UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

Form 10-Q

(Mark One)



x	QUARTERLY REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended ~~June~~September 30, 2017



o	TRANSITION REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from to

COMMISSION FILE NUMBER 001-35558

TROVAGENE, INC.

(Exact Name of registrant as specified in its charter)



Delaware		27-2004382
(State or other jurisdiction of incorporation or organization)		(I.R.S. Employer Identification No.)

11055 Flintkote Avenue, Suite B, San Diego, California		92121
(Address of principal executive offices)		(Zip Code)

(858) 952-7570
(Registrant’s telephone number, including area code)

Indicate by check mark whether the issuer (1) filed all reports required to be filed by Section 13 or 15(d) of the Exchange Act 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 x No o

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted 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 and post such files). Yes x No o

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



Large accelerated filer	o		Accelerated filer	o

Non-accelerated filer	o	(Do not check if a smaller reporting company)	Smaller reporting company	x

			Emerging growth company	o

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. o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes o No x

As of ~~July~~October 31, 2017, the issuer had ~~37,269,581~~38,106,460 shares of Common Stock issued and outstanding.

Table of Contents

TROVAGENE, INC.

Table of Contents



		Page
PART I	FINANCIAL INFORMATION

Item 1.	Financial Statements (unaudited)

	Condensed Consolidated Balance Sheets (unaudited) as of ~~June~~September 30, 2017 and December 31, 2016	3

	Condensed Consolidated Statements of Operations (unaudited) for the three and ~~six~~nine months ended ~~June~~September 30, 2017 and 2016	4

	Condensed Consolidated Statements of Comprehensive Loss (unaudited) for the three and ~~six~~nine months ended ~~June~~September 30, 2017 and 2016	5

	Condensed Consolidated Statements of Cash Flows (unaudited) for the ~~six~~nine months ended ~~June~~September 30, 2017 and 2016	6

	Notes to Condensed Consolidated Financial Statements (unaudited)	7

Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	18

Item 3.	Quantitative and Qualitative Disclosures About Market Risk	28

Item 4.	Controls and Procedures	29

PART II	OTHER INFORMATION

Item 1.	Legal Proceedings	30

Item 1A.	Risk Factors	30

Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	3130

Item 3.	Defaults Upon Senior Securities	3130

Item 4.	Mine Safety Disclosures	3130

Item 5.	Other Information	3130

Item 6:	Exhibits	3130

SIGNATURES

PART I. FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS

TROVAGENE, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(Unaudited)


	June 30, 2017			December 31, 2016			September 30, 2017			December 31, 2016
Assets
Current assets:
Cash and cash equivalents	$	7,783,891		$	13,915,094		$	7,434,298		$	13,915,094
Short-term investments	—			23,978,022			—			23,978,022
Accounts receivable	157,445			100,460			178,127			100,460
Prepaid expenses and other assets	713,913			956,616
Prepaid expenses and other current assets							939,200			956,616
Total current assets	8,655,249			38,950,192			8,551,625			38,950,192
Property and equipment, net	3,321,532			3,826,915			3,126,969			3,826,915
Other assets	583,973			1,173,304			539,309			1,173,304
Total Assets	$	12,560,754		$	43,950,411		$	12,217,903		$	43,950,411

Liabilities and Stockholders’ Equity
Current liabilities:
Accounts payable	$	602,738		$	1,130,536		$	675,499		$	1,130,536
Accrued expenses	4,929,631			4,021,365			2,620,250			4,021,365
Deferred rent	285,246			285,246			298,213			285,246
Current portion of long-term debt (in default)	1,644,567			2,360,109			1,488,041			2,360,109
Total current liabilities	7,462,182			7,797,256			5,082,003			7,797,256
Long-term debt, less current portion	—			14,176,359			—			14,176,359
Derivative financial instruments—warrants	350,862			834,940			2,037,712			834,940
Deferred rent, net of current portion	1,236,941			1,373,717			1,153,316			1,373,717
Total Liabilities	9,049,985			24,182,272			8,273,031			24,182,272

Commitments and contingencies (Note 9)

Stockholders’ equity
Preferred stock, $0.001 par value, 20,000,000 shares authorized; 60,600 shares outstanding at June 30, 2017 and December 31, 2016; designated as Series A Convertible Preferred Stock with liquidation preference of $606,000 at June 30, 2017 and December 31, 2016	60			60
Common stock, $0.0001 par value, 150,000,000 shares authorized; 31,076,872 and 30,696,791 shares issued and outstanding at June 30, 2017 and December 31, 2016, respectively	3,108			3,070
Preferred stock, $0.001 par value, 20,000,000 shares authorized; 60,600 shares outstanding at September 30, 2017 and December 31, 2016; designated as Series A Convertible Preferred Stock with liquidation preference of $606,000 at September 30, 2017 and December 31, 2016							60			60
Common stock, $0.0001 par value, 150,000,000 shares authorized; 38,105,251 and 30,696,791 shares issued and outstanding at September 30, 2017 and December 31, 2016, respectively							3,811			3,070
Additional paid-in capital	169,693,921			167,890,984			174,426,891			167,890,984
Accumulated other comprehensive loss	(13,650		)	(10,773		)	(15,194		)	(10,773		)
Accumulated deficit	(166,172,670		)	(148,115,202		)	(170,470,696		)	(148,115,202		)
Total stockholders’ equity	3,510,769			19,768,139			3,944,872			19,768,139
Total liabilities and stockholders’ equity	$	12,560,754		$	43,950,411		$	12,217,903		$	43,950,411

See accompanying notes to the unaudited condensed consolidated financial statements.

TROVAGENE, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(Unaudited)


	Three Months Ended June 30,						Six Months Ended June 30,						Three Months Ended September 30,						Nine Months Ended September 30,
	2017			2016			2017			2016			2017			2016			2017			2016
Revenues:
Royalties	$	44,810		$	47,765		$	110,636		$	160,633		$	58,779		$	47,236		$	169,415		$	207,869
Diagnostic services	55,501			23,962			84,363			31,580			58,119			37,978			142,482			69,558
Clinical research services	1,700			31,673			2,050			31,673			6,431			3,900			8,481			35,573
Total revenues	102,011			103,400			197,049			223,886			123,329			89,114			320,378			313,000
Costs and expenses:
Cost of revenues	338,203			409,463			954,629			718,734			473,202			424,559			1,427,831			1,143,293
Research and development	981,715			4,076,414			5,261,545			7,284,478			1,414,706			3,937,398			6,676,251			11,221,876
Selling and marketing	615,019			3,129,036			2,023,004			6,186,588			419,927			2,940,862			2,442,931			9,127,450
General and administrative	4,059,133			2,468,732			6,255,772			6,472,979			3,659,587			2,710,782			9,915,359			9,183,761
Restructuring (benefit) charges	(3,806		)	—			1,715,998			—			(46,472		)	—			1,669,526			—
Total operating expenses	5,990,264			10,083,645			16,210,948			20,662,779			5,920,950			10,013,601			22,131,898			30,676,380

Loss from operations	(5,888,253		)	(9,980,245		)	(16,013,899		)	(20,438,893		)	(5,797,621		)	(9,924,487		)	(21,811,520		)	(30,363,380		)

Net interest expense	(431,871		)	(274,909		)	(861,268		)	(612,529		)	(16,473		)	(354,993		)	(877,741		)	(967,522		)
Gain (loss) from change in fair value of derivative financial instruments—warrants	(71,428		)	52,876			484,078			586,626
Gain from change in fair value of derivative financial instruments—warrants													1,528,669			88,208			2,012,747			674,834
Loss on extinguishment of debt	(1,655,825		)	—			(1,655,825		)	—			—			—			(1,655,825		)	—
Other income, net	1,566			—			1,566			—
Other loss, net													(6,541		)	—			(4,975		)	—
Net loss	(8,045,811		)	(10,202,278		)	(18,045,348		)	(20,464,796		)	(4,291,966		)	(10,191,272		)	(22,337,314		)	(30,656,068		)

Preferred stock dividend	(6,060		)	(6,060		)	(12,120		)	(12,120		)	(6,060		)	(6,060		)	(18,180		)	(18,180		)

Net loss attributable to common stockholders	$	(8,051,871	)	$	(10,208,338	)	$	(18,057,468	)	$	(20,476,916	)	$	(4,298,026	)	$	(10,197,332	)	$	(22,355,494	)	$	(30,674,248	)

Net loss per common share — basic	$	(0.26	)	$	(0.34	)	$	(0.58	)	$	(0.69	)	$	(0.12	)	$	(0.34	)	$	(0.68	)	$	(1.02	)
Net loss per common share — diluted	$	(0.26	)	$	(0.34	)	$	(0.58	)	$	(0.70	)	$	(0.12	)	$	(0.34	)	$	(0.68	)	$	(1.04	)

Weighted-average shares outstanding — basic	30,991,740			29,958,037			30,976,462			29,856,611			36,465,672			30,339,774			32,826,306			30,018,841
Weighted-average shares outstanding — diluted	30,991,740			29,958,037			30,976,462			30,033,207			36,465,672			30,339,774			32,826,306			30,136,572

See accompanying notes to the unaudited condensed consolidated financial statements.

TROVAGENE, INC.

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS

(Unaudited)


	Three Months Ended June 30,						Six Months Ended June 30,						Three Months Ended September 30,						Nine Months Ended September 30,
	2017			2016			2017			2016			2017			2016			2017			2016
Net loss	$	(8,045,811	)	$	(10,202,278	)	$	(18,045,348	)	$	(20,464,796	)	$	(4,291,966	)	$	(10,191,272	)	$	(22,337,314	)	$	(30,656,068	)
Other comprehensive income (loss):
Foreign currency translation loss	(9,543		)	(1,145		)	(11,942		)	(1,796		)	(1,544		)	(81		)	(13,486		)	(1,877		)
Unrealized gain or reversal of previous losses on securities available-for-sale	9,519			5,132			9,065			5,132			—			(7,997		)	9,065			(2,865		)
Total other comprehensive income (loss)	(24		)	3,987			(2,877		)	3,336			(1,544		)	(8,078		)	(4,421		)	(4,742		)

Total comprehensive loss	(8,045,835		)	(10,198,291		)	(18,048,225		)	(20,461,460		)	(4,293,510		)	(10,199,350		)	(22,341,735		)	(30,660,810		)

Preferred stock dividend	(6,060		)	(6,060		)	(12,120		)	(12,120		)	(6,060		)	(6,060		)	(18,180		)	(18,180		)

Comprehensive loss attributable to common stockholders	$	(8,051,895	)	$	(10,204,351	)	$	(18,060,345	)	$	(20,473,580	)	$	(4,299,570	)	$	(10,205,410	)	$	(22,359,915	)	$	(30,678,990	)

See accompanying notes to the unaudited condensed consolidated financial statements.

TROVAGENE, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(Unaudited)


	Six Months Ended June 30,						Nine Months Ended September 30,
	2017			2016			2017			2016
Operating activities
Net loss	$	(18,045,348	)	$	(20,464,796	)	$	(22,337,314	)	$	(30,656,068	)
Adjustments to reconcile net loss to net cash used in operating activities:
Loss on disposal of assets	28,097			—			28,199			—
Impairment loss	485,000			—			485,000			—
Depreciation and amortization	645,962			489,708			956,995			693,485
Stock based compensation expense	1,696,184			4,113,021			3,117,364			5,942,392
Loss on extinguishment of debt	1,655,825			—			1,655,825			—
Accretion of final fee premium	293,614			181,318			293,614			266,423
Amortization of discount on debt	113,780			52,641			113,780			105,710
Net realized loss on short-term investments	6,400			—			6,400			—
Amortization of premiums on short-term investments	9,230			27,481			9,230			61,719
Deferred rent	(136,776		)	(66,689		)	(207,435		)	(133,378		)
Interest income accrued on short-term investments	(90,330		)	(75,300		)	(90,330		)	10,122
Change in fair value of derivative financial instruments—warrants	(484,078		)	(586,626		)	(2,012,747		)	(674,834		)
Changes in operating assets and liabilities:
Decrease in other assets	—			2,761			—			2,761
Increase in accounts receivable	(56,985		)	(59,801		)
Decrease (increase) in prepaid expenses	243,571			(88,678		)
Increase in accounts payable and accrued expenses	280,520			1,481,532
(Increase) decrease in accounts receivable							(77,667		)	13,584
Decrease (increase) in prepaid expenses and other current assets							18,230			(157,051		)
(Decrease) increase in accounts payable and accrued expenses							(1,908,796		)	2,490,137
Net cash used in operating activities	(13,355,334		)	(14,993,428		)	(19,949,652		)	(22,034,998		)

Investing activities:
Capital expenditures, net	(20,738		)	(670,867		)	(136,251		)	(797,781		)
Maturities of short-term investments	16,431,837			—			16,431,837			—
Purchases of short-term investments	(8,804,604		)	(27,951,611		)	(8,804,604		)	(24,451,611		)
Sales of short-term investments	16,434,553			—			16,434,553			—
Net cash provided by (used in) investing activities	24,041,048			(28,622,478		)	23,925,535			(25,249,392		)

Financing activities:
Proceeds from sales of common stock, net of expenses	106,791			—
Proceeds from sales of common stock and warrants, net of expenses							6,634,803			2,293,857
Proceeds from exercise of options	—			232,144			—			366,966
Borrowings under equipment line of credit	—			792,251			—			792,251
Borrowings under long-term debt, net of costs							—			7,805,086
Payment upon debt extinguishment	(1,613,067		)	—			(1,613,067		)	—
Repayments of long-term debt	(15,000,000		)	(2,320,083		)	(15,000,000		)	(8,896,166		)
Repayments of equipment line of credit	(313,052		)	—			(469,578		)	—
Net cash used in financing activities	(16,819,328		)	(1,295,688		)
Net cash (used in) provided by financing activities							(10,447,842		)	2,361,994
Effect of exchange rate changes on cash and cash equivalents	2,411			(2,473		)	(8,837		)	(1,544		)
Net change in cash and equivalents	(6,131,203		)	(44,914,067		)	(6,480,796		)	(44,923,940		)
Cash and cash equivalents—Beginning of period	13,915,094			67,493,047			13,915,094			67,493,047
Cash and cash equivalents—End of period	$	7,783,891		$	22,578,980		$	7,434,298		$	22,569,107

Supplementary disclosure of cash flow activity:
Cash paid for taxes	$	800		$	4,560		$	800		$	4,560
Cash paid for interest	$	629,952		$	536,727		$	650,331		$	806,228
Supplemental disclosure of non-cash investing and financing activities:
Preferred stock dividends accrued	$	12,120		$	12,120		$	18,180		$	18,180
Leasehold improvements paid for by lessor	$	—		$	1,860,000		$	—		$	1,860,000

See accompanying notes to the unaudited condensed consolidated financial statements.

TROVAGENE, INC.

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

1. Organization and Basis of Presentation

Business Organization and Overview

Trovagene, Inc. (“Trovagene” or the “Company”) ~~is a precision medicine biotechnology company~~ headquartered in San Diego, ~~California.~~California, is a clinical-stage, precision medicine oncology therapeutics company. The Company’s primary focus is to develop oncology therapeutics for improved cancer care, ~~incorporating~~optimizing drug development by leveraging its proprietary Precision Cancer Monitoring® (“PCM”) diagnostic technology in tumor genomics. The Company’s PCM technology enables detection and quantitation of oncogene mutations in various solid tumor and hematological malignancies to identify clinically actionable markers for predicting patient response to cancer therapeutics.

Trovagene’s lead ~~product~~drug candidate, PCM-075, ~~was licensed from Nerviano Medical Sciences S.r.l. (“Nerviano”),~~is a leading European oncology research and discovery organization, and is being developed for the treatment of patients with acute myeloid leukemia (“AML”). PCM-075 is an oral and highly-selective polo-like kinasePolo-like Kinase 1 (“PLK1”) selective adenosine triphosphate (“ATP”) competitive inhibitor. ~~Trovagene is uniquely positioned~~PCM-075 has shown preclinical antitumor activity as a single agent and synergy in combination with more than ten different chemotherapeutics and targeted therapies, such as Zytiga® (abiraterone acetate), Beleodaq® (belinostat), Quizartinib (AC220), a development stage FLT3 inhibitor, and Velcade® (bortezomib) in Acute Myeloid Leukemia (“AML”), metastatic Castration-Resistant Prostate Cancer (“mCRPC”) and other liquid and solid tumor cancers.

PCM-075 was developed to ~~leverage its expertise~~have high selectivity to PLK1, to be administered orally, and to have a relatively short drug half-life of approximately 24 hours compared to other PLK inhibitors. PCM-075 has completed a safety study in ~~tumor genomics to optimize the~~patients with advanced metastatic solid tumors with a phase 1b/2 clinical ~~development process. Trovagene plans to complement the development of PCM-075~~trial in patients with ~~correlative~~ AML biomarker analysis to identify and measure patient response to therapy. Trovagene offers its PCM technology at its Clinical Laboratory Improvement Amendments (“CLIA”)-certified/College of American Pathologists (“CAP”)-accredited laboratory and plans to continue to vertically integrate its PCM technology with precision cancer therapeutics.underway.

Basis of Presentation

The accompanying unaudited interim condensed consolidated financial statements of Trovagene, which include all accounts of its wholly owned subsidiary, Trovagene, Srl, have been prepared in accordance with accounting principles generally accepted in the United States of America (“GAAP”). All intercompany balances and transactions have been eliminated.

The accompanying unaudited interim condensed consolidated financial statements have been prepared in accordance with GAAP and the rules and regulations of the Securities and Exchange Commission (“SEC”) related to a quarterly report on Form 10-Q. Certain information and note disclosures normally included in annual financial statements prepared in accordance with GAAP have been condensed or omitted pursuant to those rules and regulations. The unaudited interim condensed consolidated financial statements reflect all adjustments consisting of normal recurring adjustments which, in the opinion of management, are necessary for a fair statement of the Company’s financial position and the results of its operations and cash flows for the periods presented. ~~All such adjustments are~~The unaudited condensed balance sheet at December 31, 2016 has been derived from the audited financial statements at that date but does not include all of ~~a normal~~the information and ~~recurring nature.~~disclosures required by GAAP for annual financial statements. The operating results presented in these unaudited interim condensed consolidated financial statements are not necessarily indicative of the results that may be expected for any future periods. These unaudited interim condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and the notes thereto for the year ended December 31, 2016 included in the Company’s annual report on Form 10-K filed with the SEC on March 15, 2017.

Liquidity

Trovagene’s condensed consolidated financial statements as of ~~June~~September 30, 2017 have been prepared under the assumption that Trovagene will continue as a going concern, which assumes that the Company will realize its assets and satisfy its liabilities in the normal course of business. The accompanying financial statements do not include any adjustments to reflect the possible future effects on the recoverability and classification of assets or the amounts and classifications of liabilities that may result from the outcome of the uncertainty concerning the Company’s ability to continue as a going concern.

However, the Company has incurred net losses since its inception and has negative operating cash flows. The Company also received a default letter from Silicon Valley Bank (“SVB”) regarding the Loan and Security Agreement entered in November 2015 which stated that events of default had occurred and SVB will decide in its sole discretion whether or not to exercise rights and remedies. Based on its current business plan and assumptions, the Company expects to continue to incur significant losses and require significant additional capital to further advance its clinical trial programs and support its other operations. Considering the Company’s current cash resources, including the net proceeds received from the offering of its equity securities in July 2017, management believes the Company’s existing resources will be sufficient to fund the Company’s

planned operations ~~until~~into the first quarter of 2018. In addition, the Company has based its cash sufficiency estimates on its current business plan and its assumptions that may prove to be wrong. The Company could utilize its available capital resources sooner than it currently expects, and it could need additional funding to sustain its operations even sooner than currently anticipated. These circumstances raise substantial doubt about the Company’s ability to continue as a going concern. For the foreseeable future, the Company’s ability to continue its operations is dependent upon its ability to obtain additional capital.

The Company cannot be certain that additional funding will be available on acceptable terms, or at all. To the extent that the Company can raise additional funds by issuing equity securities, the Company’s stockholders may experience significant dilution. Any debt financing, if available, may involve restrictive covenants that impact the Company’s ability to conduct its business.

If the Company is unable to raise additional capital when required or on acceptable terms, it may have to significantly delay, scale back or discontinue the development and/or commercialization of one or more of its product candidates, all of which may have a material adverse impact on the Company’s operations. The Company may also be required to:

Seek collaborators for product candidates at an earlier stage than otherwise would be desirable and on terms that are less favorable than might otherwise be available; and

Relinquish licenses or otherwise dispose of rights to technologies, product candidates or products that the Company would otherwise seek to develop or commercialize themselves, on unfavorable terms.

The Company is evaluating the following options to raise additional capital, increase revenue, as well as reduce costs, in an effort to strengthen its liquidity position:

Raising capital through public and private equity offerings;

Adding capital through short-term and long-term borrowings;

Introducing operation and business development initiatives to bring in new revenue streams by leveraging capabilities within our CLIA lab, as well as monetizing our proprietary NextCollect™ DNA collection and preservation cup;

Reducing operating costs by identifying internal synergies;

Engaging in strategic partnerships; and

Taking actions to reduce or delay capital expenditures.

On October 25, 2017, the Company filed a registration statement on Form S-1 with the SEC for a best efforts public offering of up to $17.5 million of common stock and warrants. The Company continually assesses any spending plans, including a review of its discretionary spending in connection with certain strategic contracts, to effectively and efficiently address its liquidity needs.

NASDAQ Notice

On ~~May 30,~~September 5, 2017, the Company received a written notice from the NASDAQ Stock Market LLC (“NASDAQ”) that it was not in compliance with NASDAQ Listing Rule 5550(a)(2) for continued listing on the NASDAQ Capital Market, as the minimum bid price of the Company’s common stock had been below $1.00 per share for 30 consecutive business days. In accordance with NASDAQ Listing Rule 5810(c)(3)(A), the Company has a period of 180 calendar days, or until ~~November 27, 2017,~~March 5, 2018, to regain compliance with the minimum bid price requirement. To regain compliance, the closing bid price of the Company’s common stock must meet or exceed $1.00 per share for at least ten consecutive business days during this 180 calendar day period.

On July 10, 2017, NASDAQ notified the Company that it had regained compliance with the applicable minimum bid price rule. Accordingly, the matter related to the notice it received in May 2017 was closed.

2. Summary of Significant Accounting Policies

Use of Estimates

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

Short-Term Investments

Short-term investments consisted of corporate debt securities, U.S. treasury securities, and commercial paper. The Company classified its short-term investments as available-for-sale, as the sale of such securities may be required prior to maturity to execute management strategies. Investments classified as available-for-sale are carried at fair value, with the unrealized gains and losses reported as a component of consolidated accumulated other comprehensive income (loss) in stockholders’ equity until realized. Realized gains and losses from the sale of available-for-sale securities were determined on a specific identification basis. A decline in the market value of any available-for-sale security below cost that is determined to be other than temporary will result in an impairment charge to earnings and a new cost basis for the security is established. No such impairment charges were recorded for any period presented. Premiums and discounts were amortized or accreted over the life of the related security as an adjustment to yield using the straight-line method and included in interest income. Interest income was recognized when earned. Realized gains and losses on investments in securities were included in other income (loss) within the consolidated statements of operations. As of ~~June~~September 30, 2017, all of the short-term investments have been sold to satisfy the Company’s outstanding obligations under the Loan and Security Agreement dated as of June 30, 2014 upon demanding repayment by the lenders. As a result, the Company recognized ~~$6,400~~ net realized ~~losses~~loss of approximately $6,400 for the ~~six~~nine months ended ~~June~~September 30, 2017.

Revenue Recognition

Revenue is recognized when persuasive evidence that an arrangement exists, delivery has occurred, the price is fixed or determinable, and collection is reasonably assured.

Milestone, Royalty and License Revenues

The Company licenses and sublicenses its patent rights to healthcare companies, medical laboratories and biotechnology partners. These agreements may involve multiple elements such as license fees, royalties and milestone payments. Revenue is recognized when the criteria described above have been met as well as the following:

•Up-front nonrefundable license fees pursuant to agreements under which the Company has no continuing performance obligations are recognized as revenues on the effective date of the agreement and when collection is reasonably assured.

•Minimum royalties are recognized as earned, and royalties are earned based on the licensee’s use. The Company is unable to predict licensee’s sales and thus revenue is recognized upon receipt of notification from licensee and payment when collection is assured. Notification is generally one quarter in arrears.

•Milestone payments are recognized when both the milestone is achieved and the related payment is received.

Diagnostic Service Revenues

Revenue for clinical laboratory tests may come from several sources, including commercial third-party payors, such as insurance companies and health maintenance organizations, government payors, such as Medicare and Medicaid in the United States, patient self-pay and, in some cases, from hospitals or referring laboratories who, in turn, might bill third-party payors for testing. The Company is recognizing diagnostic service revenue on the cash collection basis until such time as it is able to properly estimate collections on third party reimbursements.

Clinical Research Services Revenue

Revenue from clinical research services consists of revenue from the sale of urine and blood collection supplies and tests performed under agreements with our clinical research and business development partners. Revenue was recognized when supplies and/or test results were delivered.

Cost of Revenue

Cost of revenue represents the cost of materials, personnel costs and costs associated with processing specimens including pathological review, quality control analyses, and delivery charges necessary to render an individualized test result. Costs associated with performing tests are recorded as the tests are processed. However, the revenue on diagnostic services is recognized on a cash collection basis resulting in costs incurred before the collection of related revenue.

Derivative Financial Instruments—Warrants

The Company has issued common stock warrants in connection with the execution of certain equity financings. Such warrants are classified as derivative liabilities under the provisions of Financial Accounting Standards Board (“FASB”) ASC 815 Derivatives and Hedging (“ASC 815”) ~~and~~ or ASC 480 Distinguishing Liabilities from Equity (“ASC 480”)are recorded at their fair market value as of each reporting period. Such warrants do not meet the exemption that a contract should not be considered a derivative instrument if it is (1) indexed to its own stock and (2) classified in stockholders’ equity. The warrants within the scope of ASC 480 contain a feature that could require the transfer of cash in the event a change of control occurs without an authorization of our Board of Directors, and therefore classified as a liability. Changes in fair value of derivative liabilities are recorded in the consolidated statement of operations under the caption “Change in fair value of derivative instruments.”

The fair value of warrants is determined using the Black-Scholes option-pricing model using assumptions regarding the volatility of Trovagene’s common stock price, the remaining life of the ~~warrant,~~warrants, and the risk-free interest rates at each period end. The Company thus uses model-derived valuations where inputs are observable in active markets to determine the fair value and accordingly classifies such warrants in Level 3 per FASB ASC Topic 820, Fair Value Measurements (“ASC 820”). At ~~June~~September 30, 2017 and December 31, 2016, the fair value of these warrants was ~~$350,862~~$2,037,712 and $834,940, respectively, and was recorded as a liability under the caption “derivative financial instruments—warrants” on the consolidated balance sheets.

Net Loss Per Share

Basic and diluted net loss per share is presented in conformity with ASC Topic 260, Earnings per Share, for all periods presented. In accordance with this guidance, basic net loss per common share was determined by dividing net loss applicable to common stockholders by the weighted-average common shares outstanding during the period. Preferred dividends are included in income available to common stockholders in the computation of basic and diluted earnings per share. Diluted net loss per share is computed by dividing the net loss by the weighted average number of common shares and common share equivalents outstanding for the period. Common share equivalents are only included when their effect is dilutive.

The following table sets forth the computation of basic and diluted earnings per share:


	Three Months Ended June 30,						Six Months Ended June 30,						Three Months Ended September 30,						Nine Months Ended September 30,
	2017			2016			2017			2016			2017			2016			2017			2016
Numerator: Net loss attributable to common shareholders	$	(8,051,871	)	$	(10,208,338	)	$	(18,057,468	)	$	(20,476,916	)	$	(4,298,026	)	$	(10,197,332	)	$	(22,355,494	)	$	(30,674,248	)
Adjustment for (gain) loss from change in fair value of derivative financial instruments—warrants	—			—			—			(533,750		)
Adjustment for gain from change in fair value of derivative financial instruments—warrants													—			—			—			(533,750		)
Net loss used for diluted loss per share	$	(8,051,871	)	$	(10,208,338	)	$	(18,057,468	)	$	(21,010,666	)	$	(4,298,026	)	$	(10,197,332	)	$	(22,355,494	)	$	(31,207,998	)
Denominator for basic and diluted net loss per share:
Weighted-average shares used to compute basic loss per share	30,991,740			29,958,037			30,976,462			29,856,611			36,465,672			30,339,774			32,826,306			30,018,841
Adjustments to reflect assumed exercise of warrants	—			—			—			176,596			—			—			—			117,731
Weighted-average shares used to compute diluted net loss per share	30,991,740			29,958,037			30,976,462			30,033,207			36,465,672			30,339,774			32,826,306			30,136,572
Net loss per share attributable to common stockholders:
Basic	$	(0.26	)	$	(0.34	)	$	(0.58	)	$	(0.69	)	$	(0.12	)	$	(0.34	)	$	(0.68	)	$	(1.02	)
Diluted	$	(0.26	)	$	(0.34	)	$	(0.58	)	$	(0.70	)	$	(0.12	)	$	(0.34	)	$	(0.68	)	$	(1.04	)

The following table sets forth the outstanding potentially dilutive securities that have been excluded in the calculation of diluted net loss per share because their effect was anti-dilutive:


	June 30,		September 30,
	2017	2016	2017	2016
Options to purchase Common Stock	3,589,147	6,137,495	4,257,031	6,051,186
Warrants to purchase Common Stock	4,328,877	4,515,947	8,972,503	4,546,939
Restricted Stock Units	1,452,289	396,500	1,277,302	392,000
Series A Convertible Preferred Stock	63,125	63,125	63,125	63,125
	9,433,438	11,113,067	14,569,961	11,053,250

License Fees

The Company expenses amounts paid to acquire licenses associated with products under development when the ultimate recoverability of the amounts paid is uncertain and the technology has no alternative future use when acquired. Acquisitions of technology licenses are charged to expense or capitalized based upon management’s assessment regarding the ultimate recoverability of the amounts paid and the potential for alternative future use. The Company has determined that technological feasibility for its product candidates is reached when the requisite regulatory approvals are obtained to make the product available for sale.

Restructuring

Restructuring costs are included in loss from operations in the condensed consolidated statements of operations. The Company has accounted for these costs in accordance with ASC Topic 420, Exit or Disposal Cost Obligations. One-time termination benefits are recorded at the time they are communicated to the affected employees. In March 2017, the Company announced a restructuring plan which is expected to be completed in the last quarter of 2017. See Note 10 to the condensed consolidated financial statements for further information.

Recent Accounting Pronouncements

In August 2016, the FASB issued Accounting Standards Update (“ASU”) 2016-15, Classification of Certain Cash Receipts and Cash Payments (“ASU 2016-15”), which includes amendments that clarify how certain cash receipts and cash payments are presented in the statement of cash flows. ASU 2016-15 also provides guidance clarifying when an entity should

separate cash receipts and cash payments and classify them into more than one class of cash flows. The new amendments and guidance are effective for fiscal years beginning after December 15, 2017, including interim periods within those fiscal years. Early adoption is permitted provided that all amendments are adopted in the same period. The Company is currently evaluating the impact of adoption of ASU 2016-15 on its consolidated statements of cash flows.

In February 2016, the FASB issued ASU 2016-02, Leases. The new standard establishes a right-of-use (“ROU”) model that requires a lessee to record a ROU asset and a lease liability on the balance sheet for most leases. The new standard is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. A modified retrospective transition approach is required for capital and operating leases existing at, or entered into after, the beginning of the earliest comparative period presented in the financial statements, with certain practical expedients available. The new standard will impact the Company’s accounting for its office leases and the Company is currently evaluating the impact of the new standard on its consolidated financial statements.

In May 2014, the FASB issued ASU 2014-09, Revenue from Contracts with Customers (“ASU 2014-09”). The new standard is based on the ~~principal~~principle that revenue should be recognized to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. Since its initial release, the FASB has issued several amendments to the standard, which include clarification of accounting guidance related to identification of performance obligations, intellectual property licenses, and ~~principal~~principle versus agent considerations. ASU 2014-09 and all subsequent amendments (collectively, the “new standards”) will be effective for the Company beginning in the first quarter of fiscal year 2018 and may be applied using either the full retrospective method, in which case the ~~standard~~new standards would be applied to each prior reporting period presented, or the modified retrospective method, in which case the cumulative effect of applying the ~~standard~~new standards would be recognized at the date of initial application. ~~To date,~~The Company has reviewed its revenue streams to identify potential differences in accounting as a result of the new standards. Currently, the Company does not have any significant contracts with customers given its stage of development. The Company has derived its revenues primarily from a limited number of royalty, license and diagnostic service agreements. The

consideration the Company is eligible to receive under these agreements includes upfront license payments, milestone payments and royalties. Each of ~~its collaboration~~these agreements has unique terms that ~~will need to be~~are being evaluated separately under the new standards. ~~The Company has started its preliminary assessment of its active license and collaboration agreements.~~ The new standards differ from the current accounting standard in many respects, such as in the accounting for variable consideration, including milestone payments. For example, the Company currently recognizes milestone revenue using the milestone method specified in ASC 605-28, which generally results in recognition of milestone revenue in the period that the milestone event is achieved. However, under the new ~~accounting~~ standards, it is possible to start to recognize milestone revenue before the milestone is achieved if management determines with a high degree of certainty that amounts recorded as revenues will not have to be reversed when the uncertainty associated with the variable consideration is subsequently resolved. ~~In addition,~~The Company is also continuing to assess the ~~current accounting~~potential impact that the new standards ~~include~~may have with respect to its diagnostic service revenue which is currently recognized on a ~~presumption that~~cash collection basis. Under the new standards, the Company may recognize diagnostic service revenue ~~from upfront non-refundable fees are recognized ratably over the performance period, unless another attribution method is determined to more closely approximate the~~upon delivery of test results if management determines with a high degree of certainty that amounts recorded as revenues will not have to be reversed when the ~~goods or services to~~uncertainty associated with the customer. The new accounting standards will require entities to determine an appropriate attribution method using either output or input methods and do not include a presumption that entities would default to ratable attribution approach.variable consideration is subsequently resolved. The Company is continuing to assess the impact ~~these items~~the new standards will have on its financial ~~statements.~~statements and expects to complete the assessment on or before the year-end 2017. The Company ~~has completed~~does not expect a significant change in the timing and recognition of its ~~initial assessment of the new standards, including a detailed review of the Company’s contract portfolio and~~ revenue ~~streams, particularly around royalty revenues, to identify potential differences in accounting as a result~~upon adoption of the new standards. The Company expects to adopt the new standards using the modified retrospective method with an adjustment, if any, to beginning retained earnings for the cumulative effect of the change.

3. Fair Value Measurements

The following table presents the Company’s assets and liabilities that are measured and recognized at fair value on a recurring basis classified under the appropriate level of the fair value hierarchy as of ~~June~~September 30, 2017 and December 31, 2016:


	Fair Value Measurements at June 30, 2017								Fair Value Measurements at September 30, 2017
	Quoted Prices in Active Markets for Identical Assets and Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Total		Quoted Prices in Active Markets for Identical Assets and Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Total
Assets:
Money market fund (1)	$	6,496,826	$	—	$	—	$	6,496,826	$	6,510,214	$	—	$	—	$	6,510,214
Total Assets	$	6,496,826	$	—	$	—	$	6,496,826	$	6,510,214	$	—	$	—	$	6,510,214
Liabilities:
Derivative financial instruments—warrants	$	—	$	—	$	350,862	$	350,862	$	—	$	—	$	2,037,712	$	2,037,712
Total Liabilities	$	—	$	—	$	350,862	$	350,862	$	—	$	—	2,037,712		$	2,037,712



	Fair Value Measurements at December 31, 2016
	Quoted Prices in Active Markets for Identical Assets and Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		Total
Assets:
Money market fund (1)	$	12,095,620	$	—	$	—	$	12,095,620
Corporate debt securities (2)	—		14,160,686		—		14,160,686
Commercial paper (3)	—		2,393,948		—		2,393,948
U.S. treasury securities (2)	—		8,621,892		—		8,621,892
Total Assets	$	12,095,620	$	25,176,526	$	—	$	37,272,146
Liabilities:
Derivative financial instruments—warrants	$	—	$	—	$	834,940	$	834,940
Total Liabilities	$	—	$	—	$	834,940	$	834,940

(1) Included as a component of cash and cash equivalents on the accompanying condensed consolidated balance sheets.

(2) Included in short-term investments on the accompanying condensed consolidated balance sheets.

(3) $0 and $1,198,504 of commercial paper was included as a component of cash and cash equivalents at ~~June~~September 30, 2017 and December 31, 2016, respectively, and the remaining amount was included in short-term investments on the accompanying consolidated balance sheets.

The following table sets forth a summary of changes in the fair value of the Company’s Level 3 liabilities for the ~~six~~nine months ended ~~June~~September 30, 2017:


Description	Balance at December 31, 2016		Unrealized Gain			Balance at June 30, 2017		Balance at December 31, 2016		Issuance of Derivative Financial Instruments	Realized Gain			Balance at September 30, 2017
Derivative financial instruments—warrants	$	834,940	$	(484,078	)	$	350,862	$	834,940	3,215,519	$	(2,012,747	)	$	2,037,712

The ~~unrealized~~realized gains or losses on the derivative financial instruments—warrants are recorded as a change in fair value of derivative financial instruments—warrants in the Company’s consolidated statement of operations. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement. At each reporting period, the Company reviews the assets and liabilities that are subject to ASC Topic 815-40. At each reporting period, all assets and liabilities for which the fair value measurement is based on significant unobservable inputs or instruments that trade infrequently and therefore have little or no price transparency are classified as Level 3.

4. Short-Term Investments

As of ~~June~~September 30, 2017, all short-term investments have been sold to satisfy the Company’s outstanding obligations under the Loan and Security Agreement dated as of June 30, 2014 upon demanding repayment by the lenders.

The following table sets forth the composition of short-term investments as of December 31, 2016.



	December 31, 2016
				Unrealized
	Maturity in Years	Cost		Gains		Losses			Fair Value
Corporate debt securities	Less than 1 year	$	14,165,915	$	44	$	(5,273	)	$	14,160,686
Commercial paper	Less than 1 year	1,195,444		—		—			1,195,444
U.S. treasury securities	Less than 1 year	8,625,728		330		(4,166		)	8,621,892
Total Investment		$	23,987,087	$	374	$	(9,439	)	$	23,978,022

5. Property and Equipment

Property and equipment consist of the following:


	As of June 30, 2017			As of December 31, 2016			As of September 30, 2017			As of December 31, 2016
Furniture and office equipment	$	1,077,785		$	1,144,741		$	1,076,709		$	1,144,741
Leasehold improvements	1,994,514			1,994,514			1,994,514			1,994,514
Laboratory equipment	2,515,530			2,449,645			2,584,363			2,449,645
	5,587,829			5,588,900			5,655,586			5,588,900
Less—accumulated depreciation and amortization	(2,266,297		)	(1,761,985		)	(2,528,617		)	(1,761,985		)
Property and equipment, net	$	3,321,532		$	3,826,915		$	3,126,969		$	3,826,915

6. Debt

Equipment Line of Credit

In November 2015, the Company entered into a Loan and Security Agreement (“Equipment Line of Credit”) with ~~Silicon Valley Bank (“SVB”)~~SVB that provided for cash borrowings for equipment (“Equipment Advances”) of up to $2.0 million, secured by the equipment financed. Under the terms of the agreement, interest is equal to 1.25% above the Prime Rate. At

~~June~~ September 30, 2017, the interest rate was 5.50%. Interest only payments are due on borrowings through November 30, 2016, with both interest and principal payments commencing in December 2016. All unpaid principal and interest on each Equipment Advance will be due on November 1, 2019. The Company has an obligation to make a final payment equal to 7% of total amounts borrowed at the loan maturity date. The Company is also subject to certain affirmative and negative covenants under the Equipment Line of Credit.

On June 20, 2017, the Company received a Notice of Event of Default (“Default Letter”) from SVB which stated that Events of Default had occurred and SVB will decide in its sole discretion whether or not to exercise rights and remedies. Pursuant to the Default Letter, the Company has classified the entire balance of ~~$1,644,567~~$1,488,041 as a current liability as of ~~June~~September 30, 2017 and also started recording accrued interest at a default rate. The Company recorded ~~$171,959~~$209,082 in interest expense related to the Equipment Line of Credit during the ~~six~~nine months ended ~~June~~September 30, 2017. The Company is currently working with lender for resolution.

Loan and Security Agreement

In June 2014, the Company entered into a $15,000,000 Loan and Security Agreement (“Agreement”) under which the lenders provided the Company a term loan. On July 20, 2016, the Company signed the 5th Amendment to Loan and Security Agreement to refinance its existing term loan. Under the Amendment, interest is equal to 3.75% plus the Wall Street Journal Prime Rate, subject to a floor of 7.25%. The Company is required to make interest only payments on the outstanding amount of the loan on a monthly basis through September 1, 2017, after which equal monthly payments of principal and interest are due until the loan maturity date of February 1, 2020.

On June 1, 2017, the Company received a Notice of Event of Default from the lenders which stated that Events of Default had occurred and all of the obligation under the Agreement were immediately due and payable. On June 6, 2017, the lenders took the total pay-off amount of $16,668,583 for the principal, interest, final payment, and other amounts out of the Company’s bank accounts which satisfied all of the Company’s outstanding obligations under the Agreement. Accordingly, the Agreement was terminated in June 2017. Upon termination of the Agreement, the prepayment fee of $450,000, unamortized debt discount of $400,562 and unamortized final fee of $738,196 were recorded as loss on debt extinguishment. The Company recorded total interest expense of $801,173 related to the Agreement during the ~~six~~nine months ended ~~June~~September 30, 2017.

7. Derivative Financial Instruments — Warrants

Based upon the Company’s analysis of the criteria contained in ASC Topic 815-40, Contracts in Entity’s Own Equity (“ASC 815-40”) or ASC Topic 480-10, Distinguishing Liabilities from Equity (“ASC 480-10”), Trovagene determined that certain warrants issued in connection with the execution of certain equity financings must be recorded as derivative liabilities. In accordance with ASC ~~Topic~~ 815-40 and ASC 480-10, the warrants are also being re-measured at each balance sheet date based on estimated fair value, and any resultant change in fair value is being recorded in the Company’s condensed consolidated statements of operations. The Company estimates the fair value of these warrants using the Black-Scholes option pricing model.

The range of assumptions used to determine the fair value of the warrants valued using the Black-Scholes option pricing model during the periods indicated was:


	Six Months Ended June 30,				Nine Months Ended September 30,
	2017		2016		2017		2016
Estimated fair value of Trovagene common stock	1.15-1.26		4.53-4.65		0.73-1.26		4.49-4.65
Expected warrant term	1.5-1.8 years		2.5-2.8 years		1.3-5.5 years		2.3-2.8 years
Risk-free interest rate	1.27-1.38%		0.71-0.87%		1.27-1.95%		0.71-0.87%
Expected volatility	98-109%		82-89%		86-109%		82-89%
Dividend yield	0	%	0	%	0	%	0	%

Expected volatility is based on historical volatility of Trovagene’s common stock. The warrants have a transferability provision and based on guidance provided in Staff Accounting Bulletin (“SAB”) No. 107, Share-Based Payment (“SAB No. 107”), for instruments issued with such a provision, Trovagene used the remaining contractual term as the expected term of the warrants. The risk free rate is based on the U.S. Treasury security rates consistent with the expected remaining term of the warrants at each balance sheet date.

The following table sets forth the components of changes in the Company’s derivative financial instruments—warrants liability balance, valued using the Black-Scholes option pricing method, for the periods indicated.


Date	Description	Number of Warrants	Derivative Instrument Liability			Description	Number of Warrants	Derivative Instrument Liability
December 31, 2016	Balance of derivative financial instruments—warrants liability	967,295	$	834,940		Balance of derivative financial instruments—warrants liability	967,295	$	834,940
	Change in fair value of derivative financial instruments—warrants during the period recognized as a gain in the condensed consolidated statements of operations	—	(484,078		)	Issuance of derivative financial instruments	4,643,626	3,215,519
June 30, 2017	Balance of derivative financial instruments—warrants liability	967,295	$	350,862
						Change in fair value of derivative financial instruments—warrants during the period recognized as a gain in the condensed consolidated statements of operations	—	(2,012,747		)
September 30, 2017						Balance of derivative financial instruments—warrants liability	5,610,921	$	2,037,712

8. Stockholders’ Equity

Common Stock

During the ~~six~~nine months ended ~~June~~September 30, 2017, the Company issued a total of ~~380,081~~7,408,460 shares of Common Stock. The Company received gross proceeds of approximately $7.1 million from the sale of 6,191,500 shares of its common stock and 4,643,626 share of warrants through registered direct offering and private placement in July 2017. The Company received gross proceeds of approximately $0.1 million from the sale of 102,081 shares of its common stock at a weighted average price of $1.08 under the agreement with Cantor Fitzgerald & Co. (“Agent”). In addition, ~~278,000~~369,487 shares were issued upon vesting of restricted stock units (“RSU”), and 745,392 shares were issued upon vesting of restricted stock awards (“RSA”).

Stock Options

Stock-based compensation expense related to Trovagene equity awards have been recognized in operating results as follow:


	Three Months Ended June 30,					Six Months Ended June 30,					Three Months Ended September 30,				Nine Months Ended September 30,
	2017			2016		2017			2016		2017		2016		2017			2016
Included in research and development expense	$	206,463		$	590,536	$	578,663		$	989,277	$	219,480	$	872,792	$	798,143		$	1,862,069
Included in cost of revenue	15,209			38,228		41,365			56,525		15,633		42,639		56,998			99,164
Included in selling and marketing expense	127,351			438,158		431,883			1,016,879		118,434		476,865		550,317			1,493,744
Included in general and administrative expense	472,718			234,991		769,495			2,050,340		1,067,633		437,075		1,837,128			2,487,415
Benefit from restructuring	(46,356		)	—		(125,222		)	—		—		—		(125,222		)	—
Total stock-based compensation expense	$	775,385		$	1,301,913	$	1,696,184		$	4,113,021	$	1,421,180	$	1,829,371	$	3,117,364		$	5,942,392

The unrecognized compensation cost related to non-vested stock options outstanding at ~~June~~September 30, 2017 and 2016, net of expected forfeitures, was ~~$3,456,979~~$3,271,046 and ~~$11,419,948,~~$10,416,565, respectively, which is expected to be recognized over a weighted-average remaining vesting period of ~~2.5~~2.2 and ~~3.1~~3.0 years, respectively. The weighted-average remaining contractual term of outstanding options as of ~~June~~September 30, 2017 was approximately ~~6.9~~7.2 years. The total fair value of stock options vested during the ~~six~~nine months ended ~~June~~September 30, 2017 and 2016 was ~~$2,796,924~~$3,378,243 and ~~$4,181,755,~~$5,416,168, respectively.

The estimated fair value of stock option awards was determined on the date of grant using the Black-Scholes option valuation model with the following weighted-average assumptions during the following periods indicated:

Six Months Ended
June 30,
2017 (1) 2016
Risk-free interest rate — % 1.5 %
Dividend yield 0 % 0 %
Expected volatility — % 102 %
Expected term 0.0 years
5.5 years

~~(1) No options granted during the six months ended June 30, 2017.~~



	Nine Months Ended September 30,
	2017		2016
Risk-free interest rate	1.82	%	1.48	%
Dividend yield	0	%	0	%
Expected volatility	87	%	103	%
Expected term	5.2 years		5.5 years

A summary of stock option activity and changes in stock options outstanding is presented below:


	Total Options		Weighted-Average Exercise Price Per Share		Intrinsic Value		Total Options		Weighted-Average Exercise Price Per Share		Intrinsic Value
Balance outstanding, December 31, 2016	5,528,628		$	5.49	$	—	5,528,628		$	5.49	$	—
Granted							823,106		$	0.84
Canceled / Forfeited	(1,922,024	)	$	6.40			(2,077,246	)	$	6.24
Expired	(17,457	)	$	4.74			(17,457	)	$	4.74
Balance outstanding, June 30, 2017	3,589,147		$	5.01	$	—
Exercisable at June 30, 2017	2,329,718		$	4.96	$	—
Balance outstanding, September 30, 2017							4,257,031		$	4.23	$	381
Exercisable at September 30, 2017							2,492,242		$	4.79	$	—

On June 13, 2017, the number of authorized shares in the Trovagene 2014 Equity Incentive Plan (“2014 EIP”) was increased from 7,500,000 to 9,500,000. As of ~~June~~September 30, 2017 there were ~~5,018,758~~3,670,232 shares available for issuance under the 2014 EIP.

Restricted Stock Units

The weighted-average grant date fair value of the RSU was $1.59 and $4.06 per share during the ~~six~~nine months ended ~~June~~September 30, 2017 and 2016, respectively.

A summary of the RSU activity is presented below:


	Number of Shares		Weighted-Average Grant Date Fair Value Per Share		Intrinsic Value		Number of Shares		Weighted-Average Grant Date Fair Value Per Share		Intrinsic Value
Non-vested RSU outstanding, December 31, 2016	272,000		$	3.99	$	571,200	272,000		$	3.99	$	571,200
Granted	2,249,242		$	1.59			2,249,242		$	1.59
Vested	(278,000	)	$	3.95	$	580,180	(369,487	)	$	3.48	$	645,775
Forfeited	(790,953	)	$	1.81			(874,453	)	$	1.75
Non-vested RSU outstanding, June 30, 2017	1,452,289		$	1.46	$	1,829,884
Non-vested RSU outstanding, September 30, 2017							1,277,302		$	1.44	$	932,430

At ~~June~~September 30, 2017, total unrecognized compensation cost related to non-vested RSU was ~~$1,310,838,~~$1,011,494, which is expected to be recognized over a weighted-average period of 2.5 years. The total fair value of vested RSU during the ~~six~~nine months ended ~~June~~September 30, 2017 was ~~$1,097,880.~~$1,285,578.

Restricted Stock Awards

During the nine months ended September 30, 2017, a total of 745,392 shares of RSA were granted, all of which were vested immediately. The total fair value of vested RSA during the nine months ended September 30, 2017 was $596,314. The weighted-average grant date fair value of the RSA was $0.80 per share during the nine months ended September 30, 2017. There were no such awards granted during the nine months ended September 30, 2016.

Warrants

A summary of warrant activity and changes in warrants outstanding, including both liability and equity classifications is presented below:


	Total Warrants		Weighted-Average Exercise Price Per Share		Weighted-Average Remaining Contractual Term	Total Warrants		Weighted-Average Exercise Price Per Share		Weighted-Average Remaining Contractual Term
Balance outstanding, December 31, 2016	5,505,901		$	3.83	1.6	5,505,901		$	3.83	1.6
Granted						4,643,626		$	1.41
Expired	(1,177,024	)	$	5.32		(1,177,024	)	$	5.32
Balance outstanding, June 30, 2017	4,328,877		$	3.42	1.4
Balance outstanding, September 30, 2017						8,972,503		$	2.38	3.3

9. Commitments and Contingencies

Executive and Consulting Agreements

The Company has longer-term contractual commitments with various consultants and employees. Certain employment agreements provide for severance payments.

Lease Agreements

The Company leases approximately 26,100 square feet of office and laboratory space at a monthly rental rate of approximately $68,000. The lease will expire on December 31, 2021. The Company currently subleases certain office space and records the rental receipt under the subleases as a reduction of its rent expense. The Company also ~~leases~~leased certain lab and office space in Torino, Italy, of approximately 2,300 square feet, at a monthly rental rate of approximately $3,100 through the end of September 2017.

Research and Development and Clinical Trial Agreements

In March 2017, the Company entered into a license agreement with Nerviano which granted the Company development and commercialization rights to NMS-1286937, which Trovagene refers to as PCM-075. PCM-075 is an oral, investigative drug and a highly-selective adenosine triphosphate competitive inhibitor of the serine/threonine PLK 1. The Company plans to develop PCM-075 initially in patients with AML. Upon execution of the agreement, the Company paid $2.0 million in license fees which were expensed to research and development costs during the ~~six~~nine months ended ~~June~~September 30, 2017. The Company is committed to pay $1.0 million for future services provided by Nerviano, such as the costs to manufacture drug product, no later than June 30, 2019. Terms of the agreement also provide for the Company to pay royalties based on certain development and sales milestones.

The Company has entered into a variety of ~~collaboration~~clinical trial and ~~specimen transfer~~collaboration agreements relating to its drug development efforts. Included in research and development expense, the Company has recorded approximately ~~$88,000~~$291,000 for the ~~six~~nine months ended ~~June~~September 30, 2017 relating to services provided ~~by the collaborators~~ in connection with these agreements.

The Company is a party to various agreements under which it licenses technology on an exclusive basis in the field of human diagnostics. License fees are generally calculated as a percentage of product revenues, with rates that vary by agreement. To date, payments have not been material.

Litigation

Trovagene does not believe that the Company has legal liabilities that are probable or reasonably possible that require either accrual or disclosure, except for the following: On March 28, 2016 the Company filed a complaint in the Superior Court of the State of California for the County of San Diego against the Company’s former CEO and CFO, for, among other things, breach of fiduciary duty for failing to present a lucrative corporate opportunity to the Company concerning promising new therapeutics in the field of precision medicine and instead taking that opportunity for their own personal benefit (the “Complaint”). The Complaint asks that these two former executives be required to turn over their interests in these new therapeutics to the Company. The former CEO and CFO filed a cross complaint in the Superior Court of the State of California

for the County of San Diego against the Company on May 23, 2016 for, among other things, breach of contract (the “Cross Complaint”, and together with the Complaint, collectively, the “Litigation”). On July 28, 2017, the parties settled the Litigation. The settlement involved mutual releases by all parties involved. The net cost to Trovagene in connection with the settlement is approximately $2.1 ~~million, which has been accrued within the condensed consolidated balance sheet as of June 30, 2017.~~million. Of that amount, $975,000 was the net amount paid directly to the former CEO and CFO. From time to time, the Company may become involved in various lawsuits and legal proceedings that arise in the ordinary course of business. Litigation is subject to inherent uncertainties, and an adverse result in matters may arise from time to time that may harm the Company’s business. As of the date of this report, management believes that there are no claims against the Company, which it believes will result in a material adverse effect on the Company’s business or financial condition.

Public Offering and Controlled Equity Offering

On March 15, 2017, the Company filed a Form 424B5 to amend and supplement the information in the Company’s registration statement and prospectus, dated June 13, 2016, to offer and sell additional shares of the Company’s common stock having an aggregate offering price up to $20,698,357. The Company entered into an agreement with Cantor Fitzgerald & Co. (“Agent”) on January 25, 2013 to issue and sell up to $30,000,000 of shares of common stock through the Agent. As payment for its services, the Agent is entitled to a commission on gross proceeds of up to 3%. Gross proceeds of approximately $110,000 have been raised in 2017.

10. Restructuring Charges

On March 15, 2017, in connection with the addition of precision medicine therapeutics to its business, the Company announced a restructuring plan (the “Restructuring”) which included a reduction in force. The Restructuring is expected to be completed in the last quarter of 2017. The Company estimates that it will incur approximately $2.0 million in charges related to

this Restructuring. During the ~~six~~nine months ended ~~June~~September 30, 2017, the Company incurred approximately $1.7 million in restructuring charges which included approximately $1.2 million of personnel termination costs and an approximately $0.5 million charge related to impairment of capitalized license fees. As of ~~June~~September 30, 2017, approximately ~~$0.8~~$0.4 million of these restructuring costs were included in accrued liabilities in the condensed consolidated balance sheet.

11. Related Party Transactions

In March 2016, the Company engaged Rutan & Tucker, LLP, a law firm to represent Trovagene, Inc. with respect to various lawsuits. One of the partners from Rutan & Tucker, LLP, is the son of the Company’s Chairman of the Board. The fees for legal services are based on the hourly rates of the individuals performing the legal services. During the ~~six~~nine months ended ~~June~~September 30, 2017 and 2016, the Company has incurred approximately ~~$541,000~~$763,075 and ~~$222,000~~$377,464 of legal expenses, net of insurance reimbursements, for services performed by Rutan & Tucker, LLP, respectively.

12. Subsequent ~~Events~~

~~Removal of NASDAQ Notice~~Event

On ~~July 10,~~October 25, 2017, the Company ~~received notice from NASDAQ indicating that the Company has regained compliance~~filed a registration statement on Form S-1 with the ~~minimum bid price requirement under NASDAQ Listing Rule 5550(a)(2)~~SEC for continued listing on The NASDAQ Capital Market. Accordingly, the Company is in compliance with all applicable listing standards and its common stock will continue to be listed on The NASDAQ Capital Market and NASDAQ considers the matter closed.

~~Registered Direct Offering~~

~~On July 19, 2017, the Company closed~~ a ~~registered direct~~best efforts public offering of ~~6,191,500 shares of its common stock. In a concurrent private placement, the Company also issued warrants to purchase~~ up to 4,643,626 shares of its common stock. The warrants will be exercisable six months following the date of issuance, will expire on the fifth anniversary of the initial exercise date and have an exercise price of $1.41 per share. The combined purchase price for one registered share$17.5 million of common stock and ~~one unregistered warrant to purchase 0.75 of an unregistered share of common stock~~warrants. H.C. Wainwright & Co. is ~~$1.15. The net proceeds to the Company were approximately $6.5 million.~~acting as placement agent.

ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

Forward-Looking Statements

This Quarterly Report on Form 10-Q includes forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended (the “Securities Act”) and Section 21E of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). All statements other than statements of historical facts contained in this Quarterly Report, including statements regarding the future financial position, business strategy and plans and objectives of management for future operations, are forward-looking statements. The words “believe,” “may,” “will,” “estimate,” “continue,” “anticipate,” “intend,” “should,” “plan,” “expect,” and similar expressions, as they relate to us, are intended to identify forward-looking statements. We have based these forward-looking statements largely on current expectations and projections about future events and financial trends that we believe may affect our financial condition, results of operations, business strategy and financial needs. These forward-looking statements are subject to a number of risks, uncertainties and assumptions.

In addition, our business and financial performance may be affected by the factors that are discussed under “Risk Factors” in the Annual Report on Form 10-K for the year ended December 31, 2016, filed on March 15, 2017, ~~and~~ on Form 10-Q

for the period ended March 31, 2017, filed on May 10, 2017, and on Form 10-Q for the period ended June 30, 2017, filed on August 9, 2017. Moreover, we operate in a very competitive and rapidly changing environment. New risk factors emerge from time to time and it is not possible for us to predict all risk factors, nor can we assess the impact of all factors on our business or the extent to which any factor, or combination of factors, may cause actual results to differ materially from those contained in any forward-looking statements.

You should not rely upon forward looking statements as predictions of future events. We cannot assure you that the events and circumstances reflected in the forward looking statements will be achieved or occur. Although we believe that the expectations reflected in the forward looking statements are reasonable, we cannot guarantee future results, levels of activity, performance or achievements.

The following discussion and analysis is qualified in its entirety by, and should be read in conjunction with, the more detailed information set forth in the financial statements and the notes thereto appearing elsewhere in this Quarterly Report on Form 10-Q. This discussion should not be construed to imply that the results discussed herein will necessarily continue into the future, or that any conclusion reached herein will necessarily be indicative of actual operating results in the future. Such discussion represents only the best present assessment of our management.

Overview

We are a precision medicine biotechnology company developing oncology therapeutics for improved cancer care, optimizing drug development by leveraging our proprietary PCM technology in tumor genomics. Our broad intellectual property and proprietary technology enables us to measure ctDNA in urine and blood to identify and quantify clinically actionable markers for predicting response to cancer therapies. We offer our PCM technology at our CLIA-certified/CAP-accredited laboratory and plan to continue to vertically integrate our PCM technology with the development of precision cancer therapeutics.

We believe ~~that there is~~we have an opportunity to utilize precision diagnostics ~~in the development of our precision cancer therapeutics~~ to improve treatment outcomes for cancer patients using our proprietary technology to detect ~~oncogene~~clinically actionable mutations and monitor patient response to therapy. ~~Our lead product candidate,~~On March 15, 2017, we announced the licensing of PCM-075, ~~was licensed~~a PLK1 inhibitor, from ~~Nerviano Medical Sciences,~~Nerviano. We have a supplier agreement with NerPharMa, S.r.l., a ~~leading European oncology research~~pharmaceutical manufacturing company and ~~discovery organization,~~a subsidiary of Nerviano, to manufacture drug product for PCM-075. The agreement covers the clinical and ~~is initially being developed for the treatment~~commercial supply of ~~patients with AML.~~PCM-075, and includes both Active Pharmaceutical Ingredients and Good Manufacturing Process production of capsules. The licensing of global development and commercialization rights to PCM-075 allows us to execute our strategy to vertically integrate our ~~ctDNA~~ PCM technology with precision cancer therapeutics, by developing drugs where our deep understanding of tumor genomics may allow for effective targeting of appropriate cancer patients.

We have completed a Phase 1 safety study of PCM-075 ~~is an oral~~in patients with advanced metastatic solid tumors and ~~highly-selective PLK1 inhibitor~~we received notification from the U.S. Food and ~~allows us to leverage~~Drug Administration (“FDA”) that our ~~PCM technology,~~Phase 1b/2 clinical trial of PCM-075 in patients with AML may proceed. PCM-075 has positive preclinical data as a single agent and ~~expertise~~ in ~~tumor genomics, to optimize the clinical development process,~~combination with select chemotherapeutics and ~~uniquely positions us to bring a first-in-class PLK1 inhibitor to the market for the treatment of AML. We plan to leverage our technology~~targeted agents used in many hematologic and ~~expertise to analyze correlative~~solid cancers, including AML, ~~biomarkers to identify patients most likely to benefit from treatment with PCM-075.~~Non-Hodgkin Lymphoma, mCRPC, Adrenocortical Carcinoma, and Triple Negative Breast Cancer.

We have significant experience and expertise with biomarkers and technology in cancer, including AML. We are one of the patent ~~holder~~holders of NPM1 for diagnosis and monitoring of patients. NPM1-mutated AML is a genetic marker in leukemia and accounts for approximately one-third of all AML patients. We plan to use our PCM technology to profile other dominant AML markers, such as FLT3, DNMT3A, NRAS, and KIT, ~~to optimize the development of PCM-075.~~

A Phase 1 safety study of PCM-075 has been completed in patients with advanced metastatic solid tumor cancers and data published in July, 2017 in the peer-reviewed journal Investigational New Drugs. This study evaluated drug metabolism, first-cycle dose limiting toxicities and related maximum tolerated dose with data demonstrating that PCM-075 is generally safe and well-tolerated in patients with advanced cancers. The authors concluded that data from preclinical work, coupled with the results of the Phase 1 trial, suggest that PCM-075 could become a new therapeutic option for the treatment of solid tumors and hematological malignancies, including AML.

We submitted an Investigational New Drug (“IND”) application to the U.S. Food and Drug Administration (“FDA”) on June 26, 2017. This submission included a Phase 1b/2 clinical protocol that will identify the safety of PCM-075 in AML patients, provide a preliminary assessment of response, study the effect of different clinical dosing regimens, as well as ~~explore the potential of correlative biomarker analyses~~ to ~~select~~measure PLK1 enzymatic activity to potentially identify patients ~~more~~most likely to ~~respond. On July 24, 2017, we received FDA approval of our IND~~respond to PCM-075 and ~~protocol~~ to ~~conduct our Phase 1b/2 clinical trial of PCM-075 in patients with AML.~~

~~We believe our PCM technology can allow for improved detection and quantitation of oncogene mutations from tumors to help improve disease and cancer~~measure patient ~~management. We believe that we can successfully leverage our deep understanding of tumor genomics to optimize the development of PCM-075.~~

The genetic materials that result when cells in the body die and release their DNA into the bloodstream, are collectively referred to as “cell-free nucleic acids.” Cell-free nucleic acids can be used as genetic markers of disease and the ability to use urine or blood as liquid biopsy sample types allows for simple, noninvasive, or minimally invasive, sample collection methods.

Our fundamental ctDNA diagnostic platform is protected by significant intellectual property around cell-free nucleic acids in urine and blood, the extraction of cell-free nucleic acids from urine and blood, as well as novel assay designs, particularly our proprietary non-naturally occurring primers. As of June 30, 2017, our intellectual property portfolio consists of 125 issued patents worldwide and 56 pending patent applications globally. Our patent estate includes intellectual property for

the detection of cell-free nucleic acids that pass through the kidney into the urine, as well as their application in specific disease areas, including oncology, infectious disease, transplantation, urology, and prenatal genetics.

We believe our technology expertise and extensive patent portfolio around cell-free DNA in urine and blood gives us a competitive advantage to leverage an emerging trend of monitoring cancer using ctDNA as a marker of disease status. Our proprietary sample preparation process includes novel technology for the collection and DNA preservation (“NextCollect™”), DNA extraction and isolation of ctDNA protocol, proprietary, non-naturally occurring primers to enrich the sample for mutant alleles, and the ability to detect nucleic acids of interest using next-generation sequencing.therapy response.

Our accumulated deficit through ~~June~~September 30, 2017 is ~~$166,172,670.~~$170,470,696. To date, we have generated minimal revenues and expect to incur additional losses to perform further research and development activities and expand commercial operations. During 2017, we have advanced our business with the following activities:

Announced preclinical research demonstrating synergy of PCM-075 with Zytiga® (abiraterone acetate) in Castration-Resistant Prostate Cancer tumor cells.

Announced that the FDA granted Orphan Drug Designation to PCM-075 for the treatment of patients with AML.

Announced the expansion and strengthening of its Board of Directors with the appointment of Athena Countouriotis, M.D. Dr. Countouriotis brings significant experience in oncology clinical development and orphan indications

Announced PCM-075 synergy with a HDAC Inhibitor in Non-Hodgkin Lymphoma Cell Lines. Additionally, PCM-075 demonstrates synergy in combination with more than ten chemotherapeutic and targeted therapies across a broad range of solid tumor and hematologic cancers.

Announced preclinical AML data shows PCM-075 significantly enhances the efficacy of a FLT3 inhibitor in combination therapy.

Announced FDA approval of IND for Phase 1b/2 trial of PCM-075 in patients with AML.

Announced peer-reviewed publication of first-in-human Phase 1 trial results with PCM-075 in the journal Investigational New Drugs. The data from the trial demonstrated PCM-075’s potential as safe and effective treatment for solid tumor and hematological malignancies.

Completed a registered direct offering of 6,191,500 shares of common stock and a concurrent private placement issuing warrants to purchase up to 4,643,626 shares of common stock. The net proceeds from the registered direct offering and concurrent private placement were approximately $6.5 million in July 2017.

Entered into an agreement with Novogene Co. Ltd. (“Novogene”), a leading global provider of genomic services and solutions and the largest sequencing capacity in the world, whereby Novogene will purchase NextCollect™, our proprietary urine collection and nucleic acid preservation device for validation in the Chinese market.

Engaged PRA Health Sciences, a leading, global contract research organization, to conduct our Phase 1b/2 clinical trial of PCM-075.

Executed a supplier agreement with NerPharMa, S.r.l., a pharmaceutical manufacturing company and a subsidiary of Nerviano Medical Sciences S.r.l., to manufacture drug product for PCM-075.

Submitted an IND application to FDA to conduct a Phase 1b/2 clinical trial of PCM-075 in AML.

Announced expansion of key claims for our NPM1 patent portfolio for AML.

Entered into an agreement with a global biopharmaceutical company to utilize Trovera® ctDNA tests and services in cancer clinical trials.

Entered into an agreement with AstraZeneca to utilize Trovera® ctDNA test and services in prospective biomarker study.

Announced phase 1 safety study conducted by Nerviano Medical Sciences supports planned development of PCM-075 in AML.

Established a Clinical Advisory Board, appointing Dr. Jorge Cortes, of MD Anderson, Dr. Sandra Silberman, a leading clinical researcher in hematology/oncology, and practicing physician at the Duke VAMC, Dr. Filip Janku, of City of Hope Cancer Center, and Dr. David Berz, of the Beverly Hills Cancer Center. Dr. Cortes and Dr. Silberman have extensive experience in the development of novel therapies for the treatment of hematologic cancers. Dr. Cortes will serve as the Principal Investigator for the Phase 1b/2 clinical trial in AML.

Entered into a license agreement with Nerviano that grants us exclusive global development and commercialization rights to NMS-1286937, which we refers to as PCM-075. PCM-075 is an oral, investigative drug and a highly-selective PLK 1 inhibitor for the treatment of AML.

Our ~~product~~drug development ~~and commercialization~~ efforts are in their early stages, and we cannot make estimates of the costs or the time that our development efforts will take to complete, or the timing and amount of revenues related to the sale of

our ~~tests or our diagnostic services and revenues related to our license agreements.~~drugs. The risk of completion of any program is high because of the many uncertainties involved in developing new drug candidates ~~and/or bringing new diagnostic products~~ to market, including the long duration of clinical testing, the specific performance of proposed products under stringent clinical trial protocols, ~~and/or CLIA requirements,~~ extended regulatory approval and review cycles, our ability to raise additional capital, the nature and timing of

research and development expenses, and competing technologies being developed by organizations with significantly greater resources.

Off-Balance Sheet Arrangements

We had no off-balance sheet arrangements as of ~~June~~September 30, 2017.

Critical Accounting Policies

Financial Reporting Release No. 60 requires all companies to include a discussion of critical accounting policies or methods used in the preparation of financial statements. Our accounting policies are described in ITEM 7. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS of our Annual Report on Form 10-K as of and for the year ended December 31, 2016, filed with the SEC on March 15, 2017. There have been no changes to our critical accounting policies since December 31, 2016.

RESULTS OF OPERATIONS

Three Months Ended ~~June~~September 30, 2017 and 2016

Revenues

Our total revenues were ~~$102,011~~$123,329 and ~~$103,400~~$89,114 for the three months ended ~~June~~September 30, 2017 and 2016, respectively. The components of our revenues were as follows:


	Three Months Ended June 30,							Three Months Ended September 30,
	2017		2016		Increase (Decrease)			2017		2016		Increase (Decrease)
Royalties	$	44,810	$	47,765	$	(2,955	)	$	58,779	$	47,236	$	11,543
Diagnostic services	55,501		23,962		31,539			58,119		37,978		20,141
Clinical research services	1,700		31,673		(29,973		)	6,431		3,900		2,531
Total revenues	$	102,011	$	103,400	$	(1,389	)	$	123,329	$	89,114	$	34,215

The increase in royalty income related primarily to higher receipts of payments in excess of minimum royalties in comparison to the same period of the prior year. Revenue from diagnostic services is recognized when payment is received for the test results. The number of payments received ~~were~~was higher in 2017 as compared to the same period in the prior year. Revenue from clinical research services consists of revenue from the sale of urine and blood collection supplies and tests performed under agreements with our clinical research and business development partners. Revenue ~~was~~is recognized when supplies and/or test results ~~were~~are delivered. There were ~~less~~more sales of clinical research services for the three months ended ~~June~~September 30, 2017 as compared to the same period of 2016.

We expect our royalties to fluctuate as the royalties are based on the minimum royalty payments as well as the timing of when payments are received for royalties in excess of minimum royalties. In addition, our diagnostic service revenue may be impacted by our expansion into oncology therapeutics. We expect revenue from clinical research services to fluctuate based on timing of delivery of supplies and/or test results under agreements.

Cost of Revenues

Our total cost of revenues was ~~$338,203~~$473,202 for the three months ended ~~June~~September 30, 2017, compared to ~~$409,463~~$424,559 in the same period of 2016. Cost of revenues mainly relates to the costs of our diagnostic service revenues. The costs are recognized at the completion of testing. ~~Decrease~~Increase in cost of revenues for the three months ended ~~June~~September 30, 2017 compared to the same period of last year is mainly due to the ~~decreased~~higher percentage allocation of volume of tests processed. Due to revenue being recognized when cash is received, costs incurred in one period may relate to revenue recognized in a later period which could result in negative gross margins.

Research and Development Expenses

Research and development expenses consisted of the following:


	Three Months Ended June 30,							Three Months Ended September 30,
	2017		2016		Increase (Decrease)			2017		2016		Increase (Decrease)
Salaries and staff costs	$	291,195	$	1,553,806	$	(1,262,611	)	$	301,919	$	1,407,529	$	(1,105,610	)
Stock-based compensation	206,463		590,536		(384,073		)	219,480		872,792		(653,312		)
Outside services, consultants and lab supplies	217,570		1,440,217		(1,222,647		)	604,140		1,215,889		(611,749		)
Facilities	219,614		408,554		(188,940		)	254,681		372,891		(118,210		)
Travel and scientific conferences	28,861		63,463		(34,602		)	28,000		51,203		(23,203		)
Other	18,012		19,838		(1,826		)	6,486		17,094		(10,608		)
Total research and development	$	981,715	$	4,076,414	$	(3,094,699	)	$	1,414,706	$	3,937,398	$	(2,522,692	)

Research and development expenses decreased by ~~$3,094,699~~$2,522,692 to ~~$981,715~~$1,414,706 for the three months ended ~~June~~September 30, 2017 from ~~$4,076,414~~$3,937,398 for the same period in 2016. As a result of the two strategic restructuring activities which occurred in December 2016 and March 2017, our average internal research and development personnel decreased from ~~thirty-five~~thirty-four to ~~seven,~~six, resulting in a decrease of expenses in salaries and staff costs, stock-based compensation, and travel and scientific conferences. In addition, due to the shifting of our business focus, we terminated certain clinical studies and collaboration agreements. Research and development expenses incurred related to ~~these studies,~~ samples processed and validated in connection with the clinical collaborations, as well as lab supplies, decreased accordingly. We expect a reduction of research and development costs that relate to CLIA services as a result of our expansion into oncology therapeutics; however, other costs may increase as we complete the development of PCM-075.

Selling and Marketing Expenses

Selling and marketing expenses consisted of the following:


	Three Months Ended June 30,							Three Months Ended September 30,
	2017		2016		Increase (Decrease)			2017		2016		Increase (Decrease)
Salaries and staff costs	$	217,760	$	1,430,199	$	(1,212,439	)	$	158,097	$	1,427,254	$	(1,269,157	)
Stock-based compensation	127,351		438,158		(310,807		)	118,434		476,865		(358,431		)
Outside services and consultants	54,253		318,711		(264,458		)	51,717		441,699		(389,982		)
Facilities	59,334		131,505		(72,171		)	51,388		112,573		(61,185		)
Trade shows, conferences and marketing	135,146		497,018		(361,872		)	31,017		243,692		(212,675		)
Travel	9,791		284,191		(274,400		)	54		212,375		(212,321		)
Other	11,384		29,254		(17,870		)	9,220		26,404		(17,184		)
Total sales and marketing	$	615,019	$	3,129,036	$	(2,514,017	)	$	419,927	$	2,940,862	$	(2,520,935	)

Selling and marketing expenses decreased by ~~$2,514,017~~$2,520,935 to ~~$615,019~~$419,927 for the three months ended ~~June~~September 30, 2017 from ~~$3,129,036~~$2,940,862 for the same period in 2016. The overall decrease in selling and marketing expenses was primarily due to our strategic restructuring activities. During the three months ended ~~June~~September 30, 2017 we decreased the number of our field sales, customer support and marketing personnel, bringing our average headcount to ~~four~~two from twenty-two in the same period of the prior year. As a result, costs associated with selling and marketing activities as well as personnel related costs were decreased accordingly. We expect decreases in personnel and related costs as a result of the reduction in force.

General and Administrative Expenses

General and administrative expenses consisted of the following:


	Three Months Ended June 30,							Three Months Ended September 30,
	2017		2016		Increase (Decrease)			2017		2016		Increase (Decrease)
Personnel and outside services costs	$	749,166	$	1,114,943	$	(365,777	)	$	1,450,261	$	1,136,266	$	313,995
Board of Directors’ fees	113,501		121,058		(7,557		)	120,085		122,187		(2,102		)
Stock-based compensation	472,718		234,991		237,727			1,067,633		437,075		630,558
Legal and accounting fees	2,323,042		612,727		1,710,315			595,194		695,061		(99,867		)
Facilities and insurance	291,658		265,539		26,119			291,547		149,921		141,626
Travel	36,078		27,441		8,637			14,185		47,769		(33,584		)
Fees, licenses, taxes and other	72,970		92,033		(19,063		)	120,682		122,503		(1,821		)
Total general and administrative	$	4,059,133	$	2,468,732	$	1,590,401		$	3,659,587	$	2,710,782	$	948,805

General and administrative expenses increased by ~~$1,590,401~~$948,805 to ~~$4,059,133~~$3,659,587 for the three months ended ~~June~~September 30, 2017, from ~~$2,468,732~~$2,710,782 for the same period in 2016. The significant components of the increase were primarily due to the increase in ~~legal~~personnel and ~~accounting fees.~~outside services cost and stock-based compensation. In August 2017, a total of 745,392 shares of immediately vested RSA were granted to our CEO. Per the ~~second quarter of 2017, we have accrued a litigation related loss contingency expense of approximately $2.1 million for~~agreement, the ~~settlement of Complaints~~CEO’s income taxes associated with the RSA were also paid by our ~~former CEO~~Company. Therefore, personnel costs and ~~CFO, which is the primary reason for the increase of legal and accounting fees.~~stock-based compensation expenses were increased. Our general and administrative costs may increase in future periods in order to support fundraising activities ~~on-going litigation,~~and general business activities as we continue to develop and introduce new product offerings.

Restructuring

On March 15, 2017, we announced a strategic restructuring plan in connection with the expansion of precision medicine therapeutics to our business. The restructuring plan includes a reduction in force and is expected to be completed in the last quarter of 2017. The ~~$3,806~~$46,472 restructuring benefit for the three months ended ~~June~~September 30, 2017 was primarily due to ~~stock-based compensation reversal for~~ certain ~~terminated employees offset by increased~~ employee termination ~~costs.~~costs expensed was less than estimated.

Net ~~interest~~Interest Expense

Net interest expense was ~~$431,871~~$16,473 and ~~$274,909~~$354,993 for the three months ended ~~June~~September 30, 2017 and 2016, respectively. The ~~increase~~decrease of net interest expense is primarily due to ~~an increase~~a decrease in interest expense, resulting from ~~higher interest rates and event~~pay-off of ~~default related to~~ our equipment line of credit. Pursuant to the Default Letter we received for our equipment line of credit, we recorded all of the prepayment fee and accrued the remainder of the final fee to interest expense.$15.0 million term loan. We expect net interest expense to decrease as a result of ~~pay-off~~repayment of our ~~$15.0 million term loan.~~equipment line of credit.

Change in Fair Value of Derivative Financial Instruments — Warrants

We have issued warrants that are accounted for as derivative liabilities. As of ~~June~~September 30, 2017, the derivative financial instruments—warrants liabilities were revalued to ~~$350,862,~~$2,037,712, resulting in an increase in value of ~~$71,428~~$1,686,850 from ~~March 31,~~June 30, 2017, based primarily upon the ~~increase~~issuance of new derivative financial instruments—warrants in connection with July fundraising activities, offset by the decrease in our stock price ~~from $1.15 at March 31, 2017 to $1.26 at June 30, 2017~~ as well as the changes in the expected term, volatility, and risk free interest rates for the expected term. The ~~increase in value~~issuance of new warrants was recorded as a ~~loss~~liability under derivative financial instruments—warrants in the condensed consolidated balance sheets. The decrease in value upon remeasurement at September 30, 2017 was recorded as a gain from the change in fair value of derivative financial instruments—warrants in the condensed consolidated statement of operations.

Net Loss

Net loss and per share amounts were as follows:


	Three Months Ended June 30,									Three Months Ended September 30,
	2017			2016			Increase (Decrease)			2017			2016			Increase (Decrease)
Net loss attributable to common shareholders	$	(8,051,871	)	$	(10,208,338	)	$	(2,156,467	)	$	(4,298,026	)	$	(10,197,332	)	$	(5,899,306	)
Net loss per common share — basic	$	(0.26	)	$	(0.34	)	$	(0.08	)	$	(0.12	)	$	(0.34	)	$	(0.22	)
Net loss per common share — diluted	$	(0.26	)	$	(0.34	)	$	(0.08	)	$	(0.12	)	$	(0.34	)	$	(0.22	)

Weighted average shares outstanding — basic	30,991,740			29,958,037			1,033,703			36,465,672			30,339,774			6,125,898
Weighted average shares outstanding — diluted	30,991,740			29,958,037			1,033,703			36,465,672			30,339,774			6,125,898

The ~~$2,156,467~~$5,899,306 decrease in net loss attributable to common shareholders and the ~~$0.08~~$0.22 decrease in basic net loss per share was primarily the result of a decrease in operating expenses of ~~$4,093,381 offset by an increase in loss on extinguishment of debt of $1,655,825~~$4,092,651 for the three months ended ~~June~~September 30, 2017 compared to the same period in the prior year.

~~Six~~Nine Months Ended ~~June~~September 30, 2017 and 2016

Revenues

Our total revenues were ~~$197,049~~$320,378 and ~~$223,886~~$313,000 for the ~~six~~nine months ended ~~June~~September 30, 2017 and 2016, respectively. The components of our revenues were as follows:


	Six Months Ended June 30,							Nine Months Ended September 30,
	2017		2016		Increase (Decrease)			2017		2016		Increase (Decrease)
Royalties	$	110,636	$	160,633	$	(49,997	)	$	169,415	$	207,869	$	(38,454	)
Diagnostic services	84,363		31,580		52,783			142,482		69,558		72,924
Clinical research services	2,050		31,673		(29,623		)	8,481		35,573		(27,092		)
Total revenues	$	197,049	$	223,886	$	(26,837	)	$	320,378	$	313,000	$	7,378

The ~~$49,997~~$38,454 decrease in royalties related primarily to lower receipts of payments in excess of minimum royalties in comparison to the same period of the prior year. Revenue from diagnostic services is recognized when payment is received for the test results. The number of tests ~~billed and~~ payments received were higher for the ~~six~~nine months ended ~~June~~September 30, 2017 as compared to the same period in the prior year. Revenue from clinical research services consists of revenue from the sale of urine and blood collection supplies and tests performed under agreements with our clinical research and business development partners. Revenue was recognized when supplies and/or test results were delivered.

We expect our royalties to fluctuate as the royalties are based on the minimum royalty payments as well as the timing of when payments are received for royalties in excess of minimum royalties. Our diagnostic service revenue may be impacted by our expansion into oncology therapeutics. In addition, we expect revenue from clinical research services to fluctuate based on timing of delivery of supplies under agreements.

Cost of Revenues

Our total cost of revenues was ~~$954,629~~$1,427,831 for the ~~six~~nine months ended ~~June~~September 30, 2017, compared to ~~$718,734~~$1,143,293 in the same period of 2016. Cost of revenues relates to the costs of our diagnostic service revenues. The costs are recognized at the completion of testing. Increase in cost of revenues for the ~~six~~nine months ended ~~June~~September 30, 2017 compared to the same period of last year is mainly due to the ~~increased~~higher percentage allocation of volume of tests. Due to revenue being recognized when cash is received, costs incurred in one period may relate to revenue recognized in a later period which could result in negative gross margins.

Research and Development Expenses

Research and development expenses consisted of the following:


	Six Months Ended June 30,							Nine Months Ended September 30,
	2017		2016		Increase (Decrease)			2017		2016		Increase (Decrease)
Salaries and staff costs	$	1,166,572	$	2,856,066	$	(1,689,494	)	$	1,468,491	$	4,263,595	$	(2,795,104	)
Stock-based compensation	578,663		989,277		(410,614		)	798,143		1,862,069		(1,063,926		)
Outside services, consultants and lab supplies	852,364		2,621,596		(1,769,232		)	1,456,504		3,837,485		(2,380,981		)
Facilities	587,515		669,791		(82,276		)	842,196		1,042,682		(200,486		)
Travel and scientific conferences	44,901		106,242		(61,341		)	72,901		157,445		(84,544		)
Fees, licenses and other	2,031,530		41,506		1,990,024			2,038,016		58,600		1,979,416
Total research and development	$	5,261,545	$	7,284,478	$	(2,022,933	)	$	6,676,251	$	11,221,876	$	(4,545,625	)

Research and development expenses decreased by ~~$2,022,933~~$4,545,625 to ~~$5,261,545~~$6,676,251 for the ~~six~~nine months ended ~~June~~September 30, 2017 from ~~$7,284,478~~$11,221,876 for the same period in 2016. Our costs have decreased primarily due to the average number of our internal research and development personnel decreasing from ~~thirty-two~~thirty-three to ~~thirteen.~~eleven. In addition, research and development expenses incurred related to clinical studies, samples processed and validated in connection with the clinical collaborations, as well as lab supplies, decreased for the ~~six~~nine months ended ~~June~~September 30, 2017 as compared to the same period in 2016 as a result of the shifting of our business focus. The total decrease of research and development expenses was offset by the increase in fees, license and other. The increase in fees, license and other was primarily due to the $2.0 million license fee payment in March 2017 to Nerviano for development and commercialization rights to PCM-075. We expect a reduction of research and development costs that relate to CLIA services as a result of our expansion into oncology therapeutics; however, other costs may increase as we continue the development of PCM-075.

Selling and Marketing Expenses

Selling and marketing expenses consisted of the following:


	Six Months Ended June 30,							Nine Months Ended September 30,
	2017		2016		Increase (Decrease)			2017		2016		Increase (Decrease)
Salaries and staff costs	$	818,943	$	2,838,775	$	(2,019,832	)	$	977,040	$	4,266,029	$	(3,288,989	)
Stock-based compensation	431,883		1,016,879		(584,996		)	550,317		1,493,744		(943,427		)
Outside services and consultants	168,083		675,669		(507,586		)	219,800		1,117,368		(897,568		)
Facilities	169,472		249,766		(80,294		)	220,860		362,339		(141,479		)
Trade shows, conferences and marketing	326,216		839,191		(512,975		)	357,233		1,082,883		(725,650		)
Travel	71,811		504,098		(432,287		)	71,865		716,473		(644,608		)
Other	36,596		62,210		(25,614		)	45,816		88,614		(42,798		)
Total sales and marketing	$	2,023,004	$	6,186,588	$	(4,163,584	)	$	2,442,931	$	9,127,450	$	(6,684,519	)

Selling and marketing expenses decreased by ~~$4,163,584~~$6,684,519 to ~~$2,023,004~~$2,442,931 for the ~~six~~nine months ended ~~June~~September 30, 2017 from ~~$6,186,588~~$9,127,450 for the same period in 2016. The overall decrease in selling and marketing expenses was primarily due to our strategic restructuring activities. As part of our restructuring, we reduced the number of our field sales, customer support and marketing personnel, bringing down our average headcount to ~~six~~five from twenty-two in the same period of the prior year. We expect decreases in personnel and related costs due to the reduction in force.

General and Administrative Expenses

General and administrative expenses consisted of the following:


	Six Months Ended June 30,							Nine Months Ended September 30,
	2017		2016		Increase (Decrease)			2017		2016		Increase (Decrease)
Personnel and outside services costs	$	1,819,873	$	2,143,594	$	(323,721	)	$	3,270,134	$	3,279,860	$	(9,726	)
Board of Directors’ fees	227,120		223,053		4,067			347,205		345,240		1,965
Stock-based compensation	769,495		2,050,340		(1,280,845		)	1,837,128		2,487,415		(650,287		)
Legal and accounting fees	2,763,217		1,382,524		1,380,693			3,358,411		2,077,585		1,280,826
Facilities and insurance	450,858		401,461		49,397			742,405		551,382		191,023
Travel	66,921		103,586		(36,665		)	81,106		151,355		(70,249		)
Fees, licenses, taxes and other	158,288		168,421		(10,133		)	278,970		290,924		(11,954		)
Total general and administrative	$	6,255,772	$	6,472,979	$	(217,207	)	$	9,915,359	$	9,183,761	$	731,598

General and administrative expenses ~~decreased~~increased by ~~$217,207~~$731,598 to ~~$6,255,772~~$9,915,359 for the ~~six~~nine months ended ~~June~~September 30, 2017, from ~~$6,472,979~~$9,183,761 for the same period in 2016. The ~~significant components of the decrease were~~increase was primarily due to ~~the decrease of personnel and outside services costs, stock-based compensation offset by~~ an increase in legal ~~fees. The~~fees offset by the decrease of personnel and outside services costs is mainly due to a decrease in average headcount from eleven to eight as a result of restructuring. In January 2016, our former CEO was granted a non-qualified stock option to purchase 350,000 shares of Common Stock at an exercise price of $5.18 per share. As the stock option was vested upon grant, the fair value of the option, which approximated $1.2 million was expensed in full during the six months ended June 30, 2016.stock-based compensation. Legal fees increased primarily as a result of a litigation related loss contingency of $2.1 million expensed during the ~~six~~nine months ended ~~June~~September 30, 2017. Stock-based compensation, a non-cash expense, will fluctuate based on the timing and amount of options granted, forfeitures and the fair value of the options at the time of grant or remeasurement.

Restructuring

On March 15, 2017, we announced a strategic restructuring plan in connection with the addition of precision medicine therapeutics to our business. The restructuring plan includes a reduction in force and is expected to be completed in the last quarter of 2017. Restructuring charges of approximately $1.7 million were incurred and have been included as a component of operating loss for the ~~six~~nine months ended ~~June~~September 30, 2017. Of the total restructuring charges, approximately $1.2 million was related to termination of employees and an approximately $0.5 million charge related to impaired license fees.

Net Interest Expense

Net interest expense was ~~$861,268~~$877,741 and ~~$612,529~~$967,522 for ~~six~~nine months ended ~~June~~September 30, 2017 and 2016, respectively. The ~~increase~~decrease of net interest expense is ~~primarily~~ due to ~~an increase~~a decrease in interest expense of approximately ~~$214,000,~~$184,000, resulting from ~~higher~~pay-off of our $15.0 million term loan, offset by a decrease in interest ~~rates and costs related to the debt extinguishment and the event~~income as a result of ~~default related to~~liquidation of our ~~equipment line of credit.~~short-term investments.

Change in Fair Value of Derivative Financial Instruments — Warrants

We have issued warrants that are accounted for as derivative liabilities. As of ~~June~~September 30, 2017, the derivative financial instruments—warrants liabilities were revalued to ~~$350,862,~~$2,037,712, resulting in ~~a decrease~~an increase in value of ~~$484,078~~$1,202,772 from December 31, 2016, based primarily upon the issuance of new derivative financial instruments—warrants in connection with July fundraising activities, offset by the decrease in our stock price ~~from $2.10 at December 31, 2016 to $1.26 at June 30, 2017~~ as well as the changes in the expected term, volatility, and risk free interest rates for the expected term. The issuance of new warrants was recorded as a liability under derivative financial instruments—warrants in the condensed consolidated balance sheets. The decrease in value was recorded as a gain from the change in fair value of derivative financial instruments—warrants in the condensed consolidated statement of operations.

Net Loss

Net loss and per share amounts were as follows:


	Six Months Ended June 30,									Nine Months Ended September 30,
	2017			2016			Increase (Decrease)			2017			2016			Increase (Decrease)
Net loss attributable to common shareholders	$	(18,057,468	)	$	(20,476,916	)	$	(2,419,448	)	$	(22,355,494	)	$	(30,674,248	)	$	(8,318,754	)
Net loss per common share — basic	$	(0.58	)	$	(0.69	)	$	(0.11	)	$	(0.68	)	$	(1.02	)	$	(0.34	)
Net loss per common share — diluted	$	(0.58	)	$	(0.70	)	$	(0.12	)	$	(0.68	)	$	(1.04	)	$	(0.36	)

Weighted average shares outstanding — basic	30,976,462			29,856,611			1,119,851			32,826,306			30,018,841			2,807,465
Weighted average shares outstanding — diluted	30,976,462			30,033,207			943,255			32,826,306			30,136,572			2,689,734

The ~~$2,419,448~~$8,318,754 decrease in net loss attributable to common shareholders and the ~~$0.11~~$0.34 decrease in basic net loss per share was primarily the result of a decrease in operating expenses compared to the same period in the prior year. This decrease was offset by a loss on extinguishment of debt of $1.7 million.

LIQUIDITY AND CAPITAL RESOURCES

As of ~~June~~September 30, 2017, we had ~~$7,783,891~~$7,434,298 in cash and cash equivalents. Net cash used in operating activities for the ~~six~~nine months ended ~~June~~September 30, 2017 was ~~$13,355,334,~~$19,949,652, compared to ~~$14,993,428~~$22,034,998 for the ~~six~~nine months ended ~~June~~September 30, 2016. Our use of cash was primarily a result of the net loss of ~~$18,045,348~~$22,337,314 for the ~~six~~nine months ended ~~June~~September 30, 2017, adjusted for non-cash items related to stock-based compensation of ~~$1,696,184,~~$3,117,364, loss on extinguishment of debt of $1,655,825, impairment loss of $485,000, depreciation and amortization of ~~$645,962,~~$956,995, and the gain from the change in fair value of derivative financial instruments—warrants of ~~$484,078.~~$2,012,747. The changes in our operating assets and liabilities consisted of ~~higher~~lower accounts payable and accrued expenses, an increase in accounts receivable and a decreased prepaid expenses. At our current and anticipated level of operating loss, we expect to continue to incur an operating cash outflow for the next several years.

Net cash provided by investing activities was ~~$24,041,048~~$23,925,535 during the ~~six~~nine months ended ~~June~~September 30, 2017, compared to ~~$28,622,478~~$25,249,392 used in investing activities for the same period in 2016. Investing activities during the ~~six~~nine months ended ~~June~~September 30, 2017 consisted of net sales and maturities of short-term investments of $24,061,786 offset by net purchases for capital equipment of ~~$20,738.~~$136,251.

Net cash used in financing activities was ~~$16,819,328~~$10,447,842 during the ~~six~~nine months ended ~~June~~September 30, 2017, compared to ~~$1,295,688~~$2,361,994 provided in financing activities for the same period in 2016. Financing activities during the ~~six~~nine months ended ~~June~~September 30, 2017 related primarily to the pay-off of long-term debt resulting in debt extinguishment offset by the sale of common stock, while financing activities during the same period of the prior year consisted primarily of sales of common stock offset by repayment of long-term debt. On June 1, 2017, we received a Notice of Event of Default from the lenders which stated that Events of Default had occurred and all of the obligation under the Loan and Security Agreement dated as of June 30, 2014 were immediately due and payable. On June 6, 2017, the lenders took the total pay-off amount of $16,668,583 out of our bank accounts which satisfied all of our outstanding obligations under the Agreement. We disagree with the lenders that any Event of Default has occurred and are reserving all of our options with respect to the Agreement.

As of ~~June~~September 30, 2017, and December 31, 2016, we had working capital of ~~$1,193,067~~$3,469,622 and $31,152,936, respectively. ~~As of July 31,~~

On October 25, 2017, we ~~had cash~~filed a registration statement on Form S-1 with the SEC for a best efforts public offering of up to $17.5 million of common stock and ~~cash equivalents balance of $12,495,342 and we have not paid the litigation settlement.~~warrants. H.C. Wainwright & Co. is acting as placement agent.

Based on our current business plan and assumptions, we expect to continue to incur significant losses and require significant additional capital to further advance our clinical trial programs and support our other operations. Considering our current cash resources, including the net proceeds received from the offering of our equity securities in July 2017, we believe our existing resources will be sufficient to fund the Company’s planned operations ~~until~~into the first quarter of 2018. In addition, we have based our cash sufficiency estimates on our current business plan and assumptions that may prove to be wrong. We could utilize our available capital resources sooner than we currently expect, and we could need additional funding to sustain

our operations even sooner than currently anticipated. These circumstances raise substantial doubt about our ability to continue as a going concern.

Our working capital requirements will depend upon numerous factors including but not limited to the nature, cost and timing of our research and development programs. To date, our sources of cash have been primarily limited to the sale of equity

securities. We cannot be certain that additional funding will be available on acceptable terms, or at all. To the extent that we raise additional funds by issuing equity securities, our stockholders may experience significant dilution. Any debt financing, if available, may involve restrictive covenants that impact our ability to conduct business. If we are unable to raise additional capital when required or on acceptable terms, we may have to significantly delay, scale back or discontinue the development and/or commercialization of one or more product candidates, all of which may have a material adverse impact on our operations. We may also be required to (i) seek collaborators for product candidates at an earlier stage than otherwise would be desirable and on terms that are less favorable than might otherwise be available; or (ii) relinquish or otherwise dispose of rights to technologies, product candidates or products that we would otherwise seek to develop or commercialize ourselves on unfavorable terms. We are evaluating the following options to raise additional capital, increase revenue, as well as reduce costs, in an effort to strengthen our liquidity position: (1) Raising capital through public and private equity offerings; (2) Adding capital through short-term and long-term borrowings; (3) Introducing operation and business development initiatives to bring in new revenue streams by leveraging capabilities within our CLIA lab, as well as monetizing our proprietary NextCollect™ DNA collection and preservation cup; (4) Reducing operating costs by identifying internal synergies; (5) Engaging in strategic partnerships; and (6) Taking actions to reduce or delay capital expenditures. We continually assess any spending plans, including a review of our discretionary spending in connection with certain strategic contracts, to effectively and efficiently address our liquidity needs.

NASDAQ Notice

On ~~May 30,~~September 5, 2017, we received a written notice from the NASDAQ Stock Market LLC (“NASDAQ”) that we were not in compliance with NASDAQ Listing Rule 5550(a)(2) for continued listing on the NASDAQ Capital Market, as the minimum bid price of our common stock had been below $1.00 per share for 30 consecutive business days. The Notice had no immediate effect on the listing of our common stock, and our common stock continue to trade on the NASDAQ Capital Market under the symbol “TROV”.

In accordance with NASDAQ Listing Rule 5810(c)(3)(A), we have a period of 180 calendar days, or until ~~November 27, 2017,~~March 5, 2018, to regain compliance with the minimum bid price requirement. To regain compliance, the closing bid price of our common stock must meet or exceed $1.00 per share for at least ten consecutive business days during this 180 calendar day period.

~~On July 7, 2017, NASDAQ notified us that we had regained compliance with the applicable minimum bid price rule. Accordingly, the matter related to the notice we received in May 2017 was closed.~~

CONTRACTUAL OBLIGATIONS

For a discussion of our contractual obligations see (i) our Financial Statements and Notes to Consolidated Financial Statements Note 9. Commitments and Contingencies, and (ii) Item 7 Management Discussion and Analysis of Financial Condition and Results of Operations — Contractual Obligations and Commitments, included in our Annual Report on Form 10-K as of December 31, 2016.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Interest Rate Risk

Our primary exposure to market risk is interest income and expense sensitivity, which is affected by changes in the general level of interest rates, particularly because our equipment line of credit has a floating interest rate as of ~~June~~September 30, 2017. Changes in interest rates could affect the amounts of interest that we pay in the future.

Our cash and cash equivalent primary consists of deposits, and money market deposits managed by commercial banks as of ~~June~~September 30, 2017. The goals of our investment policy are preservation of capital, fulfillment of liquidity needs and fiduciary control of cash and investments.

Our investments are in short-term money marketable funds. Due to the short-term duration of our investment portfolio and the relatively low risk profile of our investments, a sudden change in interest rates would not have a material effect on the fair market value of our portfolio, nor our operating results or cash flows.

We do not believe our cash and cash equivalents have significant risk of default issues; however, we maintain significant amounts of cash and cash equivalents at one or more financial institutions that are in excess of federally insured limits. Given the current stability of financial institutions, we believe that we will not experience losses on these deposits.

Foreign Currency Risk

Our foreign currency exchange risk mainly arises from our operations in Italy. Our functional and reporting currency is the United States dollar. We translate our foreign operations’ assets and liabilities denominated in foreign currencies into U.S. dollars at current rates of exchange as of the balance sheet date and income and expense items at the average exchange rate for the reporting period. Translation adjustments resulting from exchange rate fluctuations are recorded in the cumulative translation account, a component of consolidated accumulated other comprehensive income. In addition, we face the foreign currency risk as a result of entering into transactions denominated in currencies other than U.S. dollars. Changes in foreign currency exchange rates can create foreign exchange gains or losses to us.

Effects of Inflation

We do not believe that inflation and changing prices during the ~~six~~nine months ended ~~June~~September 30, 2017 had a significant impact on our results of operations.

ITEM 4. CONTROLS AND PROCEDURES

Evaluation of Disclosure Controls and Procedures

We have performed an evaluation under the supervision and with the participation of our management, including our principal executive and financial officer, of the effectiveness of our disclosure controls and procedures, as defined in Rule 13a-15(e) under the Securities Exchange Act of 1934 (the “Exchange Act”). Based on that evaluation, our principal executive and financial officer concluded that our disclosure controls and procedures were effective as of ~~June~~September 30, 2017 to provide reasonable assurance that information required to be disclosed by us in the reports filed or submitted by us under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms.

Our disclosure controls and procedures are designed to provide reasonable assurance of achieving their objectives as specified above. Management does not expect, however, that our disclosure controls and procedures will prevent or detect all errors and fraud. Any control system, no matter how well designed and operated, is based upon certain assumptions and can provide only reasonable, not absolute, assurance that its objectives will be met. Further, no evaluation of controls can provide absolute assurance that misstatements due to error or fraud will not occur or that all control issues and instances of fraud, if any, within the Company have been detected.

Changes in Internal Control over Financial Reporting

There was no change in our internal control over financial reporting during the three months ended ~~June~~September 30, 2017 that materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

PART II. OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS

See Note 9 to the unaudited Condensed Consolidated Financial Statements for a summary of legal proceedings.

ITEM 1A. RISK FACTORS

~~Except for the following, there~~There have been no material changes from the risk factors disclosed in our Form 10-K for the year ended December 31, 2016, ~~and~~ Form 10-Q for the periods ended March 31, ~~2017.~~2017, and Form 10-Q for the periods ended June 30, 2017, except for the following:

~~Recent Events of Default have forced us~~Our financial statements include an explanatory paragraph that expresses substantial doubt about our ability to ~~repay outstanding indebtedness sooner than expected.~~continue as a going concern, indicating the possibility that we may not be able to operate in the future.

~~On June 1, 2017, we received a Notice of Event of Default (the “Notice”) from Oxford Finance LLC (“Oxford”) with respect to that certain Loan and Security Agreement dated~~Primarily as of June 30, 2014 (as amended, restated, supplemented or otherwise modified from time to time, the “Loan Agreement”), by and among Oxford as Collateral Agent, Oxford as a Lender, Silicon Valley Bank, as a Lender (“SVB” and together with Oxford, the “Lenders”) and us. The Notice stated that Events of Default had occurred and are continuing under Sections 8.2(a) and 8.2(b) (Covenant Defaults) (as a result of ~~violations of Section 5.2, 7.1~~our losses incurred to date, our expected continued future losses, and ~~7.2), Section 8.3 (Material Adverse Change), Section 8.6 (Other Agreements) and Section 8.8 (Misrepresentations)~~limited cash balances, we have included an explanatory paragraph in our financial statements expressing substantial doubt about our ability to continue as a going concern. Our ability to continue as a going concern is contingent upon, among other factors, the sale of the Loan Agreement. The Notice further stated that all of the obligation under the Loan Agreement are immediately due and payable. On June 6, 2017, the Lenders withdrew $16,668,583 out of our bank accounts which satisfies all of our outstanding obligations under the Loan Agreement. On March 31, 2017, we had approximately $28.8 million of cash. As of June 30, 2017, we had approximately $7.8 million of cash. We need to raise substantial additional capital to operate our business and our failure to obtain financing will force us to delay, reduce or eliminate our product development programs or collaboration efforts and would have a material adverse effect on our business.

On June 20, 2017, we received a Notice of Event of Default (the “Equipment Notice”) from SVB with respect to that certain Loan and Security Agreement in the aggregate principal amount of $1.4 million dated as of November 17, 2015 (as amended, restated, supplemented or otherwise modified from time to time, the “Equipment Loan Agreement”), between SVB and us. The Equipment Notice stated that Events of Default had occurred and are continuing under Sections 8.2(a) (Covenant Defaults) (as a result of violations of Section 7.1 and 7.2), Section 8.3 (Material Adverse Change), Section 8.6 (Other Agreements) and Section 8.8 (Misrepresentations) of the Equipment Loan Agreement. The Equipment Loan Agreement is substantially similar to the Loan Agreement by and among Oxford Finance LLC, SVB and us which also was the subject of a Notice of Event of Default on June 1, 2017. Both Notices of Event of Default are substantially similar, except that the Equipment Notice further stated that “SVB intends to monitor the default situation very carefully and will decide in their sole discretion on a “day-by-day” basis whether or not to exercise rights and remedies.” As of June 30, 2017, approximately $1.6 million of principal and accrued interest was outstanding under the equipment loan. We are currently discussing with SVB a waiver of the defaults. In the event that we cannot agree with SVB on a waiver of the defaults, SVB may accelerate the amounts outstanding under the Equipment Loan Agreement which will cause us to repay such amounts sooner than expected or foreclose on certain of our equipment, both of which could have a material adverse effect on our business.

~~If we fail to comply with the continued minimum closing bid requirements of the NASDAQ Capital Market LLC or other requirements for continued listing, our common stock may be delisted and the price~~shares of our common stock ~~and our ability to access the capital markets could be negatively impacted.~~

On May 30, 2017, we received a written notice (the “Notice”) from the NASDAQ that we were not in compliance with NASDAQ Listing Rule 5550(a)(2), as the minimum bid price of our common stock has been below $1.00 per share for 30 consecutive business days. The Notice had no immediate effect on the listing of our common stock, and our common stock continued to trade on the NASDAQ Capital Market under the symbol “TROV.” In accordance with NASDAQ Listing Rule 5810(c)(3)(A), we had a period of 180 calendar days, or until November 27, 2017, to regain compliance with the minimum bid price requirement. To regain compliance, the closing bid price of our common stock must meet or exceed $1.00 per share for at least ten consecutive business days during this 180 calendar day period. On July 7, 2017, we were informed by NASDAQ that we have regained compliance with the minimum bid price requirement under NASDAQ Listing Rule 5810(c)(3)(A) for continued listing. In the future, if we fail to comply with the continued minimum closing bid requirements of the NASDAQ or other requirements for continued listing, our common stock may be delisted and the price of our common stock and our ability to access the capital markets could be negatively impacted. A delisting of our common stock from the NASDAQ could materially reduce the liquidity of our common stock and result in a corresponding material reduction in the price of our common stock. In addition, delisting could harm our ability to raise capital through alternative financing sources on terms

~~acceptable to us, or at all, and may result in the potential loss of confidence by investors, employees and fewer business development opportunities.~~obtaining alternate financing.

ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS

None.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES

ITEM 4. MINE SAFETY DISCLOSURES

Not applicable.

ITEM 5. OTHER INFORMATION

None.

ITEM 6. EXHIBITS



Exhibit Number		Description of Exhibit

4.1		~~Form of Warrant (incorporated by reference to Exhibit 4.1 to Form 8-K filed with the SEC on July 17, 2017).~~

~~10.1~~		~~Form of Securities Purchase~~ Stock Award Agreement dated ~~July 13,~~August 15, 2017 ~~(incorporated~~ by ~~reference to Exhibit 10.1 to Form 8-K filed with the SEC on July 17, 2017).~~and between Trovagene, Inc. and William J. Welch.

31.1		Certification of Principal Executive Officer and Principal Financial Officer required by Rule 13a-14(a)/15d-14(a) under the Exchange Act.

32.1		Certification of Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

101.INS		XBRL Instance Document

101.SCH		XBRL Taxonomy Extension Schema

101.CAL		XBRL Taxonomy Extension Calculation Linkbase

101.LAB		XBRL Taxonomy Extension Labels Linkbase

101.PRE		XBRL Taxonomy Extension Presentation Linkbase

101.DEF		XBRL Taxonomy Extension Definition Linkbase

SIGNATURES

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.



	TROVAGENE, INC.

~~August~~November 9, 2017	By:	/s/ William J. Welch
		William J. Welch
		Chief Executive Officer (Principal Executive Officer and Principal Financial Officer)

3231



	Six Months Ended June 30,
	2017 (1)		2016
Risk-free interest rate	—	%	1.5	%
Dividend yield	0	%	0	%
Expected volatility	—	%	102	%
Expected term	0.0 years		5.5 years