and 2020, there was a change in the estimate of the revenue reserves related to sales made prior to January 1, 2020, as a result of which, the Company recorded $0.2 million and $1.5 million, respectively, as royalty revenue in European territory.

The Company’s share of collaboration and royalty revenue related to Crysvita was as follows (in thousands):

	Three Months Ended September 30,				Nine Months Ended September 30,				Three Months Ended June 30,				Six Months Ended June 30,
	2020		2019		2020		2019		2021		2020		2021		2020
Company's share of revenue in profit- share territory	$	34,058	$	19,534	$	91,079	$	48,721	$	41,756	$	29,806	$	78,016	$	57,021
Royalty revenue in European territory		—		1,950		1,498		5,896		228		1,498		228		1,498
Non-cash royalty revenue in European territory		3,331		—		9,428		—		4,689		3,482		8,561		6,097
Total	$	37,389	$	21,484	$	102,005	$	54,617	$	46,673	$	34,786	$	86,805	$	64,616

The Company is responsible for commercializing Crysvita in Latin America and Turkey. The Company is considered the principal in these territories as the Company controls the product before it is transferred to the customer. Accordingly, the Company records revenue on a gross basis related to the sale of Crysvita once the product is delivered and the risk and title of the product is transferred to the distributor. The Company recorded product sales of ~~$3.3~~$2.9 million and ~~$7.4~~$8.8 million for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020,~~2021, respectively, and ~~$1.1~~$2.5 million and ~~$2.7~~$4.2 million for the three and ~~nine~~six months ended ~~September~~June 30, ~~2019,~~2020, respectively, net of estimated product returns and other deductions. KKC has the option to assume responsibility for commercialization efforts in Turkey from the Company, after a certain minimum period.

Under the collaboration agreement, KKC manufactures and supplies Crysvita, which is purchased by the Company for sales in the above territories and is based on 35% of the net sales through December 31, 2022 and 30% thereafter. The Company also pays to KKC a low single-digit royalty on net sales in Latin America.

Under the collaboration agreement, KKC and the Company share certain development and commercialization costs. As a result, the Company was reimbursed for these costs and operating expenses were reduced as follows (in thousands):

	Three Months Ended September 30,				Nine Months Ended September 30,				Three Months Ended June 30,				Six Months Ended June 30,
	2020		2019		2020		2019		2021		2020		2021		2020
Research and development	$	5,156	$	7,124	$	15,814	$	20,118	$	5,171	$	5,168	$	11,356	$	10,658
Selling, general and administrative		5,492		5,633		18,509		16,009		7,576		5,965		15,071		13,017
Total	$	10,648	$	12,757	$	34,323	$	36,127	$	12,747	$	11,133	$	26,427	$	23,675

The Company had accounts receivable from KKC in the amount of ~~$23.2~~$14.7 million and ~~$28.5~~$16.4 million from profit-share revenue and royalties and other receivables recorded in prepaid and other current assets of ~~$12.9~~$3.8 million and ~~$17.8~~$9.6 million and accrued liabilities of ~~$1.6~~$2.7 million and ~~$0.9~~$2.4 million from commercial and development activity reimbursements, as of ~~September~~June 30 ~~30, 2020~~, 2021 and December 31, ~~2019,~~2020, respectively.

The Company has an agreement with Bayer Healthcare LLC (Bayer) to research, develop and commercialize AAV gene therapy products for the treatment of hemophilia A (DTX 201). Under this agreement, Bayer has been granted an exclusive license to develop and commercialize one or more novel gene therapies for hemophilia A. The agreement requires that Bayer use commercially reasonable efforts to conduct and fund a proof-of-concept (POC) clinical trial and any subsequent clinical trials and commercialization of gene therapy products for treatment of hemophilia A. Bayer ~~will have~~has worldwide rights to commercialize the potential future product.

Bayer iswas responsible for funding certain research and development services performed by the Company in the performance of its obligations under the annual research plan and budget. Under the terms of the agreement, ~~with Bayer,~~ the Company is eligible to receive development and commercialization milestone payments of up to $232.0 million, as well as, royalty payments ranging in the high single-digit to low double-digit percentages, not exceeding the mid-teens, of net sales of licensed products. The Company achieved the first milestone in December 2017, the second milestone in April 2018, and has received $15.0 million for such milestones to date.

The ~~Company’s~~Company has no further obligations under the ~~contract were completed by end of December 31, 2019 and 0 revenue was recorded for the three and nine months ended~~ ~~September~~ ~~30, 2020. The Company recorded revenue of $0.1 million and $0.5 million for the three and nine months ended~~ ~~September~~ ~~30, 2019, respectively.~~contract. The Company may record future milestone payments as revenue, if it becomes probable that a significant reversal in the amount of revenue recognized will not occur and when the uncertainty associated with the variable consideration is subsequently resolved.

~~The~~In October 2015, the Company ~~has~~entered into a Research Collaboration and License Agreement with Arcturus towhereby the Company and Arcturus would collaborate on the research and ~~develop~~development of therapies for select rare diseases. ~~Pursuant to~~Arcturus has the ~~agreement,~~primary responsibility for conducting certain research services, funded by the Company, ~~incurred NaN~~ and ~~$0.7~~the Company is responsible for development and commercialization costs.

On a product-by-product basis, the Company may be obligated to make development and regulatory milestone payments of up to $24.5 million, ~~for~~and commercial milestone payments of up to $45.0 million, if certain milestones are achieved. The Company may also be obligated to pay Arcturus royalties on any net sales of products incorporating the licensed intellectual property that range from a mid single-digit to low double-digit percentage. For the three and ~~nine~~six months ended ~~September~~June 30, ~~2019, respectively, in~~2021 and 2020, there were 0 research and development ~~expense~~expenses incurred for the funding of certain research services received from Arcturus. ~~NaN research and development expenses were recognized in 2020 related to the Arcturus agreement.~~

In May 2020, the Company exercised an option to purchase 600,000 shares of Arcturus’ common stock at $16.00 per share, or a total purchase price of $9.6 million. ~~Accordingly, after the exercise of the option,~~In December 2020, the Company ~~owned 3,000,000~~sold 800,000 shares ~~or 14.6%,~~ of Arcturus’ then outstanding common stock. The purchase was made pursuant to the equity purchase agreement between the parties entered into in June 2019 in connection with the amendment to the research collaboration and license agreement. The Arcturus common stock ~~is restricted from sale or transfer by the Company for six months from the exercise date, subject to certain conditions.~~at a weighted-average price of $100.81 per share and received net proceeds of $79.8 million. The Company has elected to apply the fair value option to account for the equity investment in Arcturus. ~~The~~As of June 30, 2021, the Company ~~had accounted for the option to purchase additional~~held 2,200,000 shares of ~~Arcturus~~Arcturus’ common ~~stock at fair value based on the Black-Scholes option pricing method.~~stock.

The changes in the fair value of the Company’s equity investment in Arcturus securities were as follows (in thousands):

	Arcturus common stock		Fair value of option to purchase additional shares of Arcturus common stock			Total		Arcturus common stock			Option to purchase additional shares of Arcturus common stock			Total
Acquisition of investment in Arcturus securities in June 2019	$	13,872	$	467		$	14,339
Change in fair value		12,216		1,197			13,413
December 31, 2019		26,088		1,664			27,752	$	26,088		$	1,664		$	27,752
Change in fair value		67,400		23,948			91,348		113,978			23,948			137,926
Transfer of value upon option exercise		35,212		(25,612	)		9,600		35,212			(25,612	)		9,600
September 30, 2020	$	128,700	$	—		$	128,700
Sale of shares									(79,842	)		—			(79,842	)
December 31, 2020									95,436			—			95,436
Change in fair value									(20,988	)		—			(20,988	)
June 30, 2021								$	74,448		$	—		$	74,448

The Company recorded ~~$11.5~~$16.4 million and $21.0 million in unrealized ~~loss~~losses for the three and six months ended ~~September~~June 30, 2021, respectively, and $95.2 million and $102.9 million in unrealized gains for the three and six months ended June 30, 2020, respectively, from the fair value ~~adjustment~~adjustments on the equity investment in Arcturus ~~common stock.~~securities.

In August 2019, the Company entered into a Program Agreement and a Unitholder Option Agreement with GeneTx ~~Biotherapeutics, LLC (GeneTx)~~ to collaborate on the development of GeneTx’s GTX-102, an ~~antisense oligonucleotide (ASO)~~ASO for the treatment of Angelman syndrome.

Pursuant to the terms of the Unitholder Option Agreement, the Company made an upfront payment of $20.0 million for an exclusive option to acquire GeneTx, which was exercisable any time prior to 30 days following FDA acceptance of the IND for GTX-102. Pursuant to the agreement, upon acceptance of the IND, which occurred in January 2020, the Company elected to extend the

option period by paying an option extension payment of $25.0 million (option extension premium) during the ~~prior~~ quarter ended March 31, 2020. The Company has athe right to acquire GeneTx for a payment of $125.0 million, at any time, until the earlier of 30 months from the first dosing of a patient in a planned Phase 1/2 study (subject to extensions) or 90 days after results are available from that study. This exclusive option to acquire GeneTx can be extended under certain circumstances, by up to 4 additional three-month periods, by paying an additional extension fee for each three-month period.

During the exclusive option period, GeneTx is responsible for conducting the program based on the development plan agreed between the parties and, subject to the terms in the Program Agreement, has the decision-making authority on all matters in connection with the research, development, manufacturing and regulatory activities with respect to the Program. The Company will provide support, at its discretion, including strategic guidance and clinical expertise. The Company and GeneTx will collaborate on the management of the Phase 1/2 study in patients with Angelman syndrome. If the Company acquires GeneTx, the Company will then be responsible for all development and commercialization activities from the date of acquisition. The Company would also be required to make payments upon achievement of certain development and commercial milestones, as well as royalties, depending upon the success of the program.

Although GeneTx is a variable interest entity, the Company is not the primary beneficiary as it currently does not have the power to direct the activities that would most significantly impact the economic performance of GeneTx. Prior to product regulatory approval, all consideration paid to GeneTx represents rights to potential future benefits associated with GeneTx’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use. Accordingly, for the ~~nine~~three months ended ~~September 30,~~March 31, 2020, the Company recorded the option extension payment of $25.0 million as an in-process research and development expense.

In March 2020, the Company executed a License Agreement with REGENXBIO, Inc. (REGENEX), for an exclusive, sublicensable, worldwide license to REGENX’s NAV AAV8 and AAV9 Vectors for the development and commercialization of gene therapy treatments for a rare metabolic disorder. In return for these rights, the Company made an upfront payment of $7.0 million, which was recorded as an in-process research and development expense during the ~~prior quarter~~three months ended March 31, 2020. The Company will pay certain annual fees of $0.1 million, milestone payments of up to $14.0 million, and royalties on any net sales of products incorporating the licensed intellectual property that range from a high single-digit to low double-digit royalty.

In March 2020, the Company executed a License and Technology Access Agreement (the License Agreement) with Daiichi Sankyo Co., Ltd. (Daiichi Sankyo). Pursuant to the License Agreement, the Company granted Daiichi Sankyo a non-exclusive license to intellectual property, including know-how and patent applications, with respect to its HeLa PCL and HEK293 transient transfection manufacturing technology platforms for AAV-based gene therapy products. The Company retains the exclusive right to use the manufacturing technology for its current target indications and additional indications identified now and in the future. The Company will provide certain technical assistance and technology transfer services during the technology transfer period of three years to enable Daiichi Sankyo to use the technologies for its internal gene therapy programs. Daiichi Sankyo has an option to extend the technology transfer period including know-how improvements by two additional one-year periods by paying a fixed amount for each additional year. Daiichi Sankyo will be responsible for the manufacturing, development, and commercialization of products manufactured with the licensed technology; however, the Company has the option to co-develop and co-commercialize rare disease products at the IND stage. Ultragenyx may also provide strategic consultation to Daiichi Sankyo on the development of both AAV-based gene therapy products and other products for rare diseases.

Under the terms of the License Agreement, Daiichi Sankyo made an upfront payment of $125.0 million and will pay an additional $25.0 million upon completion of the technology transfer of the HeLa PCL and HEK293 platforms, as well as single-digit royalties on net sales of products manufactured in either system. Daiichi Sankyo will reimburse the Company for all costs associated with the transfer of the manufacturing technology.

The Company also entered into a Stock Purchase Agreement (SPA) with Daiichi Sankyo, pursuant to which Daiichi Sankyo purchased 1,243,913 shares of the Company’s common stock in exchange for $75.0 million in cash during the first quarter of 2020. The fair market value of the common stock issued to Daiichi Sankyo was $55.3 million based on the stock price of $44.43 per share on the date of issuance, resulting in a $19.7 million premium on the SPA. Daiichi Sankyo is also subject to a three-year standstill and restrictions on sale of the shares (subject to customary exceptions or release).

In June 2020, the Company executed a subsequent license agreement (the Sublicense Agreement) with Daiichi Sankyo for transfer of certain technology in consideration for an upfront payment of $8.0 million and annual maintenance fees, milestone payments, and royalties on any net sales of products incorporating the licensed intellectual property.

The License Agreement, the Sublicense Agreement, and the SPA are being accounted for as one arrangement because they were entered into at or near the same time and negotiated in contemplation of one another. The Company evaluated the License Agreement and the Sublicense Agreement under ASC 606 and determined that the performance obligations under the agreements are (i) intellectual property with respect to its HeLa PCL and HEK293 transient transfection manufacturing technology platforms together with the initial technical assistance and technology transfer services, which are expected to be completed ~~over a period~~in the fourth quarter of ~~18 to 21 months,~~2021, and (ii) the transfer of any know-how and improvements after the completion of the initial technology transfer through the end of the three year technology transfer ~~period.~~period ending March 2023.

~~The~~As of June 30, 2021, the Company has determined that the total transaction price of the License Agreement was $183.6 million which was comprised of the $19.7 million premium from the SPA, the $125.0 million upfront payment, the $25.0 million in unconstrained milestone payments, $8.0 million from the Sublicense Agreement, and the $5.9 million estimated reimbursement amount for delivering the license and technology ~~services.~~ services. Total revenue recognized under the license agreement through June 30, 2021 is $153.9 million.

The Company allocated the total transaction price to the two performance obligations on a relative stand-alone selling price basis. Revenue allocated to the intellectual property and the technology transfer services will be recognized over an initial period which is estimated ~~period~~to end in the fourth quarter of ~~18 to 21 months,~~2021, measuring the progress toward complete satisfaction of the individual performance obligation using an input measure. Revenue for know-how and improvements after the completion of technology transfer will be recognized on a straight-line basis over the remaining technology transfer period, ~~(i.e., months 19-36) on a straight-line basis,~~which ends in March 2023, as it is expected that Daiichi Sankyo will receive and consume the benefits consistently throughout the period. ~~The performance obligations are estimated to be substantially complete by March 2023.~~ The estimated period to complete the technology transfer services and the related milestones payments, if any, are subject to revised estimates which could be impacted by limitations or delays from the COVID-19 pandemic, successful scale-up of the manufacturing, and other changes that may impact timing. Royalties from commercial sales will be accounted for as revenue upon achievement of such sales, assuming all other revenue recognition criteria are met.

~~For~~The Company recognized $22.0 million and $64.7 million for the three and ~~nine~~six months ended ~~September~~June 30, 2021, respectively, and $18.9 million for the three and six months ended June 30, 2020, ~~the Company recognized $32.9 million and $51.7 million, respectively,~~ in revenue related to this arrangement. Accordingly, the Company had recorded ~~$102.9~~$3.9 million as contract liabilities, net, as of ~~September~~June 30, ~~2020.~~2021. The Company recorded aan accounts receivable related to the above agreements of ~~$0.9~~$0.8 million as of ~~September~~June 30, 2021.

In October 2020, the Company entered into a strategic Collaboration and License Agreement with Solid Biosciences Inc., or Solid, and received an exclusive license for any pharmaceutical product that expresses Solid’s proprietary microdystrophin construct from AAV8 and variants thereof in ~~prepaid expenses~~clade E for use in the treatment of Duchenne muscular dystrophy and other ~~current assets.~~diseases resulting from lack of functional dystrophin, including Becker muscular dystrophy. The Company will collaborate to develop products that combine Solid’s differentiated microdystrophin construct, the Company’s HeLa PCL manufacturing platform, and the Company’s AAV8 variants. Solid will also provide development support and was granted an exclusive option to co-invest in products the Company develops for profit share participation in certain territories. On a product-by-product basis, the Company may be obligated to make development milestone payments of up to $25.0 million, regulatory milestone payments of up to $65.0 million, and commercial milestone payments of up to $165.0 million, if such milestones are achieved, as well as royalties on any net sales of products incorporating the licensed intellectual property that range from a low to mid-double-digit percentage. The royalty rate changes to mid to high double-digit percentage if Solid decides to co-invest in the product.

The Company also entered into a Stock Purchase Agreement and the Investor Agreement with Solid, pursuant to which, the Company purchased7,825,797 shares of Solid’s common stock for an aggregate purchase price of $40.0 million. Subject to the terms of the Investor Agreement, the Company is restricted from selling, transferring or otherwise disposing of the shares without the prior approval of Solid until the earlier of (i) 18 months following the closing of the transaction, (ii) the termination of the Collaboration and License Agreement and (iii) certain other specified events. The Company also agreed to customary standstill restrictions in accordance with the terms of the Investor Agreement until the earlier of (a) 24 months after the closing of the transaction and (b) certain specified events.

The Company’s investment in Solid is being accounted at fair value, as the fair value is readily determinable. The Company recorded the common stock investment at $26.8 million on the transaction date, which was based on the quoted market price on the closing date.

Although Solid is a variable interest entity, the Company is not the primary beneficiary as it does not have the power to direct the activities that would most significantly impact the economic performance of Solid. Prior to the achievement of certain development milestones, all consideration paid to Solid represents rights to potential future benefits associated with Solid’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use. Accordingly, the remaining $13.2 million of the total $40.0 million paid as consideration was attributed to the license rights obtained and was recorded as in-process research and development expense during the year ended December 31, 2020.

The changes in the fair value of the Company’s investment in Solid’s common stock were as follows (in thousands):

The Company recorded $14.6 million and $30.7 million in unrealized losses for the three and six months ended June 30, 2021, respectively, from the fair value adjustments on the equity investment in Solid securities.

In December 2020, the Company entered into a License and Collaboration Agreement with Mereo BioPharma 3 Limited, or Mereo, to collaborate on the development of setrusumab. Under the terms of the agreement, the Company will lead future global development of setrusumab in both pediatric and adult patients with Osteogenesis Imperfecta, or OI. The Company was granted an exclusive license to develop and commercialize setrusumab in the U.S., Turkey, and the rest of the world, excluding the European Economic Area, United Kingdom, and Switzerland, or the Mereo territory, where Mereo retains commercial rights. Each party will be responsible for post-marketing commitments and commercial supply in their respective territories.

Upon the closing of the transaction in January 2021, the Company made a payment of $50.0 million to Mereo and will be required to make payments of up to $254.0 million upon the achievement of certain clinical, regulatory, and commercial milestones. The Company will pay for all global development costs as well as tiered double-digit percentage royalties to Mereo on net sales in the U.S., Turkey, and the rest of the world (excluding the Mereo Territory), and Mereo will pay the Company a fixed double-digit percentage royalty on net sales in the Mereo Territory.

Although Mereo is a variable interest entity, the Company is not the primary beneficiary as it does not have the power to direct the activities that would most significantly impact the economic performance of Mereo. Prior to the achievement of certain development milestones, all consideration paid to Mereo represents rights to potential future benefits associated with Mereo’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use. Accordingly, for the three months ended March 31, 2021, the Company recorded the upfront payment of $50.0 million as in-process research and development expense.

In December 2019, the Company entered into a Royalty Purchase Agreement with RPI. Pursuant to the agreement, RPI paid $320.0 million to the Company in consideration for the right to receive royalty payments effective January 1, 2020, arising from the net sales of Crysvita in the European Union, the United Kingdom, and Switzerland under the terms of the Company’s Collaboration and License Agreement with KKC dated August 29, 2013, as amended. The agreement with RPI will automatically terminate, and the payment of royalties to RPI will cease, in the event aggregate royalty payments received by RPI are equal to or greater than $608.0 million prior to December 31, 2030, or in the event aggregate royalty payments received by RPI are less than $608.0 million prior to December 31, 2030, when aggregate royalty payments received by RPI are equal to $800.0 million.

~~As RPI’s rate of return is explicitly limited due to the cap on royalties they may receive, proceeds~~Proceeds from the transaction were recorded as a liability (liability related to sale of future royalties on the Consolidated Balance Sheets). The Company amortizes $320.0 million, net of transaction cost of $5.8 million using the effective interest method over the estimated life of the arrangement. In order to determine the amortization of the liability, the Company is required to estimate the total amount of future royalty payments to be received by the Company and paid to RPI, subject to the capped amount, over the life of the arrangement. The excess of future estimated royalty payments (subject to the capped amount), over the $314.2 million of net proceeds, is recorded as non-cash interest expense over the life of the arrangement. Consequently, the Company estimates an imputed interest on the unamortized portion of the liability and records interest expense relating to the transaction. The Company records the royalty revenue arising from the net sales of Crysvita in the applicable European territories as non-cash royalty revenue in the Consolidated Statements of ~~Operations.~~Operations over the term of the arrangement.

The Company periodically assesses the expected royalty payments using a combination of historical results, internal projections and forecasts from external sources. To the extent such payments are greater or less than the Company’s initial estimates or the timing of such payments is materially different than its original estimates, the Company will prospectively adjust the amortization of the liability and the effective interest rate. The Company’s effective annual interest rate was approximately ~~10.3% and 10.1% as of~~9.8% for the three months ended ~~September~~June 30 ~~30, 2020 and December 31, 2019, respectively.~~, 2021.

There are a number of factors that could materially affect the amount and timing of royalty payments from KKC in the applicable European territories, most of which are not within the Company’s control. Such factors include, but are not limited to, the

success of KKC’s sales and promotion of Crysvita, changing standards of care, delays or disruptions related to the COVID-19 pandemic, the introduction of competing products, pricing for reimbursement in various European territories, manufacturing or other delays, intellectual property matters, adverse events that result in governmental health authority imposed restrictions on the use of Crysvita, significant changes in foreign exchange rates as the royalty payments are made in U.S. dollars (USD) while significant

portions of the underlying European sales of Crysvita are made in currencies other than USD, and other events or circumstances that could result in reduced royalty payments from European sales of Crysvita, all of which would result in a reduction of non-cash royalty revenue and the non-cash interest expense over the life of the arrangement. Conversely, if sales of Crysvita in Europe are more than expected, the non-cash royalty revenue and the non-cash interest expense recorded by the Company would be greater over the term of the arrangement.

The following table shows the activity within the liability account (in thousands):

	Liability related to the sale of future royalties			Liability related to the sale of future royalties
Proceeds from sale of future royalties in December 2019	$	314,234
Non-cash interest expense		1,135
December 31, 2019		315,369		$	315,369
Non-cash collaboration royalty revenue		(9,428	)		(12,995	)
Non-cash interest expense		25,093			33,291
September 30, 2020	$	331,034
December 31, 2020					335,665
Non-cash collaboration royalty revenue					(8,561	)
Non-cash interest expense					16,935
June 30, 2021				$	344,039

The 2014 Incentive Plan (the 2014 Plan) provides for automatic annual increases in shares available for grant, beginning on January 1, 2015 through January 1, 2024. As of ~~September~~June 30, ~~2020~~,2021, there were ~~3,186,920~~4,103,718 shares reserved under the 2014 Plan for the future issuance of equity awards, ~~and 3,287,825~~3,956,907 shares reserved for the 2014 Employee Stock Purchase Plan, and 488,223 shares reserved for the Employment Inducement Plan.

The table below sets forth the stock-based compensation expense for the periods presented (in thousands):

	Three Months Ended September 30,				Nine Months Ended September 30,				Three Months Ended June 30,				Six Months Ended June 30,
	2020		2019		2020		2019		2021		2020		2021		2020
Cost of sales	$	133	$	319	$	313	$	404	$	223	$	112	$	602	$	180
Research and development		11,533		10,629		35,318		33,891		15,094		12,856		28,583		23,785
Selling, general and administrative		8,675		8,959		27,291		28,040		11,825		9,441		22,255		18,616
Total stock-based compensation expense	$	20,341	$	19,907	$	62,922	$	62,335	$	27,142	$	22,409	$	51,440	$	42,581

Basic net ~~loss~~income (loss) per share has been computed by dividing the net ~~loss~~income (loss) by the weighted-average number of shares of common stock outstanding during the period. Diluted net ~~loss~~income (loss) per share is calculated by dividing net ~~loss~~income (loss) by the weighted-average number of shares of common stock and potential dilutive securities outstanding during the period. For the three and six months ended June 30, 2021 and the six months ended June 30, 2020, there were no differences between basic and diluted net loss per share since the effect of the dilutive securities would have been antidilutive and therefore were excluded from the diluted net loss per share calculation. The following table sets forth the computation of the basic and diluted net income (loss) per share (in thousands, except share and per share data):

	Three Months Ended June 30,					Six Months Ended June 30,
	2021			2020		2021			2020
Net income (loss), basic and diluted	$	(122,428	)	$	25,315	$	(258,569	)	$	(93,710	)
Weighted-average shares used in computing net income (loss) per share, basic		67,607,752			59,995,617		67,356,443			58,996,278
Weighted-average effect of dilutive securities:
Options to purchase common stock and RSUs		—			1,150,614		—			—
Weighted-average shares used in computing net income (loss) per share, diluted		67,607,752			61,146,231		67,356,443			58,996,278
Net income (loss) per share:
Basic	$	(1.81	)	$	0.42	$	(3.84	)	$	(1.59	)
Diluted	$	(1.81	)	$	0.41	$	(3.84	)	$	(1.59	)

The following weighted-average outstanding common stock equivalents were excluded from the computation of diluted net ~~loss~~income (loss) per share for the periods presented because including them would have been antidilutive:

	Three Months Ended September 30,				Nine Months Ended September 30,				Three Months Ended June 30,				Six Months Ended June 30,
	2020		2019		2020		2019		2021		2020		2021		2020
Options to purchase common stock and restricted stock units		8,627,419		8,155,406		8,637,904		7,936,664		8,491,447		5,204,036		8,287,698		8,643,439
Employee stock purchase plan		35,282		33,094		19,701		18,547		8,621		10,952		4,334		5,476
Common stock warrants		—		149,700		39,337		149,700		—		—		—		59,222
		8,662,701		8,338,200		8,696,942		8,104,911		8,500,068		5,214,988		8,292,032		8,708,137

In July 2017, the Company entered into an At-The-Market, or ATM, sales agreement with Cowen and Company, LLC (Cowen), whereby the Company could sell up to $150.0 million in aggregate proceeds of common stock from time to time, with Cowen as its sales agent. During the three months ended June 30,October 2020, ~~the Company sold 283,333 shares of common stock, resulting in net proceeds of $20.4 million, after commissions and other offering costs. As of June 30, 2020, the Company had completed the sale of all~~

~~available amounts under the ATM facility.~~ ~~During the three and nine months ended~~ ~~September~~ 30, 2019, the Company sold NaN and 468,685 shares of common stock, respectively, resulting in net proceeds of approximately NaN and $24.8 million, respectively, after commissions and other offering costs.

~~In February 2019,~~ the Company completed an underwritten public offering in which ~~5,833,333~~5,111,110 shares of common stock were sold, which included ~~760,869~~666,666 shares purchased by the underwriters pursuant to an option granted to them in connection with the offering, at a public offering price of ~~$60.00~~$90.00 per share. ~~The~~For the year ended December 31, 2020, the total proceeds that the Company received from the offering were approximately ~~$330.4~~$435.6 million, net of underwriting discounts and commissions.

In May 2021, the Company entered into an Open Market Sale Agreement with Jefferies LLC, or Jefferies, pursuant to which the Company may offer and sell shares of the Company’s common stock having an aggregate offering proceeds up to $350.0 million, from time to time, in at-the-market offerings through Jefferies. As of June 30, 2021, the Company has 0t sold any shares under the arrangement.

Total accumulated other comprehensive income ~~(loss)~~ consisted of the following (in thousands):

On October 23, 2020, the Company announced that it had entered into a strategic collaboration and license agreement (the collaboration agreement) with Solid Biosciences, Inc. (Solid) to focus on the development and commercialization of new gene therapies for Duchenne muscular dystrophy (Duchenne) using its HeLa producer cell line (PCL) manufacturing platform. Under the terms of the collaboration agreement, Solid granted the Company an exclusive license for any pharmaceutical product that expresses Solid’s proprietary microdystrophin construct from AAV8 and variants thereof in clade E for use in the treatment of Duchenne and other diseases resulting from lack of functional dystrophin. The Company also entered into a stock purchase agreement and investor agreement with Solid in connection with the collaboration agreement, and purchased 7,825,797 shares of Solid’s common stock for an aggregate purchase price of $40.0 million. The Company will pay Solid up to $255.0 million in cumulative milestone payments per product upon achievement of specified milestone events, and tiered royalties on worldwide net sales at low double-digit to mid-teens percentages. Upon achievement of proof-of-concept, Solid has the right to opt-in to co-fund collaboration programs in return for participation in a profit share or increased royalty payments.

Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with the accompanying unaudited consolidated financial statements and related notes in Item 1 and with the audited consolidated financial statements and the related notes included in our Annual Report on Form 10-K for the year ended December 31, ~~2019~~2020 (the “Annual Report”).

Ultragenyx Pharmaceutical Inc. (we or the Company) is a biopharmaceutical company focused on the identification, acquisition, development, and commercialization of novel products for the treatment of serious rare and ultra-rare genetic diseases. We target diseases for which the unmet medical need is high, the biology for treatment is clear, and for which there are typically no approved therapies treating the underlying disease. Our strategy, which is predicated upon time- and cost-efficient drug development, allows us to pursue multiple programs in parallel with the goal of delivering safe and effective therapies to patients with the utmost urgency.

The continuing COVID-19 outbreak, which was declared a pandemic by the World Health Organization in March 2020, and the governmental efforts to mitigate the spread of the pandemic, has caused significant volatility and uncertainty in U.S. and international markets and could materially and adversely affect our business and operating results. As with so many other companies throughout the U.S. and globally, ourOur business operations have been and continue to be affected by the COVID-19 pandemic. In addition to some impact on our preclinical manufacturing activities and certain regulatory interactions, we have experienced interruptions to our clinical trial activities, primarily due to delays or disruptions to patient enrollment and dosing as a result of shelter-in-place orders or quarantines, and ~~we anticipate that~~ certain data from our gene therapy product candidates ~~may be~~was delayed as a result of the COVID-19 pandemic. The ~~FDA~~continuing outbreak has ~~also delayed certain key meetings or discussions with us related to one~~caused delays in delivery of ~~our product candidates, which may adversely impact the progression of our~~ancillary clinical ~~study for such product candidate. Although we have not experienced significant supply interruptions to date,~~trial materials as certain of our third-party manufacturers or suppliers have prioritized and allocated more resources and capacity to supply drug product or raw materials to other companies engaged in the study or manufacture of ~~potential~~ treatments or vaccinations for COVID-19. In response to these events, we are currently seeking alternative sources of supply of drug product or raw materials in an attempt to avoid future potential delays in supply of product, which may result in additional expenses. Social distancing measures and travel limitations in response to the pandemic have also made it difficult for us to identify new patients for our commercialized products, which may result in loss of revenue. We have also restricted access to our facilities to personnel and third parties who perform critical activities that must be performed on-site and as a result, most of our personnel currently work remotely. Such remote working policies may negatively impact productivity and disrupt our business operations.

As the COVID-19 global pandemic continues, we may experience lower revenue and increased expenses as a result of disruptions to our clinical trial, commercialization and regulatory activities, in addition to delays or shortages of drug product and raw materials. The magnitude and extent to which the pandemic may impact our business operations and operating results will continue to remain highly dependent on future developments, which are very uncertain and cannot be predicted with confidence. As a result, we cannot reliably estimate the extent to which the COVID-19 pandemic will impact our financial statements in ~~the fourth quarter~~2021 and beyond. See Item 1A: "Risk Factors" for additional details.

Our current approved therapies and clinical-stage pipeline consist of four product categories: biologics, small molecules, gene therapy, and nucleic acid product candidates. See section entitled “Recent Program Updates” below for a description of recent updates to certain of our approved therapies and clinical-stage pipeline products.

Our biologic products include approved therapies Crysvita® (burosumab) ~~and~~, Mepsevii® (vestronidase alfa): and UX143 in clinical development:

Crysvita is also approved in the United States for the treatment of FGF23-related hypophosphatemia in tumor-induced osteomalacia, or TIO, associated with phosphaturic mesenchymal tumors that cannot be curatively resected or localized in adults and pediatric patients 2 years of age and older. TIO can lead to severe hypophosphatemia, osteomalacia, fractures, fatigue, bone and muscle pain, and muscle weakness.

We are collaborating with ~~KHK,~~Kyowa Kirin Co., Ltd., or KKC (formerly Kyowa Hakko Kirin Co., Ltd., or KHK), and Kyowa Kirin, a wholly owned subsidiary of KKC, on the development and commercialization of Crysvita globally.

Our small molecule products include the approved therapy ~~Dojolvi™~~Dojolvi® (triheptanoin):

Our clinical-stage gene therapy pipeline includes DTX401, DTX301, DTX201 and ~~DTX401 in clinical development for the treatment of two diseases:~~UX701:

~~We have reported positive data from~~Our clinical-stage nucleic acid pipeline includes GTX-102 for the ~~three dose cohorts~~treatment of Angelman syndrome, and UX053 for the ~~Phase 1/2 study, with six responders~~treatment of the nine patients dosed in the study and all three patients at the highest dose cohort. A fourth cohort of three patients at the same cohort 2 and 3 dose of 1.0 × 10^13 GC/kg is underway using prophylactic steroids A fourth cohort of three patients at the same cohort 3 dose of 1.0 × 10^13 GC/kg is ongoing using prophylactic steroids. Data from this cohort are expected by the end of 2020. Phase 3 initiation is expected in 2021.GSDIII:

We have reported positive data from three cohorts at two dose levels of the Phase 1/2 study, with all patients showing a clinical response with improvements in glucose control and other metabolic parameters compared to baseline. The confirmatory expansion cohort of three patients at the second cohort dose of 6.0 × 10^12 GC/kg dose is ongoing, and we expect longer-term data to be available from this cohort by the end of 2020. A fourth cohort of three patients is ongoing at 6.0 x 10^12 GC/kg with a prophylactic steroid regimen. Data from this cohort is not expected to impact the timing of a Phase 3 study, which is expected to initiate in the first half of 2021.

~~Our nucleic acid pipeline includes the option to acquire GTX-102 in clinical development for the treatment of Angelman syndrome:~~

With our partner GeneTx, we have reported positive interim data from the ongoing Phase 1/2 study indicating substantial improvements in all patients in at least two disease domains including communication, behavior, sleep, gross motor function, and fine motor function as measured by the Clinical Global Impression of Improvement Scale for Angelman Syndrome, or CGI-I-AS for Patients 1 through 4 at day 128, and Patient 5 at Day 86. At the highest doses, all five patients experienced a serious adverse event (SAE) of lower extremity weakness believed to be related to local inflammation due to GTX-102. Following these events, the companies paused enrollment and dosing. These SAEs were assessed as mild or moderate in severity and have generally improved over a period of a few weeks while disease domain improvements have been sustained for three months. We and GeneTx plan to amend the study protocol to reduce the dose-level range and modify the administration process, which we expect to reduce further drug-related SAEs.

The following table summarizes our approved products and clinical product candidate pipeline:

Crysvita for the treatment of ~~X-linked hypophosphatemia, or XLH~~X-Linked Hypophosphatemia (XLH)

~~On October 5, 2020~~In July 2021, our collaboration partner KKC, announced that the European Commission (EC) approved Crysvita for self-administration as a treatment option when recommended by the treating physician, for pediatric and adult patients with XLH.

In July 2021, Crysvita wasapproved by Colombia’s Instituto Nacional de Vigilancia de Medicamentos y Alimentos, or INVIMA, for treatment of XLH in ~~older adolescents~~adult and ~~adults. Crysvita was previously approved by the EC for the treatment of XLH with radiographic evidence of bone disease in children~~pediatric patients one year of age and older and adolescents with growing skeletons. With this expanded approval, all adolescents with radiographic evidence of bone disease, regardless of growth status, as well as adults with XLH are now also eligible for treatment with Crysvita in the EU.older.

~~A fourth cohort of three patients at the same cohort 3 dose of 1.0 × 10^13 GC/kg is ongoing using prophylactic steroids. Data from this cohort are expected by the end of 2020.~~ ~~We are also continuing Phase 3 planning and discussions with the FDA, with the intent to start the Phase 3 study in 2021.~~

~~In October 2020, we announced that~~ ~~a fourth cohort of three patients is ongoing at 6.0 x 10^12 GC/kg, the same dose as cohorts two and three, with a prophylactic steroid regimen~~. Data from this cohort is not expected to impact the timing of a potential Phase 3 study. Additional data on Cohort 3, dosed at 6.0 x 10^12 GC/kg with an optimized reactive steroid regimen, are expected to be released in the fourth quarter of 2020. Following meetings with the FDA and finalization of the study design, we plan to initiate the study in the first half of 2021.

In ~~October 2020,~~the second quarter of 2021, we ~~along~~announced that Health Canada (HC) cleared a protocol amendment and that the U.K. Medicines and Healthcare Products Regulatory Agency (MHRA) approved a Clinical Trial Application (CTA) to begin treating patients in Canada and the U.K. with ~~our partner GeneTx, announced positive interim~~Angelman syndrome.

Following a productive meeting with the FDA, we submitted an amended protocol. We have received feedback on the amended protocol and will make additional revisions in order to resume the study in the U.S.

Clinical data from newly treated patients in the ~~ongoing~~U.K. and Canada are currently expected to be presented before the end of 2021.

At the American Society of Gene & Cell Therapy (ASGCT) Annual Meeting in May 2021 we presented additional long-term clinical data demonstrating a durable response lasting more than 2.5 years following treatment with DTX401 in patients with GSDIa. We are currently in the process of initiating a Phase 3 study with a 48-week primary efficacy analysis period and plan to enroll approximately 50 patients 8 years of age and older, randomized 1:1 to DTX401 (1.0 x 10^13 GC/kg dose) or placebo. The coprimary endpoints are the reduction in oral glucose replacement with cornstarch while maintaining and improved glucose control assessed by continuous glucose monitoring. The first patient in the Phase 3 study is currently expected to be dosed in the second half of 2021.

At the ASGCT Annual Meeting in May 20201 we presented additional long-term clinical data showing durable metabolic control and sustained responses lasting more than three years following treatment with DTX301 in patients with OTC deficiency. We are currently in the process of initiating a Phase 3 study that will include a 64-week primary efficacy analysis period and plan to enroll approximately 50 patients 12 years of age and older, randomized 1:1 to DTX301 (1.7 x 10^13 GC/kg dose) or placebo. The co-primary endpoints are the percentage of patients who achieve a response as measured by discontinuation or reduction in baseline disease management and the 24-hour plasma ammonia levels. The first patient in the Phase 3 study is currently expected to be dosed in the second half of 2021.

We are currently in the process of initiating a seamless, single-protocol Phase 1/2/3 study. The first part of the study is expected to enroll approximately 27 patients (nine per cohort), randomized 2:1 to DTX701, manufactured using the company’s proprietary HeLa 2.0 producer cell line (PCL) process at the 2,000 liter scale, or placebo. The dose cohorts will be enrolled sequentially using ascending doses. The patients will be followed for 52 weeks before transitioning to long-term follow-up and selecting a pivotal dose. The dose will be determined based on the safety profile, changes in biomarkers of copper metabolism, and the reduction in the use of the current standard of care. The first patient in the Phase 1/2/3 study is expected to be dosed in the second half of 2021.

In June 2021, UX053 was granted Orphan Drug Designation (ODD) in the U.S. by the FDA and in July 2021, ODD was granted by the European Commission (EC). Enrollment in a Phase 1/2 study is currently expected to begin in the second half of GTX-102, an investigational antisense oligonucleotide for the treatment of Angelman Syndrome. Preliminary results from the Phase 1/2 study indicate substantial improvements in all patients in at least two disease domains including communication, behavior, sleep, gross motor function, and fine motor function as measured by the CGI-I-AS for Patients 1 through 4 at day 128, and Patient 5 at Day 86. At the highest doses, all five patients experienced a SAE of lower extremity weakness believed to be related to local inflammation due to GTX-102. Following these events, the companies paused enrollment and dosing. These SAEs were assessed as mild or moderate in severity and have generally improved over a period of a few weeks while disease domain improvements have been sustained for three months. We and GeneTx plan to amend the study protocol to reduce the dose-level range and modify the administration process, which we expect to reduce further drug-related SAEs.

~~In September 2020, we announced the hire of Ernie Meyer, Chief Human Resources Officer and Executive Vice President.In this newly created role, Mr. Meyer will lead all aspects of the Global Human Resources and Facilities operations. He will report to Emil D. Kakkis and will serve on the Executive Leadership Team.~~

In September 2020, we also announced the hire of Mardi C. Dier, Chief Financial Officer (CFO) and Executive Vice President. In this role, Ms. Dier will be responsible for leading the corporate finance, strategy, investor relations, corporate communications, and information technology functions. She will report to Emil D. Kakkis and will serve on the Executive Leadership Team.

In October 2020, we announced a strategic collaboration with Solid Biosciences, Inc. (Solid) to develop and commercialize new gene therapies for Duchenne Muscular Dystrophy. This collaboration combines Solid’s differentiated microdystrophin construct and our HeLa Producer Cell Line, or PCL, manufacturing platform for use with AAV8 and variants. Under terms of the collaboration, Solid received a $40.0 million payment for our investment and may receive up to $255.0 million in cumulative milestone payments per product upon achievement of specified milestone events, and tiered royalties on worldwide net sales at low double-digit to mid-teens percentages. Upon achievement of proof-of-concept, Solid has the right to opt-in to co-fund collaboration programs in return for participation in a profit share or increased royalty payments.2021.

We are a biopharmaceutical company with a limited operating history. To date, we have invested substantially all of our efforts and financial resources in identifying, acquiring, and developing our products and product candidates, including conducting clinical studies and providing selling, general and administrative support for these operations. To date, we have funded our operations primarily from the sale of our equity securities, ~~and~~ the sale of certain future ~~royalties.~~royalties, and strategic collaboration arrangements.

We have incurred net losses in each year since inception. Our net loss was ~~$68.8~~$122.4 million and ~~$162.6~~$258.6 million for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020, respectively, and $113.0 million and $308.9~~2021, respectively. Our net income was $25.3 million for the three ~~and nine~~ months ended ~~September~~June 30, ~~2019, respectively.~~2020 and our net loss was $93.7 million for the six months ended June 30, 2020. Net loss for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020~~2021 included ~~a $11.5~~losses of $31.0 million ~~loss~~ and ~~a $91.3~~$51.7 million ~~gain, respectively,~~ resulting from changes in fair value of our investments in Arcturus Therapeutics Holdings Inc. (Arcturus) and Solid Biosciences Inc. (Solid) equity securities. Net income (loss) for the three and six months ended June 30, 2020 included gains of $95.2 million and $102.9 million, respectively, resulting from changes in the fair value of our investment in ~~Arcturus equity securities. Substantially~~Arcturus. Other than changes in the fair value of our investments, substantially all of our net losses have resulted from costs incurred in connection with our research and development programs and from selling, general and administrative costs associated with our operations.

For the three months ended ~~September~~June 30, ~~2020,~~2021, our total revenues increased to ~~$81.5~~$87.0 million, compared to ~~$25.8~~$61.7 million for the same period in ~~2019~~2020 and for the ~~nine~~six months ended ~~September~~June 30, ~~2020,~~2021, increased to ~~$179.5~~$186.4 million, compared to ~~$68.1~~$98.0 million for the same period in ~~2019.~~2020. Revenue for the three ~~and nine~~ months ended ~~September~~June 30, 2021 and 2020 included ~~$32.9~~$22.0 million and ~~$51.7~~$18.9 million, respectively, and for the six months ended June 30, 2021 and 2020 included $64.7 million and $18.9 million, respectively, in revenue from our collaboration and license agreement with Daiichi Sankyo Co., Ltd. (Daiichi Sankyo) which we executed in March 2020. The remainder of the increase was driven by higher revenue from Crysvita collaboration revenue in the profit-share territory, an increase in revenue for our approved products and an increase in collaboration royalty revenue.

As of ~~September~~June 30, ~~2020,~~2021, we had ~~$765.5~~$973.8 million in available cash, cash equivalents, and ~~available-for-sale investments.~~marketable debt securities.

Our management’s discussion and analysis of our financial condition and results of operations is based on our consolidated financial statements, which have been prepared in accordance with U.S. generally accepted accounting principles, or GAAP. The preparation of these consolidated financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements, as well as the reported expenses incurred during the reporting periods. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions. There have been no material changes in our critical accounting policies during the ~~nine~~six months ended ~~September~~June 30, ~~2020~~2021, as compared to those disclosed in “Management’s Discussion and Analysis of Financial Condition and Results of Operations — Critical Accounting Policies and Significant Judgments and Estimates” in our Annual Report.

Comparison of the three and ~~nine~~six months ended ~~September~~June 30, ~~2020~~2021 to the three and ~~nine~~six months ended ~~September~~June 30, ~~2019:~~2020:

	Three Months Ended September 30,				Dollar			%			Three Months Ended June 30,				Dollar			%
	2020		2019		Change			Change			2021		2020		Change			Change
Collaboration and license revenue:
Crysvita collaboration revenue in profit-share territory	$	34,058	$	19,534	$	14,524			74	%	$	41,756	$	29,806	$	11,950			40	%
Crysvita royalty revenue in European territory		—		1,950		(1,950	)		-100	%		228		1,498		(1,270	)		-85	%
Daiichi Sankyo		32,866		—		32,866		*				21,956		18,857		3,099			16	%
Bayer		—		101		(101	)		-100	%
Total collaboration and license revenue		66,924		21,585		45,339			210	%		63,940		50,161		13,779			27	%
Product sales:
Crysvita		3,277		1,140		2,137			187	%		2,900		2,549		351			14	%
Mepsevii		4,076		2,361		1,715			73	%		5,399		4,185		1,214			29	%
Dojolvi		3,862		714		3,148			441	%		10,047		1,332		8,715			654	%
Total product sales		11,215		4,215		7,000			166	%		18,346		8,066		10,280			127	%
Crysvita non-cash collaboration royalty revenue		3,331		—		3,331		*				4,689		3,482		1,207			35	%
Total revenues	$	81,470	$	25,800	$	55,670			216	%	$	86,975	$	61,709	$	25,266			41	%
* not meaningful

	Nine Months Ended September 30,				Dollar			%			Six Months Ended June 30,				Dollar			%
	2020		2019		Change			Change			2021		2020		Change			Change
Collaboration and license revenue:
Crysvita collaboration revenue in profit-share territory	$	91,079	$	48,721	$	42,358			87	%	$	78,016	$	57,021	$	20,995			37	%
Crysvita royalty revenue in European territory		1,498		5,896		(4,398	)		-75	%		228		1,498		(1,270	)		-85	%
Daiichi Sankyo		51,723		—		51,723		*				64,706		18,857		45,849			243	%
Bayer		—		453		(453	)		-100	%
Total collaboration and license revenue		144,300		55,070		89,230			162	%		142,950		77,376		65,574			85	%
Product sales:
Crysvita		7,436		2,734		4,702			172	%		8,772		4,159		4,613			111	%
Mepsevii		11,686		8,274		3,412			41	%		9,006		7,610		1,396			18	%
Dojolvi		6,638		2,043		4,595			225	%		17,081		2,776		14,305			515	%
Total product sales		25,760		13,051		12,709			97	%		34,859		14,545		20,314			140	%
Crysvita non-cash collaboration royalty revenue		9,428		—		9,428		*				8,561		6,097		2,464			40	%
Total revenues	$	179,488	$	68,121	$	111,367			163	%	$	186,370	$	98,018	$	88,352			90	%

For the three ~~months~~ and ~~nine~~six months ended ~~September~~June 30, 2021 ~~30, 2020,~~, the Company’s share of Crysvita collaboration revenue in the profit-share territory increased by $~~14.5~~12.0 million and ~~$42.4~~$21.0 million, respectively, as compared to the same periods in ~~2019.~~2020. The increase primarily reflects the continuing increase in demand for Crysvita due to an increase in the number of patients on therapy.

~~In December 2019, we sold the rights to the Crysvita royalty payments in the European territory, including the United Kingdom and Switzerland, to Royalty Pharma.~~ Beginning in 2020, we ~~record~~have recorded the royalty revenue as non-cash royalty revenues. During the ~~nine~~three months ended ~~September~~June 30, 2021 and 2020, there ~~was a change~~were changes in ~~estimate of~~the estimates on the revenue reserves, related to sales made prior to January 1, ~~2020. As~~2020 and as a result, we recorded ~~an additional~~$0.2 million and $1.5 million, respectively, as royalty revenue in European territory.

In March 2020, we executed a license agreement with Daiichi Sankyo, pursuant to which we granted Daiichi Sankyo a non-exclusive license to intellectual property, including know-how and patent applications, with respect to our HeLa PCL and HEK293 transient transfection manufacturing technology platforms for AAV-based gene therapy products. We will also provide certain technical assistance and technology transfer services during the technology transfer period of three years to enable Daiichi Sankyo to use the technologies for its internal gene therapy programs. For the three and ~~nine~~six months ended ~~September~~June 30, 2021 ~~30, 2020, we recognized $32.9 million and $51.7 million, respectively, as~~, the collaboration and license revenue from this ~~arrangement.~~arrangement, which is recognized based on the progress toward complete satisfaction of the individual performance obligation using an input measure, increased by $3.1 million and $45.8 million, respectively, as compared to the same periods in 2020. We expect to recognize ~~a substantial majority of~~ the ~~$183.6 million transaction price~~remaining revenue allocated to the intellectual property and the transfer services as revenue ~~over the technology transfer service period, which is currently estimated to be substantially complete~~ by the end of 2021.

The ~~decreases in collaboration and license revenue from our research arrangement with Bayer were due to the transition of the clinical development to Bayer as part of the research arrangement.~~

~~The~~ increases in product sales of ~~$7.0~~$10.3 million and ~~$12.7~~$20.3 million for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020,~~2021, respectively, compared to the same periods in ~~2019~~2020 were primarily due to the commercial launch of Dojolvi in the United States in the third quarter of 2020, continuing increase in demand for ~~our other products,~~Crysvita and Mepsevii, and an increase in sales of ~~certain products~~Dojolvi under our named patient program in certain countries.

The increases in Crysvita non-cash collaboration royalty revenue of $1.2 million and $2.5 million for the three and six months ended June 30, 2021, respectively, compared to the same periods in 2020 primarily reflects the launch progress by our collaboration partner in European countries and an increase in the number of patients on therapy.

Cost of sales ~~related to our approved products decreased~~increased by ~~$0.3~~$1.3 million and ~~$3.3~~$10.0 million for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020, respectively,~~2021 compared to the same periods in ~~2019.~~2020. The increase in cost of sales for the ~~nine~~three months ended ~~September~~June 30, 2021 compared to the same period in 2020 ~~includes~~was due to an increase in demand for our approved products including Dojolvi, which launched in the third quarter of 2020. The increase in cost of sales for the six months ended June 30, 2021 compared to the same period in 2020 was due to an increase in demand for our approved products including Dojolvi, which launched in the third quarter of 2020 and a credit for the manufacturing of future inventory batches ~~with an estimated value~~ of $4.6 million ~~which was recorded during the first quarter of 2020, and was agreed to during the period with one of our manufacturers~~ due to certain inventory batches that did not meet specified quality ~~standards.~~standards which we recorded during the six months ended June 30, 2020. The ~~Company previously recorded~~increase was offset by additional reserves of ~~$1.9~~$1.7 million ~~on these~~for excess inventory ~~batches~~write-downs recorded during the ~~three~~six months ended ~~September~~June 30, 2019. The decrease in cost of sales for the three months ended September 30, 2020 compared to the same period in 2019 was due to the reserve on these inventory batches recorded in 2019, offset by an increase in demand for our approved products and the launch of Dojolvi in the third quarter of 2020.2021.

Prior to the approval of our ~~approved~~ products, manufacturing and related costs were expensed; accordingly, these costs were not capitalized and as a result are not fully reflected in the costs of sales during the ~~current period.~~three and six months ended June 30, 2021 and 2020. If manufacturing and related costs were capitalized prior to the approval period and the $1.7 million in write downs for the six months ended June 30, 2021 and the credit of $4.6 million for the six months ended June 30, 2020 as noted above were excluded, we estimate that cost of sales for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020~~2021 would have been approximately ~~$2.5~~$3.2 million and ~~$5.6~~$7.0 million, respectively, and for the three and ~~nine~~six months ended ~~September~~June 30, ~~2019~~2020 would have been approximately ~~$2.7~~$1.9 million and ~~$4.4~~$3.1 million, respectively, for our commercial product sales. We expect our gross margin percentage to decrease as we produce approved products ~~at costs~~ that reflect the full costs of manufacturing ~~similar to other biologic products~~ and as we deplete inventories that we had expensed prior to receiving ~~FDA~~ approval.

Three Months Ended September 30,

Dollar

%

2020

2019

Change

Change

Crysvita
$
6,306

$
8,814

$
(2,508
)

-28
%
Mepsevii

3,117

4,005

(888
)

-22
%
Dojolvi

7,296

10,238

(2,942
)

-29
%
DTX301

7,001

11,401

(4,400
)

-39
%
DTX401

10,633

7,985

2,648

33
%
GTX102

873

20,000

(19,127
)

-96
%
Translational research

25,340

12,893

12,447

97
%
Other research costs

26,748

24,808

1,940

8
%
Total research and development expenses
$
87,314

$
100,144

$
(12,830
)

-13
%

Nine Months Ended September 30,

Dollar

%

2020

2019

Change

Change

Crysvita
$
21,405

$
29,345

$
(7,940
)

-27
%
Mepsevii

10,327

13,660

(3,333
)

-24
%
Dojolvi

26,733

27,678

(945
)

-3
%
DTX301

24,446

31,250

(6,804
)

-22
%
DTX401

20,532

24,378

(3,846
)

-16
%
GTX102

26,946

20,000

6,946

35
%
Translational research

72,547

37,910

34,637

91
%
Other research costs

78,048

90,073

(12,025
)

-13
%
Total research and development expenses
$
280,984

$
274,294

$
6,690

2
%

Research and development expenses ~~decreased $12.8~~include internal and external costs incurred for research and development of our programs and program candidates and expenses related to certain technology that we acquire or license through business development transactions. These expenses consist primarily of clinical studies performed by contract research organizations, manufacturing of drug substance and drug product performed by contract manufacturing organizations, materials and supplies, fees from collaborative and other arrangements including milestones, licenses and other fees, personnel costs including salaries, benefits and stock-based compensation, and overhead allocations consisting of various support and infrastructure costs.

Commercial programs include costs for disease monitoring programs and certain regulatory and medical affairs support activities for programs after commercial approval. Clinical programs include study conduct and manufacturing costs related to clinical program

candidates. Translational research includes costs for preclinical study work and costs related to preclinical programs prior to IND filing. Upfront license and milestone fees include any significant expenses related to strategic licensing agreements. Infrastructure costs include direct costs related to laboratory, IT, and equipment depreciation costs, and overhead allocations for human resources, IT and other allocable costs.

The following table provides a breakout of our research and development expenses by major program type and business activities:

	Three Months Ended June 30,				Dollar			%
	2021		2020		Change			Change
Commercial programs	$	12,641	$	13,839	$	(1,198	)		-9	%
Clinical programs:
Gene therapy programs		29,735		9,059		20,676			228	%
Nucleic acid and other biologic programs		10,571		429		10,142		*
Translational research		16,647		16,067		580			4	%
Upfront license and milestone fees		—		1,200		(1,200	)		-100	%
Infrastructure		14,374		12,787		1,587			12	%
Stock-based compensation		15,094		12,856		2,238			17	%
Other research and development		14,143		14,472		(329	)		-2	%
Total research and development expenses	$	113,205	$	80,709	$	32,496			40	%
* not meaningful

	Six Months Ended June 30,				Dollar			%
	2021		2020		Change			Change
Commercial programs	$	26,302	$	19,696	$	6,606			34	%
Clinical programs:
Gene therapy programs		51,097		22,259		28,838			130	%
Nucleic acid and other biologic programs		19,595		1,332		18,263		*
Small molecule programs		—		7,440		(7,440	)		-100	%
Translational research		29,260		32,372		(3,112	)
Upfront license and milestone fees		50,000		33,200		16,800			51	%
Infrastructure		29,236		25,200		4,036			16	%
Stock-based compensation		28,583		23,785		4,798			20	%
Other research and development		26,650		28,386		(1,736	)		-6	%
Total research and development expenses	$	260,723	$	193,670	$	67,053			35	%

Total research and development expenses increased $32.5 million and ~~increased $6.7~~$67.1 million for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020,~~2021, respectively, compared to the same periods in ~~2019.~~2020. The ~~changes~~change in research and development expenses was primarily due to:

We expect our annual research and development expenses to continue to increase in the future as we advance our product candidates through clinical development. The timing and amount of expenses incurred will depend largely upon the outcomes of current or future clinical studies for our product candidates as well as the related regulatory requirements, manufacturing costs, and any costs associated with the advancement of our preclinical programs.

Selling, general and administrative expenses increased ~~$1.1~~$11.2 million and ~~$12.2~~$16.9 million for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020,~~2021, respectively, compared to the same periods in ~~2019.~~2020. The increases in selling, general and administrative expenses were primarily due to increases in personnel costs resulting from an increase in the number of employees in support of our commercial activities, commercialization costs, and professional services ~~costs, partially offset by lower travel and related expenses due to travel restrictions in connection with the COVID-19 pandemic.~~costs.

We expect selling, general and administrative expenses to continue to increase in the future to support our organizational growth ~~and for our expected staged build out of our commercial organization over the next several years~~ related to our approved products and multiple clinical-stage product candidates.

Interest income decreased ~~$2.0~~$1.4 million and ~~$4.4~~$3.6 million for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020,~~2021, respectively, compared to the same periods in ~~2019,~~2020, primarily due to lower portfolio yields as a result of ~~federal reserve~~a decrease in interest ~~rate cuts that were made over the past year.~~rates, partially offset by higher balances in our marketable debt securities.

Change in Fair Value of ~~Investments in~~ Equity ~~Securities~~Investments (dollars in thousands)

The fair value of our equity investments ~~in equity securities~~ decreased by ~~$13.7~~$31.0 million and ~~increased by $79.4~~$51.7 million ~~for~~during the three and ~~nine~~six months ended ~~September~~June 30, 2021, respectively, due to decreases in the fair value of Arcturus and Solid common stock, resulting in unrealized losses on our investments in Arcturus common stock of $16.4 million and $21.0 million during the three and six months ended June 30, 2021, respectively and unrealized losses on our investments in Solid common stock of $14.6 million and $30.7 million during the three and six months ended June 30, 2021, respectively. The fair value of our equity investments increased by $95.2 million and $102.9 million during the three and six months ended June 30, 2020, respectively, due to increases in the ~~remeasurement to~~ fair value of ~~the~~ Arcturus ~~common stock and the exercise of the option to purchase additional Arcturus stock.~~equity investments. Given the historic volatility of the publicly traded stock price of Arcturus and Solid, the fair value adjustments of our equity investments ~~in Arcturus~~ may be subject to wide fluctuations which may have a significant impact on our earnings in future periods.~~See Item 1A: "Risk Factors" for additional details.~~

Non-cash Interest Expense on Liability Related to the Sale of Future Royalties (dollars in thousands)

The non-cash interest expense on liability related to the sale of future royalties ~~of $8.6~~increased by $0.1 million and ~~$25.1~~$0.4 million for the three and ~~nine~~six months ended ~~September~~June 30, 2021, respectively, compared to the same periods in 2020 ~~respectively, were~~ due to the ~~interest accreted on~~increase in the liability related to the sale of future royalties for net sales of Crysvita in the European territory, ~~pursuant~~partially offset by a decrease in the effective interest rate for the three and six months ended June 30, 2021 compared to ~~the Royalty Purchase Agreement entered into with RPI~~same periods in ~~December 2019.~~2020. To the extent the royalty payments are greater or less than our initial estimates or the timing of such payments is materially different than our original estimates, we will prospectively adjust the effective interest rate.

Other ~~income (expense)~~expense increased by ~~$0.7~~$0.3 million and ~~$1.2~~$0.6 million for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020,~~2021, respectively, compared to the same periods in ~~2019.~~2020. The ~~fluctuations were~~increase was primarily due to fluctuations in foreign exchange rates.

The provision for incomes taxes increased by a nominal amount ~~and $0.4 million~~ for the three and ~~nine~~six months ended ~~September~~June 30, ~~2020,~~2021, respectively, compared to the same periods in ~~2019. This was primarily due to the increase in commercialization activities in Europe and Latin America.~~2020.

~~We have assessed and have determined there is no expected material impact from the Coronavirus Aid Relief and Economic Security (CARES) Act on our future income tax provisions.~~

To date, we have funded our operations primarily from the sale of our equity securities, ~~and~~revenues from our commercial products, the sale of certain future ~~royalties.~~royalties, and strategic collaboration arrangements.

As of ~~September~~June 30, ~~2020,~~2021, we had ~~$765.5~~$973.8 million in available cash, cash equivalents, and ~~available-for-sale investments.~~ marketable debt securities. We believe that our existing capital resources will be sufficient to fund our projected operating requirements for at least the next twelve months. Our cash, cash equivalents, and ~~available-for-sale~~ ~~investments~~marketable debt securities are held in a variety of deposit accounts, interest-bearing accounts, corporate bond securities, U.S government securities, asset-backed securities, and money market funds. Cash in excess of immediate requirements is invested with a view toward liquidity and capital preservation, and we seek to minimize the potential effects of concentration and credit risk.

In ~~February 2019,~~May 2021, we ~~completed~~entered into an ~~underwritten public offering in~~Open Market Sale Agreement with Jefferies pursuant to which we ~~sold 5,833,333~~may offer and sell shares of our common stock ~~and received net~~having an aggregate offering proceeds ~~of approximately $330.4 million. In December 2019, we received net proceeds of $314.2~~up to $350.0 million, from time to time, in at-the-market offerings through Jefferies. As of June 30, 2021, we had not sold any shares under the ~~sale of future~~ ~~royalties to RPI.~~ arrangement.

In March 2020, we received $75.0 million in cash from the sale of 1,243,913 shares of our common stock to Daiichi Sankyo and in April 2020, we received $125.0 million infrom an upfront payment related to the Daiichi Sankyo License Agreement. ~~During the three~~In November 2020, we completed an underwritten public offering in which we sold 5,111,110 shares of common stock and ~~nine months ended~~ ~~September~~ ~~30,~~received net proceeds of $435.6 million. In December 2020, ~~the~~we sold 800,000 shares of Arcturus common stock and received net proceeds ~~from our at-the-market, or ATM, offering were none and $20.4 million, respectively, after commissions and other offering costs. As~~ of ~~September~~ ~~30, 2020, we had completed the sale of all available amounts under our ATM facility.~~$79.8 million.

The following table summarizes our cash flows for the periods indicated (in thousands):

	Nine Months Ended September 30,						Six Months Ended June 30,
	2020			2019			2021			2020
Cash used in operating activities	$	(69,768	)	$	(273,344	)	$	(224,702	)	$	(7,801	)
Cash used in investing activities		(277,022	)		(80,305	)		(223,670	)		(181,264	)
Cash provided by financing activities		110,561			363,863			25,277			91,426
Effect of exchange rate changes on cash		239			(502	)		(323	)		(198	)
Net increase (decrease) in cash, cash equivalents and restricted cash	$	(235,990	)	$	9,712
Net decrease in cash, cash equivalents and restricted cash							$	(423,418	)	$	(97,837	)

Our primary use of cash is to fund operating expenses, which consist primarily of research and development and commercial expenditures. Due to our significant research and development expenditures, we have generated significant operating losses since our inception. Cash used to fund operating expenses is affected by the timing of when we pay these expenses, as reflected in the change in our outstanding accounts payable and accrued expenses.

Cash used in operating activities for the ~~nine~~six months ended ~~September~~June 30, ~~2020~~2021 was ~~$69.8~~$224.7 million and reflected a net loss of ~~$162.6~~$258.6 million ~~$91.3~~and $8.6 million for non-cash collaboration royalty revenues related to the sale of future royalties to RPI Finance Trust (RPI), an ~~unrealized gain~~affiliate of Royalty Pharma, offset by non-cash charges of $51.3 million for stock-based compensation, $2.5 million for the amortization of the premium paid on purchased marketable debt securities, $6.5 million for depreciation and amortization, $51.7 million for a change in fair value of equity ~~securities~~investments from Arcturus and ~~$9.4~~Solid, and $16.9 million for non-cash interest incurred on the liability related to the sale of future royalties to RPI. Cash used in operating activities also reflected a $1.7 million decrease due to an increase in accounts receivable primarily related to higher revenues, a $2.2 million decrease due to an increase in inventory, a $9.0 million decrease due to an increase in prepaid expenses and other current assets primarily due to an increase in prepaid subscriptions, prepaid clinical studies, and prepaid fixed assets, a $11.5 million decrease in accounts payable, accrued liabilities, and other liabilities primarily due to the payout of 2020 annual bonuses, and a decrease of $62.7 million in contract liabilities, related to the revenue recognized from the license agreements with Daiichi Sankyo.

Cash used in operating activities for the six months ended June 30, 2020 was $7.8 million and reflected a net loss of $93.7 million, $0.1 million for the amortization of the discount paid on purchased investments, $102.9 million for changes in the fair value of equity investments from Arcturus, and $6.1 million for non-cash collaboration royalty revenues related to the sale of future royalties to Royalty Pharma, offset by non-cash charges of ~~$62.9~~$42.6 million for stock-based compensation, ~~$0.2 million for the amortization of the premium paid on purchased investments, $9.1~~$6.0 million for depreciation, ~~$0.2 million of non-cash foreign currency remeasurement losses in connection with~~ ~~fluctuations of exchange rates related to intercompany transactions with foreign subsidiaries that are denominated in our reporting currency,~~ and ~~$25.1~~$16.5 million for non-cash interest incurred on the liability related to the sale of future royalties to Royalty Pharma. Cash used in operating activities also reflected a ~~$2.6~~decrease of $6.1 million ~~decrease due to an increase in inventory for Mepsevii and Dojolvi, a $12.5 million decrease~~ due to an increase in prepaid expenses and other current assets primarily due to an increase in prepaid manufacturing and a ~~$7.3~~$8.8 million decrease in accounts payable, accrued liabilities, and other liabilities primarily due to a decrease in accrued bonus due to the ~~addition~~payout of the ~~right-of-use assets net of amortization during the period,~~2019 annual bonus, offset by ~~$5.1~~a $9.5 million increase due to a decrease in accounts receivable primarily related to change in the timing of billing to a collaboration partner offset by a ~~$2.8~~$8.5 million receivable related to the license agreement with Daiichi Sankyo in June 2020, a $0.5 million increase ~~in accounts payable, accrued liabilities, and other liabilities primarily~~ due to ~~completion of laboratory construction amounts that were accrued at the beginning of the year, net of~~ a decrease in ~~accrued bonus due to the payout of the 2019 annual bonus,~~inventory, and an increase of ~~$102.9~~$134.9 million in contract liabilities ~~net,~~ related to the license agreements with Daiichi ~~Sankyo, and a $7.6 million increase due to the addition of lease liabilities, net of amortization during the period.~~Sankyo.

~~Cash used in operating activities for the nine months ended~~ ~~September 30, 2019~~ was $273.3 million and reflected a net loss of $308.9 million, $4.9 million for the amortization of the discount paid on purchased investments, and $12.0 million for an unrealized gain in the Arcturus equity securities, offset by non-cash charges of $62.3 million for stock-based compensation, $6.4 million for depreciation and amortization of an intangible asset acquired, and $0.9 million of non-cash foreign currency remeasurement losses in connection with ~~fluctuations of exchange rates related to intercompany transactions with foreign subsidiaries that are denominated in our reporting currency~~. Cash used in operating activities also reflected a $10.4 million decrease due to an increase in accounts receivable due to the commercialization of our products, a $6.6 million decrease due to an increase in inventory as we build out our commercial inventory supplies as we commercialize Mepsevii, a decrease of $5.9 million due to an increase in prepaid expenses and other assets primarily due to an increase in general receivables, amounts due from a collaboration partner, and amounts owed for a tenant improvement allowance, and a $15.6 million decrease due to the addition of the right-of-use assets net of amortization during the period, offset by a $4.0 million increase in accounts payable, accrued liabilities, and other liabilities primarily due to increased commercial and research activities and the timing of the receipt of invoices, and $17.1 million increase due to the addition of lease liabilities net of amortization during the period.

Cash used in investing activities for the ~~nine~~six months ended ~~September 30, 2020~~June, 2021 was ~~$277.0~~$223.7 million and related to purchases of property, plant, and equipment of ~~$22.0~~$36.5 million and purchases of marketable debt securities of $664.3 million, offset by proceeds from the sale of marketable debt securities of $70.5 million and maturities of marketable debt securities of $406.6 million.

Cash used in investing activities for the six months ended June 30, 2020 was $181.3 million and related to purchases of property, plant, and equipment of $18.2 million, purchases of investments of ~~$648.5~~$456.3 million, ~~the purchase of investments in equity securities of $10.2 million related to $9.6 million for~~and the exercise of the option to purchase

additional Arcturus shares ~~and $0.6~~for $9.6 million, ~~related to the DiaCarta warrant, purchase of a convertible notes receivable of $1.9 million from DiaCarta, and the payment of $2.3 million on the FDA approval of Dojolvi recorded as intangible assets,~~ offset by proceeds from the sale of investments of ~~$40.4~~$28.9 million and maturities of investments of ~~$367.4~~$274.0 million.

~~Cash used in investing activities for the nine months ended~~ ~~September 30, 2019~~ was $80.3 million and related to purchases of investments of $610.3 million, purchases of property and equipment of $13.3 million, and purchases of equity securities from Arcturus of $14.3 million, offset by proceeds from maturities of investments of $522.5 million and the sale of investments of $35.1 million.

Cash provided by financing activities for the ~~nine~~six months ended ~~September~~June 30, 2021 was $25.3 million and was primarily comprised of $25.5 million in net proceeds from the issuance of common stock pursuant to equity plan awards.

Cash provided by financing activities for the six months ended June 30, 2020 was ~~$110.6~~$91.4 million and was comprised of $55.3 million from the sale of common stock in connection with the license agreement with Daiichi Sankyo in March 2020, $20.4 million in net proceeds from the sale of common stock in our ATM offering, and ~~$35.1~~$15.9 million in net proceeds from the issuance of common stock pursuant to the exercise of warrants and equity plan ~~awards, offset by $0.1 million in principal repayments of finance leases.~~

~~Cash provided by financing activities for the nine months ended~~ ~~September 30, 2019~~ was $363.9 million and was comprised of $330.4 million from the sale of common stock in our underwritten public offering in February 2019, $24.8 million from the sale of common stock in our ATM offering, and $8.6 million in net proceeds from the issuance of common stock pursuant to equity awards.

We anticipate that, excluding non-recurring items, we will continue to generate annual losses for the foreseeable future as we continue the development of, and seek regulatory approvals for, our product candidates, and continue with commercialization of approved products. We will ~~likely~~ require additional capital to fund our operations, to complete our ongoing and planned clinical studies, to commercialize our products, to continue investing in early-stage research capabilities to promote our pipeline growth, to continue to acquire or invest in businesses or products that complement or expand our business, and to further develop our general infrastructure, including ~~building~~construction of our ~~own Good Manufacturing Practices, or~~ GMP gene therapy manufacturing facility, and such funding may not be available to us on acceptable terms or at all.

If we are unable to raise additional capital in sufficient amounts or on terms acceptable to us, we may be required to delay, limit, reduce the scope of, or terminate one or more of our clinical studies, research and development programs, future commercialization efforts, or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves.

Our future funding requirements will depend on many factors, including the following:

We expect to satisfy future cash needs through existing capital balances, revenue from our commercial products, and through some combination of public or private equity offerings, debt financings, collaborations, strategic alliances, licensing arrangements, and other marketing and distribution arrangements. Please see “Risk Factors—Risks Related to Our Financial Condition and Capital Requirements.”

We have contractual obligations from our operating and finance leases, manufacturing and service contracts, licenses, royalties, development and collaboration arrangements, and other research and development activities. The following table summarizes our significant binding contractual obligations at ~~September~~June 30, ~~2020~~2021 (in thousands):

	Payments due by period										Payments due by period
	Less than 1 year		1 to 3 years		3 to 5 years		More than 5 years		Total		Less than 1 year		1 to 3 years		3 to 5 years		More than 5 years		Total
Operating and finance leases	$	11,493	$	23,500	$	17,651	$	4,758	$	57,402	$	13,012	$	25,144	$	13,816	$	1,351	$	53,323
Manufacturing and service contracts		7,048		49		—		—		7,097		8,768		472		—		—		9,240
Building construction agreement												6,411		—		—		—		6,411
Total	$	18,541	$	23,549	$	17,651	$	4,758	$	64,499	$	28,191	$	25,616	$	13,816	$	1,351	$	68,974

The terms of certain of our licenses, royalties, development and collaboration agreements, as well as other research and development activities, require us to pay potential future milestone payments based on product development success. The above table excludes such obligations as the amount and timing of such obligations are unknown or uncertain.

We have not engaged in any off-balance sheet arrangements, as defined in the rules and regulations of the SEC.

We have exposure to equity risk with respect to the equity ~~securities~~investments that we hold in ~~Arcturus. In May 2020, we exercised our option to acquire 600,000 shares of~~ Arcturus ~~common stock.~~and Solid. The carrying value of our equity investment ~~in common stock and the option to purchase additional equity securities~~held in Arcturus was ~~$128.7~~$74.4 million and ~~none, respectively,~~$95.4 million as of ~~September~~June 30, 2021 and December 31, 2020, respectively, and ~~$26.1~~the carrying value of our equity investment held in Solid was $28.6 million and ~~$1.7~~$59.3 million ~~respectively,~~ as of June 30, 2021 and December 31, 2020, respectively. The fair value of our equity investments decreased by $31.0 million and $51.7 million during the three and six months ended June 30, 2021, respectively, due to a decrease in the fair value of Arcturus and Solid common stock, resulting in unrealized losses on our investments in Arcturus common stock of $16.4 million and $21.0 million for the three and six months ended June 30, 2021, respectively and in unrealized losses in our investments in Solid common stock of $14.6 million and $30.7 million for the three and six months ended June 30, 2021, respectively. A hypothetical 10 percent decrease in the market price for our equity investments in Arcturus and Solid as of June 30, 2021 and December 31, ~~2019. If~~2020 would decrease the ~~Arcturus stock price had been lower at~~ ~~September~~ ~~30, 2020 compared to December 31, 2019, we may have reported an even greater net loss for the nine months ended~~ ~~September~~ ~~30, 2020.~~fair value by $10.3 million and $15.5 million, respectively. Given the historic volatility of the publicly traded stock price of Arcturus and Solid, the fair value of our investments in Arcturus ~~may be~~and Solid is subject to wide fluctuations which may have a significant impact on our ~~earnings~~net income (loss) in future periods.~~See Item 1A: "Risk Factors" for additional details.~~

Our exposure to market risk for changes in interest rates relates primarily to interest earned on our cash equivalents and ~~investments.~~marketable debt securities. The primary objective of our investment activities is to preserve our capital to fund operations. A secondary objective is to maximize income from our investments without assuming significant risk. Our investment policy provides for investments in low-risk, investment-grade debt instruments. As of ~~September~~June 30,~~, 2020,~~ 2021, we had cash, cash equivalents, and ~~investments~~marketable debt securities totaling ~~$765.5~~$973.8 million, compared to ~~$760.4~~$1,212.0 million as of December 31, ~~2019,~~2020, which include bank deposits, money market funds, U.S. government treasury and agency securities, and investment-grade corporate bond securities which are subject to default, changes in credit rating, and changes in market value. The securities in our investment portfolio are classified as available for sale and are subject to interest rate risk and will decrease in value if market interest rates increase. ~~Due to the COVID-19 pandemic and the reduction of rates by the U.S. Federal Reserve, we expect that the interest yield on our investments will decrease.~~ A hypothetical 100 basis point change in interest rates during any of the periods presented would not have had a material impact on the fair market value of our ~~consolidated financial statements.~~cash equivalents and marketable debt securities as of June 30, 2021 or December 31, 2020. To date, we have not experienced a loss of principal on any of ~~our~~these investments and as of June 30~~September~~, 2021 ~~30, 2020,~~, we did not record any allowance for credit loss from our investments.

We face foreign exchange risk as a result of entering into transactions denominated in currencies other than U.S. dollars. Due to the uncertain timing of expected payments in foreign currencies, we do not utilize any forward exchange contracts. All foreign transactions settle on the applicable spot exchange basis at the time such payments are made. Volatile market conditions arising from the COVID-19 pandemic may result in significant changes in exchange rates, and in particular a weakening of foreign currencies relative to the U.S. dollar may negatively affect our revenue and operating income as expressed in U.S. dollars. An adverse movement in foreign exchange rates could have a material effect on payments made to foreign suppliers and for license agreements. For the ~~nine~~three months ended June 30~~September~~, 2021 ~~30, 2020,~~, a majority of our revenue and expense activities and capital expenditures were denominated in U.S. dollars. A hypothetical 10% change in foreign exchange rates during any of the periods presented would not have had a material impact on our consolidated financial statements.

WeManagement carried out an evaluation, under the supervision and with the participation of ~~our management, including~~ our Chief Executive Officer and our Chief Financial Officer, of the effectiveness of our “disclosure controls and procedures” as of the end of the period covered by this Quarterly Report, pursuant to Rules 13a-15(b) and 15d-15(b) under the Securities Exchange Act of 1934, or the Exchange Act. In connection with that evaluation, our Chief Executive Officer and our Chief Financial Officer concluded that our disclosure controls and procedures were effective and designed to provide reasonable assurance that the information required to be disclosed is recorded, processed, summarized and reported within the time periods specified in the SEC rules and forms as of ~~September~~June 30, 2021~~, 2020.~~. For the purpose of this review, disclosure controls and procedures means controls and procedures designed to ensure that information required to be disclosed by us in the reports that we file or submit is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms. These disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in the reports that we file or submit is accumulated and communicated to management, including our principal executive officer and principal financial officer, as appropriate to allow timely decisions regarding required disclosure. In designing and evaluating the disclosure controls and procedures, our management recognized that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives, and our management necessarily was required to apply its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

There have been no changes in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) during our ~~third~~ quarter ended June 30~~September 30, 2020~~, 2021, that has materially affected, or is reasonably likely to materially affect our internal control over financial reporting.

We are not currently a party to any material legal proceedings. We may, however, in the ordinary course of business face various claims brought by third parties or government regulators and we may, from time to time, make claims or take legal actions to assert our rights, including claims relating to our directors, officers, stockholders, intellectual property rights, employment matters and the safety or efficacy of our products. Any of these claims could subject us to costly litigation and, while we generally believe that we have adequate insurance to cover many different types of liabilities, our insurance carriers may deny coverage, may be inadequately capitalized to pay on valid claims, or our policy limits may be inadequate to fully satisfy any damage awards or settlements. If this were to happen, the payment of any such awards could have a material adverse effect on our consolidated operations, cash flows and financial position. Additionally, any such claims, whether or not successful, could damage our reputation and business.

Investing in our common stock involves a high degree of risk. You should carefully consider the following material risks, together with all the other information in this Quarterly Report, including our financial statements and notes thereto, before deciding to invest in our common stock. The risks and uncertainties described below are not the only ones we face. Additional risk and uncertainties not presently known to us or that we presently deem less significant may also impair our business operations. If any of the following risks actually materialize, our operating results, financial condition, and liquidity could be materially adversely affected. As a result, the trading price of our common stock could decline and you could lose part or all of your investment. Our company’s business, financial condition and operating results can be affected by a number of factors, whether currently known or unknown, including but not limited to those described below, any one or more of which could, directly or indirectly, cause our actual financial condition and operating results to vary materially from past, or from anticipated future, financial condition and operating results. Any of these factors, in whole or in part, could materially and adversely affect our business, prospects, financial condition, operating results and stock price.

Because of the following factors, as well as other factors affecting our financial condition and operating results, past financial performance should not be considered to be a reliable indicator of future performance, and investors should not use historical trends to anticipate results or trends in future periods.

The following description of the risk factors associated with our business includes any material changes to and supersedes the description of the risk factors associated with our business previously disclosed in Part I, Item 1A of the Annual Report.

We have a history of operating losses and anticipate that we will continue to incur losses for the foreseeable future.

We are a biopharmaceutical company with a history of operating losses, and anticipate continuing to incur operating losses for the foreseeable future. Biopharmaceutical product development is a highly speculative undertaking and involves a substantial degree of risk. We have devoted substantially all of our financial resources to identifying, acquiring, and developing our products and product candidates, including conducting clinical studies, developing manufacturing processes, manufacturing product candidates for clinical studies, and providing selling, general and administrative support for these operations. The amount of our future net losses will depend, in part, on non-recurring events, the success of our commercialization efforts, and the rate of our future expenditures. We anticipate that our expenses will increase substantially if and as we:

The net losses we incur may fluctuate significantly from quarter to quarter and year to year, such that a period-to-period comparison of our results of operations may not be a good indication of our future performance.

Our ability to generate significant revenue from product sales depends on our ability, alone or with strategic collaboration partners, to successfully commercialize our products and to complete the development of, and obtain the regulatory and marketing approvals necessary to commercialize, ~~one or more of~~ our product candidates. Our ability to generate substantial future revenue from product sales, including named patient sales, depends heavily on our success in many areas, including, but not limited to:

If the number of our addressable rare disease patients is not as significant as we estimate, the indication approved by regulatory authorities is narrower than we expect, or the reasonably accepted population for treatment is narrowed by competition, physician choice, or treatment guidelines, we may not generate significant revenue from sales of our products, even if they receive regulatory approval.

We expect we will ~~likely~~ need to raise additional capital to fund our activities. This additional financing may not be available on acceptable terms, if at all. Failure to obtain this necessary capital when needed may force us to delay, limit, or terminate our product development efforts or other activities.

As of ~~September~~June 30, ~~2020,~~2021, our available cash, cash equivalents, and ~~investments~~marketable debt securities were ~~$765.5~~$973.8 million. We expect we will ~~likely~~ need additional capital to continue to commercialize our products, and to develop and obtain regulatory approval for, and to commercialize, all of our product candidates. In addition, our operating plans may change as a result of many factors that may currently be unknown to us, and we may need to seek additional funds sooner than planned. Our future funding requirements will depend on many factors, including but not limited to:

Any additional fundraising efforts may divert our management’s attention from their day-to-day activities, which may adversely affect our ability to develop our product candidates and commercialize our products. In addition, we cannot guarantee that future financing will be available in sufficient amounts or on terms acceptable to us, if at all. The terms of any financing may adversely affect the holdings or the rights of our stockholders and the issuance of additional securities, whether equity or debt, by us, or the possibility of such issuance, may cause the market price of our shares to decline. The sale of additional equity or convertible securities would dilute all of our stockholders. If we incur debt, it could result in increased fixed payment obligations and we may be required to agree to certain restrictive covenants, such as limitations on our ability to incur additional debt, limitations on our ability to acquire, sell, or license intellectual property rights, and other operating restrictions that could adversely impact our ability to conduct our business. We have in the past sought and may in the future seek funds through a sale of future royalty payments similar to our transaction with Royalty Pharma or through collaborative partnerships, strategic alliances, and licensing or other arrangements, such as our transaction with Daiichi Sankyo, and we may be required to relinquish rights to some of our technologies or product candidates, future revenue streams, research programs, and other product candidates or otherwise agree to terms unfavorable to us, any of which may have a material adverse effect on our business, operating results, and prospects. Even if we believe we have sufficient funds for our current or future operating plans, we may seek additional capital if market conditions are favorable or if we have specific strategic considerations.

~~In addition, as a result of the COVID-19 pandemic,~~ the stock market in general and the stock price of biopharmaceutical companies, in particular, have experienced extreme price and volume fluctuations. As a result of such volatility and the impact of the COVID-19 pandemic on financial markets in general, our access to and cost of capital may be negatively affected.

If we are unable to obtain funding on a timely basis or at all, we may be required to significantly curtail, delay, or discontinue one or more of our research or development programs or the commercialization of our products and any approved product candidates or be unable to expand our operations or otherwise capitalize on our business opportunities, as desired, which could materially affect our business, financial condition, and results of operations.

Clinical drug development involves a lengthy and expensive process with uncertain outcomes and the potential for substantial delays, and the results of earlier studies may not be predictive of future study results.

Before obtaining marketing approval from regulatory authorities for the sale of our product candidates, we must conduct extensive clinical studies to demonstrate the safety and efficacy of the product candidates in humans. Clinical testing is expensive, time consuming, and uncertain as to outcome. We cannot guarantee that any clinical studies will be conducted as planned or completed on schedule, if at all. A failure of one or more clinical studies can occur at any stage of testing, and our future clinical

studies may not be successful. Product candidates that have shown promising results in early-stage clinical studies may still suffer significant setbacks or fail in subsequent clinical studies. The safety or efficacy results generated to date in clinical studies do not ensure that later clinical studies will demonstrate similar results. For example, our Phase 3 studies that evaluated Ace-ER in patients with GNE myopathy and UX007 in patients with Glut1 DS experiencing disabling paroxysmal movement disorders did not achieve their primary or secondary endpoints. Results from investigator-sponsored studies or compassionate-use studies may not be confirmed in company-sponsored studies or may negatively impact the prospects for our programs. Additionally, given the nature of the rare diseases we are seeking to treat, we often have to devise newly-defined endpoints to be tested in our studies, which can lead to some subjectivity in interpreting study results and could result in regulatory agencies not agreeing with the validity of our endpoints, or our interpretation of the clinical data, and therefore delaying or denying approval. Given the illness of the patients in our studies and the nature of their rare diseases, we may also be required or choose to conduct certain studies on an open-label basis. We have in the past, and may in the future elect to review interim clinical data at multiple time points during the studies, which could introduce bias into the study results and potentially result in denial of approval.

In the biopharmaceutical industry, there is a high failure rate for drugs and biologics proceeding through clinical studies, and product candidates in later stages of clinical studies may fail to show the desired safety and efficacy despite having progressed through nonclinical studies and initial clinical studies. A number of companies in the biopharmaceutical industry have suffered significant setbacks in advanced clinical studies due to lack of efficacy or adverse safety profiles, notwithstanding promising results in earlier studies.

Scenarios that may prevent successful or timely completion of clinical development include but are not limited to:

Any inability to successfully complete nonclinical and clinical development could result in additional costs to us or negatively impact our ability to generate revenue. In addition, if we make manufacturing or formulation changes to our product candidates, we may need to conduct additional toxicology, comparability or other studies to bridge our modified product candidates to earlier versions. Clinical study delays could also shorten any periods during which our products have commercial exclusivity and may allow our competitors to bring products to market before we do, which could negatively impact our ability to obtain orphan exclusivity and to successfully commercialize our product candidates and may harm our business and results of operations.

If we do not achieve our projected development goals in the time frames we announce and expect, the commercialization of our products may be delayed and the credibility of our management may be adversely affected and, as a result, our stock price may decline.

For planning purposes, we estimate the timing of the accomplishment of various scientific, clinical, regulatory, and other product development goals, which we sometimes refer to as milestones. These milestones may include the commencement or completion of scientific studies and clinical trials, the timing of patient dosing, the submission or acceptance of regulatory filings, and the potential approval of such regulatory filings. We periodically make public announcements about the expected timing of some of these milestones. All of these milestones are based on a variety of assumptions, but the actual timing of these milestones can vary dramatically from our estimates. If we do not meet these publicly announced milestones, the commercialization of our products may be delayed and the credibility of our management may be adversely affected and, as a result, our stock price may decline.

We may find it difficult to identify and enroll patients in our clinical studies given the limited number of patients who have the diseases for which our product candidates are being studied. Difficulty in enrolling patients could delay or prevent clinical studies of our product candidates.

Identifying and qualifying patients to participate in clinical studies of our product candidates is critical to our success. The timing of our clinical studies depends in part on the speed at which we can recruit patients to participate in testing our product candidates, and we may experience delays in our clinical studies if we encounter difficulties in enrollment.

Each of the conditions for which we plan to evaluate our current product candidates is a rare genetic disease. Accordingly, there are limited patient pools from which to draw for clinical studies. For example,

In addition to the rarity of these diseases, the eligibility criteria of our clinical studies will further limit the pool of available study participants as we will require patients to have specific characteristics that we can measure or to assure their disease is either severe enough or not too advanced to include them in a study. The process of finding and diagnosing patients ~~may prove~~is costly, especially since the rare diseases we are studying are commonly ~~under diagnosed.~~underdiagnosed. We also may not be able to identify, recruit, and enroll a sufficient number of appropriate patients to complete our clinical studies because of demographic criteria for prospective patients, the perceived risks and benefits of the product candidate under study, the proximity and availability of clinical study sites for prospective patients, and the patient referral practices of physicians. The availability and efficacy of competing therapies and clinical studies can also adversely impact enrollment. If patients are unwilling to participate in our studies for any reason, the timeline for recruiting patients, conducting studies, and obtaining regulatory approval of potential products may be delayed, the commercial prospects of our product candidates will be harmed, and our ability to generate product revenue from any of these product candidates could be delayed or prevented. Furthermore, many of the factors that cause, or lead to, a delay in the commencement or completion of clinical studies may also ultimately lead to the denial of regulatory approval of our product candidates. Delays in completing our clinical studies will increase our costs, slow down our product candidate development and approval process, and jeopardize our ability to commence product sales and generate revenue. ~~Any of these occurrences may harm our business, financial condition, and prospects significantly.~~

The regulatory approval processes of the FDA and comparable foreign authorities are lengthy, time consuming, and inherently unpredictable. Even if we achieve positive results in our pre-clinical and clinical studies, if we are ultimately unable to obtain timely regulatory approval for our product candidates, our business will be substantially harmed.

Our future success is dependent on our ability to successfully commercialize our products and develop, obtain regulatory approval for, and then successfully commercialize one or more product candidates. We are not permitted to market or promote any of our product candidates before we receive regulatory approval from the FDA or comparable foreign regulatory authorities. We have only obtained regulatory approval for ~~two~~three products, and it is possible that none of our existing product candidates or any product candidates we may seek to develop in the future will ever obtain regulatory approval. Further, as the clinical trial requirements of regulatory authorities and the criteria these regulators use to determine the safety and efficacy of a product candidate vary substantially according to the type, complexity, novelty and intended use and market of the product candidates, the regulatory approval process for novel product candidates, such as our gene therapy product candidates, can be more expensive and take longer than for other product candidates, leading to fewer product approvals. To date, very few gene therapy products have received regulatory approval in the United States or Europe.

To obtain regulatory approval in the United States and other jurisdictions, we must comply with numerous and varying requirements regarding safety, efficacy, chemistry, manufacturing and controls, clinical studies (including good clinical practices), commercial sales, pricing, and distribution of our product ~~candidates.~~candidates, as described in “Item 1. Business – Government Regulation” of our Annual Report. Even if we are successful in obtaining approval in one jurisdiction, we cannot ensure that we will obtain approval in any other jurisdictions. In addition, approval policies, regulations, positions of the regulatory agencies on study design and/or endpoints, or the type and amount of clinical data necessary to gain approval may change during the course of a product candidate’s clinical development, which may cause delays in the approval or the decision not to approve an application. Communications with the regulatory agencies during the approval process are also unpredictable; favorable communications early in the process do not ensure that approval will be obtained and unfavorable communications early on do not guarantee that approval will be denied. ~~If we are unable to obtain approval for our product candidates in multiple jurisdictions, our revenue and results of operations could be negatively affected.~~ Applications for our product candidates could fail to receive regulatory approval, or could be delayed in receiving regulatory approval, for many reasons, including but not limited to the following:

Furthermore, the disease states we are evaluating often will not have clear regulatory paths for approval and/or do not have validated outcome measures. In these circumstances, we work closely with the regulatory authorities to define the approval path and may have to qualify outcome measures as part of our development programs. Additionally, many of the disease states we are targeting are highly heterogeneous in nature, which may impact our ability to determine the treatment benefit of our potential therapies.

This lengthy and uncertain approval process, as well as the unpredictability of the clinical and nonclinical studies, may result in our failure to obtain regulatory approval to market any of our product candidates, or delayed regulatory approval, which would significantly harm our business, results of operations, and prospects.

The regulatory approval process for novel product candidates, such as our gene therapy product candidates, can be more expensive and take longer than for other product candidates, and may change in the future.

The clinical trial requirements of regulatory authorities and the criteria these regulators use to determine the safety and efficacy of a product candidate vary substantially according to the type, complexity, novelty and intended use and market of the product candidate. As a result, the regulatory approval process for novel product candidates such as our gene therapy product candidates can be more expensive and take longer than for other, better known or more extensively studied product candidates, which can lead to fewer product approvals. To date, very few gene therapy products have received regulatory approval in the United States or Europe.

Additionally, the FDA, Health Canada, and the EMA have each expressed interest in further regulating biotechnology, including gene therapy and genetic testing. For example, the EMA, which governs the development of gene therapies in the EU and

may issue new guidelines concerning the development and marketing authorization for gene therapy products, advocates a risk-based approach to the development of a gene therapy product. Agencies at both the federal and state level in the United States, as well as U.S. congressional committees and foreign governments, have also expressed interest in further regulating the biotechnology industry. Different regulatory approaches by jurisdiction can result in different or additional preclinical studies or clinical trials being required to support regulatory approval in each jurisdiction.

~~Regulatory requirements such as review committees and advisory groups, the new guidelines they promulgate, and new guidance issued by regulatory authorities may lengthen~~ the regulatory review process, require us to perform additional studies or trials, increase our development costs, lead to changes in regulatory positions and interpretations, delay or prevent approval and commercialization of our product candidates or lead to significant post- approval limitations or restrictions. As we advance our product candidates, we will be required to consult with these regulatory and advisory groups and comply with applicable guidelines. If we fail to do so, we may be required to delay or discontinue development of such product candidates. These additional processes may result in a review and approval process that is longer than we otherwise would have expected. Delays as a result of an increased or lengthier regulatory approval process or further restrictions on the development of our product candidates can be costly and could negatively impact our or our collaborators’ ability to complete clinical trials and commercialize our current and future product candidates in a timely manner, if at all.

Our product candidates may cause undesirable side effects or have other properties that could delay or prevent their regulatory approval, limit the commercial profile of an approved label, or result in significant negative consequences following marketing approval, if any.

Undesirable side effects caused by our product candidates could cause us or regulatory authorities to interrupt, delay, or halt clinical studies or further development, and could result in a more restrictive label, the delay or denial of regulatory approval by the FDA or other comparable foreign authorities, or a Risk Evaluation and Mitigation Strategy, or REMS, plan, which could include a medication guide outlining the risks of such side effects for distribution to patients, restricted distribution, a communication plan for healthcare providers, and/or other elements to assure safe use. Our product candidates are in development and the safety profile has not been established. Further, as one of the goals of Phase 1 and/or 2 clinical trials is to identify the highest dose of treatment that can be safely provided to study participants, adverse side effects, including serious adverse effects, have occurred in certain studies as a result of changes to the dosing regimen during such studies. For instance, patients in our Phase 1/2 study of GTX-102 experienced a serious adverse event of lower extremity weakness believed to be related to local inflammation due to GTX-102 at the highest doses of the product. Gene therapy product candidates using AAV vectors, like DTX301, have been associated with immunologic reaction to the capsid protein or gene at early time points after administration. For example, in our discontinued Phase 1/2 clinical trial of DTX101 in hemophilia B, we observed elevated laboratory alanine transaminase levels, or ALTs. In previous clinical trials involving AAV viral vectors for gene therapy, some subjects experienced adverse events, including the development of a T-cell mediated immune response against the vector capsid proteins. In addition, theoretical side effects of AAV vectors include replication and spread of the virus to other parts of the body and insertional oncogenesis, which is the process whereby the insertion of a gene near a gene that is important in cell growth or division results in uncontrolled cell division, which could potentially enhance the risk of malignant transformation or cancer. Potential procedure-related events are similar to those associated with standard coronary diagnostic procedures, and may include vascular injury (e.g., damage to the femoral, radial or brachial arteries at the site of vascular access, or damage to the coronary arteries) or myocardial injury. Future product candidates may also cause these or similar side effects as development proceeds. Results of our studies or investigator-sponsored trials could reveal a high and unacceptable severity and prevalence of these or other side effects. In such an event, our studies could be suspended or terminated, and the FDA or comparable foreign regulatory authorities could order us to cease further development of or deny or withdraw approval of our product candidates for any or all targeted indications.

Drug-related side effects could affect patient recruitment and the ability of enrolled patients to complete a study. Such side effects could also result in potential product liability claims. ~~We currently carry~~There can be no assurance that our product liability insurance, which provides coverage in the amount of $10.0 million per incident and $10.0 million in the aggregate, ~~and we are required to maintain product liability insurance pursuant to certain of our agreements. We believe our product liability insurance coverage is~~will be sufficient in light of our current or planned clinical ~~programs; however, we~~programs. We may not be able to maintain insurance coverage at a reasonable cost or in sufficient amounts to protect us against losses due to liability, or losses may exceed the amount of insurance that we carry. A product liability claim or series of claims brought against us could cause our stock price to decline and, if judgments exceed our insurance coverage, could adversely affect our results of operations and business. In addition, regardless of merit or eventual outcome, product liability claims may result in impairment of our business reputation, withdrawal of clinical study participants, costs due to related litigation, distraction of management’s attention from our primary business, initiation of investigations by regulators, substantial monetary awards to patients or other claimants, the inability to commercialize our product candidates, and decreased demand for our product candidates, if approved for commercial sale.

Additionally, even though we received regulatory approval for Crysvita, Mepsevii, and Dojolvi and even if our product candidates receive marketing approval in the future, if we or others later identify undesirable side effects caused by such products, a number of potentially significant negative consequences could result, including but not limited to:

Any of these events could prevent us from achieving or maintaining market acceptance of the particular product candidate, if approved, and could significantly harm our business, results of operations, and prospects.

Serious adverse events in clinical trials involving gene therapy product candidates may damage public perception of the safety of our product candidates, increase government regulation, and adversely affect our ability to obtain regulatory approvals for our product candidates or conduct our business.

Gene therapy remains a novel technology. Public perception may be influenced by claims that gene therapy is unsafe, and gene therapy may not gain the acceptance of the public or the medical community. For example, certain gene therapy trials using AAV8 vectors (although at significantly higher doses than those used in our gene therapy product candidates) and other vectors led to several well-publicized adverse events, including cases of leukemia and death. The risk of cancer or death remains a concern for gene therapy and we cannot assure you that it will not occur in any of our planned or future clinical studies. In addition, there is the potential risk of

delayed adverse events following exposure to gene therapy products due to persistent biological activity of the genetic material or other components of products used to carry the genetic material. Serious adverse events in our clinical trials, or other clinical trials involving gene therapy products, particularly AAV gene therapy products such as candidates based on the same capsid serotypes as our product candidates, or occurring during use of our competitors’ products, even if not ultimately attributable to the relevant product candidates, and the resulting publicity, could result in increased government regulation, unfavorable public perception, potential regulatory delays in the testing or approval of our gene therapy product candidates, stricter labeling requirements for those gene therapy product candidates that are approved and a decrease in demand for any such gene therapy product candidates, all of which would have an adverse effect on our business, financial condition, results of operations and prospects. Refer to the risk factor above entitled, “Our product candidates may cause undesirable side effects or have other properties that could delay or prevent their regulatory approval, limit the commercial profile of an approved label, or result in significant negative consequences following marketing approval, if any”for a description of the serious adverse events experienced by patients in our Phase 1/2 study of GTX-102.

Even if we obtain regulatory approval for our product candidates, our products will remain subject to regulatory scrutiny.

Our products and any product candidates that are approved are subject to ongoing regulatory requirements for manufacturing, labeling, packaging, storage, distribution, advertising, promotion, sampling, record-keeping, conduct of post-marketing studies, and submission of safety, efficacy, and other post-market information, including both federal and state requirements in the United States and requirements of comparable foreign regulatory ~~authorities.~~authorities, as described in “Item 1. Business – Government Regulation” in our Annual Report.

Manufacturers and manufacturers’ facilities are required to comply with extensive FDA, and comparable foreign regulatory authority, requirements, including ensuring that quality control and manufacturing procedures conform to Good Manufacturing Practices (GMP) regulations. As such, we and our contract manufacturers ~~will be~~are subject to continual review and inspection to assess compliance with GMP and adherence to commitments made in any NDA, BLA, MAA, or other comparable application for approval in another jurisdiction. Regulatory authorities may, at any time, audit or inspect a manufacturing facility involved with the preparation of our products, product candidates or the associated quality systems for compliance with the regulations applicable to the activities being conducted. If we, our collaborators, such as KKC, or any of our third-party manufacturers fail to maintain regulatory compliance, the FDA or other applicable regulatory authority can impose regulatory sanctions including, among other things, the temporary or permanent suspension of a clinical study or commercial sales, recalls or seizures of product or the temporary or permanent closure of a facility or withdrawal of product approval. If supply from one approved manufacturer is interrupted due to failure to maintain regulatory compliance, an alternative manufacturer would need to be qualified through an NDA or BLA supplement or MAA variation, or equivalent foreign regulatory filing, which could result in delays in product supply. The regulatory agencies may also require additional studies if a new manufacturer is relied upon for commercial production. Switching manufacturers may involve substantial costs and is likely to result in a delay in our desired clinical and commercial timelines. Accordingly, we and others with whom we work ~~must~~are required continue to expend time, money, and effort in all areas of regulatory compliance, including manufacturing, production, and quality control.

Any regulatory approvals that we receive for our product candidates may be subject to limitations on the approved indicated uses for which the product may be marketed or other conditions of approval, or contain requirements for potentially costly post-marketing testing, including Phase 4 clinical studies, and surveillance to monitor the safety and efficacy of the product candidate. We could also be asked to conduct post-marketing clinical studies to verify the safety and efficacy of our products in general or in specific patient subsets. If original marketing approval was obtained via the accelerated approval or conditional marketing authorization pathways, we would be required to conduct a successful post-marketing clinical study to confirm clinical benefit for our products. An unsuccessful post-marketing study or failure to complete such a study could result in the withdrawal of marketing approval. We will be required to report certain adverse events and manufacturing problems, if any, to the FDA and comparable foreign regulatory authorities. Any new legislation addressing drug safety issues could result in delays in product development or commercialization, or increased costs to assure compliance. We will have to comply with requirements concerning advertising and promotion for our products. Promotional communications with respect to prescription drugs are subject to a variety of legal and regulatory restrictions and must be consistent with the information in the product’s approved label. As such, we may promote our products only for indications or uses for which they have approval. The holder of an approved NDA, BLA, MAA, or other comparable application must submit new or supplemental applications and obtain approval for certain changes to the approved product, product labeling, or manufacturing process.

If we fail to comply with applicable regulatory requirements, or there are safety or efficacy problems with a product, a regulatory agency or enforcement authority may, among other things:

Any government investigation of alleged violations of law could require us to expend significant time and resources in response, and could generate negative publicity. Any failure to comply with ongoing regulatory requirements may significantly and adversely affect our ability to commercialize and generate revenue from our products. If regulatory sanctions are applied or if regulatory approval is withdrawn, the value of our company and our operating results will be adversely affected.

If we are unable to identify, source, and develop effective biomarkers, or our collaborators are unable to successfully develop and commercialize companion diagnostics for our product candidates, or experience significant delays in doing so, we may not realize the full commercial potential of our product candidates.

We are developing companion diagnostic tests to identify the right patients for certain of our product candidates and to monitor response to treatment. In certain cases, diagnostic tests may need to be developed as companion diagnostics and regulatory approval obtained in order to commercialize some product candidates. We currently use and expect to continue to use biomarkers to identify the right patients for certain of our product candidates. We may also need to develop predictive biomarkers in the future. For example, to evaluate therapeutic response of DTX301, we are measuring ammonia levels and other biomarkers, including ¹³C-acetate, which are established measures of OTC deficiency disease status and ureagenesis. We offer no assurances that ¹³C-acetate or any other future potential biomarker will in fact prove predictive, be reliably measured, or be accepted as a measure of efficacy by the FDA or other regulatory authorities. In addition, our success may depend, in part, on the development and commercialization of companion diagnostics. We also expect the FDA will require the development and regulatory approval of a companion diagnostic assay as a condition to approval of our gene therapy product candidates. There has been limited success to date industrywide in developing and commercializing these types of companion diagnostics. Development and manufacturing of companion diagnostics is complex and there are limited manufacturers with the necessary expertise and capability. Even if we are able to ~~find a qualified collaborator, it~~successfully develop companion diagnostics, we may not be able to manufacture the companion diagnostics at a cost or in quantities or on timelines necessary for use with our product candidates. To be successful, we need to address a number of scientific, technical and logistical challenges. We ~~have not yet initiated development and commercialization of~~are currently working with a third party to develop companion ~~diagnostics. We~~diagnostics, however, we have little experience in the development and commercialization of diagnostics and may not ultimately be successful in developing and commercializing appropriate diagnostics to pair with any of our product candidates that receive marketing approval. The University of Pennsylvania School of Medicine currently conducts some of our clinical assays pursuant to a sponsored research agreement, one of which is required for our ongoing Phase 1/2 clinical trial. We also use third parties for the automation, characterization and validation, of our bioanalytical assays, companion diagnostics and the manufacture of its critical reagents.

Companion diagnostics are subject to regulation by FDA and similar regulatory authorities outside the United States as medical devices and require regulatory clearance or approval prior to commercialization. In the United States, companion diagnostics are cleared or approved through FDA’s 510(k) premarket notification or premarket approval, or PMA, process. Changes in marketing approval policies during the development period, changes in or the enactment of additional statutes or regulations, or changes in regulatory review for each submitted 510(k) premarket notification, PMA or equivalent application types in jurisdictions outside the United States, may cause delays in the approval, clearance or rejection of an application. Given our limited experience in developing and commercializing diagnostics, we expect to rely in part or in whole on third parties for companion diagnostic design and commercialization. We and our collaborators may encounter difficulties in developing and obtaining approval or clearance for the companion diagnostics, including issues relating to selectivity/specificity, analytical validation, reproducibility, or clinical validation. Any delay or failure by us or our collaborators to develop or obtain regulatory approval of the companion diagnostics could delay or prevent approval of our product candidates.

We rely on third parties to conduct our nonclinical and clinical studies and perform other tasks for us. If these third parties do not successfully carry out their contractual duties, meet expected deadlines, or comply with regulatory requirements, we may be exposed to sub-optimal quality and reputational harm, we may not be able to obtain regulatory approval for or commercialize our product candidates, and our business could be substantially harmed.

We have relied upon and plan to continue to rely upon third parties, including CROs, collaborative partners, and independent investigators to analyze, collect, monitor, and manage data for our ongoing nonclinical and clinical programs. We rely on third parties for execution of our nonclinical and clinical studies, and for estimates regarding costs and efforts completed, and we control only certain aspects of their activities. For example, pursuant to the terms of our collaboration with GeneTx on the development of GeneTx’s GTX-102, an antisense oligonucleotide (ASO) for the treatment of Angelman syndrome, subject to certain limited rights we have, GeneTx retains the decision-making authority on all matters in connection with the research, development, manufacturing and regulatory activities with respect to the program. ~~With respect to our collaboration with Arcturus,~~ ~~we rely on our partner Arcturus for the design and optimization of initial product candidates under our mRNA, DNA and siRNA collaborations.~~ Nevertheless, we are responsible for ensuring that each of our studies is conducted in accordance with the applicable protocol, legal, regulatory, and scientific standards, and our reliance on the CROs and other third parties does not relieve us of our regulatory responsibilities. We and our CROs and other vendors and partners are required to comply with GMP, GCP, and GLP, which are regulations and guidelines enforced by the FDA, the Competent Authorities of the Member States of the European Economic Area, and comparable foreign regulatory authorities for all of our product candidates in development. Regulatory authorities enforce these regulations through periodic inspections of study sponsors, principal investigators, study sites, and other contractors. If we or any of our CROs or other vendors and partners, including the sites at which clinical studies are conducted, fail to comply with applicable regulations, the data generated in our nonclinical and clinical studies may be deemed unreliable and the FDA, EMA, or comparable foreign regulatory authorities may deny approval and/or require us to perform additional nonclinical and clinical studies before approving our marketing applications, which would delay the approval process. We cannot make assurances that upon inspection by a given regulatory authority, such regulatory authority will determine that any of our clinical studies comply with GCP regulations or that nonclinical studies comply with GLP regulations. In addition, our clinical studies must be conducted with products produced under GMP regulations. If the regulatory authorities determine that we have failed to comply with GLP, GMP, or GCP regulations, they may deny approval of our product candidates and/or we may be required to repeat clinical or nonclinical studies, which would delay the regulatory approval process.

Our CROs and other vendors and partners are not our employees and ~~except for remedies available to us under our agreements with such third parties,~~ we cannot control whether or not they devote sufficient time and resources to our on-going nonclinical and clinical ~~programs.~~programs, except for the limited remedies available to us under our agreements with such third parties. If our vendors and partners do not successfully carry out their contractual duties or obligations or meet expected deadlines, if they need to be replaced, or if the quality or accuracy of the data they obtain is compromised due to the failure to adhere to our protocols, regulatory requirements, or for other reasons, our clinical studies may be extended, delayed, or terminated, and we may not be able to obtain regulatory approval for or successfully commercialize our product candidates. CROs and other vendors and partners may also generate higher costs than anticipated as a result of changes in scope of work or otherwise. As a result, our results of operations and the commercial prospects for our product candidates would be harmed, our costs could increase, and our ability to generate revenue could be delayed.

If any of our relationships with these third parties terminate, we may not be able to enter into arrangements with alternative vendors or do so on commercially reasonable terms. Switching or adding additional vendors involves additional cost and requires management time and focus. In addition, there is a natural transition period when a new vendor commences work. As a result, delays may occur, which can materially impact our ability to meet our desired clinical development timelines. ~~Though we carefully~~Our efforts to manage our relationships with our vendors and partners ~~there~~ can beprovide no assurance that we will not encounter similar challenges or delays in the future or that these delays or challenges will not have a material adverse impact on our business, financial condition, and business prospects.

We also rely on third parties in other ways, including efforts to support patient diagnosis and identify patients, to assist our finance and legal departments, and to provide other resources for our business. Use of these third parties could expose us to sub-optimal quality, missed deadlines, and non-compliance with applicable laws, all of which could result in reputational harm to us and negatively affect our business.

We are dependent on KKC for the clinical and commercial supply of Crysvita for all major markets and for the development and commercialization of Crysvita in certain major markets, and KKC’s failure to provide an adequate supply of Crysvita or to commercialize Crysvita in those markets could result in a material adverse effect on our business and operating results.

Under our agreement with KKC, KKC has the sole right to commercialize Crysvita in Europe and, at a specified time, in the United States, Canada, and Turkey, subject to a limited promotion right we retained. Our partnership with KKC may not be successful, and we may not realize the expected benefits from such partnership, due to a number of important factors, including but not limited to the following:

We rely on third parties to manufacture our products and most of our product candidates and to acquire the raw material components to manufacture such products and product candidates. Our business could be harmed if those third parties fail to provide us with sufficient quantities of drug product, or fail to do so at acceptable quality levels or cost.

We have limited infrastructure or capability internally to manufacture our products and product candidates, and we currently lack the resources and the capability to manufacture our products and most of our product candidates on a clinical or commercial scale. We rely on our manufacturers to purchase from third-party suppliers the materials necessary to produce our products and product candidates for our clinical studies. There are a limited number of suppliers for raw materials that we use to manufacture our drugs, placebos, or active controls, and there may be a need to identify alternate suppliers to prevent a possible disruption of the manufacture of the materials necessary to produce our products and our product candidates for our clinical studies, and, if approved, ultimately for commercial sale. We also do not have any control over the process or timing of the acquisition of these raw materials by our manufacturers. We may also experience interruptions in supply of product if the product or raw material components fail to meet our quality control standards or the quality control standards of our suppliers. Any significant interruption in the supply of products due to delays in obtaining the raw material components or for other reasons could hinder our ability to distribute products to meet commercial demand and negatively impact our business. Any significant delay or discontinuity in the supply of a product candidate, or the raw material components thereof, for an ongoing clinical study due to, among other things, the failure of a manufacturer to provide a drug substance or drug product of sufficient quantity or quality, or the need to replace a third-party manufacturer could considerably delay completion of our clinical studies, product testing, and potential regulatory approval of our product candidates, and could also impair named patient sale supply of our product candidates, which could harm our business and results of operations.

We have no experience as a company developing a manufacturing facility and may experience unexpected costs or delays or ultimately be unsuccessful in developing a facility.

~~We expect~~During the fourth quarter 2020, we completed our ~~future~~purchase of land located in the Town of Bedford, Massachusetts for construction of our gene therapy manufacturing ~~strategy to involve~~facility and began construction of the ~~use of one or more CMOs as well as our own capabilities and infrastructure, including at our Woburn, MA facility or new facilities we may develop.~~base building for the facility. We expect that ~~development of our own process development~~the new facility will provide us with enhanced control of material supply for both clinical trials and the commercial market, enable the more rapid implementation of process changes, and allow for better long-term ~~margins. However, we~~margins for our gene therapy products. We currently anticipate construction of the facility to be completed in 2023. We do not have no experience as a company, however, in developing a manufacturing facility and we may experience unexpected costs or delays or ultimately be unsuccessful in developing ~~our own manufacturing~~the facility or capability. ~~Additionally, given that cGMP gene therapy~~We are dependent on key partners for delivery of power, electricity and other utilities to our manufacturing ~~is a nascent industry, there are a small number of CMOs with the experience necessary to manufacture our gene therapy product candidates~~facility and we ~~may~~cannot assure that such services will be provided at the facility without interruptions, delays or unexpected costs. Further, as described in the risk factor below entitled, “Actual or threatened public health epidemics or outbreaks, including the ongoing COVID-19 pandemic, have ~~difficulty finding or maintaining relationships with such CMOs or hiring experts~~and could again materially and adversely impact our business and operating results,” the COVID-19 pandemic has adversely impacted delivery of raw materials, and increased costs for ~~internal manufacturing and accordingly,~~certain materials, for construction of our ~~production capacity may be limited. We may establish multiple manufacturing facilities as~~facility. As we expand our commercial footprint to multiple geographies, we may establish multiple manufacturing facilities, which may lead to regulatory delays or prove costly. Even if we are successful, our manufacturing capabilities could be affected by cost-overruns, unexpected delays, equipment failures, lack of capacity, labor shortages, natural disasters, power failures, program failures, and numerous other factors that could prevent us from realizing the intended benefits of our manufacturing strategy and have a material adverse effect on our business.

Gene therapy and mRNA, DNA and siRNA product candidates are novel, complex, expensive and difficult to manufacture. We could experience manufacturing problems that result in delays in developing and commercializing these programs or otherwise harm our business.

The manufacturing process used to produce our gene therapy, mRNA, DNA and siRNA product candidates is novel, complex, and has not been validated for commercial use. Several factors could cause production interruptions, including equipment malfunctions, regulatory inspections, facility contamination, raw material shortages or contamination, natural disasters, disruption in utility services, human error or disruptions in the operations of our suppliers. Further, given that cGMP gene therapy, mRNA, DNA and siRNA manufacturing is a nascent industry, there are a small number of CMOs with the experience necessary to manufacture our gene therapy product candidates and we may have difficulty finding or maintaining relationships with such CMOs or hiring experts for internal manufacturing and accordingly, our production capacity may be limited.

Our gene therapy, mRNA, DNA and siRNA product candidates require processing steps that are more complex than those required for most small molecule drugs. Moreover, unlike small molecules, the physical and chemical properties of a biologic such as gene therapy, mRNA, DNA and siRNA product candidates generally cannot be fully characterized. As a result, assays of the finished product candidate may not be sufficient to ensure that the product candidate is consistent from lot to lot or will perform in the intended manner. Accordingly, we employ multiple steps to control the manufacturing process to assure that the process works reproducibly, and the product candidate is made strictly and consistently in compliance with the process. Problems with the manufacturing process, even minor deviations from the normal process, could result in product defects or manufacturing failures that result in lot failures, noncompliance with regulatory requirements, product recalls, product liability claims or insufficient inventory. We may encounter problems achieving adequate quantities and quality of clinical-grade materials that meet FDA, the EMA or other applicable standards or specifications with consistent and acceptable production yields and costs.

In addition, FDA, the EMA and other foreign regulatory authorities may require us to submit samples of any lot of any approved product together with the protocols showing the results of applicable tests at any time. Under some circumstances, FDA, the EMA or other foreign regulatory authorities may require that we not distribute a lot until the agency authorizes its release. Slight deviations in the manufacturing process, including those affecting quality attributes and stability, may result in unacceptable changes in the product that could result in lot failures or product recalls. Lot failures or product recalls could cause us to delay product launches or clinical trials, which could be costly to us and otherwise harm our business, financial condition, results of operations and prospects.

We ~~also may encounter problems hiring~~rely on third parties to manufacture our products and ~~retaining the experienced scientific, quality-control and manufacturing personnel needed to operate the manufacturing processes for~~ our ~~gene therapy, mRNA, DNA and siRNA~~ product candidates which could result in delays in production or difficulties in maintaining compliance with applicable regulatory requirements. We may be unable to scale up existing or new facilities, including our facility in Woburn, MA, and ~~such facilities may not enable the expansion of our internal manufacturing process discovery and development to the extent~~ we ~~anticipate, or at all.~~

We are subject to a multitude of manufacturing risks, any of which could substantially increase our costs and limit the supply of our product and product candidates.

As we currently lack the resources and the capability to manufacture our products and most of our product candidates on a clinical or commercial scale, we rely on third parties to manufacture our products and product candidates. Although we oversee the contract manufacturers, we cannot control the manufacturing process of, and are substantially dependent on, our contract manufacturing partners for compliance with the regulatory requirements. See “- Even if we obtain regulatory approval for our product candidates, our products will remain subject to regulatory scrutiny” risk factor above. Further, we depend on our manufacturers to purchase from third-party suppliers the materials necessary to produce our products and product candidates. There are a limited number of suppliers for raw materials that we use to manufacture our drugs, placebos, or active controls, and there may be a need to identify alternate suppliers to prevent a possible disruption of the manufacture of the materials necessary to produce our products and our product candidates for our clinical studies, and, if approved, ultimately for commercial sale. We also do not have any control over the process or timing of the acquisition of these raw materials by our manufacturers. We may also experience interruptions in supply of product if the product or raw material components fail to meet our quality control standards or the quality control standards of our suppliers.

Further, manufacturers that produce our products and product candidates may not have experience producing our products and product candidates at commercial levels and may not produce our products and product candidates at the cost, quality, quantities, locations, and timing needed to support profitable commercialization. We have not yet secured manufacturing capabilities for commercial quantities of all of our product candidates and may be unable to negotiate binding agreements with manufacturers to support our commercialization activities on commercially reasonable terms. Even if our third-party product manufacturers develop acceptable manufacturing processes that provide the necessary quantities of our products and product candidates in a compliant and timely manner, the cost to us for the supply of our products and product candidates manufactured by such third parties may be high and could limit our profitability. For instance, KKC is our sole supplier of commercial quantities of Crysvita. The supply price to us for commercial sales of Crysvita in Latin America and the transfer price for commercial sales of the product in the United States and Canada is 35% of net sales through December 31, 2022 and 30% thereafter, which is higher than the typical cost of goods sold by companies focused on rare diseases.

The process of manufacturing our products and product candidates is complex, highly regulated, and subject to several risks, including but not limited to those listed below.

Any adverse developments affecting manufacturing operations for our products and product candidates may result in shipment delays, inventory shortages, lot failures, withdrawals or recalls, or other interruptions in the supply of our products and product candidates. For instance, during the fourth quarter of 2019, we experienced disruptions from our third-party supplier related to the fill and finish activities for the manufacture of Mepsevii, which negatively impacted our inventory of the product. Due to their stage of development, small volume requirements, and infrequency of batch production runs, we carry limited amounts of safety stock for our products and product candidates. We have, and may ~~also have~~in the future, be required to take inventory write-offs and incur other charges and expenses for products and product candidates that fail to meet specifications, undertake costly remediation efforts, or seek more costly manufacturing alternatives.

The drug substance and drug product for our products and most of our product candidates are currently acquired from single-source suppliers. The loss of these suppliers, or their failure to supply us with the necessary drug substance or drug product, could materially and adversely affect our business.

We acquire most of the drug substances and drug products for our products and product candidates from single sources. If any single source supplier breaches an agreement with us, or terminates the agreement in response to an alleged breach by us or otherwise becomes unable to fulfill its supply obligations, we would not be able to manufacture and distribute the product or product candidate until a qualified alternative supplier is identified, which could significantly impair our ability to commercialize such product or delay the development of such product candidate. The drug substance and drug product for Crysvita are made by KKC pursuant to our license and collaboration agreement with KKC. The drug substance and drug product for Mepsevii are currently manufactured by Rentschler under a commercial supply and services agreement, accompanying purchase orders, and other agreements. ~~The pharmaceutical-grade~~We experienced disruptions related to the fill and finish activities for the drug product for Mepsevii during the fourth quarter of 2019 and as a result, we identified an alternative supplier to conduct such activities. We are currently in the process of qualifying and transferring the activities to such alternative supplier, which may take a significant amount of time and expense. If we fail to qualify our alternative supplier, we could experience delays or disruptions in the supply of Mepsevii, which would negatively impact sales of the product. Pharmaceutical-grade drug substance for Dojolvi is manufactured by IOI Oleo pursuant to our supply agreement with IOI Oleo, and the drug product for Dojolvi is prepared by Haupt Pharma AG ~~and CPM~~ pursuant to ~~purchase orders.~~a master services agreement. Single source suppliers are also used for our gene therapy programs. WeOther than as described above, we have not currently secured any other suppliers for the drug substance or drug product of our products and product candidates and, although we believe that there are alternate sources of supply that could satisfy our clinical and commercial requirements, we cannot provide assurance that identifying alternate sources and establishing relationships with such sources would not result in significant expense or delay in the commercialization of our products or the development of our product candidates. For instance, we experienced disruptions from our third-party supplier related to the fill and finish activities for the manufacture of Mepsevii during the fourth quarter of 2019 and as a result, we have identified an alternative supplier to conduct such activities. It may take a significant amount of time and expense to qualify such alternative supplier and to transfer activities to such supplier, which are currently ongoing. If we fail to qualify our alternative supplier in a timely manner, we could experience delays or disruptions in the supply of Mepsevii, which would negatively impact sales of the product. Additionally, we may not be able to enter into supply arrangements with ~~our~~an alternative supplier on commercially reasonable terms or at all.�� The terms of any new agreement ~~such as any agreement with our alternative supplier for Mepsevii,~~ may also be less favorable or more costly than the terms we have with our current supplier. A delay in the commercialization of our products or the development of our product candidates or having to enter into a new agreement with a different third-party on less favorable terms than we have with our current suppliers could have a material adverse impact upon on ~~our business.~~

We and our collaborators and contract manufacturers are subject to significant regulation with respect to manufacturing our products and our product candidates. The manufacturing facilities on which we rely may not continue to meet regulatory requirements or may not be able to meet supply demands.

All entities involved in the preparation of therapeutics for clinical studies or commercial sale, including our existing contract manufacturers and collaboration partners for our product and product candidates, are subject to extensive regulation. Components of a finished therapeutic product approved for commercial sale or used in clinical studies must be manufactured in accordance with GMP. These regulations govern manufacturing processes and procedures (including record keeping) and the implementation and operation of quality systems to control and assure the quality of investigational products and products approved for sale. Poor control of production processes can lead to the introduction of contaminants or to inadvertent changes in the properties or stability of our products and product candidates that may not be detectable in final product testing. We, our collaborators, or our contract manufacturers must supply all necessary documentation in support of an NDA, BLA, MAA, or other application for regulatory approval, on a timely basis and must adhere to GLP, GMP, and similar regulations enforced by the FDA and other regulatory agencies through their facilities inspection programs. Some of our contract manufacturers have never produced a commercially approved pharmaceutical product and therefore have not obtained the requisite regulatory authority approvals to do so. The facilities and quality systems of some or all of our collaborators and third-party contractors must pass a pre-approval inspection for compliance with the applicable regulations as a condition of regulatory approval of our product candidates or any of our other potential products. In addition, the regulatory authorities may, at any time, audit or inspect a manufacturing facility involved with the preparation of our products, product candidates or our other potential products or the associated quality systems for compliance with the regulations applicable to the activities being conducted. Although we oversee the contract manufacturers, we cannot control the manufacturing process of, and are substantially dependent on, our contract manufacturing partners for compliance with the regulatory requirements. If these facilities cannot schedule manufacturing to meet inspectional demands or do not initially pass and continue to pass regulatory inspections, including pre-approval plant inspections, regulatory approval of our product candidates may not be granted or may be substantially delayed until any violations are corrected to the satisfaction of the regulatory authority, if ever.

The regulatory authorities also may, at any time following approval of a product for sale, audit the manufacturing facilities of our collaborators, such as KKC, and third-party contractors. If any such inspection or audit identifies a failure to comply with applicable regulations or if a violation of our product specifications or applicable regulations occurs independent of such an inspection or audit, we or the relevant regulatory authority may require remedial measures that may be costly and/or time consuming for us or a third-party to implement, and that may include the temporary or permanent suspension of a clinical study or commercial sales, recalls or seizures of product or the temporary or permanent closure of a facility. Any such remedial measures imposed upon us, our collaborators, or third parties with whom we contract could materially harm our business.

If we, our collaborators, including KKC, or any of our third-party manufacturers fail to maintain regulatory compliance, the FDA or other applicable regulatory authority can impose regulatory sanctions including, among other things, refusal to approve a pending application for a new drug product or biologic product, withdrawal of an approval, or suspension of production. As a result, our business, financial condition, and results of operations may be materially harmed.

Additionally, if supply from one approved manufacturer is interrupted, an alternative manufacturer would need to be qualified through an NDA or BLA supplement or MAA variation, or equivalent foreign regulatory filing, which could result in further delay. The regulatory agencies may also require additional studies if a new manufacturer is relied upon for commercial production. Switching manufacturers may involve substantial costs and is likely to result in a delay in our desired clinical and commercial timelines.

These factors could cause us to incur higher costs and could cause interruptions in the supply of our products or a delay or termination of clinical studies, regulatory submissions, required approvals, or commercialization of our product candidates. Furthermore, if our suppliers fail to meet contractual requirements and we are unable to secure one or more replacement suppliers capable of production at a substantially equivalent cost, we could experience supply interruptions of product that would impact our ability to meet commercial demand and result in loss of revenue, or our clinical studies may be delayed, which could delay regulatory approval for our product candidates, any and all of which could materially and adversely affect our business.

The actions of distributors and specialty pharmacies could affect our ability to sell or market products profitably. Fluctuations in buying or distribution patterns by such distributors and specialty pharmacies could adversely affect our revenues, financial condition, or results of operations.

We rely on commercial distributors and specialty pharmacies for a considerable portion of our product sales and such sales are concentrated within a small number of distributors and specialty pharmacies. The financial failure of any of these parties could adversely affect our revenues, financial condition or results of operations. Our revenues, financial condition or results of operations may also be affected by fluctuations in buying or distribution patterns of such distributors and specialty pharmacies. These fluctuations may result from seasonality, pricing, wholesaler inventory objectives, or other factors.

Our reliance on third parties requires us to share our trade secrets, which increases the possibility that a competitor will discover them or that our trade secrets will be misappropriated or disclosed.

Because we rely on third parties in connection with the development and manufacture of our products and product candidates and will likely rely on third parties in connection with the commercialization of our approved products, we must, at times, share trade secrets with them. We seek to protect our proprietary technology in part by entering into confidentiality agreements and, if applicable, material transfer agreements, collaborative research agreements, consulting agreements, letters of engagement, or other similar agreements with our collaborators, advisors, employees, and consultants prior to beginning research or disclosing proprietary information. These agreements typically limit the rights of the third parties to use or disclose our confidential information, such as trade secrets. Despite the contractual provisions employed when working with third parties, the need to share trade secrets and other confidential information increases the risk that such trade secrets become known by our competitors, are inadvertently incorporated into the technology of others, or are disclosed or used in violation of these agreements. Given that our proprietary position is based, in part, on our know-how and trade secrets, a competitor’s discovery of our trade secrets or other unauthorized use or disclosure would impair our competitive position and may have a material adverse effect on our business.

If the market opportunities for our products and product candidates are smaller than we believe they are, our revenue may be adversely affected, and our business may suffer. Because the target patient populations of our products and product candidates are small, and the addressable patient population potentially even smaller, we must be able to successfully identify patients and acquire a significant market share to achieve profitability and growth.

We focus our research and product development on treatments for rare and ultra-rare genetic diseases. Given the small number of patients who have the diseases that we are targeting, it is critical to our ability to grow and become profitable that we continue to successfully identify patients with these rare and ultra-rare genetic diseases. Some of our current clinical programs may be most appropriate for patients with more severe forms of their disease. For instance, ~~our Phase 2 study of Dojolvi in LC-FAOD enrolled patients with more severe disease. In addition,~~ while adults make up the majority of the XLH patients, they often have less severe disease that may reduce the penetration of Crysvita in the adult population relative to the pediatric population. Given the overall rarity of the diseases we target, it is difficult to project the prevalence of the more severe forms, or the other subsets of patients that may be most suitable to address with our products and product candidates, which may further limit the addressable patient population to a small subset. Our projections of both the number of people who have these diseases, as well as the subset of people with these diseases who have the potential to benefit from treatment with our products and product candidates, are based on our beliefs and estimates. These estimates have been derived from a variety of sources, including the scientific literature, surveys of clinics, patient foundations, or market research, and may prove to be incorrect. Further, new studies may change the estimated incidence or prevalence of these diseases. The number of patients may turn out to be lower than expected. The effort to identify patients with diseases we seek to treat is in early stages, and we cannot accurately predict the number of patients for whom treatment might be possible. Additionally, the potentially addressable patient population for each of our products and product candidates may be limited or may not be amenable to treatment with our products and product candidates, and new patients may become increasingly difficult to identify or access, which would adversely affect our results of operations and our business. Further, even if we obtain significant market share for our products and product candidates, because the potential target populations are very small, we may never become or remain profitable nor generate sufficient revenue growth to sustain our business.

Manufacturers that produce our products and product candidates may not have experience producing our products and product candidates at commercial levels and may not achieve the necessary regulatory approvals or produce our products and product candidates at the cost, quality, quantities, locations, and timing needed to support profitable commercialization.

We rely on third-party manufacturers to produce our products and product candidates. These manufacturers may not have the experience or ability to produce our products and product candidates at commercial levels. We may run into technical or scientific issues related to manufacturing or development that we may be unable to resolve in a timely manner or with available funds. We also have not completed all of the characterization and validation activities necessary for commercialization and regulatory approvals for all of our product candidates. If our manufacturing partners are not able to conduct all such necessary activities in accordance with applicable regulations, our commercialization efforts will be harmed. We have not yet secured manufacturing capabilities for commercial quantities of all of our product candidates and may be unable to negotiate binding agreements with manufacturers to support our commercialization activities on commercially reasonable terms.

Even if our third-party product manufacturers develop an acceptable manufacturing process, if such third-party manufacturers are unable to produce the necessary quantities of our products and product candidates, are unable to comply with GMP or other pertinent regulatory requirements, or are unable to produce our products and product candidates within our planned timeframe and cost parameters, the development and sales of our products and product candidates, if approved, may be materially harmed.

Additionally, the cost to us for the supply of our products and product candidates manufactured by such third parties may be high and could limit our profitability, even if our third-party product manufacturers develop acceptable manufacturing processes that provide the necessary quantities of our products and product candidates in a compliant and timely manner. Furthermore, KKC is our sole supplier of commercial quantities of Crysvita. The supply price to us for commercial sales of Crysvita in Latin America and the transfer price for commercial sales of the product in the United States and Canada is 35% of net sales through December 31, 2022 and 30% thereafter, which is higher than the typical cost of goods sold by companies focused on rare diseases.

We face intense competition and rapid technological change and the possibility that our competitors may develop therapies that are similar, more advanced, or more effective than ours, which may adversely affect our financial condition and our ability to successfully commercialize our product candidates.

The biotechnology and pharmaceutical industries are intensely competitive and subject to rapid and significant technological change. We are currently aware of various existing treatments that may compete with our products and product candidates. For example, XLH is treated with oral phosphate and vitamin D therapy, which may compete with Crysvita; LC-FAOD is managed with diet therapy and medium-chain triglyceride oil, which may compete with Dojolvi; OTC deficiency is currently treated ~~with nitrogen scavenging drugs and severe limitations~~See “Item 1. Business – Competition” in ~~dietary protein, which may compete with DTX30; and~~ ~~GSDIa is currently treated with corn starch, which may compete with DTX401. Triheptanoin is available in food-grade form, which may compete with~~ our pharmaceutical-grade product. Furthermore, investigator-sponsored trials evaluating triheptanoin in multiple indications are ongoing. Gene therapy, gene correction, RNA-based therapies, and other approaches may also emerge for the treatment of any of the disease areas in which we focus.Annual Report.

We have competitors both in the United States and internationally, including major multinational pharmaceutical companies, specialty pharmaceutical companies, biotechnology companies, startups, academic research institutions, government agencies, and public and private research institutions. Many of our competitors have substantially greater financial, technical, and other resources, such as larger research and development staff and experienced marketing and manufacturing organizations. Additional mergers and acquisitions in the biotechnology and pharmaceutical industries may result in even more resources being concentrated in our competitors. As a result, these companies may obtain regulatory approval more rapidly than we are able to and may be more effective in selling and marketing their products as well. Smaller or early-stage companies may also prove to be significant competitors, particularly through collaborative arrangements with large, established companies. Competition may increase further as a result of advances in the commercial applicability of technologies and greater availability of capital for investment in these industries. Our competitors may succeed in developing, acquiring, or licensing on an exclusive basis, products that are more effective or less costly than any product candidate that we may develop, or achieve earlier patent protection, regulatory approval, product commercialization, and market penetration than we do. Additionally, technologies developed by our competitors may render our potential products and product candidates uneconomical or obsolete, and we may not be successful in marketing our products and product candidates against competitors.

We ~~continue~~may not be able to ~~build and evolve~~effectively manage the expansion of our organization, including building an integrated commercial organization. If we are unable to expand our existing commercial infrastructure or enter into agreements with third parties to market and sell our products and product candidates, as needed, we may be unable to ~~generate significant~~increase our revenue.

We expect we will need additional managerial, operational, marketing, financial, legal, and other resources to support our development and commercialization plans and strategies. In order to successfully commercialize our products as well as any additional products that may result from our development programs, we are building aand expanding our commercial infrastructure in North America, Europe and Latin America. This infrastructure consists of both office based as well as field teams with technical expertise, and will be expanded as we approach the potential approval dates of additional products that result from our development programs. ~~This will~~Our management may need to divert a disproportionate amount of its attention away from our day-to-day activities and devote a substantial amount of time to managing these growth activities. We may not be ~~expensive and time consuming. Any failure or delay in~~able to effectively manage the expansion of ~~this~~our operations, which may result in weaknesses in our infrastructure, operational mistakes, loss of business opportunities, loss of employees, and reduced productivity among remaining employees. Our expected growth could require significant capital expenditures and may ~~adversely impact~~divert financial resources from other projects, such as the ~~commercialization~~development of additional product candidates. If our ~~approved products.~~management is unable to effectively manage our growth, our expenses may increase more than expected, our ability to generate and/or grow revenue could be reduced, and we may not be able to implement our business strategy. Our future financial performance and our ability to commercialize product candidates and compete effectively will depend, in part, on our ability to effectively manage any future growth.

~~Although our employees may have promoted other similar products in the past while employed at other companies, we,~~We, as a company, have limited, recent experience selling and marketing our ~~product.~~product and only some of our employees have prior experience promoting other similar products in the past while employed at other companies. As we increase the number and range of our commercialized products, we may experience additional complexities to our sales process and strategy and have difficulties in allocating sufficient resources to sales and marketing of certain products. Further, ~~given~~as we launch additional products or as demand for our ~~limited experience in marketing and selling biopharmaceutical~~ products change, our initial estimate of the size of the required field force may be materially more or less than the size of the field force actually required to effectively commercialize our product candidates. As such, we may be required to hire large teams to adequately support the commercialization of our products and product candidates or we may incur excess costs in an effort to optimize the hiring of commercial personnel. With respect to certain geographical markets, we may enter into collaborations with other entities to utilize their local marketing and distribution capabilities, but we may be unable to enter into such agreements on favorable terms, if at all. If our future collaborators do not commit sufficient resources to commercialize our future products, if any, and we are unable to develop the necessary marketing capabilities on our own, we will be unable to generate sufficient product revenue to sustain our business. We may be competing with companies that currently have extensive and well-funded marketing and sales operations. Without a large internal team or the support of a third-party to perform key commercial functions, we may be unable to compete successfully against these more established companies.

Our exclusive right to promote Crysvita in the United States and Canada expires in 2023.

Pursuant to the terms of our collaboration and license agreement with KKC, we have the sole right to promote Crysvita in the United States and Canada, or the profit-share territory, for a specified period of time, with KKC increasingly participating in the promotion of the product until the transition date of April 2023, which is the fifth anniversary of the commercial launch of the product in the United States. After the transition date, KKC will have the right to promote the product, subject to a limited promotion right retained by us. ~~Although we expect that we will use our North America commercial infrastructure to promote our other commercialized products after the transition date, we~~We cannot assure that we will have adequate commercial activity to support our North America field force and other aspects of our commercial infrastructure in the ~~territory.~~territory after the transition date. After the transition date, we will also solely bear the expenses related to the promotion of Crysvita in the profit-share territory pursuant to our limited promotion right, rather than share such expenses with KKC. ~~We expect to collaborate~~Collaboration with KKC ~~to provide for~~may not result in a seamless transition of responsibilities for KKC to promote the product in the profit-share territory after the transition date ~~however,~~and the commercial success of Crysvita in the profit-share territory after the transition date will depend on, among other things, the efforts and allocation of resources of KKC.

The commercial success of any current or future product will depend upon the degree of market acceptance by physicians, patients, third-party payors, and others in the medical community.

Even with the requisite approvals from the FDA and comparable foreign regulatory authorities, the commercial success of our current and future products will depend in part on the medical community, patients, and payors accepting our current and future products as medically useful, cost-effective, and safe. Any product that we bring to the market may not gain market acceptance by physicians, patients, payors, and others in the medical community. The degree of market acceptance of any of our current and future products will depend on a number of factors, including:

Even if a potential product displays a favorable efficacy and safety profile in nonclinical and clinical studies, market acceptance of the product will not be fully known until after it is launched. Our efforts to educate the medical community and payors on the benefits of the product candidates ~~may~~ require significant resources and may never be successful. If our current and future products fail to achieve an adequate level of acceptance by physicians, patients, payors, and others in the medical community, we will not be able to generate sufficient revenue to become or remain profitable.

The insurance coverage and reimbursement status of newly approved products is uncertain. Failure to obtain or maintain adequate coverage and reimbursement for new or current products could limit our ability to market those products and decrease our ability to generate revenue.

Our target patient populations are small, and accordingly the pricing, coverage, and reimbursement of our products and product candidates, if approved, must be adequate to support our commercial infrastructure. Our per-patient prices must be sufficient to recover our development and manufacturing costs and potentially achieve profitability. We expect the cost of a single administration of gene therapy products, such as those we are developing, to be substantial, when and if they achieve regulatory approval. Accordingly, the availability and adequacy of coverage and reimbursement by governmental and private payors are essential for most patients to afford expensive treatments such as ours, assuming approval. Sales of our products and product candidates, if approved, will depend substantially, both domestically and abroad, on the extent to which their costs will be paid for by health maintenance, managed care, pharmacy benefit, and similar healthcare management organizations, or reimbursed by government authorities, private health insurers, and other payors. If coverage and reimbursement are not available, are available only to limited levels, or are not available on a timely basis, we may not be able to successfully commercialize our products and product candidates, if approved. For example, deteriorating economic conditions and political instability in certain Latin American countries and in Turkey may cause us to experience significant delays in receiving approval for reimbursement for our products and consequently impact our product commercialization timelines in such regions. Even if coverage is provided, the approved reimbursement amount may not be high enough to allow us to establish or maintain pricing sufficient to sustain our overall enterprise.

There is significant uncertainty related to the insurance coverage and reimbursement of newly approved products. In the United States, the Centers for Medicare & Medicaid Services, or CMS, an agency within the U.S. Department of Health and Human Services, decides whether and to what extent a new drug will be covered and reimbursed under Medicare. Private payors tend to follow the coverage reimbursement policies established by CMS to a substantial degree. It is difficult to predict what CMS or private payors will decide with respect to reimbursement for products such as ours, especially our gene therapy product candidates as there is a limited body of established practices and precedents for gene therapy products.

Outside the United States, international operations are generally subject to extensive governmental price controls and other market regulations, and we believe the increasing emphasis on cost-containment initiatives in Europe, Canada, and other countries will put pressure on the pricing and usage of our products and product candidates. In many countries, the prices of medical products are subject to varying price control mechanisms as part of national health systems. Other countries allow companies to fix their own prices for medicinal products, but monitor and control company profits. Additional foreign price controls or other changes in pricing regulation could restrict the amount that we are able to charge for our product candidates. Accordingly, in markets outside the United States, the reimbursement for our products may be reduced compared with the United States and may be insufficient to generate commercially reasonable revenue and profits.

Moreover, increasing efforts by governmental and third-party payors in the United States and abroad to cap or reduce healthcare costs may cause such organizations to limit both coverage and the level of reimbursement for new products and, as a result, they may not cover or provide adequate payment for our products and product candidates. We expect to experience pricing pressures in connection with the sale of any of our products and product candidates due to the trend toward managed healthcare, the increasing influence of health maintenance organizations, additional legislative changes, and statements by elected officials. For example, proposals ~~are being~~have been discussed to tie U.S. drug prices to the cost in other countries, several states in the U.S. have introduced legislation to require pharmaceutical companies to disclose their costs to justify the prices of their products, and an “Affordable Drug Pricing Task-Force” has been formed in the U.S. House of Representatives with the goal of combating the increased costs of prescription drugs. ~~Although~~Drug pricing is also expected to remain a ~~number of these proposals~~focus for the new Presidential Administration and other measures, including the executive orders announced by the U.S. Presidential administration in July 2020 and September 2020 aimed to lower drug prices, may require additional authorization to become effective, Congress and the U.S. Presidential administration have each indicated that it will continue to seek new legislative and/or administrative measures to control drug costs.Congress. The downward pressure on healthcare costs in general, and with respect to prescription drugs, surgical procedures, and other treatments in particular, has become very intense. As a result, increasingly high barriers are being erected to the entry of new products.

The ~~results of the~~ United Kingdom’s ~~referendum on~~ withdrawal from the EU may have a negative effect on our business, global economic conditions, and financial markets.

~~On June 23, 2016, the electorate in the United Kingdom voted in favor of leaving the EU, commonly referred to as Brexit.~~ On January 30, 2020, the United Kingdom formally withdrew from the ~~EU. Following the United Kingdom’s formal withdrawal from the~~ EU, ~~the United Kingdom will~~commonly referred to ~~continue to follow all of the EU’s rules~~as Brexit, and ~~its trading relationship with the EU will remain the same during a transition period which will expire on December 31, 2020. Several aspects of~~ the United Kingdom and EU ~~relationship will need~~subsequently entered into a trading agreement effective January 1, 2021. In anticipation of Brexit, we had previously adjusted our product inventory and storage plans and as such, our business and operations to ~~be determined during~~date have not been materially or adversely impacted by Brexit. However, the ~~transition period, including free~~full effects of Brexit and the impact from the trade agreement and other formal agreements ~~and rules and regulations affecting the biotechnology or pharmaceutical industries. Since a significant proportion of the regulatory framework in~~between the United Kingdom ~~is derived from~~and EU ~~directives and regulations, Brexit could materially~~that may impact the regulatory regime with respect to the approval of product candidates, disrupt the manufacture of our products and product candidates in the United Kingdom or the EU, disrupt the importation and export of active substances and other components of drug formulations, and disrupt the supply chain for clinical trial product and final authorized formulations. Any delay in obtaining, or an inability to obtain, any marketing approvals, or disruption to our and our collaborators’ supply chain as a result of Brexit or otherwise, would prevent us from commercializing our product candidates in the United Kingdom and/or the EU and restrict our ability to generate revenue and achieve and sustain profitability. The cumulative effect of disruptions to the regulatory framework or supply chains may add considerably to the development lead time to, and expense of, marketing authorization and commercialization of products in the EU and/or the United Kingdom. In view of the uncertainty surrounding the Brexit implementation, we are unable to predict the effects of such disruption to the regulatory framework and supply chain in ~~Europe.~~

Further, these developments, or the perception that any of them could occur, have had and may continue to have a material adverse effect on global economic conditions and the stability of global financial markets, and could significantly reduce global market liquidity and restrict the ability of key market participants to operate in certain financial markets. Asset valuations, currency exchange rates and credit ratings may be especially subject to increased market volatility. Lack of clarity about future U.K. laws and regulations as the United Kingdom determines which EU laws to replace or replicate following the expiration of the transition period, including financial laws and regulations, tax and free trade agreements, intellectual property rights, supply chain logistics, environmental, health and safety laws and regulations, immigration laws and employment laws, could decrease foreign direct investment in the United Kingdom, increase costs and depress economic activity. In addition,Europe remain uncertain. For instance, we expect that Brexit could lead to ~~legal uncertainty~~additional processes and ~~potentially divergent national laws and regulations as the United Kingdom determines which EU laws to replicate or replace. We are taking certain precautionary measures~~steps with respect to ~~Brexit~~certain regulatory applications and ~~its~~activities, which may impact to the ~~EU, and will continue to monitor the situation. If~~timing of approvals or result in additional costs. Further, if the United Kingdom were to significantly alter its regulations affecting the biotechnology or pharmaceutical industries, we could face significant ~~new~~additional costs. It may also be time-consuming and expensive for us to alter our internal operations in order to comply with new regulations. Any of these factors could have a material adverse effect on our business, financial condition and results of operations and affect our strategy in the U.K. and EU biotech market.

If we are unable to obtain and maintain effective patent rights for our products, product candidates, or any future product candidates, we may not be able to compete effectively in our markets.

We rely upon a combination of patents, trade secret protection, and confidentiality agreements to protect the intellectual property related to our technologies, our products, and our product candidates. Our success depends in large part on our and our licensors’ ability to obtain and maintain patent and other intellectual property protection in the United States and in other countries with respect to our proprietary ~~technology,~~technologies, our products, and our product candidates.

We have sought to protect our proprietary position by filing patent applications in the United States and abroad related to our novel technologies, products and ~~products~~product candidates that are important to our business. This process is expensive and time consuming, and we may not be able to file and prosecute all necessary or desirable patent applications at a reasonable cost or in a timely manner. It is also possible that we will fail to identify patentable aspects of our research and development output before it is too late to obtain patent protection.

The patent position of biotechnology and pharmaceutical companies generally is highly uncertain and involves complex legal and factual questions for which legal principles remain unsolved. The patent applications that we own or in-license may fail to result in issued patents with claims that cover our products or product candidates in the United States or in other foreign countries. There is no assurance that all potentially relevant prior art relating to our patents and patent applications has been found, which can invalidate a patent or prevent a patent from issuing from a pending patent application. Even if patents do successfully issue, and even if such patents cover our products or product candidates, third parties may challenge their validity, enforceability, or scope, which may result in such patents being narrowed, found unenforceable, or invalidated. Furthermore, even if the patents and patent applications we own or in-license are unchallenged, they may not adequately protect our intellectual property, provide exclusivity for our products or product candidates, or prevent others from designing around our claims. Any of these outcomes could impair our ability to prevent competition from third parties, which may have an adverse impact on our business.

We, independently or together with our licensors, have filed several patent applications covering various aspects of our products or product candidates. We cannot offer any assurances about which, if any, patents will issue, the breadth of any such patent or whether any issued patents will be found invalid and unenforceable or will be threatened by third parties. Any successful opposition to these patents could impair the exclusivity position of our products or ~~any other patents owned by or licensed to us after patent issuance could~~ deprive us of rights necessary for the successful commercialization of any product candidates that ~~we may develop.~~are approved. Further, if we encounter delays in regulatory approvals, the period of time during which we could market a product candidate under patent protection could be reduced.

~~Although we have a number of~~Our current patents or applications covering methods of use and certain compositions of matter we do not ~~have~~provide complete patent protection for our products and product candidates in all territories. For example, there are no issued patents covering the Crysvita composition of matter in Latin America where we have rights to commercialize the compound. Therefore, a competitor could develop the same antibody or a similar antibody as well as other approaches that target FGF23 for potential commercialization in Latin America, subject to any intellectual property rights or regulatory exclusivities awarded to us. If we cannot obtain and maintain effective patent rights for our products or product candidates, we may not be able to compete effectively and our business and results of operations would be harmed.

We may not have sufficient patent terms to effectively protect our products and business.

Patents have a limited lifespan. In the United States, the natural expiration of a patent is generally 20 years after its effective filing date. Although various extensions may be available, the life of a patent, and the protection it affords, is limited. Even if patents covering our product candidates are obtained, once the patent life has expired for a product, we may be open to competition from generic or biosimilar medications.

~~While patent~~Patent term extensions under the Hatch-Waxman Act in the United States and under supplementary protection certificates in Europe may not be available to extend the patent exclusivity term for ~~Crysvita, Mepsevii, Dojolvi, DTX301,~~our products and ~~DTX401,~~product candidates, and we cannot provide any assurances that any such patent term extension will be obtained and, if so, for how long. Furthermore, we may not receive an extension if we fail to apply within applicable deadlines, fail to apply prior to expiration of relevant patents or otherwise fail to satisfy applicable requirements. Moreover, the length of the extension could be less than we request. If we do not have sufficient patent terms or regulatory exclusivity to protect our products, our business and results of operations may be adversely affected.

Patent policy and rule changes could increase the uncertainties and costs surrounding the prosecution of our patent applications and the enforcement or defense of our issued patents.

Changes in either the patent laws or interpretation of the patent laws in the United States and other countries may diminish the value of our patents or narrow the scope of our patent protection. The laws of foreign countries may not protect our rights to the same extent as the laws of the United States. Publications of discoveries in the scientific literature often lag behind the actual discoveries, and patent applications in the United States and other jurisdictions are typically not published until 18 months after filing, or in some cases not at all. We therefore cannot be certain that we or our licensors were the first to make the invention claimed in our owned and ~~licensed~~in-licensed patents or pending applications, or that we or our licensor were the first to file for patent protection of such inventions. Assuming the other requirements for patentability are met, in the United States prior to March 16, 2013, the first to make the claimed invention is entitled to the patent, while outside the United States, the first to file a patent application is entitled to the patent. After March 15, 2013, under

In 2011, the Leahy-Smith America Invents Act ~~or the~~(the Leahy-Smith ~~Act, enacted on September 16, 2011, the United States has also moved to a first to file system. The Leahy-Smith Act included a number of~~Act) was signed into law and introduced significant changes ~~that affect~~to the ~~way~~prosecution of U.S. patent applications ~~are prosecuted~~ and to the ~~way patents can be challenged.~~procedures for challenging U.S. patents. The effects of these changes ~~are currently~~still remain unclear asowing to the ~~courts have only begun to address these provisions. In general,~~evolving nature of the law and the lengthy timelines associated with court system review and interpretation. However, the Leahy-Smith Act and its implementation could increase the uncertainties and costs surrounding the prosecution of our patent applications and the enforcement or defense of our issued patents, all of which could have a material adverse effect on our business and financial condition.

If we are unable to maintain effective proprietary rights for our products, product candidates, or any future product candidates, we may not be able to compete effectively in our markets.

In addition to the protection afforded by patents, we rely on trade secret protection and confidentiality agreements to protect proprietary know-how that is not patentable or that we elect not to patent, processes for which patents are difficult to enforce and any other elements of our products or product candidate discovery and development processes that involve proprietary know-how, information, or technology that is not covered by patents. However, trade secrets can be difficult to protect. ~~We seek to protect our proprietary technology and processes, in part, by entering into~~The confidentiality agreements entered into with our employees, consultants, scientific advisors, and ~~contractors. We also seek~~contractors may not be sufficient to ~~preserve the integrity~~protect our proprietary technology and ~~confidentiality of our data and trade secrets by maintaining~~processes. The physical security of our premises and physical and electronic security of our information technology ~~systems. While we have confidence in these~~systems may not preserve the integrity and confidentiality of our data and trade secrets. These individuals, organizations and systems, agreements or security measures may be breached, and we may not have adequate remedies for any breach. In addition, our trade secrets may otherwise become known or be independently discovered by competitors.

~~Although~~The assignment agreements we ~~expect all of~~enter into with our employees and consultants to assign their inventions to us, and ~~all of~~the confidentiality agreements we enter into with our employees, consultants, advisors, and any third parties who have access to our proprietary know-how, information, or technology ~~to enter into confidentiality agreements, we cannot provide any assurances that all such agreements~~may not have been duly executed orand we cannot assure that our trade secrets and other confidential proprietary information will not be disclosed or that competitors will not otherwise gain access to our trade secrets or independently develop substantially equivalent information and techniques. Misappropriation or unauthorized disclosure of our trade secrets could impair our competitive position and may have a material adverse effect on our business. Additionally, if the steps taken to maintain our trade secrets are deemed inadequate, we may have insufficient recourse against third parties for misappropriating the trade secret.

Claims of intellectual property infringement may prevent or delay our development and commercialization efforts.

Our commercial success depends in part on our avoiding infringement of the patents and proprietary rights of others. There have been many lawsuits and other proceedings involving patent and other intellectual property rights in the biotechnology and pharmaceutical industries, including patent infringement lawsuits, interferences, inter partes reviews, post grant reviews, oppositions, and reexamination proceedings before the USPTO and corresponding foreign patent offices. Numerous U.S. and foreign issued patents and pending patent applications, which are owned by other parties, exist in the fields in which we are developing product candidates. As the biotechnology and pharmaceutical industries expand and more patents are issued, the risk increases that our products or product candidates may be subject to claims of infringement of the patent rights of these other parties.

Other parties may assert that we are employing their proprietary technology without authorization. There may be patents or patent applications with claims to materials, formulations, methods of manufacture, or methods for treatment related to the use or manufacture of our products or product candidates. We have conducted freedom to operate analyses with respect only to our products and certain of our product candidates, and therefore we do not know whether there are any patents of other parties that would impair our ability to commercialize all of our product candidates. We also cannot guarantee that any of our analyses are complete and thorough, nor can we be sure that we have identified each and every patent and pending application in the United States and abroad that is relevant or necessary to the commercialization of our products or product candidates. Because patent applications can take many years to issue, there may be currently pending patent applications that may later result in issued patents that our products or product candidates may infringe.

We are aware of ~~four third-party patent families~~certain U.S. and foreign patents owned by third parties that ~~include issued U.S. patents with claims that, if valid and enforceable, could~~a court might construe to be ~~construed~~relevant to ~~cover~~ one or more of our gene therapy product candidates, if and when approved, or methods of their manufacture. We are also aware of two third-party patent families that include issued European claims that, if valid and enforceable, could be construed to cover certain methods that may be used in ~~the~~their manufacture, ofor certain formulations comprising one or more of our gene therapy ~~product~~ candidates. ~~In addition, other~~We are also aware of certain U.S. and foreign patents owned by third parties that relate to anti-sclerostin antibodies and their use, and which a court might construe to be relevant to setrusumab. There is a risk that one or more of these third parties may ~~obtain patents~~choose to engage in ~~the future and claim that use of our technologies infringes upon these patents. If any of these patents were held by~~litigation with us to enforce or to otherwise assert their patent rights against us. Even if we believe such claims are without merit, a court of competent jurisdiction ~~to cover aspects~~could hold that one or more of ~~our formulations,~~these patents is valid, enforceable, and infringed, in which case the ~~manufacturing process of our products or any of our product candidates, methods of use, any molecules formed during the manufacturing process or any final product itself, the holders~~owners of any such patents may be able to block our ability to commercialize ~~our products or~~ a product candidate unless we obtained a license under the applicable patents, or until such patents ~~expire or are finally determined to be invalid or unenforceable. Such~~expire. However, such a license may not be available on commercially reasonable terms or at all.

Parties making claims against us may obtain injunctive or other equitable relief, which could effectively block our ability to continue commercialization of our products, or block our ability to develop and commercialize one or more of our product candidates. Defense of these claims, regardless of their merit, would involve substantial litigation expense and would be a substantial diversion of employee resources from our business. In the event of a successful claim of infringement against us, we may have to pay substantial damages, including treble damages and attorneys’ fees for willful infringement, pay royalties, redesign our infringing products, or obtain one or more licenses from third parties, which may be impossible or require substantial time and monetary expenditure.

We may not be successful in obtaining or maintaining necessary rights to our product candidates through acquisitions and in-licenses.

We currently have rights to the intellectual property, through licenses from third parties and under patents that we own, to commercialize our product candidates. Because our programs may require the use of proprietary rights held by third parties, the growth of our business will likely depend in part on our ability to acquire, in-license, or use these proprietary rights. For example, our product candidates may require specific formulations to work effectively and efficiently and the rights to these formulations may be held by others. We may be unable to acquire or in-license any compositions, methods of use, processes, or other third-party intellectual property rights from third parties that we identify as necessary for our product candidates. The licensing and acquisition of third-party intellectual property rights is a competitive area, and a number of more established companies are also pursuing strategies to license or acquire third-party intellectual property rights that we may consider attractive. These established companies may have a competitive advantage over us due to their size, cash resources, and greater clinical development and commercialization capabilities. In addition, companies that perceive us to be a competitor may be unwilling to assign or license rights to us. We also may be unable to license or acquire third-party intellectual property rights on terms that would allow us to make an appropriate return on our investment.

We sometimes collaborate with U.S. and foreign academic institutions to accelerate our preclinical research or development under written agreements with these institutions. Typically, these institutions provide us an option to negotiate a license to any of the institution’s rights in technology resulting from the collaboration. Regardless of such option, we may be unable to negotiate a license within the specified timeframe or under terms that are acceptable to us. If we are unable to do so, the institution may offer the intellectual property rights to other parties, potentially blocking our ability to pursue our program.

If we are unable to successfully obtain rights to required third-party intellectual property rights or maintain the existing intellectual property rights we have, we may have to abandon development of that program and our business and financial condition could suffer.

We may face competition from biosimilars, which may have a material adverse impact on the future commercial prospects of ~~Crysvita, Mepsevii, DTX301,~~our biological products and ~~DTX401.~~product candidates.

Even if we are successful in achieving regulatory approval to commercialize a product candidate faster than our competitors, we may face competition from biosimilars with respect to ~~Crysvita, Mepsevii, DTX301,~~our biological products (Crysvita and ~~DTX401.~~Mepsevii) and our biological product candidates. In the United States, the Biologics Price Competition and Innovation Act of 2009, or BPCI Act, was included in the Affordable Care Act and created an abbreviated approval pathway for biological products that are demonstrated to be “highly similar,” or biosimilar, to or “interchangeable” with an FDA-approved biological product. The BPCI Act prohibits the FDA from approving a biosimilar or interchangeable product that references a brand biological product until 12 years after the licensure of the reference product, but permits submission of an application for a biosimilar or interchangeable product to the FDA four years after the reference product was first licensed. The BPCI Act does not prevent another company from developing a product that is highly similar to the innovative product, generating its own data, and seeking approval. Moreover, it is not known whether the BPCI Act will survive in whole or in part if the Affordable Care Act is repealed by Congress or held unconstitutional by courts. As a result, its ultimate impact, implementation, meaning, and long-term existence are subject to uncertainty. Elimination or modification of the BPCI Act, or changes to the FDA’s interpretation or implementation of the BPCI Act, could have a material adverse effect on the future commercial prospects for ~~Crysvita, Mepsevii, DTX301,~~our biological products and ~~DTX401.~~product candidates.

In Europe, the European Commission has granted marketing authorizations for several biosimilars pursuant to a set of general and product class-specific guidelines for biosimilar approvals issued over the past few years. In Europe, a competitor may reference data supporting approval of an innovative biological product, but will not be able to get on the market until 10 years after the time of approval of the innovative product. This 10-year marketing exclusivity period will be extended to 11 years if, during the first eight of those 10 years, the marketing authorization holder obtains an approval for one or more new therapeutic indications that bring significant clinical benefits compared with existing therapies. In addition, companies may be developing biosimilars in other countries that could compete with our products.

If competitors are able to obtain marketing approval for biosimilars referencing our products, our products may become subject to competition from such biosimilars, with the attendant competitive pressure and consequences.

Competitors could enter the market with generic versions of Dojolvi or our small-molecule product candidates, which may result in a material decline in sales of affected products.

Under the Hatch-Waxman Act, a pharmaceutical manufacturer may file an abbreviated new drug application, or ANDA, seeking approval of a generic copy of an approved innovator product. Under the Hatch-Waxman Act, a manufacturer may also submit an NDA under section 505(b)(2) that references the FDA’s finding of safety and effectiveness of a previously approved drug. A 505(b)(2) NDA product may be for a new or improved version of the original innovator product. Innovative small molecule drugs may be eligible for certain periods of regulatory exclusivity (e.g., five years for new chemical entities, three years for changes to an approved drug requiring a new clinical study, and seven years for orphan drugs), which preclude FDA approval (or in some circumstances, FDA filing and review of) an ANDA or 505(b)(2) NDA relying on the FDA’s finding of safety and effectiveness for the innovative drug. In addition to the benefits of regulatory exclusivity, an innovator NDA holder may have patents claiming the active ingredient, product formulation or an approved use of the drug, which would be listed with the product in the “Orange Book.” If there are patents listed in the Orange Book, a generic applicant that seeks to market its product before expiration of the patents must include in the ANDA or 505(b)(2) what is known as a “Paragraph IV certification,” challenging the validity or enforceability of, or claiming non-infringement of, the listed patent or patents. Notice of the certification must be given to the innovator, too, and if within 45 days of receiving notice the innovator sues to enforce its patents, approval of the ANDA is stayed for 30 months, or as lengthened or shortened by the court.

Accordingly, competitors could file ANDAs for generic versions of our small-molecule product, Dojolvi, or 505(b)(2) NDAs that reference Dojolvi. For ~~any~~the patents listed for Dojolvi in the Orange Book, those ANDAs and 505(b)(2) NDAs would be required to include a certification as to each listed patent indicating whether the ANDA applicant does or does not intend to challenge the patent. We cannot predict how any generic competitor would address such patents, whether we would sue on any such patents, or the outcome of any such suit.

We may not be successful in securing or maintaining proprietary patent protection for products and technologies we develop or license. Moreover, if any patents that are granted and listed in the Orange Book are successfully challenged by way of a Paragraph IV certification and subsequent litigation, the affected product could more immediately face generic competition and its sales would likely decline materially. Should sales decline, we may have to write off a portion or all of the intangible assets associated with the affected product and our results of operations and cash flows could be materially and adversely affected.

The patent protection and patent prosecution for some of our products and product candidates is dependent on third parties.

While we normally seek and gain the right to fully prosecute the patents relating to our products or product candidates, there may be times when patents relating to our products or product candidates are controlled by our licensors. This is the case with our agreement with KKC, who is primarily responsible for the prosecution of certain patents and patent applications covering Crysvita which are licensed to us under the collaboration agreement.

In addition, we have in-licensed patents and patent applications owned by the University of Pennsylvania, relating to the AAV8 vector used in DTX301 and DTX401. These patents and patent applications are licensed or sublicensed by REGENXBIO and sublicensed to us. We do not have the right to control the prosecution of these patent applications, or the maintenance of any of these patents. In addition, under our agreement with REGENXBIO, we do not have the first right to enforce the licensed patents, and our enforcement rights are subject to certain limitations that may adversely impact our ability to use the licensed patents to exclude others from commercializing competitive products. Moreover, REGENXBIO and the University of Pennsylvania may have interests which differ from ours in determining whether and the manner in which to enforce such patents.

If KKC, the University of Pennsylvania, or any of our future licensing partners fail to appropriately prosecute, maintain, and enforce patent protection for the patents covering any of our products or product candidates, our ability to develop and commercialize those products or product candidates may be adversely affected and we may not be able to prevent competitors from making, using, and selling competing products. In addition, even where we now have the right to control patent prosecution of patents and patent applications we have licensed from third parties, we may still be adversely affected or prejudiced by actions or inactions of our licensors and their counsel that took place prior to us assuming control over patent prosecution.

If we fail to comply with our obligations in the agreements under which we license intellectual property and other rights from third parties or otherwise experience disruptions to our business relationships with our licensors, we could lose license rights that are important to our business.

We are a party to a number of intellectual property license agreements that are important to our business and expect to enter into additional license agreements in the future. Our existing license agreements impose, and we expect that future license agreements will impose, various diligence, milestone payment, royalty, and other obligations on us. If we fail to comply with our obligations under these agreements, or we are subject to a bankruptcy, we may be required to make certain payments to the licensor, we may lose the exclusivity of our license, or the licensor may have the right to terminate the license, in which event we would not be able to develop or market products covered by the license. Additionally, the milestone and other payments associated with these licenses will make it less profitable for us to develop our ~~drug~~product candidates.

In certain cases, we control the prosecution of patents resulting from licensed technology. In the event we breach any of our obligations related to such prosecution, we may incur significant liability to our licensing partners. Licensing of intellectual property is of critical importance to our business and involves complex legal, business, and scientific issues. Disputes may arise regarding intellectual property subject to a licensing agreement, including but not limited to:

If disputes over intellectual property and other rights that we have licensed prevent or impair our ability to maintain our current licensing arrangements on acceptable terms, we may be unable to successfully develop and commercialize the affected product candidates.

~~Although we are not currently involved in any intellectual property litigation, we~~We may bebecome involved in lawsuits to protect or enforce our patents or the patents of our licensors, or be subject to claims that challenge the inventorship or ownership of our patents or other intellectual property, which could be expensive, time consuming, and ~~unsuccessful.~~result in unfavorable outcomes.

Competitors may infringe our patents or the patents of our licensors. ~~Although we are not currently involved in any intellectual property litigation, if~~If we or one of our licensing partners were to initiate legal proceedings against a third party to enforce a patent covering our products or one of our product candidates, the defendant could counterclaim that the patent covering our product or product candidate is invalid and/or unenforceable. In patent litigation in the United States, defendant counterclaims alleging invalidity and/or unenforceability are commonplace. Grounds for a validity challenge could be an alleged failure to meet any of several statutory requirements, including lack of novelty, obviousness, or non-enablement. Grounds for an unenforceability assertion could be an allegation that someone connected with prosecution of the patent withheld relevant information from the USPTO, or made a misleading statement, during prosecution. The outcome following legal assertions of invalidity and unenforceability is unpredictable.

Interference proceedings or derivation proceedings now available under the Leahy-Smith Act provoked by third parties or brought by us or declared or instituted by the USPTO may be necessary to determine the priority of inventions with respect to our patents or patent applications or those of our licensors. An unfavorable outcome could require us to cease using the related technology or to attempt to license rights to it from the prevailing party. Our business could be harmed if the prevailing party does not offer us a license on commercially reasonable terms. In addition, the validity of our patents could be challenged in the USPTO by one of the new post grant proceedings (i.e., inter partes review or post grant review) now available under the Leahy-Smith Act. Our defense of litigation, interference proceedings, or post grant proceedings under the Leahy-Smith Act may fail and, even if successful, may result in substantial costs and distract our management and other employees.

We may in the future also be subject to claims that former employees, collaborators, or other third parties have an interest in our patents as an inventor or co-inventor. In addition, ~~the uncertainties associated with litigation could~~we may have ~~a material adverse effect on our ability to raise sufficient capital to continue our clinical studies, continue our research programs, license necessary technology~~ownership disputes arise from ~~third parties,~~conflicting obligations of consultants or ~~enter into development partnerships that would help us bring~~others who are involved in developing our product ~~candidates~~candidates. Litigation may be necessary to ~~market.~~defend against these and other claims challenging inventorship or ownership. If we fail to successfully defend against such litigation or claims, in addition to paying monetary damages, we may lose valuable intellectual property rights, such as exclusive ownership of, or right to use, valuable intellectual property.

~~Furthermore, because~~Even if we are successful in defending against such litigation and claims, such proceedings could result in substantial costs and distract our management and other employees. Because of the substantial amount of discovery required in connection with intellectual property litigation, there is a risk that some of our confidential information could be compromised by disclosure during ~~this type of~~ litigation. There could also be public announcements of the results of hearings, motions, or other interim proceedings or ~~developments.~~developments related to such litigation or claims. If securities analysts or investors perceive these results to be negative, it could have a material adverse effect on the price of our common stock.

We may be subject to claims that our employees, consultants, or independent contractors have wrongfully used or disclosed confidential information of third parties or that our employees have wrongfully used or disclosed alleged trade secrets of their former employers.

We employ certain individuals who were previously employed at universities or other biotechnology or pharmaceutical companies, including our competitors or potential competitors. ~~Although we try~~Our efforts to ~~ensure that~~vet our employees, consultants, and independent contractors ~~do not~~and prevent their use of the proprietary information or know-how of others in their work for us may not be successful, and we ~~are not currently~~may in the future be subject to ~~any~~ claims that our employees, consultants, or independent contractors have wrongfully used or disclosed confidential information of third ~~parties, we may in the future be subject to such claims. Litigation may be necessary to defend against these claims.~~parties. If we fail in defending any such claims, in addition to paying monetary damages, we may lose valuable intellectual property rights or personnel, which could adversely impact ~~our business. Even if we are successful in defending against such claims, litigation could result in substantial costs and distract management and other employees.~~

~~We may be subject to claims challenging the inventorship of our patents and other intellectual property.~~

Although we are not currently experiencing any claims challenging the inventorship of our patents or ownership of our intellectual property, we may in the future be subject to claims that former employees, collaborators, or other third parties have an interest in our patents or other intellectual property as an inventor or co-inventor. For example, we may have inventorship disputes arise from conflicting obligations of consultants or others who are involved in developing our product candidates. Litigation may be necessary to defend against these and other claims challenging inventorship. If we fail to successfully defend against such claims, in addition to paying monetary damages, we may lose valuable intellectual property rights, such as exclusive ownership of, or right to use, valuable intellectual property. Such an outcome could have a material adverse effect on our business. Even if we are successful in defending against such claims, litigation could result in substantial costs and distract management and other employees.

Changes in U.S. patent law could diminish the value of patents in general, thereby impairing our ability to protect our products.

As is the case with other biotechnology and pharmaceutical companies, our success is heavily dependent on intellectual property, particularly patents. Obtaining and enforcing patents in the biotechnology and pharmaceutical industries involves both technological and legal complexity. Therefore, obtaining and enforcing such patents is costly, time consuming, and inherently uncertain. In addition, the United States has recently enacted and is currently implementing wide-ranging patent reform legislation. Recent U.S. Supreme Court rulings have narrowed the scope of patent protection available in certain circumstances and weakened the rights of patent owners in certain situations. For example, in Association for Molecular Pathology v. Myriad Genetics, Inc., the Supreme Court ruled that a “naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated,” invalidating Myriad Genetics’ patents on the BRCA1 and BRCA2 genes. Certain claims of our licensed U.S. patents covering DTX301 and DTX401 relate to isolated AAV8 vectors, capsid proteins, or nucleic acids. To the extent that such claims are deemed to be directed to natural products, or to lack an inventive concept above and beyond an isolated natural product, a court may decide the claims are invalid under Myriad. Additionally, there have been recent proposals for additional changes to the patent laws of the United States and other countries that, if adopted, could impact our ability to obtain patent protection for our proprietary technology or our ability to enforce our proprietary technology. Depending on future actions by the U.S. Congress, the U.S. courts, the USPTO and the relevant law-making bodies in other countries, the laws and regulations governing patents could change in unpredictable ways that would weaken our ability to obtain new patents or to enforce our existing patents and patents that we might obtain in the future.

We may not be able to protect our intellectual property rights throughout the world.

Filing, prosecuting, and defending patents on our products or product candidates in all countries throughout the world would be prohibitively expensive, and our intellectual property rights in some countries outside the United States can be less extensive than those in the United States. In addition, the laws of some foreign countries do not protect intellectual property rights to the same extent as federal and state laws in the United States. Further, licensing partners such as KKC may not prosecute patents in certain jurisdictions in which we may obtain commercial rights, thereby precluding the possibility of later obtaining patent protection in these countries. Consequently, we may not be able to prevent third parties from practicing our inventions in all countries outside the United States, or from selling or importing products made using our inventions in and into the United States or other jurisdictions. Competitors may use our technologies in jurisdictions where we have not obtained patent protection to develop their own products and may also export infringing products to territories where we have patent protection, but enforcement is not as strong as that in the United States. These products may compete with our products, and our patents or other intellectual property rights may not be effective or sufficient to prevent them from competing.

Many companies have encountered significant problems in protecting and defending intellectual property rights in foreign jurisdictions. The legal systems of certain countries, particularly certain developing countries, do not favor the enforcement of patents, trade secrets, and other intellectual property protection, particularly those relating to biotechnology products, which could make it difficult for us to stop the infringement of our patents or marketing of competing products in violation of our proprietary rights generally. Proceedings to enforce our patent rights in foreign jurisdictions, whether or not successful, could result in substantial costs and divert our efforts and attention from other aspects of our business, could put our patents at risk of being invalidated or interpreted narrowly, could put our patent applications at risk of not issuing, and could provoke third parties to assert claims against us. We may not prevail in any lawsuits that we initiate and the damages or other remedies awarded, if any, may not be commercially meaningful. Accordingly, our efforts to enforce our intellectual property rights around the world may be inadequate to obtain a significant commercial advantage from the intellectual property that we develop or license.

Actual or threatened public health epidemics or outbreaks, including the ~~current~~ongoing COVID-19 pandemic, have and could again materially and adversely impact our business and operating results.

A public health epidemic or outbreak, and the public and governmental efforts to mitigate the spread of such disease, could materially and adversely impact the commercialization of our products, development and regulatory approval of our product candidates and our clinical trial operations and significantly disrupt our business operations as well as those of our third party suppliers, CRO and collaboration partners that we rely on. In December 2019, a new strain of novel coronavirus (COVID-19) emerged in Wuhan, Hubei Province, China. In March 2020, the World Health Organization declared COVID-19 a pandemic. ~~The spread of this pandemic has caused significant volatility and uncertainty in U.S. and international markets and could materially and adversely affect our business and operating results.~~

The rapid global spread of COVID-19 has led to the implementation of various responses, including government-imposed quarantines, business closures and lockdowns, shelter-in-place and social distancing mandates, sweeping restrictions on travel and other public health safety measures, as well as reported adverse impacts on healthcare resources, facilities and providers across the United States and in other countries where we operate. Although COVID-19 has already impacted our operations and those of our third-party partners, the ultimate scope and magnitude of such impact will depend on future developments, which are highly uncertain and cannot be predicted with confidence, including the scope and duration of the outbreak, additional or modified government actions, new information which may emerge concerning the severity of the coronavirus and the actions taken to contain the pandemic or treat its impact, among others.

Our clinical trial activities, including the initiation and completion of such activities and the timing thereof, have been and are expected to continue to be significantly delayed or disrupted by COVID-19. For instance, enrollment of patients in certain of our clinical trials for our gene therapy product candidates have been disrupted and dosing was delayed in ~~certain~~one of our ~~trials has been delayed as shelter-in-place orders or quarantines have impeded patient movement. We may also experience difficulties in recruiting clinical site investigators and clinical site staff.~~trials. Changes in local regulations in response to COVID-19 have also required us to change the way our clinical trials are conducted and certain ~~anticipated~~ data from our clinical trials ~~will be~~were delayed as a result. Further, healthcare resources have been and may continue to be diverted away from the conduct of clinical trials, such as the diversion of hospitals serving as our clinical trial sites, in response to the COVID-19 pandemic. We have also had difficulties in recruiting clinical site investigators and clinical staff for our studies, and may continue to experience such difficulties. Any of these events, including if we are required to initiate new or additional sites in response to such events, could require us to incur substantial increased expenses, delay the development and commercialization of our product candidates, delay the timing of anticipated data releases, and impact our operating results.

The COVID-19 pandemic ~~may~~has also ~~impact~~impacted the timing of review of our submissions. The FDA has delayed certain key meetings or discussions with us related to one of our product candidates, which may adversely impact the progression of our clinical study for such product candidate. The pandemic has also significantly impacted our commercialization efforts for our ~~products, including the launch of our recently approved product, Dojolvi.~~products. Social distancing measures and travel limitations have prevented our field sales and medical teams from meeting with health care professionals, customers and patients in person and it has become increasingly difficult to maintain consistent contact with our current patients or identify new patients for our commercialized products and product candidates. Further, certain of our patients may experience interruptions in insurance coverage due to job loss or change in

employment status due to the economic impact from the ~~pandemic.~~pandemic, which would limit patient access to our products. Effects from government budgetary constraints, either in the United States or internationally, due to the economic impact of the pandemic, such as changes to state coverage rules under Medicaid programs in the United States, could also impact continued insurance coverage and reimbursement for our products. Any of these events could impact our ability to commercialize our products and adversely affect our operating results and revenue.

We have experienced delays in delivery of ~~the~~ancillary clinical trial materials due to government-imposed mandates and other restrictions from COVID-19 ~~pandemic~~and may ~~also result~~ in the ~~inability~~future experience delays or interruptions in supply of ~~our suppliers to deliver~~ drug product or raw materials, ~~on a timely basis, if at all,~~ or ~~result in~~incur increased costs or expenses. ~~Facility shutdowns or operational restrictions imposed by government-imposed mandates could result in supply disruptions that could impact~~For instance, the ~~availability~~Presidential Executive Order invoking the Defense Production Act of ~~drug product for our clinical trials as well as our commercialized products. For instance,~~1950 has caused certain of our third party manufacturers or suppliers ~~have prioritized~~to prioritize and ~~allocated~~allocate more resources and capacity to supply ~~drug product or raw~~ materials to other companies engaged in the study or manufacture of ~~potential~~ treatments or vaccinations for COVID-19, which ~~may result~~has resulted in delays or shortages in supply of such ~~product or~~ materials to us. Any of these events could adversely impact our clinical trial activities and our ability to meet commercial demand for our product and product candidates and result in loss of revenue. In response to these events, we are currently seeking alternative sources of supply of drug product or raw materials in an attempt to avoid future potential delays in supply of product, which may result in additional expenses. We have also experienced interruptions or delays in sourcing certain equipment, materials and resources, and increased costs for certain raw materials, related to construction of our gene therapy manufacturing facility as a result of COVID-19, which could delay the anticipated timing for completion of the plant or result in significant additional expenses.

In an effort to protect the health of our employees, their families and our communities, and in accordance with shelter-in-place direction from state and local government authorities, we have restricted access to our facilities to personnel and third parties who must perform critical activities that must be completed on-site, limited the number of such personnel that can be present at our facilities at any one time, and requested that most of our personnel work remotely, including significant limitations on access to our laboratory space. As vaccines against COVID-19 become more widely available, we plan to ease restrictions to our facilities and allow our employees to return to work on-site. The ~~effects of the shelter-in-place and~~safety protocols we implement as our ~~remote working policies~~employees return to work may negatively impact productivity and disrupt our business operations. Further, notwithstanding these measures, the COVID-19 pandemic could affect the health and availability of our workforce, including members of our management.not prevent employees from contracting COVID-19. If members of our management and other key personnel in critical functions across our organization are unable to perform their duties or have limited availability due to illness from COVID-19, we may not be able to execute on our business strategy and/or our operations may be negatively impacted. Further, despite the safety protocols we may implement, employees may still contract COVID-19 at the workplace if and when we ease restrictions to our facilities and our employees return to work on-site. The magnitude of the adverse effect on our business operations will depend, in part, on the length and severity of the restrictions and other limitations on our ability to conduct our business in the ordinary course.

The COVID-19 pandemic has negatively impacted the global economy, disrupted global supply chains and created significant volatility and disruption of financial markets, which could adversely impact our operating results. For instance, delays or defaults in payments by our customer and third-party partners could adversely impact our accounts receivables. The value of our investments currently held in a variety of accounts could also be negatively impacted by the volatility in certain markets, such as the fixed income market, and impact our sources of liquidity. The stock market in general and the stock price of biopharmaceutical companies, in particular, have also experienced extreme price and volume fluctuations. Broad market and industry factors, including worsening economic conditions or a recession resulting from the ongoing COVID-19 pandemic, may adversely impact the value of our common stock and our ability to raise capital. If we do raise additional capital and issue equity securities when the value of our common stock is depressed, the dilutive impact on our stockholders may be greater compared to when the value of our common stock is higher.

The COVID-19 pandemic ~~continues to rapidly evolve.~~has already impacted our operations and those of our third-party partners. The magnitude and extent to which the outbreak may impact or continue to impact our business operations, clinical trial activities, product candidate approvals, supply chain and commercialization of our products and product candidates will continue to remain highly dependent on future developments, which are very uncertain and cannot be predicted with confidence, such as the ~~ultimate geographic spread of the disease, the~~ duration of the outbreak, the scope and magnitude of any resurgence in the outbreak due to virus mutations or other factors, the timing and availability of treatments and vaccines against the virus, the duration of, or implementation of additional, restrictions to contain the outbreak and the effectiveness of ~~such~~other actions taken in the United States and other countries to contain and address the pandemic. This pandemic ~~may~~ also ~~amplify~~amplifies many of the other risks described throughout the “Risk Factors” section of this Quarterly Report on Form 10-Q.

Our future success depends in part on our ability to retain our Founder, President, and Chief Executive Officer and to attract, retain, and motivate other qualified personnel.

We are dependent on Emil D. Kakkis, M.D., Ph.D., our Founder, President, and Chief Executive Officer, the loss of whose services may adversely impact the achievement of our objectives. Dr. Kakkis could leave our employment at any time, as he is an “at will” employee. Recruiting and retaining other qualified employees, consultants, and advisors for our business, including scientific and technical personnel, will also be critical to our success. There is currently a shortage of skilled personnel in our industry, which is likely to continue. As a result, competition for skilled personnel is intense and the turnover rate can be high. WeOur investments and efforts in human capital management may not ~~be able to~~ attract and retain personnel on acceptable terms given the competition among numerous pharmaceutical and biotechnology companies for individuals with similar skill sets. In addition, failure to succeed in preclinical or clinical studies may make it more challenging to recruit and retain qualified personnel. The inability to recruit and retain qualified personnel, or the loss of the services of Dr. Kakkis, may impede the progress of our research, development, and commercialization objectives.

If we fail to obtain or maintain orphan drug exclusivity for our products, our competitors may sell products to treat the same conditions and our revenue will be reduced.

Our business strategy focuses on the development of drugs that are eligible for FDA and EU orphan drug designation. In the United States, orphan drug designation entitles a party to financial incentives such as opportunities for grant funding towards clinical study costs, tax advantages, and user-fee waivers. In addition, if a product receives the first FDA approval for the indication for which it has orphan designation, the product is entitled to orphan drug exclusivity, which means the FDA may not approve any other application to market the same drug for the same indication for a period of seven years, except in limited circumstances, such as a showing of clinical superiority over the product with orphan exclusivity or where the manufacturer is unable to assure sufficient product quantity. In the EU, orphan drug designation entitles a party to financial incentives such as reduction of fees or fee waivers and ten years of market exclusivity following drug or biological product approval. This period may be reduced to six years if the orphan drug designation criteria are no longer met, including where it is shown that the product is sufficiently profitable not to justify maintenance of market exclusivity.

Because the extent and scope of patent protection for our products may in some cases be limited, orphan drug designation is especially important for our products for which orphan drug designation may be available. For eligible drugs, we plan to rely on the exclusivity period under the Orphan Drug Act to maintain a competitive position. If we do not obtain orphan drug exclusivity for our drug products and biologic products that do not have broad patent protection, our competitors may then sell the same drug to treat the same condition sooner than if we had obtained orphan drug exclusivity, and our revenue will be reduced.

Even though we have orphan drug designation for Dojolvi for the treatment of fatty acid oxidation disorders in the United States and for various subtypes of LC-FAOD in Europe, as well as for Crysvita, Mepsevii, DTX301, DTX401 and ~~DTX401~~UX701 in the United States and Europe, we may not be the first to obtain marketing approval for any particular orphan indication due to the uncertainties associated with developing pharmaceutical products. Further, even if we obtain orphan drug exclusivity for a product, that exclusivity may not effectively protect the product from competition because different drugs with different active moieties can be approved for the same condition or the same drug can be approved for a different indication unless there are other exclusivities such as new chemical entity exclusivity preventing such approval. Even after an orphan drug is approved, the FDA or EMA can subsequently approve the same drug with the same active moiety for the same condition if the FDA or EMA concludes that the later drug is safer, more effective, or makes a major contribution to patient care. Orphan drug designation neither shortens the development time or regulatory review time of a drug nor gives the drug any advantage in the regulatory review or approval process.

~~We will need to expand our organization and we may experience difficulties in managing this growth, which could disrupt our operations.~~

As our development and commercialization plans and strategies develop, we expect to need additional managerial, operational, field forces, marketing, financial, legal, and other resources. Our management may need to divert a disproportionate amount of its attention away from our day-to-day activities and devote a substantial amount of time to managing these growth activities. We may not be able to effectively manage the expansion of our operations, which may result in weaknesses in our infrastructure, operational mistakes, loss of business opportunities, loss of employees, and reduced productivity among remaining employees. Our expected growth could require significant capital expenditures and may divert financial resources from other projects, such as the development of additional product candidates. If our management is unable to effectively manage our growth, our expenses may increase more than expected, our ability to generate and/or grow revenue could be reduced, and we may not be able to implement our business strategy. Our future financial performance and our ability to commercialize product candidates and compete effectively will depend, in part, on our ability to effectively manage any future growth.

Our operating results would be adversely impacted if our intangible assets become impaired.

As a result of the accounting for our acquisition of Dimension Therapeutics, Inc. (Dimension) in November 2017, we have recorded on our balance sheet intangible assets for in-process research and development (IPR&D) related to DTX301 and DTX401. Following the FDA approval of Dojolvi in June 2020, we have also recorded contract-based intangible assets related to our license from third parties for certain assets related to the product. We test the intangible assets for impairment annually during the fourth quarter and more frequently if events or changes in circumstances indicate that it is more likely than not that the asset is impaired. If the associated research and development effort is abandoned, the related assets will be written-off and we will record a noncash impairment loss on our statement of operations. We have not recorded any impairments related to our intangible assets through the end of ~~September~~June 30, ~~2020~~2021.

We may not be successful in our efforts to identify, license, discover, develop, or commercialize additional product candidates.

~~Although a substantial amount of our effort will focus on the continued clinical testing, potential approval, and commercialization of our existing product candidates, the~~The success of our business ~~also~~ depends upon our ability to identify, license, discover, develop, or commercialize additional product candidates in addition to the continued clinical testing, potential approval, and commercialization of our existing product candidates. Research programs to identify and develop new product candidates, such as those under our collaboration with Arcturus, require substantial technical, financial, and human resources. We may focus our efforts and resources on potential programs or product candidates that ultimately prove to be unsuccessful. Our research programs or licensing efforts may fail to yield additional product candidates for clinical development and commercialization for a number of reasons, including but not limited to the following:

If any of these events occur, we may be forced to abandon our development efforts for a program or programs, or we may not be able to identify, license, discover, develop, or commercialize additional product candidates, which would have a material adverse effect on our business and could potentially cause us to cease operations.

We may expend our limited resources to pursue a particular product, product candidate or indication and fail to capitalize on products, product candidates or indications that may be more profitable or for which there is a greater likelihood of success.

Because we have limited financial and managerial resources, we focus our sales, marketing and research programs on certain products, product candidates or for specific indications. As a result, we may forego or delay pursuit of opportunities with other products or product candidates or other indications that later prove to have greater commercial potential. Our resource allocation decisions may cause us to fail to capitalize on viable commercial products or profitable market opportunities. Our spending on current and future research and development programs and product candidates may not yield any commercially viable products. If we do not accurately evaluate the commercial potential or target market for a particular product or product candidate, we may relinquish valuable rights through collaboration, licensing, or other royalty arrangements in cases in which it would have been advantageous for us to retain sole development and commercialization rights or we may allocate internal resources to a product candidate in a therapeutic area in which it would have been more advantageous to enter into a partnering arrangement.

If we are unable to maintain effective internal control over financial reporting, investors may lose confidence in the accuracy and completeness of our financial reports and the market price of our stock may decrease.

The Sarbanes-Oxley Act requires, among other things, that we maintain effective internal controls for financial reporting and disclosure controls and procedures. In particular, we are required to perform system and process evaluation and testing of our internal controls over financial reporting to allow management to report on the effectiveness of our internal controls over financial reporting, as required by Section 404(a) of the Sarbanes-Oxley Act. Section 404(b) of the Sarbanes-Oxley Act also requires our independent auditors to attest to, and report on, this management assessment. Ensuring that we have adequate internal controls in place so that we can produce accurate financial statements on a timely basis is a costly and time-consuming effort that will need to be evaluated frequently. If we are not able to comply with the requirements of Section 404 or if we or our independent registered public accounting firm are unable to attest to the effectiveness of our internal control over financial reporting, investors may lose confidence in the accuracy and completeness of our financial reports, the market price of our stock could decline and we could be subject to sanctions or investigations by Nasdaq, the SEC, or other regulatory authorities, which would require additional financial and management resources.

Changes to healthcare and FDA laws, regulations, and policies may have a material adverse effect on our business and results of operations.

InAs described under “Item 1. Business - Government Regulation” in our Annual Report and in the ~~United States,~~Risk Factor above entitled “ – The insurance coverage and reimbursement status of newly approved products is uncertain” there have been and continue to be a number of legislative initiatives to contain healthcare costs and to modify the regulation of drug and biologic products. For example, the Affordable Care Act, as amended, substantially changed the way health care is financed by both governmental and private insurers, and significantly impacts the U.S. pharmaceutical industry. The Affordable Care Act, among other things, subjects biologic products to potential competition by lower-cost biosimilars, addresses a new methodology by which rebates owed by manufacturers under the Medicaid Drug Rebate Program are calculated for drugs that are inhaled, infused, instilled, implanted, or injected, increases the minimum Medicaid rebates owed by manufacturers under the Medicaid Drug Rebate Program and extends the rebate program to individuals enrolled in Medicaid managed care organizations, and establishes annual fees and taxes on manufacturers of certain branded prescription drugs. A federal district court ruled the entire Affordable Care Act to be unconstitutional in December 2018, but issued a stay, meaning the law will remain in effect while the ruling is appealed. Implementation of the Affordable Care Act remains ongoing, but there is uncertainty as to how the law’s various provisions will ultimately affect the industry and whether the law will remain in place.

Other legislative changes have been adopted in the United States, including the Cures Act and the Budget Control Act of 2011, or the Budget Act, signed into law on August 2, 2011. The Cures Act introduced a wide range of reforms and the Budget Act, among other things, required reductions in federal spending, which eventually triggered Medicare sequestration—the requirement to reduce Medicare payments to providers up to 2% per fiscal year. In 2013, the 2% Medicare payment reductions were applied to fee-for-service claims with dates of service or dates of discharge on or after April 1, 2013. Sequestration was initially set to expire in fiscal year 2021 but has been extended to 2025.

We expect that additional state and federal healthcare reform measures and regulations will be adopted in the future, including proposals to reduce the exclusivity protections provided to already approved biological products and to provide biosimilar and interchangeable biologic products an easier path to approval. Any of these measures and regulations could limit the amounts that federal and state governments will pay for healthcare products and services, result in reduced demand for our product candidates or additional pricing pressures and affect our product development, testing, marketing approvals and post-market activities.

In the EU, the European Commission has adopted detailed rules for the safety features appearing on the packaging of medicinal products for human use. The regulations set forth the rules for the features appearing on the packaging of these medicinal products, including, inter alia, the characteristics and technical specifications of the unique identifier that enables the authenticity of medicinal products to be verified and individual packs to be identified, the modalities for the verification of the safety features, and the list of medicinal products and product categories subject and not subject to prescription which shall not bear and bear (respectively) safety features.

The European Commission has also launched a series of public consultations that are aimed at the adoption of notices and guidelines which will serve the interpretation of currently applicable regulations and directives. For example, between August 2015 and December 2016, the European Commission launched public consultations which concerned good manufacturing practices, clinical trials for human medicinal products, and orphan medicinal products. The purpose of the consultation on orphan medicinal products (which will be replaced with a Notice) is to streamline the regulatory framework and to adapt the applicable regulations to technical progress. The consultation focuses on a variety of elements of Regulation (EC) No 141/2000, which include the encouragement of development of orphan medicinal products for communicable diseases and the simplification of the procedure for the reassessment of orphan criteria when two authorization application procedures are pending in parallel for two orphan medicinal products.

We are subject, directly and indirectly, to federal and state healthcare fraud and abuse laws, false claims laws, and health information privacy and security laws. If we are unable to comply, or have not fully complied, with such laws, we could face substantial penalties.

Our operations are directly, and indirectly through our customers, subject to various federal and state fraud and abuse laws, including, without limitation, the federal Anti-Kickback Statute, the federal False Claims Act, and physician sunshine laws and regulations. These laws impact, among other things, our field marketing and education programs. In addition, we are subject to patient privacy regulation by both the federal government and the states in which we conduct our business. The laws that may affect our ability to operate, including the EU General Data Protection Regulation, are described in our Annual Report on Form 10-K for the fiscal year ended December 31, 2019. Further, in the United States, California recently enacted the California Consumer Privacy Act (CCPA), which became effective on January 1, 2020. The CCPA gives California residents expanded rights to access and delete their personal information, opt out of certain personal information sharing, and receive detailed information about how their personal information is used. The CCPA provides for civil penalties for violations, as well as a private right of action for data breaches that is expected to increase data breach litigation. Because of the breadth of these laws and the narrowness of the statutory exceptions and safe harbors available, it is possible that some of our business activities could be subject to challenge under one or more of such laws. If our operations are found to be in violation of any of the laws described above or any other governmental regulations that apply to us, we may be subject to penalties, including civil and criminal penalties, damages, fines, exclusion from participation in government health care programs, such as Medicare and Medicaid, imprisonment, and the curtailment or restructuring of our operations, any of which could adversely affect our ability to operate our business and our results of operations. We may also incur increased costs as a result of complying with new legislations such as the CCPA.

~~International expansion of our business exposes us to business, regulatory, political, operational, financial, and economic risks associated with doing business outside of the United States.~~

Our business strategy includes international expansion. We currently conduct clinical studies and regulatory activities and we also commercialize products outside of the United States. Doing business internationally involves a number of risks, including but not limited to:

~~Any of these factors could significantly harm our future international expansion and operations and, consequently, our results of operations.~~

We have a multinational tax structure and are subject to income tax in the United States and various foreign jurisdictions. Our effective tax rate is influenced by many factors including changes in our operating structure, changes in the mix of our earnings among countries, our allocation of profits and losses among our subsidiaries, our intercompany transfer pricing agreements and rules relating to transfer pricing, the availability of U.S. research and development tax credits, and future changes in tax laws and regulations in the U.S. and foreign countries. Significant judgment is required in determining our tax liabilities including management’s judgment for uncertain tax positions. The Internal Revenue Service, other domestic taxing authorities, or foreign taxing authorities may disagree with our interpretation of tax laws as applied to our operations. Our reported effective tax rate and after-tax cash flows may be materially and adversely affected by tax assessments in excess of amounts accrued for our financial statements. This could materially increase our future effective tax rate thereby reducing net income and adversely impacting our results of operations for future periods.

Failure to comply with laws and regulations could harm our business and our reputation.

Our business is subject to regulation by various federal, state, local and foreign governmental agencies, including agencies responsible for monitoring and enforcing employment and labor laws, workplace safety, and tax laws and regulations. In certain jurisdictions, these regulatory requirements may be more stringent than those in the United States, and in other circumstances these requirements may be more stringent in the United States. ~~Noncompliance~~

In particular, our operations are directly, and indirectly through our customers, subject to various federal and state fraud and abuse laws, including, without limitation, the federal Anti-Kickback Statute, the federal False Claims Act, and physician sunshine laws and regulations and patient privacy regulations, including the EU General Data Protection Regulation and the California Consumer Privacy Act (CCPA), as described in “Item 1. Business – Government Regulation” of our Annual Report. Because of the breadth of these laws and the narrowness of the statutory exceptions and safe harbors available, it is possible that some of our business activities could be subject to challenge under one or more of such laws. For instance, as we and our employees increasingly use social media tools as a means of communication with the public, there is a risk that the use of social media by us or our employees to communicate about our products or business may cause to be found in violation of applicable laws, despite our attempts to monitor such social media communications through company policies and guidelines. In addition, our employees may knowingly or inadvertently make use of social media in ways that may not comply with our company policies or other legal or contractual requirements, which may give rise to liability, lead to the loss of trade secrets or other intellectual property, or result in public exposure of personal information of our employees, clinical trial patients, customers, and others. If our operations are found to be in violation of any of the laws described above or any other governmental regulations ~~or requirements could~~that apply to us, we may be subject us to ~~investigations, sanctions, mandatory recalls, enforcement actions, disgorgement of profits, fines, damages,~~penalties, including civil and criminal penalties, damages, fines, exclusion from participation in government health care programs, such as Medicare and Medicaid, imprisonment, disgorgement of profits, and the curtailment or ~~injunctions.~~restructuring of our operations. If any governmental sanctions, fines or penalties are imposed, or if we do not prevail in any possible civil or criminal litigation, our business, operating results, financial condition and our reputation could be harmed. In addition, responding to any action will likely result in a significant diversion of management’s attention and resources and an increase in professional fees. ~~Enforcement actions and sanctions could further harm our business, operating results, financial condition, and our reputation.~~

Our research and development activities, including our process and analytical development activities in our quality control laboratory, and our and our third-party manufacturers’ and suppliers’ activities involve the controlled storage, use, and disposal of hazardous materials, including the components of our product candidates, such as viruses, and other hazardous compounds, which subjects us to laws and regulations governing such activities. In some cases, these hazardous materials and various wastes resulting from their use are stored at our or our manufacturers’ facilities pending their use and disposal. We cannot eliminate the risk of contamination, which could cause an interruption of our commercialization efforts, research and development efforts, and business operations or environmental damage that could result in costly clean-up and liabilities under applicable laws and regulations governing the use, storage, handling, and disposal of these materials and specified waste products. We cannot guarantee that the safety procedures utilized by us and our third-party manufacturers for handling and disposing of these materials comply with the standards prescribed by these laws and regulations, or eliminate the risk of accidental contamination or injury from these materials. In such an event, we may be held liable for any resulting damages—and such liability could exceed our resources—and state or federal or other applicable authorities may curtail our use of certain materials and/or interrupt our business operations. Furthermore, environmental laws and regulations are complex, change frequently, and have tended to become more stringent. We cannot predict the impact of such changes and cannot be certain of our future compliance. We do not currently carry biological or hazardous waste insurance coverage.

International expansion of our business exposes us to business, regulatory, political, operational, financial, and economic risks associated with doing business outside of the United States.

Any of these factors could significantly harm our future international expansion and operations and, consequently, our results of operations.

Risks generally associated with a company-wide implementation of an enterprise resource planning (ERP) system may adversely affect our business and results of operations or the effectiveness of our internal controls over financial reporting.

We are in the process of implementing a company-wide ERP system to upgrade certain existing business, operational, and financial processes. Our ERP implementation is a complex and time-consuming project that we expect will require multiple years to complete. Our results of operations could be adversely affected if we experience time delays or cost overruns during the ERP implementation process, or if the ERP system or associated process changes do not give rise to the benefits that we expect. This project has required and may continue to require investment of capital and human resources, the re-engineering of processes of our business, and the attention of many employees who would otherwise be focused on other aspects of our business. Any deficiencies in the design and implementation of the new ERP system could result in potentially much higher costs than we had incurred and could adversely affect our ability to develop and launch solutions, provide services, fulfill contractual obligations, file reports with the SEC in a timely manner, operate our business or otherwise affect our controls environment. Any of these consequences could have an adverse effect on our results of operations and financial condition.

Our business and operations may be materially adversely affected in the event of computer system failures or security breaches.

~~Despite the implementation of security measures,~~Cybersecurity incidents, including phishing attacks and attempts to misappropriate or compromise confidential or proprietary information or sabotage enterprise IT systems are becoming increasingly frequent and more sophisticated. The information and data processed and stored in our ~~internal computer~~technology systems, and those of our strategic partners, CROs, ~~and~~contract manufacturers, suppliers, distributors or other third parties onfor which we ~~rely, are~~depend to operate our business, may be vulnerable to loss, damage, ~~from computer viruses,~~denial-of-service, unauthorized access ~~cyber-attacks, natural disasters, fire, terrorism, war,~~or misappropriation. Data security breaches may be due to malware, hacking, business email compromise, ransomware attacks, phishing or other cyberattacks directed by third parties. We, and ~~telecommunication~~certain of the third parties for which we depend on to operate our business, have experienced cybersecurity incidents, including third party unauthorized access to and ~~electrical failures.~~misappropriation of financial information. Further, r ~~Risks~~isks of unauthorized access and cyber-attacks have increased as most of our personnel, and the personnel of many third-parties with which we do business, have adopted remote working arrangements as a result of the COVID-19 pandemic. Improper or inadvertent employee behavior, including data privacy breaches by employees, contractors and others with permitted access to our systems, may also pose a risk that sensitive data may be exposed to unauthorized persons or to the public. If a system failure or security breach occurs and interrupts our operations or the operations at one of our third-party vendors or partners, it could result in intellectual property and other proprietary or confidential information being lost or stolen or a material disruption of our drug development ~~programs.~~programs and commercial operations. For example, the loss of clinical trial data from ongoing or planned clinical trials could result in delays in our regulatory approval efforts and significantly increase our costs to recover or reproduce the data. To the extent that any disruption or security breach results in a loss of or damage to our data or applications, loss of trade secrets or inappropriate disclosure of confidential or proprietary information, including protected health information or personal ~~data~~identifiable information of employees or former employees, access to our clinical data, or disruption of the manufacturing process, we could incur liability and the further development of our drug candidates could be delayed. ~~We may~~Further, we could incur significant costs to investigate and mitigate such cybersecurity incidents. A security breach that results in the unauthorized access, use or disclosure of personal identifiable information also ~~be vulnerable~~requires us to ~~cyber-attacks by hackers~~notify individuals, governmental authorities, credit reporting agencies, or other ~~malfeasance. This type~~parties, as applicable, pursuant to privacy and security laws and regulations or other obligations. Such a security breach could harm our reputation, erode confidence in our information security measures, and lead to regulatory scrutiny and result in penalties, fines, indemnification claims, litigation and potential civil or criminal liability, any of ~~breach of our cybersecurity may compromise our confidential information and/or our financial information and~~which could materially adversely affect our ~~business or reputation or result in legal or regulatory proceedings.~~business.

We or the third parties upon whom we depend may be adversely affected by earthquakes or other natural disasters and our business continuity and disaster recovery plans may not adequately protect us from a serious disaster.

Our corporate headquarters and one of our laboratories are located in the San Francisco Bay Area, and our collaboration partner for Crysvita, KKC, is located in Japan, which have both in the past experienced severe earthquakes and other natural disasters. We do not carry earthquake insurance. Earthquakes or other natural disasters could severely disrupt our operations or those of our collaborators, and have a material adverse effect on our business, results of operations, financial condition, and prospects. If a natural disaster, power outage, or other event occurred that prevented us from using all or a significant portion of our headquarters, that damaged critical infrastructure (such as the manufacturing facilities of our third-party contract manufacturers) or that otherwise disrupted operations, it may be difficult or, in certain cases, impossible for us to continue our business for a substantial period of time. The disaster recovery and business continuity plans we have in place currently are limited and are may be inadequate in the event of a serious disaster or similar event. We may incur substantial expenses as a result of the limited nature of our disaster recovery and business continuity plans, which, particularly when taken together with our lack of earthquake insurance, could have a material adverse effect on our business.

We may acquire companies or products or engage in strategic transactions, which could divert our management’s attention and cause us to incur various costs and expenses, or result in fluctuations with respect to the value of such investment, which could impact our operating results.

We may acquire or invest in businesses or products that we believe could complement or expand our business or otherwise offer growth opportunities. For example, we acquired Dimension in November 2017 and during the third quarter 2019, we entered into an agreement with GeneTx to collaborate on the development of a product for the treatment of Angelman Syndrome which ~~included~~includes an exclusive option to acquire GeneTx. The pursuit of potential acquisitions or investments may divert the attention of management and may cause us to incur various costs and expenses in identifying, investigating, and pursuing them, whether or not they are consummated. We may not be able to identify desirable acquisitions or investments or be successful in completing or realizing anticipated benefits from such transactions. In addition, we may receive inquiries relating to potential strategic transactions, including collaborations, licenses, and acquisitions. Such potential transactions may divert the attention of management and may cause us to incur various costs and expenses in investigating and evaluating such transactions, whether or not they are consummated.

The value of our investments in other companies or businesses may also fluctuate significantly and impact our operating results quarter to quarter or year to year. For instance, in June 2019, we purchased 2.4 million shares of common stock of Arcturus ~~Therapeutics Holdings, Inc. (Arcturus)~~ and in May 2020, we exercised our option to purchase an additional 600,000 shares of Arcturus’ common stock pursuant to the terms of our equity purchase agreement with ~~Arcturus.~~Arcturus; we subsequently sold an aggregate of 800,000 shares in December 2020. We also purchased 7,825,797 shares of common stock of Solid in October 2020. We have elected to apply the fair value option to account for our equity investments in ~~Arcturus.~~Arcturus and Solid. As a result, increases or decreases in the stock price of Arcturus and Solid common stock will result in accompanying changes in the fair value of our investments, ~~and impact,~~ and cause substantial volatility in, our operating results for the reporting period. For instance, the changes in fair value of the Arcturus and Solid investments recognized in the ~~Condensed~~ Consolidated Statements of Operations for the three and ~~nine~~six months ended ~~September~~June 30,~~, 2020 were~~ 2021 was a ~~$11.5~~$31.0 million and a $51.7 million decrease, respectively, primarily due to the lower Arcturus and Solid stock price as of June 30, 2021 compared to the prior period. The changes in fair value of the Arcturus investment recognized in the Consolidated Statements of Operations for the three and six months ended June 30, 2020 was a $95.2 and a ~~$91.3~~$102.9 million increase, respectively, primarily due to the ~~lower Arcturus stock price at September~~ 30~~, 2020 compared to June 30, 2020 and the~~ higher Arcturus stock price ~~at September~~as of June 30, 2020 compared to ~~December 31, 2019, respectively.~~the prior period. The ~~gain~~losses and gains in fair value of the ~~investment~~equity investments for the ~~nine~~three and six months ended ~~September~~June 30, 2021 and for the three and six months ended June 30, 2020 increased and decreased, respectively, the amount of our net loss during ~~that period and the loss in fair value of the investment for the three months ended September 30, 2020 increased the amount of our net loss during that period.~~those periods. If the Arcturus or Solid stock price had been lower at ~~September~~June 30,, 2021 and 2020 compared to ~~December 31, 2019,~~the prior period, we ~~may~~would have reported an even greater net loss for the three and ~~nine~~six months ended ~~September~~June 30, 2021 and for the six months ended June 30, 2020. As the fair value of our ~~investment~~investments in Arcturus and Solid is dependent on the stock price of Arcturus and Solid, which has recently seen wide fluctuations, the value of our investments and the impact on our operating results may similarly fluctuate significantly from quarter to quarter and year to year such that period-to-period comparisons may not be a good indication of the future value of the investments and our future operating results.

We have been, and may in the future become, party to lawsuits including, without limitation, actions and proceedings in the ordinary course of business relating to our directors, officers, stockholders, intellectual property, and employment matters, which will cause us to incur legal fees and other costs related thereto, including potential expenses for the reimbursement of legal fees of officers and directors under indemnification obligations. The expense of defending against such litigation may be significant and there can be no assurance that we will be successful in any defense. Further, the amount of time that may be required to resolve such lawsuits is unpredictable, and these actions may divert management’s attention from the day-to-day operations of our business, which could adversely affect our business, results of operations, and cash flows. Litigation is subject to inherent uncertainties, and an adverse result in such matters that may arise from time to time could have a material adverse effect on our business, results of operations, and financial condition.

The market price of our common stock has been, and is likely to continue to be, volatile, including for reasons unrelated to changes in our business. Our stock price could be subject to wide fluctuations in response to a variety of factors, including but not limited to the following:

In addition, biotechnology and biopharmaceutical companies in particular have experienced extreme price and volume fluctuations that have often been unrelated or disproportionate to the operating performance of these companies. Broad market and industry factors may negatively affect the market price of our common stock, regardless of our actual operating performance.

Future sales and issuances of our common stock or rights to purchase common stock, including pursuant to our equity incentive plans, could result in additional dilution of the percentage ownership of our stockholders and could cause our stock price to fall.

We will need additional capital in the future to continue our planned operations. To the extent we raise additional capital by issuing equity securities, our stockholders may experience substantial dilution. We may sell common stock, convertible securities, or other equity securities in one or more transactions at prices and in a manner we determine from time to time. If we sell common stock, convertible securities, or other equity securities in more than one transaction, investors may be materially diluted by subsequent sales. These sales may also result in material dilution to our existing stockholders, and new investors could gain rights superior to our existing stockholders.

Pursuant to our 2014 Incentive Plan, or the 2014 Plan, our management is authorized to grant stock options and other equity-based awards to our employees, directors, and consultants. At ~~September~~June 30,~~, 2020, 3,186,920~~ 2021, 4,103,718 shares were available for future grants under the 2014 Plan. Through January 1, 2024, the number of shares available for future grant under the 2014 Plan will automatically increase on January 1 of each year by the lesser of 2,500,000 shares or 4% of all shares of our capital stock outstanding as of December 31 of the prior calendar year, subject to the ability of our compensation committee to take action to reduce the size of the increase in any given year.

Pursuant to our 2014 Employee Stock Purchase Plan, or 2014 ESPP, eligible employees can acquire shares of our common stock at a discount to the prevailing market price. At ~~September~~June 30,~~, 2020, 3,287,825~~ 2021, 3,956,907 shares were available for issuance under the 2014 ESPP. Through January 1, 2024, the number of shares available for issuance under the 2014 ESPP will automatically increase on January 1 of each year by the lesser of 1,200,000 shares or 1% of all shares of our capital stock outstanding as of December 31 of the prior calendar year, subject to the ability of our compensation committee to take action to reduce the size of the increase in any given year.

~~Currently~~In February 2021, our board of directors adopted an employment inducement plan with a maximum of 500,000 shares available for grant under the plan. At June 30, 2021, 488,223 shares were available for issuance under the inducement plan. We have registered all the shares under our inducement plan. In addition, we currently plan to register the increased number of shares available under the 2014 Plan and the 2014 ESPP each year. If our board of directors elects to increase the number of shares available for future grant

under the 2014 Plan, or the 2014 ESPP or the inducement plan, our stockholders may experience additional dilution, which could cause our stock price to fall.

65We do not intend to pay dividends on our common stock so any returns will be limited to the value of our stock.

We have never declared or paid any cash dividends on our common stock. We currently intend to retain all available funds and any future earnings, if any, for the development, operation, and expansion of our business and do not anticipate declaring or paying any cash dividends for the foreseeable future. Any return to stockholders will therefore be limited to the appreciation of their stock.

Provisions in our amended and restated certificate of incorporation and by-laws, as well as provisions of Delaware law, could make it more difficult for a third-party to acquire us or increase the cost of acquiring us, even if doing so would benefit our stockholders, or remove our current management.

Our amended and restated certificate of incorporation, amended and restated by-laws, and Delaware law contain provisions that may have the effect of delaying or preventing a change in control of us or changes in our management. Our amended and restated certificate of incorporation and by-laws include provisions that:

These provisions, alone or together, could delay, deter, or prevent hostile takeovers and changes in control or changes in our management.

In addition, because we are incorporated in Delaware, we are governed by the provisions of Section 203 of the Delaware General Corporation Law, which limits the ability of stockholders owning in excess of 15% of our outstanding voting stock to merge or combine with us. Further, no stockholder is permitted to cumulate votes at any election of directors because this right is not included in our amended and restated certificate of incorporation.

Any provision of our amended and restated certificate of incorporation or amended and restated by-laws or Delaware law that has the effect of delaying or deterring a change in control could limit the opportunity for our stockholders to receive a premium for their shares of our common stock, and could also affect the price that some investors are willing to pay for our common stock.

Our amended and restated certificate of incorporation provides that the Court of Chancery of the State of Delaware is the sole and exclusive forum for substantially all disputes between us and our stockholders, which could limit our stockholders’ ability to obtain a favorable judicial forum for disputes with us or our directors, officers or employees.

Our amended and restated certificate of incorporation provides that the Court of Chancery of the State of Delaware is the sole and exclusive forum for (1) any derivative action or proceeding brought on our behalf, (2) any action asserting a claim of breach of fiduciary duty owed by any of our directors, officers, or other employees to us or to our stockholders, (3) any action asserting a claim against us arising under the Delaware General Corporation Law or under our amended and restated certificate of incorporation or bylaws, or (4) any action against us asserting a claim governed by the internal affairs doctrine. The choice of forum provision may limit a stockholder’s ability to bring a claim in a judicial forum that it finds favorable for disputes with us or our directors, officers, or other employees, which may discourage such lawsuits against us and our directors, officers, and other employees. Alternatively, if a court were to find the choice of forum provision contained in our amended and restated certificate of incorporation to be inapplicable or unenforceable in an action, we may incur additional costs associated with resolving such action in other jurisdictions, which could harm our business, operating results and financial condition.

Our ability to use our net operating loss carryforwards and certain other tax attributes may be limited.

We have incurred substantial losses during our history. To the extent that we continue to generate taxable losses, unused taxable losses will, subject to certain limitations, carry forward to offset future taxable income, if any, until such unused losses expire. Under Sections 382 and 383 of the Internal Revenue Code of 1986, as amended, or the IRC, if a corporation undergoes an “ownership change,” generally defined as a greater than 50% change (by value) in its equity ownership over a three-year period, the corporation’s ability to use its pre-change net operating loss carryforwards, or NOL carryforwards, and other pre-change tax attributes (such as research tax credits) to offset its post-change income may be limited. An analysis to determine limitations upon our NOL carryforwards and other pre-change tax attributes for ownership changes that have occurred previously has been performed, resulting in a permanent decrease of federal and state NOL carryforwards in the amount of $7.2 million and a permanent decrease in federal research tax credit carryforwards in the amount of $0.2 million. As a result of these decreases and others that may occur as a result of future ownership changes, our ability to use our pre-change NOL carryforwards and other tax attribute carryforwards to offset U.S. federal taxable income and tax liabilities is limited and may become subject to even greater limitations, which could potentially accelerate or permanently increase future federal tax liabilities for us. In addition, there may be periods during which the use of state income tax NOL carryforwards and other state tax attribute carryforwards (such as state research tax credits) are suspended or otherwise limited, which could potentially accelerate or permanently increase future state tax liabilities for us.

~~We do not intend to pay dividends on~~Litigation may substantially increase our ~~common stock so any returns will be limited to the value of~~costs and harm our ~~stock.~~business.

We have ~~never declared or paid any cash dividends on~~been, and may in the future become, party to lawsuits including, without limitation, actions and proceedings in the ordinary course of business relating to our ~~common stock. We currently intend~~directors, officers, stockholders, intellectual property, and employment matters, which will cause us to ~~retain all available funds~~incur legal fees and ~~any future earnings, if any,~~other costs related thereto, including potential expenses for the ~~development, operation,~~reimbursement of legal fees of officers and ~~expansion~~directors under indemnification obligations. The expense of defending against such litigation may be significant and there can be no assurance that we will be successful in any defense. Further, the amount of time that may be required to resolve such lawsuits is unpredictable, and these actions may divert management’s attention from the day-to-day operations of our business, which could adversely affect our business, results of operations, and ~~do not anticipate declaring or paying any~~ cash ~~dividends for the foreseeable future. Any return~~flows. Litigation is subject to ~~stockholders will therefore be limited to the appreciation of their stock.~~

~~Provisions~~inherent uncertainties, and an adverse result in our amended and restated certificate of incorporation and by-laws, as well as provisions of Delaware law, could make it more difficult for a third-party to acquire us or increase the cost of acquiring us, even if doing so would benefit our stockholders, or remove our current management.

~~Our amended and restated certificate of incorporation, amended and restated by-laws, and Delaware law contain provisions~~such matters that may arise from time to time could have ~~the~~a material adverse effect ~~of delaying or preventing a change in control of us or changes in our management. Our amended and restated certificate of incorporation and by-laws include provisions that:~~

~~These provisions, alone or together, could delay, deter, or prevent hostile takeovers and changes in control or changes in our management.~~

~~Our amended and restated certificate of incorporation provides that the Court of Chancery of the State of Delaware is the sole and exclusive forum for (1) any derivative action or proceeding brought~~ on our ~~behalf, (2) any action asserting a claim~~business, results of breach of fiduciary duty owed by any of our directors, officers, or other employees to us or to our stockholders, (3) any action asserting a claim against us arising under the Delaware General Corporation Law or under our amended and restated certificate of incorporation or bylaws, or (4) any action against us asserting a claim governed by the internal affairs doctrine. The choice of forum provision may limit a stockholder’s ability to bring a claim in a judicial forum that it finds favorable for disputes with us or our directors, officers, or other employees, which may discourage such lawsuits against us and our directors, officers, and other employees. Alternatively, if a court were to find the choice of forum provision contained in our amended and restated certificate of incorporation to be inapplicable or unenforceable in an action, we may incur additional costs associated with resolving such action in other jurisdictions, which could harm our business, operating resultsoperations, and financial condition.

† Certain confidential portions of this exhibit were omitted by means of marking such portions with asterisks because the identified confidential portions (i) are not material and (ii) would be competitively harmful if publicly disclosed.

*The certification attached as Exhibit 32.1 that accompanies this Quarterly Report is furnished to, and not deemed filed with, the SEC and is not to be incorporated by reference into any filing of the Registrant under the Securities Act or the Exchange Act, whether made before or after the date of this Form 10-Q, irrespective of any general incorporation language contained in such filing.

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

Delaware			27-2546083
(State or other jurisdiction of incorporation or organization)			(I.R.S. Employer Identification No.)

60 Leveroni Court Novato, California		94949
(Address of principal executive offices)		(Zip Code)


Title of each class	Trading Symbol	Name of each exchange on which registered
Common Stock, $0.001 par value	RARE	The Nasdaq Global Select Market

			Page

CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS			1

Part I –	Financial Information

	Item 1.	Financial Statements

		Condensed Consolidated Balance Sheets	2

		Condensed Consolidated Statements of Operations	3

		Condensed Consolidated Statements of Comprehensive Loss	4

		Condensed Consolidated Statements of Stockholders’ Equity	5

		Condensed Consolidated Statements of Cash Flows	7

		Notes to Condensed Consolidated Financial Statements	8

	Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	2021

	Item 3.	Quantitative and Qualitative Disclosures About Market Risk	3132

	Item 4.	Controls and Procedures	32

Part II –	Other Information

	Item 1.	Legal Proceedings	3233

	Item 1A.	Risk Factors	3233

	Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	67

	Item 3.	Defaults Upon Senior Securities	6768

	Item 4.	Mine Safety Disclosures	6768

	Item 5.	Other Information	6768

	Item 6.	Exhibits	6869

	Signatures		6970

	Solid common stock
Acquisition of investment in Solid common stock in October 2020	$	26,843
Change in fair value		32,477
December 31, 2020		59,320
Change in fair value		(30,677	)
June 30, 2021	$	28,643

Large accelerated filer	☑	Accelerated filer	☐
Non-accelerated filer	☐	Smaller reporting company	☐
		Emerging growth company	☐

		Incorporated by Reference
Exhibit Number	Exhibit Description	Form	Date	Number	Furnished or Filed Herewith
3.1	Amended and Restated Certificate of Incorporation	8-K	2/5/2014	3.1
3.2	Amended and Restated Bylaws	8-K	2/5/2014	3.2
10.1	Offer Letter between Mardi C. Dier and Ultragenyx Pharmaceutical Inc. dated August 28, 2020.	8-K	9/2/2020	10.1
10.2	Amendment dated October 9, 2020 to the Offer Letter between Mardi C. Dier and Ultragenyx Pharmaceutical Inc. dated August 28, 2020	8-K	10/13/2020	10.1
10.3	Amendment, dated as of August 28, 2020, to Transition Letter Agreement between Shalini Sharp and Ultragenyx Pharmaceutical Inc. dated March 5, 2020.	8-K	9/2/2020	10.2
10.4	Amendment No. 2 dated October 8, 2020 to the Transition Letter Agreement between Shalini Sharp and Ultragenyx Pharmaceutical Inc. dated as of March 5, 2020, as amended on August 28, 2020	8-K	10/13/2020	10.2
10.5	Fourth Amended and Restated Amendment to Lease Agreement between Ultragenyx Pharmaceutical Inc. and ARE-MA Region No. 20, LLC				X
31.1	Certification of Principal Executive Officer Required Under Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act				X
31.2	Certification of Principal Financial Officer Required Under Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act				X
32.1*	Certification of Principal Executive Officer and Principal Financial Officer Required Under Rule 13a-14(b) or Rule 15d-14(b) of the Exchange Act and 18 U.S.C. 1350				X
101.INS	XBRL Instance Document, formatted in Inline XBRL				X
101.SCH	Inline XBRL Taxonomy Extension Schema Document				X
101.CAL	Inline XBRL Taxonomy Extension Calculation Linkbase Document				X
101.DEF	Inline XBRL Taxonomy Extension Definition Linkbase Document				X
101.LAB	Inline XBRL Taxonomy Extension Labels Linkbase Document				X
101.PRE	Inline XBRL Taxonomy Extension Presentation Linkbase Document				X
104	Cover Page Interactive Data File, formatted in Inline XBRL (included in Exhibit 101).

	ULTRAGENYX PHARMACEUTICAL INC.

Date: ~~October 27, 2020~~August 2, 2021	By:	/s/ Emil D. Kakkis
		Emil D. Kakkis, M.D., Ph.D.
		President and Chief Executive Officer (Duly Authorized Officer)

Date: ~~October 27, 2020~~August 2, 2021	By:	/s/ Mardi C. Dier
		Mardi C. Dier
		Executive Vice President and Chief Financial Officer (Principal Financial Officer)

Date: August 2, 2021	By:	/s/ Theodore A. Huizenga
		Theodore A. Huizenga
		Senior Vice President and ~~Corporate Controller~~Chief Accounting Officer (Principal Accounting Officer)