Table of Contents

 
UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
 
Form 10-Q
 
(Mark One)
xQUARTERLY REPORT UNDER SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the quarterly period ended September 30, 20162017
 
OR
oTRANSITION 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(I.R.S. Employer
incorporation or organization) (I.R.S. Employer Identification No.)
11055 Flintkote Avenue, Suite B, San Diego, California92121
(Address of principal executive offices)(Zip Code)
(858) 952-7570
(Registrant’s telephone number, including area code)
11055 Flintkote Avenue, Suite B, San Diego, California 92121
(Address of principal executive offices) (Zip Code)
Issuer’s telephone Number: (858) 952-7570
 
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, or a smaller reporting company, or an emerging growth company. See definitions of “large accelerated filer,” “accelerated filer,” and “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act. (Check one):
 
Large accelerated filer o 
Accelerated filer xo
   
Non-accelerated filer o
 
Smaller reporting company o
Non-accelerated filer o(Do not check if a smaller reporting company) Smaller reporting company x
Emerging growth companyo
 
 
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 October 31, 2016,2017, the issuer had 30,615,40638,106,460 shares of Common Stock issued and outstanding.
 


Table of Contents

TROVAGENE, INC.
 
Table of Contents
 
  Page
 
   
 
   
 
   
 
   
 
   
 
   
 
   
   
   
   
 
   
   
 


PART I. FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS

TROVAGENE, INC. 
CONDENSED CONSOLIDATED BALANCE SHEETS
(Unaudited)
 
September 30, 2016 December 31, 2015September 30, 2017 December 31, 2016
Assets      
Current assets:      
Cash and cash equivalents$22,569,107
 $67,493,047
$7,434,298
 $13,915,094
Short-term investments24,376,904
 

 23,978,022
Accounts receivable85,152
 98,736
178,127
 100,460
Prepaid expenses and other assets946,388
 789,285
Prepaid expenses and other current assets939,200
 956,616
Total current assets47,977,551
 68,381,068
8,551,625
 38,950,192
Property and equipment, net4,654,876
 2,690,579
3,126,969
 3,826,915
Other assets371,243
 374,004
539,309
 1,173,304
Total Assets$53,003,670
 $71,445,651
$12,217,903
 $43,950,411
      
Liabilities and Stockholders’ Equity      
Current liabilities:      
Accounts payable$925,173
 $1,040,868
$675,499
 $1,130,536
Accrued expenses4,558,809
 1,903,797
2,620,250
 4,021,365
Deferred rent279,710
 30,614
298,213
 285,246
Current portion of long-term debt801,024
 5,225,818
Current portion of long-term debt (in default)1,488,041
 2,360,109
Total current liabilities6,564,716
 8,201,097
5,082,003
 7,797,256
Long-term debt, less current portion15,595,400
 11,246,188

 14,176,359
Derivative financial instruments - warrants2,622,243
 3,297,077
Derivative financial instruments—warrants2,037,712
 834,940
Deferred rent, net of current portion1,446,912
 
1,153,316
 1,373,717
Total Liabilities26,229,271
 22,744,362
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 September 30, 2016 and December 31, 2015; designated as Series A Convertible Preferred Stock with liquidation preference of $606,000 at September 30, 2016 and December 31, 201560
 60
Common stock, $0.0001 par value, 150,000,000 shares authorized; 30,599,140 and 29,737,601 shares issued and outstanding at September 30, 2016 and December 31, 2015, respectively3,060
 2,974
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, 201660
 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, respectively3,811
 3,070
Additional paid-in capital166,337,512
 157,585,498
174,426,891
 167,890,984
Accumulated other comprehensive loss(4,742) 
(15,194) (10,773)
Accumulated deficit(139,561,491) (108,887,243)(170,470,696) (148,115,202)
Total stockholders’ equity26,774,399
 48,701,289
3,944,872
 19,768,139
Total liabilities and stockholders’ equity$53,003,670
 $71,445,651
$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 September 30, Nine Months Ended September 30,Three Months Ended September 30, Nine Months Ended September 30,
2016 2015 2016 20152017 2016 2017 2016
Revenues:              
Royalties$47,236
 $51,301
 $207,869
 $222,931
$58,779
 $47,236
 $169,415
 $207,869
Diagnostic services37,978
 6,026
 69,558
 10,712
58,119
 37,978
 142,482
 69,558
Clinical research services3,900
 
 35,573
 
6,431
 3,900
 8,481
 35,573
Total revenues89,114
 57,327
 313,000
 233,643
123,329
 89,114
 320,378
 313,000
Costs and expenses:              
Cost of revenues424,559
 173,537
 1,143,293
 429,992
473,202
 424,559
 1,427,831
 1,143,293
Research and development3,937,398
 2,546,533
 11,221,876
 7,428,349
1,414,706
 3,937,398
 6,676,251
 11,221,876
Selling and marketing2,940,862
 1,798,263
 9,127,450
 4,508,766
419,927
 2,940,862
 2,442,931
 9,127,450
General and administrative2,710,782
 1,948,546
 9,183,761
 5,756,047
3,659,587
 2,710,782
 9,915,359
 9,183,761
Restructuring (benefit) charges(46,472) 
 1,669,526
 
Total operating expenses10,013,601
 6,466,879
 30,676,380
 18,123,154
5,920,950
 10,013,601
 22,131,898
 30,676,380
              
Loss from operations(9,924,487) (6,409,552) (30,363,380) (17,889,511)(5,797,621) (9,924,487) (21,811,520) (30,363,380)
              
Net interest expense(354,993) (335,359) (967,522) (1,100,080)(16,473) (354,993) (877,741) (967,522)
Gain (loss) from change in fair value of derivative financial instruments — warrants88,208
 4,017,212
 674,834
 (1,105,270)
Other income (loss), net
 (8,130) 
 4,617
Gain from change in fair value of derivative financial instruments—warrants1,528,669
 88,208
 2,012,747
 674,834
Loss on extinguishment of debt
 
 (1,655,825) 
Other loss, net(6,541) 
 (4,975) 
Net loss(10,191,272) (2,735,829) (30,656,068) (20,090,244)(4,291,966) (10,191,272) (22,337,314) (30,656,068)
              
Preferred stock dividend(6,060) (6,060) (18,180) (18,180)(6,060) (6,060) (18,180) (18,180)
              
Net loss attributable to common stockholders$(10,197,332) $(2,741,889) $(30,674,248) $(20,108,424)$(4,298,026) $(10,197,332) $(22,355,494) $(30,674,248)
              
Net loss per common share — basic$(0.34) $(0.10) $(1.02) $(0.80)$(0.12) $(0.34) $(0.68) $(1.02)
Net loss per common share — diluted$(0.34) $(0.23) $(1.04) $(0.96)$(0.12) $(0.34) $(0.68) $(1.04)
              
Weighted average shares outstanding — basic30,339,774
 28,560,211
 30,018,841
 25,014,966
Weighted average shares outstanding — diluted30,339,774
 29,128,235
 30,136,572
 25,204,307
Weighted-average shares outstanding — basic36,465,672
 30,339,774
 32,826,306
 30,018,841
Weighted-average shares outstanding — diluted36,465,672
 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 September 30, Nine Months Ended September 30,Three Months Ended September 30, Nine Months Ended September 30,
2016 2015 2016 20152017 2016 2017 2016
Net loss$(10,191,272) $(2,735,829) $(30,656,068) $(20,090,244)$(4,291,966) $(10,191,272) $(22,337,314) $(30,656,068)
Other comprehensive loss:       
Other comprehensive income (loss):       
Foreign currency translation loss(81) 
 (1,877) 
(1,544) (81) (13,486) (1,877)
Unrealized loss on securities available-for-sale(7,997) 
 (2,865) 
Total other comprehensive loss(8,078) 
 (4,742) 
Unrealized gain or reversal of previous losses on securities available-for-sale
 (7,997) 9,065
 (2,865)
Total other comprehensive income (loss)(1,544) (8,078) (4,421) (4,742)
              
Total comprehensive loss(10,199,350) (2,735,829) (30,660,810) (20,090,244)(4,293,510) (10,199,350) (22,341,735) (30,660,810)
              
Preferred stock dividend(6,060) (6,060) (18,180) (18,180)(6,060) (6,060) (18,180) (18,180)
              
Comprehensive loss attributable to common stockholders$(10,205,410) $(2,741,889) $(30,678,990) $(20,108,424)$(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)
 
Nine Months Ended
September 30,
Nine Months Ended
September 30,
2016 20152017 2016
Operating activities      
Net loss$(30,656,068) $(20,090,244)$(22,337,314) $(30,656,068)
Adjustments to reconcile net loss to net cash used in operating activities:      
Net gain on disposal of fixed assets
 4,562
Loss on disposal of assets28,199
 
Impairment loss485,000
 
Depreciation and amortization693,485
 250,600
956,995
 693,485
Stock based compensation expense5,942,392
 2,758,847
3,117,364
 5,942,392
Loss on extinguishment of debt1,655,825
 
Accretion of final fee premium266,423
 253,028
293,614
 266,423
Amortization of discount on debt105,710
 59,665
113,780
 105,710
Net realized loss on short-term investments6,400
 
Amortization of premiums on short-term investments61,719
 
9,230
 61,719
Deferred rent(133,378) 
(207,435) (133,378)
Interest income accrued on short-term investments10,122
 
(90,330) 10,122
Change in fair value of derivative financial instruments - warrants(674,834) 1,105,270
Change in fair value of derivative financial instruments—warrants(2,012,747) (674,834)
Changes in operating assets and liabilities:      
Decrease (increase) in other assets2,761
 (10,273)
Decrease (increase) in accounts receivable13,584
 (231,672)
Increase in prepaid expenses(157,051) (26,238)
Increase in accounts payable and accrued expenses2,490,137
 616,366
Decrease in other assets
 2,761
(Increase) decrease in accounts receivable(77,667) 13,584
Decrease (increase) in prepaid expenses and other current assets18,230
 (157,051)
(Decrease) increase in accounts payable and accrued expenses(1,908,796) 2,490,137
Net cash used in operating activities(22,034,998) (15,310,089)(19,949,652) (22,034,998)
      
Investing activities:      
Capital expenditures, net(797,781) (1,256,988)(136,251) (797,781)
Net purchases of short-term investments(24,451,611) 
Net cash used in investing activities(25,249,392) (1,256,988)
Maturities of short-term investments16,431,837
 
Purchases of short-term investments(8,804,604) (24,451,611)
Sales of short-term investments16,434,553
 
Net cash provided by (used in) investing activities23,925,535
 (25,249,392)
      
Financing activities:      
Proceeds from sales of common stock, net of expenses2,293,857
 61,215,398
Proceeds from sales of common stock and warrants, net of expenses6,634,803
 2,293,857
Proceeds from exercise of options366,966
 818,251

 366,966
Proceeds from exercise of warrants
 1,389,427
Borrowings under equipment line of credit792,251
 

 792,251
Borrowings under long-term debt, net of costs7,805,086
 

 7,805,086
Payment upon debt extinguishment(1,613,067) 
Repayments of long-term debt(8,896,166) 
(15,000,000) (8,896,166)
Net cash provided by financing activities2,361,994
 63,423,076
Repayments of equipment line of credit(469,578) 
Net cash (used in) provided by financing activities(10,447,842) 2,361,994
Effect of exchange rate changes on cash and cash equivalents(1,544) 
(8,837) (1,544)
Net change in cash and equivalents(44,923,940) 46,855,999
(6,480,796) (44,923,940)
Cash and cash equivalents—Beginning of period67,493,047
 27,293,798
13,915,094
 67,493,047
Cash and cash equivalents—End of period$22,569,107
 $74,149,797
$7,434,298
 $22,569,107
      
Supplementary disclosure of cash flow activity:      
Cash paid for taxes$4,560
 $800
$800
 $4,560
Cash paid for interest$806,228
 $795,375
$650,331
 $806,228
Supplemental disclosure of non-cash investing and financing activities:      
Preferred stock dividends accrued$18,180
 $18,180
$18,180
 $18,180
Warrants issued in connection with Amendment to the Loan and Security Agreement$148,885
 $
Reclassification of derivative financial instruments - warrants to additional paid in capital$
 $435,365
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 molecular diagnostics company headquartered in San Diego, California.California, is a clinical-stage, precision medicine oncology therapeutics company. The Company’s primary focus is to leverage its cell-free DNA molecular diagnostic technology in cancer and other diseases. Trovagene's goal is to broadly commercialize its molecular diagnostic technology via direct sales as well as external license agreements and/or collaborations to democratizedevelop oncology therapeutics for improved cancer care, optimizing drug development by establishing the best access for patient care. The Company’sleveraging its proprietary Precision Cancer Monitoring® (“PCM”) platform measures circulating tumor DNA (“ctDNA”) in urine and blood, enabling personalized patient care.  The Company’s PCM platform as well as urine and blood based tests, also known as liquid biopsies, have the potential to dramatically improve cancer care and usher in an era of precision oncology. Trovagene’s tests are available to clinicians for the assessment of known driver mutations in lung, pancreatic, colorectal, neuroendocrine cancers, melanoma and histiocytic disorders. The Company’s noninvasivediagnostic technology provides for clinically actionable information through the detection of cancer mutations and the monitoring of changes in tumor dynamics before, during,genomics.

Trovagene’s lead drug candidate, PCM-075, is a Polo-like Kinase 1 (“PLK1”) selective adenosine triphosphate (“ATP”) competitive inhibitor. PCM-075 has shown preclinical antitumor activity as a single agent and after treatment.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 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 patients with advanced metastatic solid tumors with a phase 1b/2 clinical trial in patients with AML 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 areThe 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 normalthe 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, 20152016 included in the Company’s annual report on Form 10-K filed with the SEC on March 10, 2016.15, 2017.

Liquidity
 
Trovagene’s condensed consolidated financial statements as of September 30, 20162017 have been prepared under the assumption that Trovagene will continue as a going concern.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 concernconcern.
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 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 equity or debt financing, attain further operating efficiencies and, ultimately, to generate additional revenue. Based on current plans, the Company will be required to raise additional capital in the next twelve months to complete the development and commercialization of current product candidates and to continue to fund operations at its current projected cash expenditure levels.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.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 has approximately $44.4is 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 cash, cash equivalentscommon stock and short-term investments at October 31, 2016.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 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 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.


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 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 net realized loss of approximately $6,400 for the nine months ended 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 in excess of minimum amounts 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”) or ASC 480 Distinguishing Liabilities from Equity (“ASC 480”) and 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 condensed consolidated statementsstatement of operations under the caption “Gain (loss) from change“Change in fair value of derivative financial instruments - warrants.instruments.
 
The fair value of warrants is determined using the Black-Scholes option-pricing model using assumptions regarding the volatility of Trovagene’s common sharestock price, the fair value of the underlying common shares, 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 September 30, 2016,2017 and December 31, 2015,2016, the fair value of these warrants was $2,622,243$2,037,712 and

$3,297,077, $834,940, respectively, and arewas recorded as a liability under the caption "Derivative“derivative financial instruments - warrants"warrants” on the consolidated balance sheet.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 September 30,
 Nine Months
Ended September 30,
Three Months
Ended September 30,
 Nine Months
Ended September 30,
2016 2015 2016 20152017 2016 2017 2016
Numerator: Net loss attributable to common shareholders$(10,197,332) $(2,741,889) $(30,674,248) $(20,108,424)$(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
 (4,017,212) (533,750) (4,017,212)
Adjustment for gain from change in fair value of derivative financial instrumentswarrants

 
 
 (533,750)
Net loss used for diluted loss per share$(10,197,332) $(6,759,101) $(31,207,998) $(24,125,636)$(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 share30,339,774
 28,560,211
 30,018,841
 25,014,966
Weighted-average shares used to compute basic loss per share36,465,672
 30,339,774
 32,826,306
 30,018,841
Adjustments to reflect assumed exercise of warrants
 568,024
 117,731
 189,341

 
 
 117,731
Weighted average shares used to compute diluted net loss per share30,339,774
 29,128,235
 30,136,572
 25,204,307
Weighted-average shares used to compute diluted net loss per share36,465,672
 30,339,774
 32,826,306
 30,136,572
Net loss per share attributable to common stockholders:              
Basic$(0.34) $(0.10) $(1.02) $(0.80)$(0.12) $(0.34) $(0.68) $(1.02)
Diluted$(0.34) $(0.23) $(1.04) $(0.96)$(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:
 
September 30,September 30,
2016 20152017 2016
Options to purchase Common Stock6,051,186
 6,514,130
4,257,031
 6,051,186
Warrants to purchase Common Stock4,546,939
 4,565,947
8,972,503
 4,546,939
Restricted Stock Units392,000
 
1,277,302
 392,000
Series A Convertible Preferred Stock63,125
 63,125
63,125
 63,125
11,053,250
 11,143,202
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 DisposalCost 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 Accounting Standards Update (“ASU”)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 all leases with terms longer than 12 months. Leases will be classified as either finance or operating, with classification affecting the pattern of expense recognition in the income statement.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 the adoption of the new standard will have on its consolidated financial statements.
In August 2014, the FASB issued ASU 2014-15, Presentation of Financial StatementsGoing Concern, which impacts the accounting guidance related to the evaluation of an entity’s ability to continue as a going concern. The amendment establishes management’s responsibility to evaluate whether there is substantial doubt about an entity’s ability to continue as a going concern in connection with preparing financial statements for each annual and interim reporting period. The amendment also gives guidance to determine whether to disclose information about relevant conditions and events when there is substantial doubt about an entity’s ability to continue as a going concern. The amended guidance is effective prospectively for fiscal years beginning after December 15, 2016. The new guidance is not expected to have a material impact on the Company’s financial position, results of operations or cash flows.
 
In May 2014, the FASB issued ASU 2014-9,2014-09, Revenue from Contracts with Customers (“ASU 2014-9”2014-09”). ASU 2014-9 provides companies with a single model for accounting forThe new standard is based on the principle that revenue arising from contracts with customers and supersedes current revenue recognition guidance, including industry-specific revenue guidance. The core principleshould be recognized to depict the transfer of the model is to recognize revenue when control of thepromised goods or services transfersto 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 customer, as opposedstandard, which include clarification of accounting guidance related to recognizing revenue when the risksidentification of performance obligations, intellectual property licenses, and rewards transfer to the customer under the existing revenue guidance. The guidance permits companies to either apply the requirements retrospectively to all prior periods presented, or apply the requirements in the year of adoption, through a cumulative adjustment. In August 2015, the FASB issued ASU 2015-14, Deferral of the Effective Date, which defers the required adoption date ofprinciple versus agent considerations. ASU 2014-09 by one year. As a result ofand all subsequent amendments (collectively, the deferred effective date, ASU 2014-09“new standards”) will be effective for the Company beginning in its first quarter of fiscal year 2018. Early adoption is permitted but not before the original effective date of the first quarter of fiscal year 2018 and may be applied using either the full retrospective method, in which case the 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 new standards would be recognized at the date of initial application. 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 these agreements has unique terms that are being evaluated separately under the new standards. 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 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. The Company is also continuing to assess the potential impact that the new standards may have with respect to its diagnostic service revenue which is currently recognized on a cash collection basis. Under the new standards, the Company may recognize diagnostic service revenue 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 uncertainty associated with the variable consideration is subsequently resolved. The Company is continuing to assess the impact the new standards will have on its financial statements and expects to complete the assessment on or before the year-end 2017. The Company isdoes not expect a significant change in the processtiming and recognition of evaluating the transition method that will be elected and the impact ofits revenue upon adoption of ASU 2014-09 on its consolidated financial statement.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 September 30, 20162017 and December 31, 2015:2016:
 
 Fair Value Measurements at
September 30, 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)$19,841,032
 $
 $
 $19,841,032
Corporate debt securities (2)
 15,887,439
 
 15,887,439
    Commercial paper (2)
 8,489,465
 
 8,489,465
Total Assets$19,841,032
 $24,376,904
 $
 $44,217,936
Liabilities:       
Derivative financial instruments - warrants$
 $
 $2,622,243
 $2,622,243
Total Liabilities$
 $
 $2,622,243
 $2,622,243

Fair Value Measurements at
December 31, 2015
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)$65,016,222
 $
 $
 $65,016,222
$6,510,214
 $
 $
 $6,510,214
Total Assets$65,016,222
 $
 $
 $65,016,222
$6,510,214
 $
 $
 $6,510,214
Liabilities:              
Derivative financial instruments - warrants$
 $���
 $3,297,077
 $3,297,077
Derivative financial instrumentswarrants
$
 $
 $2,037,712
 $2,037,712
Total Liabilities$
 $
 $3,297,077
 $3,297,077
$
 $
 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 instrumentswarrants
$
 $
 $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 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 nine months ended September 30, 2016:2017:
 
Description Balance at
December 31, 2015
 
Unrealized
Gain
 Balance at
September 30, 2016
 Balance at
December 31, 2016
 Issuance of Derivative Financial Instruments 
Realized
Gain
 Balance at
September 30, 2017
Derivative financial instruments - warrants $3,297,077
 $(674,834) $2,622,243
Derivative financial instrumentswarrants
 $834,940
 3,215,519
 $(2,012,747) $2,037,712
 
The unrealized gainrealized gains or losses on the derivative financial instruments - instruments—warrants isare recorded as a change in fair value of derivative financial instruments - instruments—warrants in the Company’s condensed consolidated statementsstatement 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 whichthat trade infrequently and therefore have little or no price transparency are classified as Level 3.

4. Short-Term Investments

Investments consistAs of corporate debt securities and commercial paper. The Company classifies debt securities 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 accumulated other comprehensive income (loss) in stockholders’ equity until realized. Realized gains and losses from the sale of available-for-sale securities, if any, are 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 are 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 is recognized when earned. Realized gains and losses on investments in securities will be included in other income (loss) within the condensed consolidated statements of operations. There were no realized gains and losses for the nine months ended September 30, 2016.2017, 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 securities available-for-saleshort-term investments as of September 30,December 31, 2016.

   Unrealized  December 31, 2016
Maturity in Years Cost Gains Losses Fair Value   Unrealized  
        Maturity in Years Cost Gains Losses Fair Value
Corporate debt securitiesLess than 1 year $15,890,304
 $2,162
 $(5,027) $15,887,439
Less than 1 year $14,165,915
 $44
 $(5,273) $14,160,686
Commercial paperLess than 1 year 8,489,465
 
 
 8,489,465
Less than 1 year 1,195,444
 
 
 1,195,444
U.S. treasury securitiesLess than 1 year 8,625,728
 330
 (4,166) 8,621,892
Total Investment $24,379,769
 $2,162
 $(5,027) $24,376,904
 $23,987,087
 $374
 $(9,439) $23,978,022


5. Property and Equipment
 
Property and equipment consist of the following:
 
As of September 30,
2016
 As of December 31,
2015
As of September 30,
2017
 As of December 31,
2016
Furniture and office equipment$1,727,321
 $1,483,227
$1,076,709
 $1,144,741
Leasehold improvements1,994,514
 39,401
1,994,514
 1,994,514
Laboratory equipment2,472,444
 2,022,733
2,584,363
 2,449,645
6,194,279
 3,545,361
5,655,586
 5,588,900
Less—accumulated depreciation and amortization(1,539,403) (854,782)(2,528,617) (1,761,985)
Property and equipment, net$4,654,876
 $2,690,579
$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 BankSVB 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 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. Any equipment advances after November 30, 2016 are subject to principal and interest payments immediately over a 36-month period following the advance. 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. As

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 $1,488,041 as a current liability as of September 30, 2016, the Company was in compliance with all covenants.

As of September 30, 2016, $1,878,312 has been borrowed under the Equipment Line of Credit. As of September 30, 2016, amounts due under the Equipment Line of Credit included $573,929 in current liabilities2017 and $1,328,355 in long-term liabilities, which includes $23,972 of final fee premium accretion.also started recording accrued interest at a default rate. The Company recorded $80,176$209,082 in interest expense related to the Equipment Line of Credit during the nine months ended September 30, 2016.
Future principal payments of long-term debt at September 30, 2016 are as follows:

Year Ended December 31,
2016$104,351
2017626,104
2018626,104
2019521,753
Total principal1,878,312
Plus final fee premium accretion23,972
Total long-term obligations$1,902,284
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 loanLoan and security agreementSecurity Agreement (“Agreement”) under which the lenders provided the Company a term loan. The loan is secured by a security interest in all of the Company’s assets except intellectual property, which is subject to a negative pledge. In connection with the loan, the lenders received a warrant to purchase an aggregate 85,470 shares of the Company’s common stock at an exercise price of $3.51 per share exercisable for ten years from the date of issuance. 

On July 20, 2016, the Company signed the 5th Amendment to Loan and Security Agreement (“Amendment”) 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. In addition,

On June 1, 2017, the Company received a Notice of Event of Default from the lenders received a warrant to purchase an aggregate 30,992 shareswhich 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 common stock at an exercise price of $4.84 per share exercisable for ten years from the date of issuance. The fair value of the warrants, totaling $148,885, was recorded as debt discount and additional paid-in capital as the warrants were equity classified. As of September 30, 2016, warrants to purchase 73,727 shares of common stock remains outstanding.
At the Company’s option, it may prepaybank accounts which satisfied all of the Company’s outstanding principal balance, subject to certain pre-payment fees ranging from 1% to 3%obligations under the Agreement. Accordingly, the Agreement was terminated in June 2017. Upon termination of the Agreement, the prepayment amount. In the eventfee of a final payment$450,000, unamortized debt discount of the loans under the Amendment, either in the event of repayment of the loan at maturity or upon any prepayment, the Company is obligated to pay the$400,562 and unamortized final fee of $1,125,000.
The Company is also subject to certain affirmative and negative covenants under the Agreement, including limitations$738,196 were recorded as loss on its ability to undergo certain change of control events, and is required to maintain its primary operating, deposit and securities accounts with the lender. In addition, the Company is required to be in compliance with healthcare laws and regulations and terms and conditions of healthcare permits. The Company was in compliance with all covenants as of September 30, 2016.
As of September 30, 2016, amounts due under the Agreement include $227,095 in current liabilities, which include $272,905 of current portion of debt discount, and $14,267,045 in long-term liabilities, which include $76,575 of final fee premium accretion.extinguishment. The Company recorded $1,113,943 intotal interest expense of $801,173 related to the Agreement during the nine months ended September 30, 2016.
Future principal payments of long-term debt at September 30, 2016 are as follows:
Year Ended December 31,
2016$
20172,000,000
20186,000,000
20196,000,000
20201,000,000
Total principal15,000,000
Less discount(582,435)
Plus final fee premium accretion76,575
Total long-term obligations$14,494,140
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:
 

Nine Months Ended September 30,Nine Months Ended September 30,
2016 20152017 2016
Estimated fair value of Trovagene common stock4.49-4.65
 5.69-10.15
0.73-1.26
 4.49-4.65
Expected warrant term2.3-2.8 years
 3.3-3.8 years
1.3-5.5 years
 2.3-2.8 years
Risk-free interest rate0.71-0.87%
 0.89-1.01%
1.27-1.95%
 0.71-0.87%
Expected volatility82-90%
 75-77%
86-109%
 82-89%
Dividend yield0% 0%0% 0%

Expected volatility is based on historical volatility.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 107 No. 107”), for instruments issued with such a provision, Trovagene used the fullremaining 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
December 31, 2015 Balance of derivative financial instruments - warrants liability 967,295
 $3,297,077
  Change in fair value of derivative financial instruments - warrants during the period recognized as a gain in the condensed consolidated statements of operations 
 (674,834)
September 30, 2016 Balance of derivative financial instruments - warrants liability 967,295
 $2,622,243
Date Description Number of Warrants 
Derivative
Instrument
Liability
December 31, 2016 
Balance of derivative financial instrumentswarrants liability
 967,295
 $834,940
  Issuance of derivative financial instruments 4,643,626
 3,215,519
  
Change in fair value of derivative financial instrumentswarrants during the period recognized as a gain in the condensed consolidated statements of operations
 
 (2,012,747)
September 30, 2017 
Balance of derivative financial instrumentswarrants liability
 5,610,921
 $2,037,712
 
8. Stockholders’ Equity
 
Common Stock
 
During the nine months ended September 30, 2016,2017, the Company issued a total of 861,5397,408,460 shares of Common Stock. The Company received gross proceeds of approximately $2.4$7.1 million from the sale of 421,8106,191,500 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 $5.61$1.08 under the agreement with Cantor Fitzgerald & Co. (“Agent”). In addition, 98,396369,487 shares were issued upon exercisevesting of options for a weighted average price of $3.73,restricted stock units (“RSU”), and 341,333745,392 shares were issued upon net exercisevesting of 1,236,875 options at a weighted average exercise price of $3.81.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
September 30,
 Nine Months Ended
September 30,
Three Months Ended
September 30,
 Nine Months Ended
September 30,
2016 2015 2016 20152017 2016 2017 2016
Included in research and development expense$872,792
 $342,122
 $1,862,069
 $1,054,443
$219,480
 $872,792
 $798,143
 $1,862,069
Included in cost of revenue42,639
 7,518
 99,164
 22,468
15,633
 42,639
 56,998
 99,164
Included in selling and marketing expense476,865
 225,892
 1,493,744
 480,006
118,434
 476,865
 550,317
 1,493,744
Included in general and administrative expense437,075
 348,127
 2,487,415
 1,201,929
1,067,633
 437,075
 1,837,128
 2,487,415
Benefit from restructuring
 
 (125,222) 
Total stock-based compensation expense$1,829,371
 $923,659
 $5,942,392
 $2,758,846
$1,421,180
 $1,829,371
 $3,117,364
 $5,942,392
 
The unrecognized compensation cost related to non-vested stock options outstanding at September 30, 20162017 and 2015,2016, net of expected forfeitures, was $3,271,046 and $10,416,565, and $10,308,131, respectively, bothwhich is expected to be recognized over a weighted-average remaining vesting period of approximately three years.2.2 and 3.0 years, respectively. The weighted averageweighted-average remaining contractual term of outstanding options as of September 30, 2017 was approximately 7.2 years. The total fair value of stock options vested during the nine months ended September 30, 2017 and 2016 was approximately eight years.$3,378,243 and $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 averageweighted-average assumptions during the following periods indicated:
 
Nine Months Ended
September 30,
Nine Months Ended
September 30,
2016 20152017 2016
Risk-free interest rate1.48% 1.77%1.82% 1.48%
Dividend yield0% 0%0% 0%
Expected volatility103% 76%87% 103%
Expected term5.5 years
 6.1 years
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
Balance outstanding, December 31, 20156,948,630
 $5.45
 $5,903,466
Granted3,234,750
 5.02
  
Exercised(1,335,271) 3.81
  
Canceled / Forfeited(2,690,146) 5.44
  
Expired(106,777) 11.14
  
Balance outstanding, September 30, 20166,051,186
 5.49
 1,724,990
Exercisable at September 30, 20162,287,028
 5.13
 1,325,134
 Total Options 
Weighted-Average
Exercise Price
Per Share
 
Intrinsic
Value
Balance outstanding, December 31, 20165,528,628
 $5.49
 $
Granted823,106
 $0.84
  
Canceled / Forfeited(2,077,246) $6.24
  
Expired(17,457) $4.74
  
Balance outstanding, September 30, 20174,257,031
 $4.23
 $381
Exercisable at September 30, 20172,492,242
 $4.79
 $
 
DuringOn June 13, 2017, the nine months ended September 30, 2016, the Company had issued 996,000 options to its executive officers and non-employee directors that were over the authorized number of authorized shares available in the Trovagene 2014 Equity Incentive Plan (2014 EIP) and were subject(“2014 EIP”) was increased from 7,500,000 to shareholder approval. As per ASC Topic 815-40, the options were accounted for as liabilities and recorded at fair value with the changes in fair value being recorded in the Company’s condensed consolidated statements of operations. Stockholder approval was obtained on May 17, 2016 to increase the number of authorized shares in the 2014 EIP from 5,000,000 to 7,500,000. Accordingly, the options were remeasured as of the date of stockholder approval with the change recorded in stock based compensation expense and the $217,333 liability was reclassified to additional paid in capital.9,500,000. As of September 30, 20162017 there were 2,346,4783,670,232 shares available for issuance under the 2014 EIP.



Restricted Stock Units

Under guidance provided by ASC Topic 718 “Compensation—Stock Compensation” for share-based payments, the fair value of our restricted stock units is based on the grant date fair value of our common stock. All restricted stock units were granted with no purchase price. Vesting of the restricted stock units is generally subject to service conditions, while vesting of certain units are based on attainment of specific performance objectives. The weighted-average grant date fair value of the restricted stock unitsRSU was $1.59 and $4.06 per share during the nine months ended September 30, 2016. There were no restricted stock units granted during the year ended December 31, 2015.2017 and 2016, respectively.

A summary of the restricted stock unitRSU activity is presented below:
Number of Shares 
Weighted Average
Grant Date Fair Value
Per Share
Number of Shares 
Weighted-Average
Grant Date Fair Value
Per Share
 Intrinsic Value
Non-vested restricted stock units outstanding, December 31, 2015
 $
Non-vested RSU outstanding, December 31, 2016272,000
 $3.99
 $571,200
Granted402,000
 4.06
2,249,242
 $1.59
  
Vested(369,487) $3.48
 $645,775
Forfeited(10,000) 3.99
(874,453) $1.75
  
Non-vested restricted stock units outstanding, September 30, 2016392,000
 4.06
Non-vested RSU outstanding, September 30, 20171,277,302
 $1.44
 $932,430


None of the restricted stock units vested during the nine months ended September 30, 2016. At September 30, 2016,2017, total unrecognized compensation cost related to non-vested restricted stock unitsRSU was $537,134,$1,011,494, which is expected to be recognized over a weighted-average period of three months.2.5 years. The total fair value of vested RSU during the nine months ended September 30, 2017 was $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, 20155,533,242
 $3.86
 2.50
Balance outstanding, December 31, 20165,505,901
 $3.83
 1.6
Granted30,992
 4.84
 4,643,626
 $1.41
 
Expired(50,000) 8.00
  (1,177,024) $5.32
  
Balance outstanding, September 30, 20165,514,234
 3.82
 1.85
Balance outstanding, September 30, 20178,972,503
 $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 previously leasedleases approximately 22,60026,100 square feet of office and laboratory space at a monthly rental rate of approximately $60,000. On April 4, 2016, the Company entered into an amendment to the lease agreement which expanded the square footage of its office space to approximately 26,100 square feet at a revised monthly rental rate of approximately $68,000. Under the amendment, the lessor provided the Company with a $1,860,000 tenant improvement allowance which the Company recorded as a deferred rent obligation. The Company will amortize the deferred rent on a straight-line basis over the life of the lease. The new 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 leasesleased certain lab and office space in Torino, Italy, of approximately 2,300 square feet, at a monthly rental rate of approximately $3,100. The lease is for a period$3,100 through the end of three years and expires December 31, 2018.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 nine months ended 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 collaborationclinical trial and specimen transfercollaboration agreements relating to its drug development efforts. Included in research and development expense, the Company has recorded approximately $0.8 million$291,000 for the nine months ended September 30, 20162017 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.

TheLitigation
Trovagene does not believe that the Company has entered intolegal 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 collaborative research program under which it will workcomplaint 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 designpresent a lucrative corporate opportunity to the Company concerning promising new therapeutics in the field of precision medicine and validate custom enrichment panels--as specified byinstead 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 research partner will be reimbursed former CEO and CFO filed a cross complaint in the Superior Court of the State of California

for a portionthe County of incurred costs, plus a fixed fee for target services performed. The research agreement includes an outline for a provisional commercial agreement that providesSan 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. 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 exclusive licenseadverse result in matters may arise from time to usetime that may harm the research partner's technologyCompany’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 exchange for two milestone payments. The commercial agreement has not been finalized as of September 30, 2016.a material adverse effect on the Company’s business or financial condition.

Public Offering and Controlled Equity Offering

On May 27, 2016March 15, 2017, the Company filed a Form S-3 Registration Statement424B5 to amend and supplement the information in the Company’s registration statement and prospectus, dated June 13, 2016, to offer and sell in one or more offerings, any combinationadditional shares of the Company’s common stock preferred stock, debt securities, warrants, or units having an aggregate initial offering price not exceeding $250,000,000. The preferred stock, debt securities, warrants, and units may be convertible or exercisable or exchangeable for common stock or preferred stock or other Trovagene securities. This form was declared effective on June 13,

2016.up to $20,698,357. The Company hadentered 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 3% commission on gross proceeds.proceeds of up to 3%. Gross proceeds of $2.4 millionapproximately $110,000 have been raised since the date of effectiveness of the Form S-3 on June 13, 2016.

Database Usage

In March 2016 the Company entered into an agreement with an outside vendor to develop an online database for test requisition and test results. Under the agreement, the Company is obligated to pay a fixed development fee, and a usage fee each time an external user completes and submits a test order form to the database. To date, the Company has paid the fixed development fee, but has incurred no costs in connection with the usage fees.

Other Matters

The Company may be subject to litigation or administrative proceedings related to our business, such as claims related to employment practices, commercial disputes, or patent infringement. Responding to litigation or administrative proceedings, regardless of whether they have merit, can be expensive and disruptive to normal business operations. We are not able to predict the timing or outcome of these matters.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 nine months ended 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 September 30, 2017, approximately $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. As ofDuring the nine months ended September 30, 2017 and 2016, the Company has incurred approximately $376,000$763,075 and $377,464 of legal expenses, net of insurance reimbursements, for services performed by Rutan & Tucker, LLP.

In September 2015, the Company entered into a research agreement with University of Turin (“University”) to collaborate on a program of research to develop, optimize and test molecular profiling tools for plasma and urine ctDNA in cancer. Dr. Alberto Bardelli, the Principal Investigator of the University who oversees this research program is also a member of the Scientific Advisory Board of the Company. Under the agreement, the Company has committed to pay up to $743,000 for the services performed by the University. In addition, the Company may pay royalties to the University on revenue generated by the Company from the commercialization of any tools developed during the collaboration. As of September 30, 2016, the Company has incurred and recorded approximately $555,000 of research and development expenses related to the agreement. No royalty expense has been incurred as of September 30, 2016.LLP, respectively.

12. Subsequent Event

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. H.C. Wainwright & Co. is 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, 2015,2016, filed on March 15, 2017, on Form 10-Q

for the period ended March 31, 2017, filed on May 10, 2016,2017, and on Form 10-Q for the periodsperiod ended June 30, 2016,2017, filed on August 4, 2016.9, 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 molecular diagnosticsprecision medicine biotechnology company that focuses ondeveloping 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 and commercialization of both proprietary urine and blood-based cell-free molecular diagnostic technologies for use in the detection and monitoring ofprecision cancer mutations across a variety of medical disciplines. Our primary internal focus istherapeutics.

We believe we have an opportunity to leverage our novel urine-based molecular diagnostic platform to facilitate improvements in the field of oncology, while our external focus includes entering into collaborations to develop the Company’s technology in areas such as infectious disease, urology transplantation, and prenatal genetics. Our current goal isutilize precision diagnostics to improve treatment outcomes for cancer patients using our proprietary technology to detect clinically actionable mutations and quantitatively monitor cell-free DNA in urine and/or blood.patient response to therapy. On March 15, 2017, we announced the licensing of PCM-075, a PLK1 inhibitor, from Nerviano. We have a supplier agreement with NerPharMa, S.r.l., a pharmaceutical manufacturing company and a subsidiary of Nerviano, to manufacture drug product for PCM-075. The agreement covers the clinical and commercial supply of 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 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 in patients with advanced metastatic solid tumors and we received notification from the U.S. Food and Drug Administration (“FDA”) that our 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 in combination with select chemotherapeutics and targeted agents used in many hematologic and solid cancers, including AML, 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 leveraging our proprietary molecular diagnostic technologyone of the patent holders of NPM1 for the detectiondiagnosis and monitoring of cell-free DNA originating from diseased cell death that can be isolated and detected from urine, blood, and tissue samples to improve disease management. 
These genetic materials are also collectively referred to as “cell-free nucleic acids,” which result when cells in the body die and release their DNA contents into the bloodstream. The circulating fragments of genetic material are eventually filtered through the kidneys and therefore, can be detected and measured in urine and blood. Cell-free nucleic acids can be used as genetic markers of disease. As such, the contents of urine or blood samples represent systemic liquid biopsies that can allow for simple, noninvasive or minimally invasive sample collection methods. Circulating tumor DNApatients. NPM1-mutated AML is a subtypegenetic marker in leukemia and accounts for approximately one-third of cell-free DNA,all AML patients. We plan to use our PCM technology to profile other dominant AML markers, such as FLT3, DNMT3A, NRAS, and represents the mutant cell-free DNA that we use to detect and monitor cancer mutations.
Our fundamental ctDNA diagnostic platform, also known as Precision Cancer Monitoring®, (“PCM”) is protected by a strong intellectual property portfolio. We have developed significant intellectual property around cell-free nucleic acids in urine, the extraction of cell-free nucleic acids from urine,KIT, as well as novel assay designs, particularly our proprietary non-naturally occurring primers. Through this proprietary technology, we believe that we are at the forefront of a shift in the way diagnostic medicine is practiced, using simple, noninvasive or minimally invasive sampling and analysis of nucleic acids, which we believe will ultimately lead to more effective treatment monitoring, better management of serious illnesses such as cancer, and the ability to detect the recurrence of cancer earlier. As of September 30, 2016, our intellectual property portfolio consists of 101 issued patents worldwide and over 70 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 that our proprietary PCM platform is uniquely positioned to address a high unmet clinical need in the field of oncology. Our PCM platform is designed to offer improved cancer monitoring by tracking and analyzing levels of cell-free DNA from either urine or blood samples, and is intended to provide important clinical information beyond the current standard of care. Using urine as a sample, our cancer monitoring technology enables more frequent, noninvasive monitoring of cancer mutation status, disease progression and disease recurrence. Our research and development efforts were made commercially feasible following improved Next Generation Sequencing (“NGS”) technologies which are now available at a significantly lower cost. This, combined with our extensive patent portfolio around cell-free DNA in urine, gives us a competitive advantage to leverage an emerging trend toward monitoring cancer using ctDNA as a marker of disease status. Our proprietary sample preparation process forms the basis of our PCM platform. It includes a novel technology for the extraction and isolation of ctDNA from either a urine or blood sample, proprietary non-naturally occurring primers to enrich the sample for mutant alleles, and the ability to detect nucleic acids of interest using one of several leading gene sequencing technologies such as NGS or droplet digital Polymerase Chain Reaction ("PCR"). We believe that our quantitative ctDNA detection and monitoring platform offers industry-leading sensitivity, featuring single nucleic acid molecule detection.
Our PCM platform is poised to overcome a significant clinical dilemma in the area of cancer treatment. Recent scientific evidence supports the molecular basis of cancer, and has resulted in a paradigm shift in the way cancer is treated. Researchers and clinicians are now focused on specific mutations that are believed to be the molecular drivers of cancer, and, as

a result, there is a trend in the pharmaceutical research community toward developing targeted therapies. As such, there is a need for oncologists to have an ability to track the mutational status of their patients' tumor, including a given patient’s response to treatments that are designed to target driver cancer mutations. Current monitoring tools such as imaging procedures, tissue biopsy, and circulating tumor cells are insufficient to meet the challenge of monitoring cancer mutations. Cancer imaging provides a rough indication of tumor size, but provides no information to oncologists regarding mutational status which is important for the use of molecular targeted therapies. Tissue biopsy usually involves a major surgical procedure and, in many cases, is not repeatable as there are limitations related to tissue access for serial biopsies. In some cases, biopsies may not be feasible, significantly increasing the need to determine mutational status using an alternative method. In addition, tumor heterogeneity can create challenges, as the surgeon may not obtain the proper tissue from the tumor sample. With circulating tumor cells, which are typically measured using blood tests, sensitivity is low, and such tests are technically difficult and can be expensive.
While an improvement over chemotherapy in many cases, targeted drug therapies are not without issues, such as their high cost and potential side effects. In order to measure effectiveness of these therapies, repeated monitoring is neededPLK1 enzymatic activity to potentially identify patients most likely to respond to PCM-075 and imaging and serial biopsies have their challenges or may not be optimal. If resistance develops to a targeted cancermeasure patient therapy fast and accurate detection of emerging or changing cancer mutation status has potential to provide critical information early. Our PCM platform provides a novel solution for early detection of cancer progression using urine, a noninvasive, plentiful sample source. We continue to generate positive data supporting the clinical utility of our technology to monitor cancer using ctDNA.response.

Our accumulated deficit through September 30, 20162017 is $139,561,491.$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 2016,2017, we have advanced our business with the following activities:

Entered into preferred provider agreementsAnnounced preclinical research demonstrating synergy of PCM-075 with Blue Cross Blue Shield Illinois, Stratose, Inc., Multiplan, Inc., Three Rivers Provider Network, Fortified Provider Network, FedMed, Inc., American’s Choice Provider Network, and Galaxy Health Network. These combined agreements represent in-network coverage for approximately 168 million covered lives.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.
Presented

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 resultsconducted 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 2016 American Association forDuke VAMC, Dr. Filip Janku, of City of Hope Cancer Research (“AACR”) Annual Meeting that demonstrated ctDNA assay performance for detectionCenter, and monitoring KRAS mutations in urine from patients with advanced cancers.

Appointed William J. Welch, as our Chief Executive Officer, after announcingDr. David Berz, of the departure of Matthew Posard, Chief Commercial OfficerBeverly Hills Cancer Center. Dr. Cortes and the termination of Antonius Schuh and Stephen Zaniboni as our previous CEO and CFO, respectively.

Presented clinical study results for our Trovera™ ctDNA tests at the 2016 ASCO Annual Meeting. Results demonstrated highly sensitive detection of EGFR T790M mutations and validated urine ctDNA testing as an alternative to tissue and plasma.

Entered into a clinical collaboration with the University of Michigan for monitoring and early detection of pancreatic cancer utilizing the TroveraTMKRAS ctDNA liquid biopsy test.

Entered into a clinical collaboration with the USC Norris Comprehensive Cancer Center to standardize the use of TroveraTM ctDNA liquid biopsy test in patient care.

Published study resultsDr. Silberman have extensive experience in the Journaldevelopment of Thoracic Oncology that demonstratenovel therapies for the treatment of hematologic cancers. Dr. Cortes will serve as the Principal Investigator for the Phase 1b/2 clinical and analytical validity of the Trovera™ urine and blood-based liquid biopsy tests to assess EGFR T790M mutational status. The data shows that the Trovera™ test successfully identifies EGFR mutations, and has high concordance with tumor tissue.trial in AML.

Presented clinical study results for our Trovera™ tests at the 3rd Annual Precision Medicine Congress. The presentation highlighted Trovera'sTM clinical utility in identifying driver mutations as well as the potential benefits of liquid biopsies, including: patient response to therapy, progression monitoring, and early detection.

Entered into a partnershiplicense agreement with the Pancreatic Cancer Action Network (PanCAN)Nerviano that grants us exclusive global development and commercialization rights to be the liquid biopsy provider for Precision Promise--the first large-scale precision medicine trial designedNMS-1286937, which we refers to transform careas PCM-075.  PCM-075 is an oral, investigative drug and treatment for patients with pancreatic cancer.


Published study results in Experimental Hematology & Oncology that illustrates the clinical utility of using Trovera™ urine liquid biopsy to confirm the presence of EGFR T790M mutational status in a patient with late-stage non-small cell lung cancer. The study concluded that ctDNA analysis should be considered a valuable diagnostic tool in treatment decision-making.

Invited to present four abstracts at the International Associationhighly-selective PLK 1 inhibitor for the Studytreatment of Lung Cancer's (IASLC) 17th World Conference on Lung Cancer. The presentation will focus on the clinical utility of Trovera™ in detection and monitoring of the EGFR T790M resistance mutation in non-small cell lung cancer. The presentation will also include first health outcomes and a total cost of care analysis, demonstrating that a urine-testing strategy shows improved cost-savings and patients' experiences compared to a tissue-testing strategy.

Invited to present at the 31st International Papillomavirus Conference. Two abstracts will be presented. The first demonstrates clinical performance of urine and cervical samples in a Chinese screening population. These results support the utility of urine testing for cervical cancer screening among this population. The second abstract describes the analytical performance of the Trovagene HPV-UR urine test.AML.

Our productdrug 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 bringingdeveloping new diagnostic productsdrug candidates to market, including the long duration of clinical testing, the specific performance of proposed products under stringent clinical trial protocols, and/or Clinical Laboratory Improvement Amendments (“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 September 30, 2016.2017.
 
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, 2015,2016, filed with the SEC on March 10, 2016.15, 2017. There have been no changes to our critical accounting policies since December 31, 2015.2016.

RESULTS OF OPERATIONS
 
Three Months Ended September 30, 20162017 and 20152016
 
Revenues
 
Our total revenues were $89,114$123,329 and $57,327$89,114 for the three months ended September 30, 20162017 and 2015,2016, respectively. The components of our revenues were as follows:
 
Three Months Ended September 30,Three Months Ended September 30,
2016 2015 Increase (Decrease)2017 2016 Increase (Decrease)
Royalties$47,236
 $51,301
 $(4,065)$58,779
 $47,236
 $11,543
Diagnostic services37,978
 6,026
 31,952
58,119
 37,978
 20,141
Clinical research services$3,900
 $
 3,900
6,431
 3,900
 2,531
Total revenues$89,114
 $57,327
 $31,787
$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 tests billed and payments received werewas higher in 20162017 as compared to the same period in the prior year. Revenue from clinical research services consists primarily 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 wasis recognized when supplies wereand/or test results are delivered. There was no such revenuewere more sales of clinical research services for the three months ended September 30, 2015.2017 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, we expect our diagnostic service revenue from diagnostic services to increase in future periods, but as the revenue recognition is based on cash receipts, the timing of these revenues is also uncertain.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 $424,559$473,202 for the three months ended September 30, 2016,2017, compared to $173,537$424,559 in the same period of 2015.2016. Cost of revenues mainly 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 three months ended September 30, 2017 compared to the same period of last year is mainly due to the 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. Gross margins areperiod which could result in negative as we begin to build test volume to cover costs associated with running our diagnostic tests as well as inefficiencies in realizing capacity related issues. Increase in cost of revenues for the three months ended September 30, 2016 compared to the same period of last year is mainly due to the increased volume of tests processed offset by decreased average cost per test.gross margins. 
 

Research and Development Expenses
 
Research and development expenses consisted of the following:
 
Three Months Ended September 30,Three Months Ended September 30,
2016 2015 Increase (Decrease)2017 2016 Increase (Decrease)
Salaries and staff costs$1,407,529
 $1,037,831
 $369,698
$301,919
 $1,407,529
 $(1,105,610)
Stock-based compensation872,792
 342,122
 530,670
219,480
 872,792
 (653,312)
Outside services, consultants and lab supplies1,215,889
 901,662
 314,227
604,140
 1,215,889
 (611,749)
Facilities372,891
 193,926
 178,965
254,681
 372,891
 (118,210)
Travel and scientific conferences51,203
 52,684
 (1,481)28,000
 51,203
 (23,203)
Other17,094
 18,308
 (1,214)6,486
 17,094
 (10,608)
Total research and development$3,937,398
 $2,546,533
 $1,390,865
$1,414,706
 $3,937,398
 $(2,522,692)
 
Research and development expenses increaseddecreased by $1,390,865$2,522,692 to $3,937,398$1,414,706 for the three months ended September 30, 20162017 from $2,546,533$3,937,398 for the same period in 2015. Our2016. 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-four to six, resulting in a decrease of expenses in salaries and staff costs, have increased mainlystock-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 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 internal research and development personnel increasing from twenty-seven to thirty-four and the use of additional consulting and outside services. We utilize clinical studies to provide data that supports our technology for the monitoring of responsiveness to therapy and the status of diseases. The number of samples processed in connection with our research and development clinical studies increased for the three months ended September 30, 2016 as compared to the same period in 2015. We expect research and development expenses toexpansion into oncology therapeutics; however, other costs may increase as we enter into additional collaborations, and complete the development of our urine collection and DNA extraction kits and multi-plex panels.

PCM-075.

Selling and Marketing Expenses
 
Selling and marketing expenses consisted of the following:
 
Three Months Ended September 30,Three Months Ended September 30,
2016 2015 Increase (Decrease)2017 2016 Increase (Decrease)
Salaries and staff costs$1,427,254
 $681,421
 $745,833
$158,097
 $1,427,254
 $(1,269,157)
Stock-based compensation476,865
 225,892
 250,973
118,434
 476,865
 (358,431)
Outside services and consultants441,699
 218,582
 223,117
51,717
 441,699
 (389,982)
Facilities112,573
 70,665
 41,908
51,388
 112,573
 (61,185)
Trade shows, conferences and marketing243,692
 432,123
 (188,431)31,017
 243,692
 (212,675)
Travel212,375
 157,163
 55,212
54
 212,375
 (212,321)
Other26,404
 12,417
 13,987
9,220
 26,404
 (17,184)
Total sales and marketing$2,940,862

$1,798,263

$1,142,599
$419,927

$2,940,862

$(2,520,935)
 
Selling and marketing expenses increaseddecreased by $1,142,599$2,520,935 to $2,940,862$419,927 for the three months ended September 30, 20162017 from $1,798,263$2,940,862 for the same period in 2015.2016. The overall decrease in selling and marketing expenses was primarily due to our strategic restructuring activities. During the three months ended September 30, 20162017 we increaseddecreased the number of our field sales, customer support and marketing personnel, bringing our average headcount to twenty-twotwo from fourteentwenty-two in the same period of the prior year. These additions to our commercial team support our salesAs a result, costs associated with selling and marketing activities resulting in the increase in salaries and staffas well as personnel related costs and stock-based compensation. The increase in outside services and consultants is due to our utilization of outside marketing consultants and agents for targeted marketing activities such as website design, product branding and printing services.were decreased accordingly. We expect our sellingdecreases in personnel and marketing expenses to change based onrelated costs as a result of the composition of commercial team members that are focused on increasing market acceptance of our commercially available tests and the commercial introduction of future product offerings, such as our urine collection and DNA extraction kits.reduction in force.
 

General and Administrative Expenses
 
General and administrative expenses consisted of the following:
 
Three Months Ended September 30,Three Months Ended September 30,
2016 2015 Increase (Decrease)2017 2016 Increase (Decrease)
Personnel and outside services costs$1,136,266
 $879,722
 $256,544
$1,450,261
 $1,136,266
 $313,995
Board of Directors’ fees122,187
 108,612
 13,575
120,085
 122,187
 (2,102)
Stock-based compensation437,075
 348,127
 88,948
1,067,633
 437,075
 630,558
Legal and accounting fees695,061
 286,312
 408,749
595,194
 695,061
 (99,867)
Facilities and insurance149,921
 152,714
 (2,793)291,547
 149,921
 141,626
Travel47,769
 97,106
 (49,337)14,185
 47,769
 (33,584)
Fees, licenses, taxes and other122,503
 75,953
 46,550
120,682
 122,503
 (1,821)
Total general and administrative$2,710,782

$1,948,546
 $762,236
$3,659,587

$2,710,782
 $948,805
 
General and administrative expenses increased by $762,236$948,805 to $2,710,782$3,659,587 for the three months ended September 30, 2016,2017, from $1,948,546$2,710,782 for the same period in 2015.2016. The overallsignificant components of the increase waswere primarily due to the increase of personnel and outside services costs and legal and accounting fees. The increase ofin personnel and outside services cost is primarily dueand stock-based compensation. In August 2017, a total of 745,392 shares of immediately vested RSA were granted to an increase in generalour CEO. Per the agreement, the CEO’s income taxes associated with the RSA were also paid by our Company. Therefore, personnel costs and administrative employees, an increase in investor relations activities as our investor base has grown, and increased services related to information technology to support our overall headcount growth. The increase in legal and accounting fees primarily resulted from the lawsuit against the Company’s former CEO and CFO. Stock-basedstock-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. We expect ourexpenses were increased. Our general and administrative costs may increase in future periods in order to increasesupport fundraising activities and general business activities as our commercial operationswe continue to develop and research and development teams grow and if we need to retain additional legal resources.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 $46,472 restructuring benefit for the three months ended September 30, 2017 was primarily due to certain employee termination costs expensed was less than estimated.

Net interestInterest Expense
 
Net interest expense was $354,993$16,473 and $335,359$354,993 for the three months ended September 30, 20162017 and 2015,2016, respectively. The increasedecrease of net interest expense is primarily due to an increasea decrease in interest expense, offset by an increase in interest income of approximately $62,000. This increase is due to the investment of a portionresulting from pay-off of our cash and cash equivalents in short-term investments which have a higher average yield as well as overall higher average cash and investment balances during the three months ended September 30, 2016 as compared to the same period of the prior year.$15.0 million term loan. We expect net interest expense to increasedecrease as a result of repayment of our debt refinancing and as our average cash and investment balances decrease.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 September 30, 2016,2017, the derivative financial instruments - warrants liabilities were revalued to $2,622,243,$2,037,712, resulting in a decreasean increase in value of $88,208$1,686,850 from June 30, 2016,2017, 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 $4.53 at June 30, 2016 to $4.49 at September 30, 2016 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 instrumentswarrants 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 September 30,Three Months Ended September 30,
2016 2015 Increase 2017 2016 Increase (Decrease)
Net loss attributable to common shareholders$(10,197,332) $(2,741,889) $7,455,443
$(4,298,026) $(10,197,332) $(5,899,306)
Net loss per common share — basic$(0.34) $(0.10) $0.24
$(0.12) $(0.34) $(0.22)
Net loss per common share — diluted$(0.34) $(0.23) $0.11
$(0.12) $(0.34) $(0.22)
          
Weighted average shares outstanding — basic30,339,774
 28,560,211
 1,779,563
36,465,672
 30,339,774
 6,125,898
Weighted average shares outstanding — diluted30,339,774
 29,128,235
 1,211,539
36,465,672
 30,339,774
 6,125,898
 
The $7,455,443 increase$5,899,306 decrease in net loss attributable to common shareholders and the $0.24 increase$0.22 decrease in basic net loss per share was primarily the result of an increasea decrease in operating expenses of $3,546,722, and a decrease in gain from the change in fair value of derivative financial instruments - warrants of $3,929,004$4,092,651 for the ninethree months ended September 30, 20162017 compared to the same period in the prior year.
 
Nine Months Ended September 30, 20162017 and 20152016
 
Revenues
 
Our total revenues were $313,000$320,378 and $233,643$313,000 for the nine months ended September 30, 20162017 and 2015,2016, respectively. The components of our revenues were as follows:

Nine Months Ended September 30,Nine Months Ended September 30,
2016 2015 Increase (Decrease)2017 2016 Increase (Decrease)
Royalties$207,869
 $222,931
 $(15,062)$169,415
 $207,869
 $(38,454)
Diagnostic services69,558
 10,712
 58,846
142,482
 69,558
 72,924
Clinical research services35,573
 
 35,573
8,481
 35,573
 (27,092)
Total revenues$313,000
 $233,643
 $79,357
$320,378
 $313,000
 $7,378
 
The $15,062$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 nine months ended September 30, 20162017 as compared to the same period in the prior year. Revenue from clinical research services consists primarily 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. There was no such revenue for the nine months ended September 30, 2015.

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. We expectOur diagnostic service revenue may be impacted by our revenue from diagnostic services to increase in future periods, but as the revenue recognition is based on cash receipts, the timing of these revenues is also uncertain.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 $1,143,293$1,427,831 for the nine months ended September 30, 2016,2017, compared to $429,992$1,143,293 in the same period of 2015.2016. 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 nine months ended September 30, 2017 compared to the same period of last year is mainly due to the 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. Gross margins areperiod which could result in negative as we begin to build test volume to cover costs associated with running our diagnostic tests as well as inefficiencies in realizing capacity related issues. Increase in cost of revenues for the nine months ended September 30, 2016 compared to the same period of last year is mainly due to the increased volume of test processed offset by decreased average cost per test.gross margins. 
 

Research and Development Expenses
 
Research and development expenses consisted of the following:

Nine Months Ended September 30,Nine Months Ended September 30,
2016 2015 Increase 2017 2016 Increase (Decrease)
Salaries and staff costs$4,263,595
 $2,679,951
 $1,583,644
$1,468,491
 $4,263,595
 $(2,795,104)
Stock-based compensation1,862,069
 1,054,443
 807,626
798,143
 1,862,069
 (1,063,926)
Outside services, consultants and lab supplies3,837,485
 2,955,738
 881,747
1,456,504
 3,837,485
 (2,380,981)
Facilities1,042,682
 552,259
 490,423
842,196
 1,042,682
 (200,486)
Travel and scientific conferences157,445
 148,766
 8,679
72,901
 157,445
 (84,544)
Other58,600
 37,192
 21,408
Fees, licenses and other2,038,016
 58,600
 1,979,416
Total research and development$11,221,876
 $7,428,349
 $3,793,527
$6,676,251
 $11,221,876
 $(4,545,625)

Research and development expenses increaseddecreased by $3,793,527$4,545,625 to $11,221,876$6,676,251 for the nine months ended September 30, 20162017 from $7,428,349$11,221,876 for the same period in 2015.2016. Our costs have increaseddecreased primarily due to the average number of our internal research and development personnel growingdecreasing from twentythirty-three to thirty-three.eleven. In addition, we purchased additional lab suppliesresearch and development expenses incurred related to clinical samples to support the number ofstudies, samples processed and validated in connection with our research and developmentthe clinical studiescollaborations, as well as the development of our urine collection and DNA extraction kits. We utilize clinical studies to provide data that supports our technology for the monitoring of responsiveness to therapy and the status of diseases. The number of samples processed in connection with our research and development clinical studies increasedlab supplies, decreased for the nine months ended September 30, 20162017 as compared to the same period in 2015. We expect2016 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 enter into additional collaborations or studies and completecontinue the development of our urine collection and DNA extraction kits and multi-plex panels.PCM-075. 

Selling and Marketing Expenses
 
Selling and marketing expenses consisted of the following:

Nine Months Ended September 30,Nine Months Ended September 30,
2016 2015 Increase2017 2016 Increase (Decrease)
Salaries and staff costs$4,266,029
 $1,758,789
 $2,507,240
$977,040
 $4,266,029
 $(3,288,989)
Stock-based compensation1,493,744
 480,006
 1,013,738
550,317
 1,493,744
 (943,427)
Outside services and consultants1,117,368
 654,512
 462,856
219,800
 1,117,368
 (897,568)
Facilities362,339
 210,153
 152,186
220,860
 362,339
 (141,479)
Trade shows, conferences and marketing1,082,883
 1,005,859
 77,024
357,233
 1,082,883
 (725,650)
Travel716,473
 330,399
 386,074
71,865
 716,473
 (644,608)
Other88,614
 69,048
 19,566
45,816
 88,614
 (42,798)
Total sales and marketing$9,127,450
 $4,508,766
 $4,618,684
$2,442,931
 $9,127,450
 $(6,684,519)
 
Selling and marketing expenses increaseddecreased by $4,618,684$6,684,519 to $9,127,450$2,442,931 for the nine months ended September 30, 20162017 from $4,508,766$9,127,450 for the same period in 2015. During the nine months ended September 30, 20162016. The overall decrease in selling and marketing expenses was primarily due to our strategic restructuring activities. As part of our restructuring, we increasedreduced the number of our field sales, customer support and marketing personnel, bringing down our average headcount to twenty-twofive from eleventwenty-two in the same period of the prior year. We also increased utilization of outside marketing consultantsexpect decreases in personnel and agents for targeted marketing activities such as social media engagements and website design services.related costs due to the reduction in force.
 

General and Administrative Expenses
 
General and administrative expenses consisted of the following:

Nine Months Ended September 30,Nine Months Ended September 30,
2016 2015 Increase (Decrease)2017 2016 Increase (Decrease)
Personnel and outside services costs$3,279,860
 $2,582,108
 $697,752
$3,270,134
 $3,279,860
 $(9,726)
Board of Directors’ fees345,240
 339,823
 5,417
347,205
 345,240
 1,965
Stock-based compensation2,487,415
 1,201,929
 1,285,486
1,837,128
 2,487,415
 (650,287)
Legal and accounting fees2,077,585
 855,101
 1,222,484
3,358,411
 2,077,585
 1,280,826
Facilities and insurance551,382
 366,109
 185,273
742,405
 551,382
 191,023
Travel151,355
 206,741
 (55,386)81,106
 151,355
 (70,249)
Fees, licenses, taxes and other290,924
 204,236
 86,688
278,970
 290,924
 (11,954)
Total general and administrative$9,183,761
 $5,756,047
 $3,427,714
$9,915,359
 $9,183,761
 $731,598
 
General and administrative expenses increased by $3,427,714$731,598 to $9,183,761$9,915,359 for the nine months ended September 30, 2016,2017, from $5,756,047$9,183,761 for the same period in 2015. The significant components of the increase were primarily due to the increase of personnel and outside services costs, stock-based compensation and legal fees.2016. The increase of personnel and outside services costs iswas primarily due to an increase in average headcount from six to eleven to supportlegal fees offset by the growth in our research, development and sales and marketing organizations, an increase in investor relations activities as our investor base has grown, and increased services related to information technology to support our overall headcount growth. In January 2016, our former CEO was granted a non-qualified stock option to purchase 350,000 sharesdecrease 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 nine months ended September 30, 2016.stock-based compensation. Legal fees increased primarily as a result of a lawsuit againstlitigation related loss contingency of $2.1 million expensed during the Company’s former CEOnine months ended September 30, 2017. Stock-based compensation, a non-cash expense, will fluctuate based on the timing and CFO,amount of options granted, forfeitures and reviewthe fair value of federalthe 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 state tax regulations with respectis expected to certain executive compensation.

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 nine months ended 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 $967,522$877,741 and $1,100,080$967,522 for nine months ended September 30, 20162017 and 2015,2016, respectively. The decrease of net interest expense is primarily due to an increasea decrease in interest expense of approximately $184,000, resulting from pay-off of our $15.0 million term loan, offset by a decrease in interest income as a result of approximately $193,518, resulting from the investment of a portionliquidation of our cash and cash equivalents in short-term investments which have a higher average yield as well as overall higher average cash and investment balances during the nine months ended September 30, 2016 as compared to the same period of the prior year.investments.

Change in Fair Value of Derivative Financial Instruments - Warrants
 
We have issued warrants that are accounted for as derivative liabilities. As of September 30, 2016,2017, the derivative financial instruments - warrants liabilities were revalued to $2,622,243,$2,037,712, resulting in a decreasean increase in value of $674,834$1,202,772 from December 31, 2015,2016, 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 $5.40 at December 31, 2015 to $4.49 at September 30, 2016 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 instrumentswarrants 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:

Nine Months Ended September 30,Nine Months Ended September 30,
2016 2015 Increase 2017 2016 Increase (Decrease)
Net loss attributable to common shareholders$(30,674,248) $(20,108,424) $10,565,824
$(22,355,494) $(30,674,248) $(8,318,754)
Net loss per common share — basic$(1.02) $(0.80) $0.22
$(0.68) $(1.02) $(0.34)
Net loss per common share — diluted$(1.04) $(0.96) $0.08
$(0.68) $(1.04) $(0.36)
          
Weighted average shares outstanding — basic30,018,841
 25,014,966
 5,003,875
32,826,306
 30,018,841
 2,807,465
Weighted average shares outstanding — diluted30,136,572
 25,204,307
 4,932,265
32,826,306
 30,136,572
 2,689,734
 
The $10,565,824 increase$8,318,754 decrease in net loss attributable to common shareholders and the $0.22 increase$0.34 decrease in basic net loss per share was primarily the result of an increasea decrease in operating expenses of $12,553,226 compared to the same period in the prior year. This increasedecrease was offset by a $674,834 gain from the change in the fair valueloss on extinguishment of derivative financial instruments - warrants for the nine months ended September 30, 2016, as compared to a loss from the change in the fair valuedebt of derivative financial instruments - warrants of $1,105,270 for the same period in the prior year.$1.7 million.

LIQUIDITY AND CAPITAL RESOURCES
 
As of September 30, 2016,2017, we had $22,569,107$7,434,298 in cash and cash equivalents. Net cash used in operating activities for the nine months ended September 30, 20162017 was $22,034,998,$19,949,652, compared to $15,310,089$22,034,998 for the nine months ended September 30, 2015.2016. Our use of cash was primarily a result of the net loss of $30,656,068$22,337,314 for the nine months ended September 30, 2016,2017, adjusted for non-cash items related to stock-based compensation of $5,942,392, accretion$3,117,364, loss on extinguishment of final fee premium of $266,423, amortization of discount on debt of $105,710,$1,655,825, impairment loss of $485,000, depreciation and amortization of $693,485, amortization of premiums on short-term investments of $61,719, deferred rent of $133,378, interest income accrued on short-term investments of $10,122,$956,995, and the gain from the change in fair value of derivative financial instruments - warrants of $674,834.$2,012,747. The changes in our operating assets and liabilities consisted of higherlower accounts payable and accrued expenses, an increase in prepaid expenses, and a decrease in accounts receivable and other assets.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 used inprovided by investing activities was $25,249,392$23,925,535 during the nine months ended September 30, 2016,2017, compared to $1,256,988$25,249,392 used in investing activities for the same period in 2015.2016. Investing activities consisted of net purchases for capital equipment that used $797,781 in cash, and net purchase of short-term investments of $24,451,611.
Net cash provided by financing activities was $2,361,994 during the nine months ended September 30, 2016,2017 consisted of net sales and maturities of short-term investments of $24,061,786 offset by net purchases for capital equipment of $136,251.
Net cash used in financing activities was $10,447,842 during the nine months ended September 30, 2017, compared to $63,423,076$2,361,994 provided in financing activities for the same period in 2015.2016. Financing activities during the nine months ended September 30, 20162017 related primarily to the sale of our common stock through a controlled equity offering and net paymentpay-off of long-term debt resulting in debt extinguishment offset by

borrowings under equipment line the sale of credit. Financingcommon stock, while financing activities during the same period of the prior year consisted primarily of proceedssales of common stock offset by repayment of long-term debt. On June 1, 2017, we received a Notice of Event of Default from the salelenders 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 common stock in underwritten public offerings.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 September 30, 2016,2017, and December 31, 2015,2016, we had working capital of $41,412,835$3,469,622 and $60,179,971,$31,152,936, respectively. As
On October 25, 2017, we filed a registration statement on Form S-1 with the SEC for a best efforts public offering of October 31, 2016,up to $17.5 million of common stock and warrants. H.C. Wainwright & Co. is acting as placement agent.

Based on our workingcurrent business plan and assumptions, we expect to continue to incur significant losses and require significant additional capital was $52.3 million.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 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 and ramp up of our sales and marketing function. We will be required to raise additional capital during 2017 to complete the development and commercialization of current product candidates, to fund the potential working capital deficit and to continue to fund operations at our current cash expenditure levels.programs. To date, our sources of cash have been primarily limited to the sale of equity securities and debentures and a venture capital loan.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 (i) significantly delay, scale back or discontinue the development and/or commercialization of one or more product candidates, all of product candidates; (ii)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 (iii)(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 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 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.

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, 2015.2016.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK
 
Interest Rate Risk
 
Our primary exposure to market risk due tois 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 September 30, 2017. Changes in interest rates relates tocould affect the increase or decreaseamounts of interest that we pay in the valuefuture.

Our cash and cash equivalent primary consists of debt securities indeposits, and money market deposits managed by commercial banks as of September 30, 2017. The goals of our short-term investment portfoliopolicy are preservation of capital, fulfillment of liquidity needs and fiduciary control of cash and investments.

Our investments are in short-term money marketable funds, as well as interest expense under our equipment line of credit.

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 or illiquidity,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.

Under our current policies, we do not use interest rate derivative instruments to manage exposure to interest rate changes. We attempt to increase the safety and preservation of our invested principal funds by limiting default risk, market risk, and reinvestment risk. We mitigate default risk by investing in investment grade securities. Changes in interest rates over time will increase or decrease our interest income.

Borrowings under the Company’s equipment line of credit bear interest at floating rates. Changes in interest rates could affect the amounts of interest that we pay in the future.
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. GainsIn 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 from foreign currency transactions are included in other expense (income), net.to us.
 
Effects of Inflation
 
We do not believe that inflation and changing prices during the nine months ended September 30, 20162017 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 CEOprincipal executive and principal financial officer concluded that our disclosure controls and procedures were effective as of September 30, 20162017 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 September 30, 20162017 that materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.


PART II.  OTHER INFORMATION

ITEM 1. LEGAL PROCEEDINGS
 
We are not a party to any pending legal proceeding, nor is our property the subject of a pending legal proceeding, that is not in the ordinary course of business or otherwise materialSee Note 9 to the financial conditionunaudited Condensed Consolidated Financial Statements for a summary of our business, except for the following:  On March 28, 2016 we filed a complaint against Dr. Schuh and Mr. Zaniboni, for, among other things, breach of fiduciary duty.  The complaint was filed in the Superior Court of the State of California for the County of San Diego.  We are alleging that Dr. Schuh and Mr. Zaniboni failed to present a lucrative corporate opportunity to us concerning promising new therapeutics in the field of precision medicine and instead took that opportunity for their own personal benefit.  The complaint asks that Dr. Schuh and Mr. Zaniboni be required to turn over their interests in these new therapeutics to us. The parties are currently engaged in the discovery process.legal proceedings.

On April 29, 2016, a complaint was filed against William Welch, our CEO, and our company by Pathway Genomics Corporation alleging, among other things, breach of contract and intentional interference with contractual relations. We believe the complaint is unfounded, and consists largely of baseless speculation that is contrary to fact. We plan to vigorously defend against these allegations. The parties are currently engaged in the discovery process.
ITEM 1A. RISK FACTORS
 
There have been no material changes from the risk factors disclosed in our Form 10-K for the year ended December 31, 2015,2016, Form 10-Q for the periods ended March 31, 2017, and Form 10-Q for the periods ended June 30, 2016.
2017, except for the following:

Our financial statements include an explanatory paragraph that expresses substantial doubt about our ability to continue as a going concern, indicating the possibility that we may not be able to operate in the future.

Primarily as a result of our losses incurred to date, our expected continued future losses, and 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 shares of our common stock or obtaining alternate financing.

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

None.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES

None.

ITEM 4. MINE SAFETY DISCLOSURES

Not applicable.

ITEM 5. OTHER INFORMATION

None.

ITEM 6. EXHIBITS
 
Exhibit
Number
 Description of Exhibit
   
31.1 
   
 
   
101 
Financial statements from the quarterly report on Form 10-Q of the Company for the quarter ended September 30, 2016 filed on November 9, 2016, formatted in Extensible Business Reporting Language (XBRL): (i) the Condensed Consolidated Statements of Operations, (ii) the Condensed Consolidated Balance Sheets, (iii) the Condensed Consolidated Statements of Cash Flows and (iv) the Notes to the Condensed Consolidated Financial Statements tagged as blocks of text.XBRL Instance Document


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.
   
November 9, 20162017By:/s/ William J. Welch
  William J. Welch
  Chief Executive Officer (Principal Executive Officer and Principal Financial Officer)


31