10-Q

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-Q

(Mark One)

ý QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE

SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended September 30, 2015

OR

¨ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE

SECURITIES EXCHANGE ACT OF 1934

For the transition period from to

Commission file number: 001-36538

ROKA BIOSCIENCE, INC.

(Exact name of registrant as specified in its charter)

DELAWARE	27-0881542
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

20 Independence Boulevard

Warren, NJ, 07059

(Address of principal executive offices)(Zip code)

(908) 605-4700

(Registrant’s telephone number, including area code)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  ý    No  ¨

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  ý    No  ¨

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

Large accelerated filer	¨	Accelerated filer	¨
Non-accelerated filer	¨  (Do not check if a smaller reporting company)	Smaller reporting company	ý

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

The number of shares outstanding of the registrant’s common stock, par value of $0.001 per share, as of November 9, 2015 was 18,069,968.

ROKA BIOSCIENCE, INC

REPORT ON FORM 10-Q

For the Quarterly Period Ended September 30, 2015

	PAGE
PART I. FINANCIAL INFORMATION
Item 1. Financial Statements (unaudited)
a) Condensed Balance Sheets as of September 30, 2015 and December 31, 2014	3
b)  Condensed Statements of Operations and Comprehensive Loss for the three and nine months ended September 30, 2015 and September 30, 2014	4
c)  Condensed Statements of Convertible Preferred Stock and Stockholders’ Equity (Deficit) as of and for the nine months ended September 30, 2015 and the year ended December 31, 2014	5
d) Condensed Statements of Cash Flows for the nine months ended September 30, 2015 and September 30, 2014	6
e) Notes to Condensed Financial Statements	7
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations	20
Item 3. Quantitative and Qualitative Disclosures About Market Risk	32
Item 4. Controls and Procedures	32
PART II. OTHER INFORMATION
Item 1. Legal Proceedings	32
Item 1A. Risk Factors	33
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds	34
Item 6. Exhibits	34
SIGNATURES	35

2

PART I – FINANCIAL INFORMATION

ROKA BIOSCIENCE, INC.

Condensed Balance Sheets

(unaudited)

(amounts in thousands except share and per share data)

	September 30,			December 31,
	2015			2014
ASSETS
Current Assets:
Cash and cash equivalents	$	6,949		$	7,503
Short-term marketable securities	30,946			36,231
Trade accounts receivable, net of $0 allowance for doubtful accounts	681			670
Inventories	4,366			4,930
Prepaid expenses and other current assets	1,975			2,115
Total current assets	44,917			51,449
Long-term marketable securities	—			13,366
Property and equipment, net	10,524			12,186
Intangible assets, net	23,345			26,156
Goodwill	360			360
Other assets	264			262
Total assets	$	79,410		$	103,779
LIABILITIES AND STOCKHOLDERS’ EQUITY
Current Liabilities:
Accounts payable	$	413		$	1,134
Short-term deferred payments	1,660			695
Notes payable, current	9,811			9,910
Accrued expenses and other current liabilities	2,723			2,125
Total current liabilities	14,607			13,864
Deferred payments	10,187			10,457
Deferred tax liabilities	49			49
Other long-term liabilities	321			334
Total liabilities	25,164			24,704
Commitments and Contingencies (See Note 11)
Common stock, $0.001 par value:
500,000,000 shares of Common Stock authorized; 18,077,197 shares issued and 18,070,878 shares outstanding, respectively at September 30, 2015; 17,660,432 shares issued and 17,658,373 shares outstanding at December 31, 2014	18			18
Additional paid-in capital	213,846			212,069
Treasury stock, at cost: 6,319 shares at September 30, 2015 and 2,059 shares at December 31, 2014	(22		)	(8		)
Accumulated deficit	(159,596		)	(133,004		)
Total stockholders’ equity	54,246			79,075
Total liabilities and stockholders’ equity	$	79,410		$	103,779

The accompanying notes are an integral part of these financial statements

3

ROKA BIOSCIENCE, INC.

Condensed Statements of Operations and Comprehensive Loss

(unaudited)

(amounts in thousands except share and per share data)

	Three Months Ended September 30,						Nine Months Ended September 30,
	2015			2014			2015			2014
Revenue	$	1,508		$	1,483		$	4,484		3,701
Operating expenses:
Cost of revenue	1,672			2,578			5,391			5,416
Research and development	2,058			1,922			5,823			5,991
Selling, general and administrative	4,924			4,618			15,453			14,214
Amortization of intangible assets	937			738			2,811			822
Total operating expenses	9,591			9,856			29,478			26,443
Loss from operations	(8,083		)	(8,373		)	(24,994		)	(22,742		)
Other income (expense):
Change in fair value of financial instruments	—			(223		)	—			(785		)
Interest income (expense), net	(404		)	(476		)	(1,588		)	(1,244		)
Loss before income taxes	(8,487		)	(9,072		)	(26,582		)	(24,771		)
Income tax provision (benefit)	4			11			10			28
Net loss and comprehensive loss	$	(8,491	)	$	(9,083	)	$	(26,592	)	$	(24,799	)
Net Loss per Common Share:
Basic and diluted	$	(0.49	)	$	(0.64	)	$	(1.54	)	$	(4.78	)
Weighted average common shares outstanding used in computing net loss per common share:
Basic and diluted	17,303,490			14,153,715			17,262,033			5,188,516

The accompanying notes are an integral part of these financial statements

4

ROKA BIOSCIENCE, INC.

Condensed Statement of Convertible Preferred Stock and Stockholders’ Equity (Deficit)

(unaudited)

(amounts in thousands except share and per share data)

	Preferred Stock					Common Stock				Treasury Stock			Additional Paid-in Capital		Accumulated Deficit			Total
	Shares		Amount			Shares		Amount
Balance at December 31, 2013	114,737,351		$	127,797		1,185,065		$	8	$	—		$	19,422	$	(100,774	)	$	(81,344	)
Series E convertible preferred stock issuance costs	—		(99		)	—		—		—			—		—			—
Stock-based compensation expense	—		—			—		—		—			1,019		—			1,019
Issuance of common stock from initial public offering, net of underwriters’ discounts and issuance costs	—		—			5,000,000		5					53,209		—			53,214
Conversion of convertible preferred stock into Common Stock	(114,737,351	)	(127,698		)	10,494,557		4		—			127,694		—			127,698
Reclassification of warrants to purchase redeemable convertible preferred stock into warrants to purchase Common Stock	—		—			—		—		—			1,364		—			1,364
Issuance of common stock upon exercise of option in amended license agreement	—		—			865,063		1		—			9,091		—			9,092
Issuance of restricted shares to employees, net of shares withheld for taxes	—		—			(2,059	)	—		(8		)	—		—			(8		)
Exercise of options for Common Stock	—		—			115,747		—		—			270		—			270
Net loss	—		—			—		—		—			—		(32,230		)	(32,230		)
Balance at December 31, 2014	—		$	—		17,658,373		$	18	$	(8	)	$	212,069	$	(133,004	)	$	79,075
Issuance of restricted shares to employees, net of shares withheld for taxes	—		—			370,766		—		(14		)	—		—			(14		)
Issuance of Warrants for Common Stock													100					100
Exercise of options for Common Stock	—		—			41,739		—		—			77		—			77
Stock-based compensation expense	—		—			—		—		—			1,600		—			1,600
Net loss	—		—			—		—		—			—		(26,592		)	(26,592		)
Balance at September 30, 2015	—		—			18,070,878		$	18	$	(22	)	$	213,846	$	(159,596	)	$	54,246

The accompanying notes are an integral part of these financial statements

5

ROKA BIOSCIENCE, INC.

Condensed Statements of Cash Flows

(unaudited)

(amounts in thousands)

	Nine Months Ended September 30,
	2015			2014
Cash flows from operating activities
Net loss	$	(26,592	)	$	(24,799	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	4,543			2,690
Change in fair value of financial instruments	—			785
Loss on disposal of property and equipment	—			98
Provisions for inventory	374			991
Share-based compensation expense	1,600			765
Non-cash interest expense	1,138			800
Changes in operating assets and liabilities:
Accounts receivable	(154		)	(549		)
Inventories	189			(2,005		)
Prepaid expenses and other assets	607			492
Accounts payable and accrued expenses	—			(397		)
Deferred taxes	—			3,135
Other liabilities	(12		)	(2		)
Net cash used in operating activities	(18,307		)	(17,996		)
Cash flows from investing activities
Purchases of property and equipment	(165		)	(199		)
Proceeds from sale of property and equipment	71			60
Purchase of marketable securities	(9,856		)	—
Proceeds from maturities of marketable securities	28,040			—
Payment pursuant to amended license agreement and option exercise	—			(10,500		)
Net cash provided by (used in) investing activities	18,090			(10,639		)
Cash flows from financing activities
Net proceeds from issuance of convertible preferred stock and warrants	—			(99		)
Net proceeds from issuance of debt and warrants	4,950			5,000
Principal repayments	(5,350		)	—
Proceeds from exercise of stock options	77			270
Restricted shares withheld for taxes	(14		)	—
Proceeds from issuance of common stock, net of issuance costs	—			53,585
Net cash provided by financing activities	(337		)	58,756
Net change in cash and cash equivalents	(554		)	30,121
Cash and cash equivalents, beginning of period	7,503			32,728
Cash and cash equivalents, end of period	$	6,949		$	62,849

The accompanying notes are an integral part of these financial statements

6

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

1. BUSINESS OVERVIEW

Business

Roka Bioscience, Inc. (“Roka” or “the Company”) is focused on the development and commercialization of molecular assay technologies for the detection of foodborne pathogens. The Company was established in September 2009 through the acquisition of industrial testing assets and technology from Gen-Probe Incorporated, which was subsequently acquired by Hologic, Inc. (herein referred to as “Gen-Probe”).

The Company has limited capital resources, has experienced negative cash flows from operations and has incurred net losses since inception. The Company expects to continue to experience negative cash flows from operations and incur net losses in the near term as it devotes substantially all of its efforts on commercialization of its products and continued product development. The Company’s business is subject to significant risks and its ability to successfully develop, manufacture and commercialize proprietary products is dependent upon many factors which include, but are not limited to, risks and uncertainties associated with the supply of molecular diagnostic instruments (“Atlas instruments”) and materials, product development, manufacturing scale-up, attracting and retaining key personnel, customer acceptance as well as competition.

On July 22, 2014, the Company completed an initial public offering ("IPO") in which it sold 5,000,000 shares of common stock at $12.00 per share, before underwriting discounts. The Company received $53.2 million of net proceeds from the offering after deducting underwriting discounts, commissions and offering expenses. In connection with the closing of the IPO, all shares of the Company’s Class A common stock (“Common A”) and Class B common stock (“Common B”) were converted into a new class of common stock ("Common Stock") on a 1:1 basis and all shares of Series B Convertible Preferred Stock (“Series B”), Series C Convertible Preferred Stock (“Series C”), Series D Convertible Preferred Stock (“Series D”) and Series E Convertible Preferred Stock (“Series E”), collectively referred to as “Convertible Preferred Stock”, were converted into Common Stock at their respective conversion ratios.

The Company will need to raise additional capital through the sale of equity and/or debt securities in the future. There is no assurance that the Company will be able to raise needed capital under acceptable terms, if at all. The sale of additional equity may dilute existing shareholders and newly issued shares may contain senior rights and preferences compared to currently outstanding common stock. Issued debt securities may contain covenants and limit the Company’s ability to pay dividends or make other distributions to stockholders. In addition, the Company’s debt agreement contains certain clauses which allow the lenders to require repayment of the debt based on subjective factors regarding the Company’s business and performance if considered a material adverse change by the lender.

Concentration of Suppliers

The Company relies on single source suppliers, including Gen-Probe, for certain components and materials used in its products, including its Atlas Detection Assays. Since the Company’s contracts with these suppliers, including Gen-Probe, do not commit the suppliers to carry inventory or to make available any minimum quantities, the Company may be unable to obtain adequate supplies in a timely manner or on commercially reasonable terms.  If the Company loses such suppliers, or its suppliers encounter financial hardships, the Company may not be able to identify or enter into agreements with alternative suppliers on a timely basis on acceptable terms, if at all. Transitioning to a new supplier could be time consuming, may be expensive, may result in an interruption in the Company’s operations and could affect the performance specifications of the Company’s products. If the Company should encounter delays or difficulties in securing the quality and quantity of materials required for its products, the Company’s ability to manufacture its products would be interrupted which could adversely affect sales.

2. SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Basis of Presentation

The accompanying unaudited condensed financial statements of Roka Bioscience, Inc. have been prepared by the Company in accordance with United States generally accepted accounting principles (“U.S. GAAP”) for interim financial reporting, which do not conform in all respects to the requirements of U.S. GAAP for annual financial statements. The information included in this quarterly report on Form 10-Q should be read in conjunction with the Company’s audited financial statements included in the

7

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

Company’s Annual Report on Form 10-K for the year ended December 31, 2014 filed with the SEC on March 27, 2015 (the “2014 Form 10-K”). Accordingly, these condensed notes to the unaudited financial statements should be read in conjunction with the 2014 audited financial statements and notes thereto prepared in accordance with U.S. GAAP. The unaudited financial statements have been prepared using accounting policies that are consistent with the policies used in preparing the Company’s audited financial statements for the year ended December 31, 2014. The condensed Balance Sheet as of December 31, 2014 was derived from the Company’s audited financial statements, but does not include all disclosures required by accounting principles generally accepted in the United States. The unaudited financial statements reflect all normal and recurring adjustments necessary, if any, for a fair statement of the Company’s financial position and results of operations for the interim periods presented. The results of operations for the three and nine months ended September 30, 2015 are not necessarily indicative of the results to be expected for the year ending December 31, 2015 or for any other future annual or interim period. There have been no changes in the significant accounting policies from those included in the 2014 Form 10-K. However, in order to further clarify the Company's policy with respect to impairment of long-lived assets, below please find a description of such policy.

Impairment of Long-Lived Assets

The Company’s long-lived assets are primarily comprised of intangible assets and property, plant and equipment. The Company evaluates its finite-lived intangible assets and property, plant and equipment, for impairment whenever events or changes in circumstances indicate the carrying value of an asset or group of assets is not recoverable. If these circumstances exist, recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset group to future undiscounted cash flows expected to be generated by the asset group. If the Company’s estimated undiscounted future cash flows are below the asset group’s carrying value, the Company may recognize an impairment charge measured by its fair value.

Common A and Common B Reverse Stock Split

In July 2014, the Company’s board of directors authorized and the Company’s shareholders approved an 11.04:1 reverse stock split of the Company’s Common A and Common B shares, effective on July 3, 2014. In addition, effective on the date of the reverse stock split, the conversion ratio of Convertible Preferred Stock was adjusted by a factor of 11.04 and consequently, each share of Series B, Series C and Series E became convertible into approximately 0.0906 shares of Common Stock and each share of Series D became convertible into approximately 0.0937 shares of Common Stock. As stated in Note 1, all shares of Common A, Common B and Convertible Preferred Stock converted into Common Stock upon the completion of the Company's IPO. The Company’s historical share and per share information have been retroactively adjusted to give effect to this reverse split and corresponding change in conversion ratio.

New Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (“FASB”) or other standard setting bodies and adopted by the Company as of the specified effective date.

In July 2015, the FASB issued ASU No. 2015-11, Simplifying the Measurement of Inventory. This standard amends existing guidance and requires entities to measure most inventory at the lower of cost and net realizable value. This standard is effective for annual reporting periods beginning after December 15, 2016, and early adoption is permitted. This standard is to be applied on a prospective basis and upon adoption, entities must disclose the nature of and reason for the accounting change. The Company is currently in the process of evaluating the impact this new guidance will have on its financial statements.

In April 2015, the FASB issued ASU No. 2015-05, Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Fees Paid in a Cloud Computing Arrangement. This standard provides guidance to customers about whether a cloud computing arrangement includes a software license. If a cloud computing arrangement includes a software license, then the customer should account for the software license element of the arrangement consistent with the acquisition of other software licenses. If a cloud computing arrangement does not include a software license, the customer should account for the arrangement as a service contract. This amendment is effective for annual periods, including interim periods within those annual periods, beginning after December 15, 2015, and early adoption is permitted. The Company has evaluated this new guidance and determined it will not have an impact on the Company's financial statements.

In August 2014, the FASB issued ASU No. 2014-15, Presentation of Financial Statements—Going Concern (Subtopic 205-40): Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern, which is intended to define management’s responsibility to evaluate whether there is substantial doubt about an organization’s ability to continue as a going concern and to provide related footnote disclosures. This ASU provides guidance to an organization’s management, with principles and definitions that are intended to reduce diversity in the timing and content of disclosures that are commonly provided by

8

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

organizations today in the financial statement footnotes. The amendments are effective for annual periods ending after December 15, 2016, and interim periods within annual periods beginning after December 15, 2016, and early adoption is permitted. The Company does not believe this new guidance will have a material impact on its financial statements.

In May 2014, the FASB issued ASU 2014-09, Revenue from Contracts with Customers. This standard outlines a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers and supersedes most current revenue recognition guidance. ASU 2014-09 provides companies with two implementation methods. Companies can choose to apply the standard retrospectively to each prior reporting period presented (full retrospective application) or retrospectively with the cumulative effect of initially applying the standard as an adjustment to the opening balance of retained earnings of the annual reporting period that includes the date of initial application (modified retrospective application). This ASU is effective for annual periods ending after December 15, 2016, and interim periods within annual periods beginning after December 15, 2016. In August 2015, the FASB issued ASU 2015-14, Revenue from Contracts with Customers - Deferral of the Effective Date. This ASU defers the effective date of Update 2014-09 for all entities by one year, requiring the guidance in ASU 2014-09 to be applied for annual reporting periods beginning after December 15, 2017, including interim reporting periods within that reporting period. Additionally, this ASU permits earlier application only as of annual reporting periods beginning after December 15, 2016, including interim reporting periods within that reporting period. The Company is currently in the process of evaluating the impact this new guidance will have on its financial statements.

Adoption of New Accounting Principle

In April 2015, the FASB issued Accounting Standards Update (“ASU”) No. 2015-03, Interest - Imputation of Interest: Simplifying the Presentation of Debt Issuance Costs which is intended to simplify the accounting for and presentation of debt issuance costs. This ASU requires debt issuance costs to no longer be capitalized as an asset on the balance sheet and amortized as a deferred charge, and instead be treated as a direct deduction from the face amount of the note. This guidance is effective for annual reporting periods beginning after December 15, 2015, including interim periods within that reporting period, and early application is permitted. The Company adopted the new guidance beginning in the interim period ended June 30, 2015 and has applied the guidance to its financial statements on a retrospective basis, wherein the balance sheet of each individual period presented has been adjusted to reflect the period-specific effects of applying the new guidance. The application of this new guidance did not have a material impact on the Company's financial statements. There were no cumulative changes to the Statement of Operations and Comprehensive Loss or the Statement of Convertible Preferred Stock and Stockholders’ Equity (Deficit); changes to the Balance Sheet as of December 31, 2014 as a result of this new accounting principle are noted below (amounts in thousands):

	As of December 31, 2014
	Adjusted	As previously reported	Change
Other assets	262	308	(46	)
Total assets	103,779	103,825	(46	)
Notes payable, current	9,910	9,956	(46	)
Total current liabilities	13,864	13,910	(46	)
Total liabilities	24,704	24,750	(46	)
Total liabilities and stockholders' equity	103,779	103,825	(46	)

3. CASH AND CASH EQUIVALENTS

The Company’s entire balance of Cash and cash equivalents as of September 30, 2015 was held in demand accounts with one financial institution, which subjects the Company to significant concentrations of credit risk.

4. MARKETABLE SECURITIES

9

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

As of September 30, 2015 and December 31, 2014, the fair value of held-to-maturity marketable securities by type of security was as follows (amounts in thousands):

	Amortized Cost	Gross Unrealized Holding Gains	Gross Unrealized Holding Losses		Aggregate Fair Value
September 30, 2015
Short-term marketable securities
Debt securities	30,946	3	(13	)	30,936
December 31, 2014
Short-term marketable securities
Debt securities	36,231	2	(36	)	36,197
Long-term marketable securities
Debt securities	13,366	4	(32	)	13,338

Marketable securities held by the Company consist of United States treasury bills, commercial paper, U.S. government-related debt, and corporate debt securities. All short-term marketable securities held by the Company mature within one year and all long-term marketable securities mature after one year but in less than five years from the respective balance sheet date.

5. INVENTORIES

The following table provides details of the Company’s net inventories (amounts in thousands):

	As of September 30,		As of December 31,
	2015		2014
Raw materials	$	1,744	$	1,914
Work in process	—		11
Finished goods	2,622		3,005
	$	4,366	$	4,930

6. PROPERTY AND EQUIPMENT

The following table provides details of the Company’s property and equipment (amounts in thousands):

	As of September 30,			As of December 31,
	2015			2014
Atlas instruments placed with customers	$	4,589		$	3,875
Atlas instruments intended for placement(1)	5,314			6,204
Manufacturing equipment	2,779			2,753
Laboratory equipment	3,026			2,953
Computer and office equipment	1,480			1,469
Leasehold improvements	1,435			1,380
Software	1,142			1,142
Total property and equipment	$	19,765		$	19,776
Less: Accumulated depreciation	(9,241		)	(7,590		)
Total	$	10,524		$	12,186

(1) The Company does not depreciate Atlas instruments prior to the instruments being placed with customers.

As of September 30, 2015 and December 31, 2014, the cost of Atlas instruments, which represents equipment on lease or held for lease, was $8.2 million and $8.9 million, respectively, net of accumulated depreciation of $1.7 million and $1.2 million, respectively.

Expenses for depreciation of property and equipment were incurred as follows (amounts in thousands):

10

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

	For the Three Months Ended September 30,				For the Nine Months Ended September 30,
	2015		2014		2015		2014
Depreciation expense	$	548	$	623	$	1,732	$	1,867

7. INTANGIBLE ASSETS

In June 2014, the Company entered into an amendment to its license agreement with Gen-Probe. Under the amendment, the Company obtained a two-year option to reduce the royalty rate it pays to Gen-Probe in exchange for an option payment of $2.5 million. Upon completion of its IPO in July 2014, the Company exercised its option and issued to Gen-Probe 865,063 shares of common stock valued at $10.51 per share on the issuance date and made a cash payment of $8.0 million. The Company is required to make additional cash payments of $5.0 million on January 1, 2018 and $5.0 million on January 1, 2020.

The aggregate cash and stock payments made to Gen-Probe along with the present value of the two $5.0 million payments described above were recorded as a $26.6 million addition to the Company's intangible technology asset in Intangible assets on the Balance Sheet and will be amortized on a straight-line basis through December 31, 2021, the end of the estimated remaining life of the technology asset. See Note 9 for further details on the additional required future cash payments described above.

Pursuant to the terms of the license agreement amendment, the Company committed to additional future contingent payments, as described in Note 11 below. If made, such additional payments will further reduce the royalty rate the Company pays to Gen-Probe, and will be recorded as additions to the Company's intangible technology asset upon payment and amortized over the estimated remaining life of the technology asset.

The Company assesses its intangible and other long-lived assets for impairment whenever events or other changes in circumstances suggest that the carrying value of an asset group may not be recoverable based on its undiscounted future cash flows. If the Company’s estimated undiscounted future cash flows are below the asset group’s carrying value, the Company may recognize an impairment charge measured by its fair value.

During the third quarter of 2015, the Company prepared revised projections for revenue and expenses, which indicated continued cash flow losses for the Company, and as a result, the Company determined a triggering event had occurred. The Company completed an assessment of the asset group including the intangible asset for recoverability. The recoverability assessment was based upon probability-weighted cash flow estimates resulting from updated revenue and expense projections and an appropriate terminal value. Based on the impairment assessment, the Company determined that the asset group including the intangible asset was not impaired.

The following table summarizes the Company's intangible asset as of the periods presented (amounts in thousands):

	September 30, 2015		December 31, 2014
Intangible asset, gross	28,259		28,259
Accumulated amortization	(4,914	)	(2,103	)
Intangible asset, net	23,345		26,156

8. ACCRUED EXPENSES AND OTHER CURRENT LIABILITIES

The following table provides details of the Company’s accrued expenses (amounts in thousands):

11

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

	As of September 30,		As of December 31,
	2015		2014
Employee related	$	2,016	$	1,116
Professional services	296		235
Other	411		774
Total accrued expenses and other current liabilities	$	2,723	$	2,125

9. DEFERRED PAYMENTS

Gen-Probe supply agreement

In May 2011, the Company entered into a supply agreement with Gen-Probe to purchase Atlas instruments. Pursuant to the terms of the agreement, the Company can defer up to one half of the purchase price for up to 54 months from the date of delivery. The deferred amounts do not bear interest, and the Company has recorded the imputed interest component as a reduction of the deferred payment and as a reduction of the asset cost. The supply agreement provides for variable repayment terms based on a percentage of net sales as defined in the agreement, and the Company has estimated its net sales in determining amounts due for the 54 month term. The following table summarizes the amounts deferred under this agreement (amounts in thousands):

	As of September 30,			As of December 31,
	2015			2014
Current
Deferred payments, gross	$	1,990		$	1,079
Imputed interest	(330		)	(384		)
Deferred payments, net	$	1,660		$	695
Long-term
Deferred payments, gross	$	2,729		$	3,683
Imputed interest	(226		)	(464		)
Deferred payments, net	$	2,503		$	3,219

The Company estimated the interest rate implicit in the extended payment terms by considering the rate at which it could obtain financing of a similar nature from other sources at the date of each transaction, as well as prevailing rates for similar debt instruments of issuers with similar credit ratings. The estimated effective interest rate used ranges from 9.9% to 11.2%.

In the three and nine months ended September 30, 2015, the Company recorded approximately $0.1 million and $0.3 million, respectively, and in the three and nine months ended September 30, 2014, the Company recorded approximately $0.1 million and $0.3 million, respectively as non-cash interest expense related to the deferred payments pursuant to the supply agreement with Gen-Probe.

Gen-Probe license amendment

The amendment to the license agreement with Gen-Probe detailed in Note 7 includes a $5.0 million payment due on January 1, 2018 and a $5.0 million payment due on January 1, 2020. Under the terms of the amendment, no interest payments are required and no interest rate is stated. The Company determined that imputed interest must be calculated and recognized in accordance with ASC-835, and the payments are recorded in Deferred payments on the Balance Sheet at their present value based upon a 7.6% interest rate for the payment due on January 1, 2018 and a 9.0% interest rate for the payment due on January 1, 2020. The difference between the present value and the amount payable is accreted to Deferred payments over the respective term with a corresponding charge to Interest expense.

10. NOTES PAYABLE

In November 2013, the Company entered into two loan and security agreements. One agreement was entered into with Comerica Bank (“Comerica”) and another agreement was entered into with TriplePoint Capital LLC (“TriplePoint”). Upon closing

12

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

of the two agreements, the Company borrowed $5.0 million under the loan and security agreement with Comerica (the “Comerica Loan”). In March 2014, the Company borrowed $5.0 million under the loan and security agreement with TriplePoint (the “TriplePoint Loan”).

In May 2015, the Company paid off the remaining amounts outstanding and due under the TriplePoint Loan, which consisted of $4.6 million in principal and a $0.4 million final payment fee, and simultaneously amended the Comerica Loan (the “Comerica Amendment”). The Comerica Amendment increased the borrowing under the Comerica Loan to $10.0 million and extended the interest-only period until December 31, 2015. Beginning January 1, 2016, the Company will make monthly payments which will consist of accrued interest and equal principal payments in accordance with a 30-month amortization schedule. The interest rate under the Comerica Amendment remains the same as under the original Comerica Loan, which accrues interest at Comerica’s Prime Referenced Rate (as defined in the loan agreement with Comerica) plus 3.15%, subject to a floor of the daily adjusting LIBOR rate plus 2.5%. As of September 30, 2015, and since inception, the rate was 6.4%.

If the Company has at least $30.0 million in cash and marketable securities as of December 31, 2015, the Company has the option to extend the interest-only period through March 31, 2016. If such interest-only election is made, the interest rate will increase by 0.25%. Additionally, the Company will then make monthly payments which will consist of accrued interest and equal principal payments in accordance with a 22-month amortization schedule.

In connection with the Comerica Loan and the Comerica Amendment, the Company recorded a liability for the note of $9.8 million, net of expenses paid to Comerica, the value of the warrants issued to Comerica and the incremental value due to the amendment of the original Comerica warrant at the time of the repricing. The difference between the liability recorded and the face value of the note will be accreted to Notes payable over the term of the loan with a corresponding charge to Interest expense.

Pursuant to the Comerica Amendment, the Company is required to maintain at least $5.0 million of unrestricted cash and/or marketable securities with Comerica at all times. As of September 30, 2015 and during the period since the Company entered into the Comerica Amendment, the Company has been in compliance with this requirement. Additionally, the Comerica Loan contains various covenants that limit the Company’s ability to engage in specified types of transactions, including limiting the Company’s ability to; sell, transfer, lease or dispose of certain assets; engage in certain mergers and consolidations; incur debt or encumber or permit liens on certain assets, make certain restricted payments, including paying dividends on, or repurchasing or making distributions with respect to, the Company’s Common Stock; and enter into certain transactions with affiliates.

In connection with the closing of the loan and security agreements in November 2013, the Company issued warrants to Comerica and TriplePoint, see Note 15 for further details. In connection with the Comerica Amendment, the Company issued an additional warrant to Comerica to purchase up to an aggregate of 52,265 shares of Common Stock at $2.87 per share and modified the exercise price of the original warrant granted to Comerica under the Comerica Loan from $14.08 per share to $2.87 per share. The value of the new warrant and the incremental value due to the amendment of the original Comerica warrant were recorded as a reduction to Notes payable with a corresponding offset to Additional paid-in capital.

In connection with the repayment of the TriplePoint Loan, the Company recorded approximately $0.2 million of Interest expense as the difference between the amount recorded in the Company's financial records and the amount paid.

As of September 30, 2015, the entire balance of $9.8 million has been classified as Notes payable, current on the Balance Sheet, although only $3.0 million is due within one year. The remaining $6.8 million has also been classified as Notes payable, current because the Comerica Loan agreement contains a material adverse change clause which allows Comerica to require repayment of the debt based on subjective factors regarding the Company’s business and performance.

11. COMMITMENTS AND CONTINGENCIES

Operating Leases

The Company has not entered into any new operating leases or amended any existing operating leases during the nine months ended September 30, 2015.

Commitments

During the nine months ended September 30, 2015, there have been no significant changes to the Company’s commitments as disclosed in the Company’s most recent audited financial statements.

13

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

Contingent liabilities

In addition to the commitments disclosed in the Company’s most recent audited financial statements, the amendment to the license agreement with Gen-Probe detailed in Note 9 provides for additional milestone payments of up to $6.0 million which will further reduce the royalty rate paid. Such payments are required to be made upon meeting certain revenue milestones or may be made at the election of the Company prior to meeting the revenue milestones.

Legal Matters

The Company may periodically become subject to legal proceedings and claims arising in connection with its business. Except as set forth below, the Company is not currently involved in any legal proceedings, nor are any claims pending against the Company.

A putative securities class action originally captioned Ding v. Roka Bioscience, Inc., Case No. 3:14-cv-8020, was filed against the Company and certain of its officers and directors in the United States District Court for the District of New Jersey on December 24, 2014, on behalf of a putative class of persons and entities who had purchased or otherwise acquired securities pursuant or traceable to the Registration Statement for the Company’s IPO. The original putative class period ran from July 17 through November 6, 2014.  The original complaint asserted claims under the Securities Act of 1933 and contended that the IPO Registration Statement was false and misleading, or omitted allegedly material information, in connection with the Company’s statements about its placement of Atlas instruments and its expectations of future growth and increased market share, and the Company’s alleged failure to disclose “known trends and uncertainties about the Company’s sales.”  The alleged misrepresentations and omissions purportedly came to light when the Company issued its third-quarter 2014 earnings release on November 6, 2014.

Pursuant to the Private Securities Litigation Reform Act of 1995, two applicants filed motions on February 23, 2015 for appointment as lead plaintiff.  On March 23, 2015, the applicant with the smaller loss agreed not to oppose the application for lead plaintiff filed by the applicant with the larger loss. The court appointed Stanley Yedlowski as lead plaintiff and The Rosen Law Firm as lead counsel on April 21, 2015. The lead plaintiff then filed an amended complaint, captioned Stanley Yedlowski v. Roka Bioscience, Inc., Case No. 14-cv-8020, on June 23, 2015. The amended complaint pleads Securities Act claims on behalf of persons and entities who purchased or otherwise acquired Roka securities pursuant or traceable to the IPO Registration Statement during an extended putative class period, running from July 17, 2014 through March 26, 2015. The amended complaint alleges that the Registration Statement was false or misleading in that it failed to disclose that the Company’s customers purportedly were experiencing false positives and other usage issues with the Company’s Listeria assays apparently arising from the customers’ employees’ inability to follow the Company’s Listeria assay workflow. The amended complaint alleges that the full extent of the purported misstatements and omissions was not revealed until March 26, 2015. Defendants filed a motion on August 25, 2015 to dismiss the amended complaint, and plaintiffs filed an opposition to that motion on October 9, 2015. The parties have agreed to attempt to resolve the case through mediation in December 2015.

The Company believes that the claims in the securities class action are without merit and, if the mediation is unsuccessful, the Company intends to defend the litigation vigorously, and expects to incur costs associated with defending the securities class action. The Company has various insurance policies related to the risks associated with its business, including directors’ and officers’ liability insurance policies. However, there is no assurance that the Company will be successful in its defense of the securities class action, and there is no assurance that the insurance coverage will be sufficient or that the insurance carriers will cover all claims or litigation costs. At this early stage of the litigation, the Company cannot accurately predict the ultimate outcome of this matter. Due to the inherent uncertainties of litigation, the Company cannot reasonably predict the timing or outcomes, or estimate the amount of loss, if any, or their effect, if any, on its financial statements.

The Company sells its products in various jurisdictions and is subject to federal, state and local taxes including, where applicable, sales and use tax. While the Company believes that it has properly paid or accrued for all such taxes based on its interpretation of applicable law, tax laws are complex and interpretations differ. Periodically, the Company may be audited by taxing authorities, and it is possible that additional assessments may be made in the future.

12. FAIR VALUE MEASUREMENTS

The Company’s financial instruments consist of cash and cash equivalents, marketable securities, trade accounts receivable, accounts payable, short-term deferred payments, deferred payments, notes payable, accrued expenses and Convertible Preferred Stock Warrants. The carrying amounts of cash and cash equivalents, trade accounts receivable, accounts payable, short-term deferred payments and accrued expenses approximate their fair values because of the short-term nature of the instruments,

14

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

or, in the case of the deferred payments and notes payable, because the interest rates the Company believes it could obtain for similar borrowings is similar to its existing interest rates.  The carrying amount of the Company's marketable securities is the amortized cost basis based upon their held-to-maturity classification.

The following table summarizes the fair value information for the Company’s cash held in money market deposit accounts and its marketable securities at September 30, 2015 and December 31, 2014 (amounts in thousands):

			Fair value measurements using:
	Carrying Value		Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)	Significant Unobservable Inputs (Level 3)
Financial Assets and Liabilities Carried at Fair Value
As of September 30, 2015
Financial Assets:
Money market deposit accounts	$	4,547	$	4,547	—	—
As of December 31, 2014
Financial Assets:
Money market deposit accounts	$	5,741	$	5,741	—	—
Financial Assets Carried at Amortized Cost
As of September 30, 2015
Short-term marketable securities	$	30,946	$	5,004	25,932	—
As of December 31, 2014
Short-term marketable securities	$	36,231	$	10,081	26,116	—
Long-term marketable securities	$	13,366	$	2,001	11,337	—

A portion of the Company’s cash and cash equivalents are held in money market deposit accounts and a portion of the Company's short-term marketable securities are United States treasury bills, each of which are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices.

The Company's short-term marketable securities and long-term marketable securities not classified within Level 1 of the fair value hierarchy are comprised of commercial paper, U.S. government-related debt, and corporate debt securities, all of which are classified as  Level 2 within the fair value hierarchy. The Company estimates the fair values of these marketable securities by taking into consideration valuations obtained from its investment manager, which utilizes industry standard valuation models, including both income and market-based approaches, for which all significant inputs are observable, either directly or indirectly, to estimate fair value. There have been no transfers between levels during the reporting period.

There were no convertible preferred stock warrants outstanding during the nine months ended September 30, 2015. In conjunction with the closing of the Company’s IPO, the warrants exercisable for shares of Preferred Stock were automatically converted into warrants exercisable for shares of its Common Stock, resulting in the reclassification of the related convertible preferred stock warrant liability to Additional paid-in capital as the warrants to purchase shares of common stock met the criteria for equity classification. Per ASC 820, Fair Value Measurements and Disclosures, (“ASC 820”) the Convertible Preferred Stock Warrants which were outstanding during the nine months ended September 30, 2014 were revalued to their fair value, using the Black-Scholes option-pricing model, at September 30, 2014 and the change in fair value is reflected in the Statement of Operations and Comprehensive Loss. The table below provides a summary of the changes in the Convertible preferred stock warrant liability during the nine months ended September 30, 2014 (amounts in thousands):

	For the Nine Months Ended September 30, 2014
Balance at beginning of period	$	212
Increase in Series E warrant shares	135
Change in fair value of warrants(1)	1,017
Reclassification to equity(2)	$	(1,364	)
Balance at end of period	$	—

15

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

(1) Amount includes $0.7 million of prior period fair value adjustments.

(2) The warrants were re-measured to fair value and reclassified to additional paid-in capital upon the completion of the Company's initial public offering.

13. CONVERTIBLE PREFERRED STOCK AND STOCKHOLDERS’ EQUITY

Registration rights

Prior to the IPO, the Company had multiple classes of preferred stock for which shares were authorized, issued and outstanding. At the closing of the Company's IPO, all shares of Convertible Preferred Stock converted into 10,494,557 shares of Common Stock. The holders of these shares have demand, short-form and piggyback registration rights under the terms of an investor rights agreement between such holders and the Company which will expire upon the earlier of (i) five years after the Company's IPO and (ii) as to a holder, at such time as all registrable securities held by such holder may be sold without restriction under Rule 144. Upon request of holders of at least 51% of the registrable securities, the Company is required to file a registration statement under the Securities Act covering the registration of such shares, subject to terms and conditions set forth in the agreement.

Authorized stock

In connection with the seventh amended and restated certificate of incorporation effective on July 22, 2014, the total authorized shares of stock was changed to 520,000,000 of which 500,000,000 shares are designated as common stock with a par value of $0.001 per share and 20,000,000 shares are designated as "blank check" preferred stock with a par value of $0.001 per share.

14. STOCK-BASED COMPENSATION

Effective upon the closing of the IPO, the Company adopted the Roka Bioscience, Inc. 2014 Equity Incentive Plan (the "2014 Plan"). The 2014 Plan initially made available 1,086,956 shares to be granted to employees, officers, directors, consultants, advisors or other individual service providers of the Company. The number of shares of Common Stock available for issuance under the 2014 Plan shall automatically increase on January 1st of each year for a period of ten years commencing on January 1, 2015 and ending on (and including) January 1, 2024, in an amount equal to 3% of the total number of shares of Common Stock outstanding on December 31st of the preceding calendar year.

Under the Roka Bioscience, Inc. 2009 Equity Incentive Plan (the “2009 Plan”), as amended on June 13, 2013, incentive and non-qualified stock options and restricted stock may be granted for up to a maximum of 2,028,850 shares to employees, consultants and directors of the Company. Effective upon adoption of the 2014 Plan, the Company does not intend to issue additional shares under the 2009 Plan.

Stock options and shares of restricted stock granted under the 2009 Plan and the 2014 Plan have a maximum contractual term of ten years from the date of grant and generally vest over four years. For stock options, the exercise price may not be less than the fair value of the stock on the grant date.

The Company recognized stock compensation expense as follows (amounts in thousands):

	For the Three Months Ended   September 30,				For the Nine Months Ended September 30,
	2015		2014		2015		2014
Stock options	$	209	$	41	$	584	$	174
Restricted stock	$	300	$	200	$	1,016	$	591

Under the 2014 Plan, the Company granted approximately 940,000 stock options and approximately 375,000 shares of restricted stock during the nine months ended September 30, 2015, valued at approximately $2.7 million and $1.6 million,

16

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

respectively. Under the 2009 Plan, the Company granted approximately 4,000 stock options valued at approximately $0.02 million and no shares of restricted stock during the nine months ended September 30, 2014.

The Company determines the fair value of stock option awards at the date of grant using a Black-Scholes valuation model. This model requires the Company to make assumptions and judgments on the expected volatility, dividend yield, the risk-free interest rate and the expected term of the stock options. The following ranges of assumptions were utilized for stock options granted during the periods indicated:

	For the Nine Months Ended September 30,
	2015	2014
Expected life in years	5.8-6.3	5.9-6.0
Interest rate	1.06%-1.80%	2.01%-2.04%
Volatility	75% - 90%	60%
Dividend yield	—	—

The Company estimates the expected life of its employee stock options using the “simplified” method, whereby the expected life equals the arithmetic average of the vesting term and the original contractual term of the option due to its lack of sufficient historical data. The risk-free interest rates are based on the U.S. Treasury yield curve in effect at the time of grant for periods corresponding with the expected life of the option. The expected stock price volatility rates are based on average historical volatilities of the common stock of the Company and a group of public companies in similar industries. The Company has no history or expectations of paying dividends on its Common Stock and therefore uses a zero percent dividend yield in the Black-Scholes option pricing model.

15. WARRANTS

As of September 30, 2015, there were 323,078 warrant shares outstanding with a weighted average exercise price of $9.78 per share. See Note 12 for a summary of the changes in the Convertible preferred stock warrant liability for the nine months ended September 30, 2014.

Warrants Issued prior to IPO

Immediately prior to the Company's IPO, the Company had Series B Warrants outstanding which allowed their holders to purchase 2,480,000 shares of Series B at an exercise price of $1.00 per share. In connection with the IPO, the warrants converted into warrants to purchase Common Stock at their conversion rate of approximately 0.0906 common warrant shares to one Series B warrant share. Such warrants expire in September 2016, whereupon any warrants that remain unexercised will be exercised automatically in whole in a cashless exercise resulting in an issuance, to the holders of the warrants, the number of shares with a value equal to the intrinsic value of the warrants at the time of expiry.

In connection with the closing of the loan and security agreements in November 2013 discussed in Note 10, the Company issued warrants to Comerica and TriplePoint to purchase up to an aggregate of 352,941 shares of Series E with an exercise price of $1.28. Upon issuance, the Company recorded liabilities of approximately $0.03 million and $0.06 million for the warrants issued to Comerica and TriplePoint, respectively. The initial fair value of the warrant issued to Comerica of approximately $0.03 million was deemed a discount on the debt issued by Comerica and is being accreted to interest expense over the term of the Comerica Loan. The initial fair value of the warrants issued to TriplePoint of approximately $0.06 million were capitalized in Other assets on the Balance Sheet as part of debt issuance costs and were amortized to Interest expense. In connection with the borrowings made under the TriplePoint Loan in March 2014, one of the TriplePoint warrants became exercisable for an additional 156,863 shares of Series E. The related fair value of approximately $0.1 million was deemed a discount on the debt issued by TriplePoint and was accreted to interest expense over the term of the TriplePoint Loan through the early payoff in May 2015, at which time the remaining discount was charged to interest expense. In connection with the IPO, the Series E warrants converted into warrants to purchase common stock at their conversion rate of approximately 0.0906 common warrant shares to one Series E warrant share and as a result became exercisable for 31,968 shares of Common Stock with an exercise price of $14.08.

Warrants Issued Subsequent to IPO

In connection with the Comerica Amendment on May 29, 2015, the Company issued an additional warrant to Comerica to purchase up to an aggregate of 52,265 shares of Common Stock at $2.87 per share and modified the exercise price of the original

17

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

warrant granted to Comerica to purchase up to an aggregate of 10,656 shares of common stock from $14.08 per share to $2.87 per share.

16. NET LOSS PER SHARE

Basic net loss per share is calculated by dividing net loss applicable to common stockholders by the weighted-average shares outstanding during the period, without consideration for common stock equivalents. The weighted-average common shares outstanding excludes unvested restricted stock which although such shares are legally issued and outstanding, are not required to share in losses of the Company and are therefore excluded from the net loss per share calculation. Diluted net loss per share is calculated by adjusting the weighted-average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury-stock method. For purposes of the diluted net loss per share calculation, Convertible Preferred Stock, stock options and warrants are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive. Therefore, basic and diluted net loss per share applicable to common stockholders were the same for all periods presented. Prior to the IPO, the Company had two classes of common stock outstanding, and in connection with the IPO, the two classes were converted into a new class of Common Stock. The tables in this footnote are retroactively adjusted to show the results as if only the new class of Common Stock was outstanding for the entirety of each of the respective periods.

	For the Three Months Ended September 30,						For the Nine Months Ended September 30,
	2015			2014			2015			2014
Net loss applicable to common shareholders (thousands)	$	(8,491	)	$	(9,083	)	$	(26,592	)	$	(24,799	)
Basic and diluted weighted average common shares outstanding	17,303,490			14,153,715			17,262,033			5,188,516
Basic and diluted loss per share	$	(0.49	)	$	(0.64	)	$	(1.54	)	$	(4.78	)

As the Company incurred a loss for the three and nine months endedSeptember 30, 2015 and 2014, all unvested restricted stock awards were excluded from the calculation of basic net loss per share and all potential Common Stock shares issuable for Convertible Preferred Stock, stock options and warrants were excluded from the calculation of diluted net loss per share, as the effect of including them would have been anti-dilutive. Had the Company not incurred a loss, the dilutive effect of the unvested restricted stock awards on basic weighted average common shares outstanding and the dilutive effect of potential Common Stock shares issuable for Convertible Preferred Stock, stock options and warrants on the weighted-average number of Common Stock shares outstanding would have been as follows:

	For the Three Months Ended September 30,		For the Nine Months Ended September 30,
	2015	2014	2015	2014
Basic weighted average shares outstanding	17,303,490	14,153,715	17,262,033	5,188,516
Dilutive effect of unvested restricted stock	—	301,846	71,860	262,861
Basic weighted average shares outstanding had the Company not incurred a loss	17,303,490	14,455,561	17,333,893	5,451,377
Dilutive effect of Convertible Preferred Stock	—	1,939,212	—	7,642,775
Dilutive effect of warrants	—	208	—	69
Dilutive effect of stock options	78,284	339,272	97,444	363,792
Diluted weighted average shares outstanding had the Company not incurred a loss	17,381,774	16,734,253	17,431,337	13,458,013

17. SEGMENT INFORMATION

The Company operates in a single reportable segment. During each of the nine months endedSeptember 30, 2015, and the nine months endedSeptember 30, 2014, the Company had four customers which each generated more than 10% of the Company’s revenues. These customers accounted for revenues as follows (amounts in thousands):

18

ROKA BIOSCIENCE, INC.

NOTES TO FINANCIAL STATEMENTS

(unaudited)

	Nine Months Ended September 30,
	2015	2014
Customer A	1,040	648
Customer B	889	1,086
Customer C	623	631
Customer D	463	411

19

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

In this Quarterly Report on Form 10-Q, the words “Roka”, the “Company”, “our”, “we” and “us” refer to Roka Bioscience, Inc.

The following discussion of the financial condition and results of operations of the Company should be read in conjunction with the audited Financial Statements and Notes thereto included in the Company's Annual Report on Form 10-K.

SPECIAL NOTE REGARDING FORWARD LOOKING STATEMENTS

This Quarterly Report on Form 10-Q contains a number of forward-looking statements made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995 under 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”). Any statements contained herein (including, without limitation, statements to the effect that we “believe”, “expect”, “anticipate”, “plan” and similar expressions) that are not statements of historical fact should be considered forward-looking statements. These forward-looking statements are based on current expectations, estimates, forecasts and projections about the industry and markets in which we operate and management’s current beliefs and assumptions.

These forward-looking statements are subject to a number of risks, uncertainties and assumptions, including, but not limited to:

• the ability of our Atlas Detection Assays and Atlas instrument to gain market acceptance, particularly from key thought leaders in the industry, major food companies and third-party food safety testing laboratories;

• our ability to increase our revenue, instrument placements and average revenue per instrument;

• our relationship with Gen-Probe under our license and supply agreements;

• our relationships with key suppliers, including certain single source suppliers such as Gen-Probe, from whom we obtain our Atlas instrument and supplies for Atlas Detection Assays and certain components and materials used in our assays;

• our ability to manufacture our complex assays in accordance with precise technological specifications and in sufficient quantities, on a timely basis;

• our ability to enhance existing products and to develop, introduce and commercialize new products;

• our ability to protect our intellectual property rights, including the patent rights we license from Gen-Probe;

• our ability to defend against any future claims that our Atlas Detection Assays and Atlas instrument infringe the patent rights of any third parties;

• our ability to manage lengthy and variable sales cycles and to forecast revenue and operating expenses;

• our ability to defend against the securities class action lawsuit, the resolution of which in a manner adverse to us could have an adverse effect on our financial condition and business;

• our anticipated cash needs and our estimates regarding our capital requirements and our needs for additional financing;

• anticipated trends and challenges in our business and the markets in which we operate; and

• the factors listed under the heading “Risk Factors” in the Company’s annual report on Form 10-K for the year ended December 31, 2014 and other reports that we file with the Securities and Exchange Commission.

Moreover, we operate in a very competitive and rapidly changing environment. New risks emerge from time to time. It is not possible for our management to predict all risks, 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 we may make. In light of these risks, uncertainties and assumptions, the forward-looking events and circumstances discussed in this report may not occur and actual results could differ materially and adversely from those anticipated or implied in the forward-looking statements.

You should not rely upon forward-looking statements as predictions of future events. Although we believe that the expectations reflected in the forward-looking statements are reasonable, we cannot guarantee that the future results, levels of activity, performance or events and circumstances reflected in the forward-looking statements will be achieved or occur. Moreover, except as required by law, neither we nor any other person assumes responsibility for the accuracy and completeness of the forward-looking statements. We undertake no obligation to update publicly any forward-looking statements for any reason after the date of this report to conform these statements to actual results or to changes in our expectations.

Overview

Background

20

We are a molecular diagnostics company initially focused on providing advanced testing solutions for the detection of foodborne pathogens. The proprietary molecular technology used in our assays enables us to offer accurate and rapid testing solutions while our fully automated Atlas instrument helps our customers reduce labor costs and minimize operator error. In late 2012, we launched our proprietary Atlas Detection Assays and Atlas instrument in the North American food safety testing market and we have worldwide rights to develop and commercialize our advanced molecular testing solutions for a wide range of other industrial applications.

Our company was founded in 2009 through the acquisition of the industrial application market assets of Gen-Probe. The acquisition included a worldwide license for Gen-Probe’s molecular assay technologies in the industrial application markets, access to certain instrument platforms as well as 18 key development personnel. Our advanced molecular assays and automated instruments are derived from Gen-Probe technologies, which Gen-Probe uses in the highly regulated clinical diagnostics and blood screening markets.

We are initially focused on the commercialization, under the Atlas brand name, of a comprehensive menu of molecular diagnostic products for the detection of foodborne pathogens. We believe that other available pathogen test methods have significant performance gaps with respect to accuracy, time to results and automation, which are areas of critical importance to food processors, third-party contract testing laboratories and the government agencies that regulate food safety. Our Atlas solution is designed to provide our customers with accurate and rapid test results with reduced labor costs and improved laboratory efficiencies.

Our commercial success is dependent upon our ability to increase sales of our Atlas Detection Assays through increased utilization of Atlas instruments with current customers and the placement of additional Atlas instruments. We are in the early stages of commercialization and rely on a limited number of customers, and as of September 30, 2015, we have placed 39 Atlas instruments. Although we generally expect that placement of additional instruments will result in higher revenue, our customer agreements do not have minimum purchase obligations for Atlas Detection Assays. Our sales cycle is lengthy, often lasting longer than 12 months, which makes it difficult for us to accurately forecast revenue and other operating results. Additionally, this lengthy sales cycle may cause revenue and operating results to vary significantly from period to period.

We have incurred significant losses since our inception, and as of September 30, 2015, our accumulated deficit was $159.6 million. We expect to continue to incur operating losses over the near term as we continue our commercialization efforts. In order to achieve and sustain profitability, we will need to significantly increase the demand for our Atlas Detection Assays.

Financial Operations Overview

Revenue

Our revenue is derived primarily from the sale of our Atlas Detection Assays and consumable supplies for our Atlas instruments. Our Atlas Detection Assays and our consumable supplies are designed to be used only on our Atlas instruments and our Atlas instruments will only accept our Atlas Detection Assays and our consumable supplies. This closed system model enables us to generate recurring revenue from the sale of our Atlas Detection Assays and other consumable supplies for use with each Atlas instrument we place. We mostly place our Atlas instruments with customers through reagent rental agreements, and recover the cost of providing the Atlas instruments, including services related to instrument maintenance, repairs, installation and training to our customers, in the amount charged for our Atlas Detection Assays. The reagent rental agreements are typically for a one-year initial period with automatic renewal provisions, and the agreements have no minimum purchase obligations.

Shipping and handling costs incurred by us are included in our billings to customers. Revenue is generally recognized when our Atlas Detection Assays and other consumable supplies are shipped to the customer.

In addition to the sale of our Atlas Detection Assays, we generate limited revenue from instrument rental and service and maintenance contracts. Revenue from instrument rental and service and maintenance contracts is recognized ratably over the term of the contract. We also offer our Atlas instruments for sale, and during the nine months ended September 30, 2015, we sold one Atlas instrument.

Potential customers for our products typically need to commit significant time and resources to evaluate our products, due to the nature and cost of our products and their impact on the potential customers’ businesses. To date, it has been difficult for us to accurately project revenues and other operating results due to these and other factors. In addition, the revenue generated from sales of our Atlas Detection Assays may fluctuate from time to time due to changes in the testing volumes of our customers. As a result, our financial results may fluctuate on a quarterly basis or over other measurement periods. Our future revenue growth is dependent on our ability to place additional commercial instruments with customers and increased usage of our Atlas Detection Assays.

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In the spring of 2014, several of our customers experienced sporadic false positive test results due to sample contamination in their early-stage implementation of our Listeria assay, primarily in connection with environmental testing. In collaboration with our customers, we developed revised sample workflow procedures that we believed successfully minimized the risk of sample contamination with our Listeria assay. However, in late August 2014, we became aware that while some of our customers successfully implemented the revised sample workflow procedures, one of our high-volume customers found it difficult to consistently follow these revised sample workflow procedures and sporadically experienced false positive test results due to inadvertent sample contamination, primarily in connection with environmental testing. These difficulties caused the customer to delay further implementation of the Listeria assay. In late 2014, we commenced an initiative to develop a new Listeria assay, specifically for use in environmental testing, intended to be less susceptible to inadvertent sample contamination. In July 2015, we announced that we received AOAC approval for our new Listeria assay, the Atlas Listeria Environmental Detection Assay. We presently expect to make this new assay available to customers in the fourth quarter of 2015. We are currently unable to accurately forecast customer adoption of the new assay, as current and potential customers are expected to conduct thorough evaluations of the new assay. The outcome of such customer evaluations is uncertain, and we may experience only modest impact on our sales in the near term. As a result, we do not expect our revenue to increase significantly in the near term until we place additional instruments and successfully commercialize the new Atlas Listeria Environmental Detection Assay.

Operating Expenses

Cost of revenue

Cost of revenue primarily consists of the cost of materials, direct labor and manufacturing overhead costs associated with the production and distribution of our Atlas Detection Assays and consumable supplies for our Atlas instruments. Cost of revenue also includes depreciation on Atlas instruments placed with our customers under reagent rental or rental agreements, expenses related to service and maintenance of instruments, and royalties payable under a technology license agreement with Gen-Probe. We purchase our Atlas instruments from Gen-Probe pursuant to a supply agreement entered into in 2011.

We manufacture our Atlas Detection Assays and consumable supplies in our San Diego facility, which has significant capacity for expansion. To date, the underutilized capacity in this facility has contributed to a high cost of revenue relative to revenue.

We expect our cost of revenue to increase as we place additional Atlas instruments and manufacture and sell an increasing number of our Atlas Detection Assays and consumable supplies. We believe cost of revenue as a percentage of revenue will decrease in future periods to the extent our manufacturing and sales volumes of Atlas Detection Assays increase.

Research and development

Our research and development expenses are primarily associated with costs incurred for development, improvements and support activities for our Atlas instruments and Atlas Detection Assays, such as our assays for Salmonella, Listeria, E. coli O157:H7, Shiga toxin-producing E. coli and Listeria monocytogenes. These expenses consist principally of payroll, employee benefits, as well as fees for contract research, consulting services and laboratory supplies. We expense all research and development costs as incurred.

We expect to remain focused on improving our existing Atlas Detection Assays as well as developing additional assays and instrument platforms in the near term, and we expect our research and development expenses to remain approximately at their current level during the remainder of 2015.

Selling, general and administrative

Our selling, general and administrative expenses include costs associated with our sales organization as well as our executive, accounting, information technology and human resources functions. These expenses consist principally of payroll, employee benefits, travel, and stock-based compensation, as well as professional services fees such as consulting, audit, tax and legal fees, and general corporate costs. We expense all general and administrative expenses as incurred.

We expect our selling, general and administrative expenses to remain at approximately the current level during the remainder of 2015.

Amortization of Intangible Assets

In connection with the acquisition of the industrial application market assets of Gen-Probe, we acquired certain in-process research and development projects that were recorded as an intangible asset with an indefinite life. Upon completion of the development of our first Atlas Detection Assay in January 2012, this asset was transferred from in-process research and development to a definite life intangible asset and we initiated amortization of the asset over its estimated useful life of 10 years. In June 2014,

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we entered into an amendment to our license agreement with Gen-Probe. Under the amendment, we obtained a two-year option to reduce the royalty rate we pay to Gen-Probe in exchange for an option payment of $2.5 million. Upon completion of our IPO we exercised our option and issued to Gen-Probe 865,063 shares of common stock and made a cash payment of $8.0 million. We are required to make additional cash payments of $5.0 million on January 1, 2018 and $5.0 million on January 1, 2020. The aggregate cash and stock payments made to Gen-Probe along with the present value of the two $5.0 million payments described above were recorded as a $26.6 million addition to our intangible technology asset in Intangible assets on the Balance Sheet in the third quarter of 2014. This addition is being amortized through December 31, 2021, the end of the estimated remaining life of the technology asset. As a result, amortization expense for these intangible assets has increased over prior periods. We assess our intangible and other long-lived assets for impairment whenever events or other changes in circumstances suggest that the carrying value of an asset group may not be recoverable based on its undiscounted future cash flows. For example, if our commercialization efforts are not successful, or if commercialization progress takes longer than anticipated, we may recognize a non-cash impairment charge with respect to the asset group including our intangible asset and other long-lived assets in future periods.

Other Income (Expenses)

Change in Fair Value of Financial Instruments

We recognize changes in fair value of certain financial instruments outstanding during the reporting period. These instruments are comprised of warrants and rights to purchase our preferred stock. Upon completion of our initial public offering in July 2014, the preferred stock warrants were automatically converted into warrants to purchase common stock, and were reclassified into additional paid-in capital at that time. As a result, periods beyond the third quarter of 2014 do not have any change in fair value of certain financial instruments recognized due to these warrants.

Interest Income (Expense), net

Interest income is derived from cash and cash equivalents held with our banking institutions as well as our short-term and long-term marketable securities. Interest income fluctuates based on the current interest rate available from our banking institutions and the amount of funds held in cash accounts and marketable securities. Interest expense during the periods presented is associated with the $10.0 million of debt outstanding under the two loan and security agreements we entered into in November 2013, the repayment of the TriplePoint loan and the amendment to the Comerica loan in the three months ended June 30, 2015, the two individual $5.0 million payments due to Gen-Probe on January 1, 2018 and January 1, 2020, respectively, under the terms of the royalty reduction option exercised under the terms of the amendment to our license agreement, as well as the extended payment terms provided to us by Gen-Probe on the purchase of Atlas instruments. See “—Liquidity and Capital Resources” below for further details.

We expect our interest expense to remain at approximately the current level for the remainder of 2015.

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Results Of Operations

Comparison of the Three Months Ended September 30, 2015 to the Three Months Ended September 30, 2014

	Three Months Ended September 30,						Change
	2015			2014			$			%
	(amounts in thousands, except percentages)
Statement of Operations Data:
Revenue	$	1,508		$	1,483		$	25		2	%
Operating Expenses
Cost of revenue	1,672			2,578			(906		)	(35	)%
Research and development	2,058			1,922			136			7	%
Selling, general and administrative	4,924			4,618			306			7	%
Amortization of intangible asset	937			738			199			27	%
Total operating expenses	9,591			9,856			(265		)	(3	)%
Loss from operations	(8,083		)	(8,373		)	290			(3	)%
Other (expense) income:
Change in fair value of financial instruments	—			(223		)	223			(100	)%
Interest income (expense), net	(404		)	(476		)	72			(15	)%
Net loss	$	(8,491	)	$	(9,083	)	$	592		(7	)%

Revenue

Revenue increased slightly for the three months ended September 30, 2015, compared to the three months ended September 30, 2014. During the three months ended September 30, 2015, we sold 183,000 Atlas Detection Assays compared to 152,000 during the three months ended September 30, 2014.

As of September 30, 2015, we had 39 instruments placed with customers under commercial agreements, compared to 36 instruments as of September 30, 2014. For the three months ended September 30, 2015, the average revenue per instrument placed under commercial agreements was approximately $39,000, compared to $38,000 for the three months ended September 30, 2014. During the three months ended September 30, 2015, four customers each accounted for more than 10% of revenues and generated approximately $1.1 million of revenue compared to four customers who generated $1.0 million of revenue in the three months ended September 30, 2014.

Operating Expenses

Cost of Revenue

Cost of revenue decreased by $0.9 million, to $1.7 million for the three months ended September 30, 2015, from $2.6 million for the three months ended September 30, 2014. The decrease was primarily due to inventory provisions in the three months ended September 30, 2015 which were lower than the inventory provisions in the three months ended September 30, 2014 by $0.7 million.

Research and Development

Research and development expense increased by $0.2 million to $2.1 million for the three months ended September 30, 2015, from $1.9 million for the three months ended September 30, 2014. The increase was primarily due to an increased use of supplies totaling approximately $0.3 million, which was partially offset by a decrease in external development services of approximately $0.1 million.

Selling, General and Administrative

Selling, general and administrative expense increased by $0.3 million, to $4.9 million for the three months ended September 30, 2015, from $4.6 million for the three months ended September 30, 2014. Payroll related expenses increased by approximately $0.3 million and consulting services increased by approximately $0.3 million, these increases were partially offset by a decrease in promotional expenses of approximately $0.2 million and a $0.1 million decrease in travel and depreciation.

Amortization of intangible assets

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Amortization of intangibles increased by $0.2 million to $0.9 million for the three months ended September 30, 2015 from $0.7 million for the three months ended September 30, 2014. The increase was due to the addition to our intangible asset in July 2014 in connection with the amendment to our license agreement with Gen-Probe.

Other (Expense) Income

Change in Fair Value of Financial Instruments

For the three months ended September 30, 2014, we recorded $0.2 million of income which was due to changes in the fair value of our Series B and Series E preferred stock warrants which were outstanding from the beginning of the year through June 30, 2014. Upon completion of our IPO in July 2014, these warrants were converted into warrants to purchase common stock and they were reclassified into additional paid-in capital at their fair value on that date. As a result of the conversion of our warrants to purchase shares of convertible preferred stock into warrants to purchase shares of common stock, we did not recognize any changes in fair value of these warrants in the three months ended September 30, 2015.

Interest Income (Expense), net

Net interest expense decreased by $0.1 million to $0.4 million for the three months ended September 30, 2015, from net interest expense of $0.5 million for the three months ended September 30, 2014. The decrease was primarily due to higher interest expense on the TriplePoint loan in 2014 which was replaced by the amendment to the Comerica Loan in 2015.

Comparison of the nine months ended September 30, 2015 to the nine months ended September 30, 2014

	Nine Months Ended September 30,						Change
	2015			2014			$			%
	(amounts in thousands, except percentages)
Statement of Operations Data:
Revenue	$	4,484		$	3,701		$	783		21	%
Operating Expenses
Cost of revenue	5,391			5,416			(25		)	—	%
Research and development	5,823			5,991			(168		)	(3	)%
Selling, general and administrative	15,453			14,214			1,239			9	%
Amortization of intangible asset	2,811			822			1,989			242	%
Total operating expenses	29,478			26,443			3,035			11	%
Loss from operations	(24,994		)	(22,742		)	(2,252		)	10	%
Other (expense) income:
Change in fair value of financial instruments	—			(785		)	785			(100	)%
Interest income (expense), net	(1,588		)	(1,244		)	(344		)	28	%
Net loss	$	(26,592	)	$	(24,799	)	$	(1,793	)	7	%

Revenue

Revenue increased by $0.8 million, to $4.5 million for the nine months ended September 30, 2015, from $3.7 million, for the nine months ended September 30, 2014, primarily as a result of increased demand for our Atlas Detection Assays and the sale of one Atlas instrument. During the nine months ended September 30, 2015, we sold 512,000 Atlas Detection Assays compared to 414,000 in the nine months ended September 30, 2014.

As of September 30, 2015, we had 39 instruments placed with customers under commercial agreements, compared to 36 instruments as of September 30, 2014. For the nine months ended September 30, 2015, the average revenue per instrument placed under commercial agreements was approximately $115,000, compared to $99,000 for the nine months ended September 30, 2014. This increase was due to higher utilization of the instruments placed under commercial agreements. Our four largest customers, which each accounted for more than 10% of revenues, generated approximately $3.0 million of revenue in the nine months ended September 30, 2015, compared to $2.8 million in the nine months ended September 30, 2014.

Operating Expenses

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Cost of Revenue

Cost of revenue decreased slightly for the nine months ended September 30, 2015, compared to the nine months ended September 30, 2014. The decrease was primarily due inventory provisions in the nine months ended September 30, 2015 being lower than the inventory provisions in the nine months ended September 30, 2014 by approximately $0.6 million, which was partially offset by higher sales volumes.

Research and Development

Research and development expense decreased by $0.2 million, to $5.8 million for the nine months ended September 30, 2015, from $6.0 million for the nine months ended September 30, 2014. External development services decreased by approximately $0.4 million, depreciation decreased by approximately $0.1 million and payroll related expenses decreased by approximately $0.1 million, these decreases were partially offset by a $0.4 million increase in supplies.

Selling, General and Administrative

Selling, general and administrative expense increased by $1.3 million, to $15.5 million for the nine months ended September 30, 2015, from $14.2 million for the nine months ended September 30, 2014. Payroll related expenses increased by approximately $1.0 million, consulting services increased by approximately $0.8 million and administrative expenses increased by approximately $0.2 million. These increases were partially offset by a $0.3 million decrease in promotional expenses, a $0.3 million decrease in supplies and a $0.2 million decrease in travel and depreciation.

Amortization of intangible assets

Amortization of intangibles increased by $2.0 million to $2.8 million for the nine months ended September 30, 2015 from $0.8 million for the nine months ended September 30, 2014. The increase was due to the addition to our intangible asset in July 2014 in connection with the amendment to our license agreement with Gen-Probe.

Other (Expense) Income

Change in Fair Value of Financial Instruments

For the nine months ended September 30, 2014, we recorded $0.8 million of income which was due to changes in the fair value of our Series B and Series E preferred stock warrants which were outstanding from the beginning of the year through June 30, 2014. Upon completion of our IPO in July 2014, these warrants were converted into warrants to purchase common stock and they were reclassified into additional paid-in capital at their fair value on that date. As a result of the conversion of our warrants to purchase shares of convertible preferred stock into warrants to purchase shares of common stock, we did not recognize any changes in fair value of these warrants in the nine months ended September 30, 2015.

Interest Income (Expense), net

Net interest expense increased by $0.4 million to $1.6 million for the nine months ended September 30, 2015, from net interest expense of $1.2 million for the nine months ended September 30, 2014. The increase was primarily due to $0.2 million recognized upon the early repayment of the TriplePoint loan in May 2015 and the $5.0 million increase in debt in March 2014 and interest expense accretion recognized in accordance with the amounts payable to Gen-Probe on January 1, 2018 and January 1, 2020 in connection with the amendment to our license agreement with Gen-Probe.

Liquidity and Capital Resources

Prior to our IPO in July 2014, our operations were primarily financed through private sales of shares of our preferred stock and debt. Upon closing of our IPO on July 22, 2014 we received approximately $53.2 million of net proceeds, after deduction of underwriting discounts, commissions and expenses.

In October 2015, we filed a shelf registration statement with the Securities and Exchange Commission to register for sale any combination of the types of securities described in the filing up to a dollar amount of $100 million. The shelf registration went effective on October 7, 2015. No securities have been sold by us from this shelf registration. On October 30, 2015, we entered into a Controlled Equity Offering^SM Sales Agreement, or the Sales Agreement, with Cantor Fitzgerald & Co., or Cantor Fitzgerald, as sales agent, pursuant to which we may offer and sell, from time to time, through Cantor Fitzgerald shares of its common stock, par value $0.001 per share up to an aggregate offering price of $6,750,000. We will pay Cantor Fitzgerald a commission of 3.0%

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of the aggregate gross proceeds from each sale of shares and have also agreed to reimburse Cantor Fitzgerald for certain specified expenses. As of November 11, 2015, we had not sold any shares of common stock under the Sales Agreement.

We have incurred negative cash flows from operating and investment activities since our inception in 2009, and as of September 30, 2015, we have an accumulated deficit of $159.6 million. Since inception, we have devoted our resources to funding research and development and to commercializing the assets and technology acquired from Gen-Probe. Our business generally involves placement of Atlas instruments with our customers under reagent rental agreements. As a result, as our business expands, we expect to incur significant negative upfront cash outlays for the purchase and installation of additional Atlas instruments, to be offset by later positive operating cash flows from sales of Atlas Detection Assays and consumable supplies. At September 30, 2015, we had cash and cash equivalents of $6.9 million and marketable securities of $30.9 million.

The following table shows a summary of our cash flows for the nine months ended September 30, 2015 and 2014, respectively (amounts in thousands):

	Nine Months Ended September 30,
	2015			2014
Net cash used in operating activities	$	(18,307	)	$	(17,996	)
Net cash provided by (used in) investing activities	18,090			(10,639		)
Net cash provided by (used in) financing activities	(337		)	58,756
Net decrease in cash and cash equivalents	$	(554	)	$	30,121

Operating Activities

Net cash used in operating activities was $18.3 million for the nine months ended September 30, 2015and resulted from $26.6 million net loss, partially offset by $7.7 million in non-cash items, principally depreciation and amortization, share-based compensation expense and non-cash interest expense, and $0.6 million net changes in operating assets and liabilities.  Net cash used in operating activities was$18.0 million for the nine months ended September 30, 2014and resulted from $24.8 million net loss, partially offset by $6.1 million in non-cash items, principally depreciation and amortization, change in fair value of financial instruments, provisions for inventory, share-based compensation expense and non-cash interest expense, and $0.7 million net changes in operating assets and liabilities.

Investing Activities

Net cash provided by investing activities was $18.1 million for the nine months ended September 30, 2015 and was primarily the result of maturities of marketable securities that were not reinvested. Net cash used in investing activities during the nine months ended September 30, 2014 was primarily the result of $10.5 million in payments to Gen-Probe for payments due under the license amendment.

Financing Activities

Net cash used in financing activities was $0.3 million for the nine months ended September 30, 2015 and consisted primarily of the repayment of amounts outstanding under our loan and security agreement with TriplePoint Capital of $5.4 million, partially offset by proceeds under the amendment of our loan and security agreement with Comerica of $5.0 million. Net cash provided by financing activities for the nine months ended September 30, 2014 was $58.8 million and consisted of proceeds from our initial public offering of $53.6 million, which excludes offering expenses of $0.4 million paid in 2013, borrowings under our loan and security agreements of $5.0 million and $0.3 million of proceeds from the exercise of stock options.

Operating Capital Requirements

We have limited capital resources and have experienced negative cash flows from operations and have incurred net losses since inception. We expect to continue to experience negative cash flows from operations and incur net losses in the near term as we devote substantially all of our efforts to commercializing our products and continued product development. We expect future operating, investment and financing activities to be funded by our product revenue, our existing cash and cash equivalents, our existing marketable securities and sales of our common stock, if any, pursuant to our sales agreement with Cantor Fitzgerald. Based on our current business plan, we believe that our cash, cash equivalents and marketable securities as of September 30, 2015 will be sufficient to fund our projected operating requirements at least through the middle of 2016. Our liquidity requirements have and will continue to consist of research and development expenses, sales and marketing expenses, capital expenditures, working capital and general corporate expenses. Our future liquidity requirements will also include interest and principal payments

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on our debt and future payments to Gen-Probe of $5.0 million on January 1, 2018 and $5.0 million on January 1, 2020. As we place additional instruments and demand for our Atlas Detection Assays increases, we expect that our capital requirements will also increase as we purchase additional Atlas instruments for placement with customers and fund working capital requirements such as inventory and accounts receivable.

Our present and future funding requirements will depend on many factors, including our revenue growth and ability to generate cash flows from operating activities; the level of our sales and marketing and research and development activities; the effect of competing technological and market developments; the cost of and potential delays in product development; any change in regulatory oversight applicable to our products; and our ability to comply with the provisions of our debt agreement with Comerica.

In addition to the proceeds from sales of our common stock, if any, pursuant to the sales agreement with Cantor Fitzgerald, we will need additional financing to fund our long-term liquidity needs.  We may seek such financing by selling common or preferred equity or convertible debt securities, entering into an additional credit facility or another form of third-party funding, or seeking other debt financing. Such additional capital may not be available to us on reasonable terms or at all.  In addition, we may raise additional capital to expand our business, to pursue strategic investments, to take advantage of financing opportunities, or for other reasons. The sale of equity and convertible debt securities may result in dilution to our stockholders and those securities may have rights senior to those of our common shares. If we raise additional funds through the issuance of preferred stock, convertible debt securities or other debt financing, these securities or other debt could contain covenants that would restrict our operations. Any other third-party funding arrangement could require us to relinquish valuable rights.

These statements regarding our future liquidity requirements are forward-looking statements and involve risks and uncertainties and actual results could vary materially and negatively as a result of a number of factors, including the factors discussed in the section “Risk Factors” of our most recent Annual Report on Form 10-K. We have based our estimates regarding our future liquidity requirements on assumptions that may prove to be wrong and we could utilize our available capital resources sooner than we currently expect. If we cannot expand our operations or otherwise capitalize on our business opportunities because we lack sufficient capital, our business, financial condition, and results of operations could be materially adversely affected.

Term Loan and Security Agreements

In November 2013, we entered into loan and security agreements with each of Comerica Bank, or Comerica, and with TriplePoint Capital LLC, or TriplePoint.

Under the terms of our loan agreement with Comerica, we borrowed $5.0 million in November 2013. The Comerica loan bears interest at Comerica’s Prime Referenced Rate (as defined in the loan agreement with Comerica) plus 3.15 %, subject to a floor of the daily adjusting LIBOR rate plus 2.5%, which was 6.4% as of September 30, 2015.

Pursuant to the terms of our loan agreement with TriplePoint, we borrowed $5.0 million in March 2014. The borrowings under the TriplePoint loan accrued interest at the Prime Rate plus 6.25%, but not less than 9.5% and were repayable over 36 months from the borrowing date with an interest-only period of 12 months, and equal monthly installments of principal and interest over the remaining term of the loan after the interest only period.

In May 2015, we paid off the remaining amounts due under the TriplePoint Loan, which consisted of $4.6 million in principal and a $350,000 final payment fee and simultaneously amended the Comerica Loan (the “Comerica Amendment”). The Comerica Amendment increased the borrowing under the Comerica Loan to $10.0 million, extended the interest-only period from June 1, 2015 until December 31, 2015 and extended the overall term by 12 months. Beginning January 1, 2016, we will make monthly payments which will consist of accrued interest and equal principal payments in accordance with a 30-month amortization schedule. The interest rate under the Comerica Amendment remains unchanged.

At our option, if we have at least $30 million in cash and marketable securities as of December 31, 2015, we may extend the interest only period through March 31, 2016. If such interest-only election is made, the interest rate will increase by 0.25%. Additionally, we will then make monthly payments which will consist of accrued interest and equal principal payments in accordance with a 22-month amortization schedule.

Pursuant to the Comerica Amendment we are required to maintain at least $5,000,000 of unrestricted cash and/or marketable securities with Comerica at all times. As of September 30, 2015 and during the period since we entered into the Comerica Amendment, we have been in compliance with this requirement. Additionally, the Comerica Loan contains various covenants that limit our ability to engage in specified types of transactions, including limiting our ability to; sell, transfer, lease or dispose of certain assets; engage in certain mergers and consolidations; incur debt or encumber or permit liens on certain assets, make certain restricted payments, including paying dividends on, or repurchasing or making distributions with respect to, our Common Stock; and enter into certain transactions with affiliates.

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As of September 30, 2015, we had $10.0 million outstanding under the amended Comerica Loan. We may prepay the loan to Comerica, in full or in part at any time, provided that no event of default has occurred and is continuing.

In connection with entering into the loan and security agreements in November 2013, we issued to Comerica a ten-year warrant to purchase an aggregate of 117,647 shares of our Series E preferred stock at an exercise price of $1.28 per share, and we issued to TriplePoint ten-year warrants to purchase an aggregate of 235,294 shares of our Series E preferred stock at an exercise price of $1.28 per share. In connection with the borrowings in March 2014, the TriplePoint warrants became exercisable for an additional 156,863 shares. The warrants issued to TriplePoint contain net issuance exercise provisions. The Comerica and TriplePoint warrants contain anti-dilution adjustment provisions for stock splits, dividends, combinations, reclassifications or exchanges and as such in connection with the IPO, these warrants converted into warrants to purchase common stock at their conversion rate of approximately 0.0906 common warrant shares to one Series E warrant share.

In connection with the Comerica Amendment in May 2015, we issued an additional warrant to Comerica to purchase up to an aggregate of 52,265 shares of Common Stock at $2.87 per share and modified the exercise price of the original warrant granted to Comerica to purchase up to an aggregate of 10,656 shares of common stock from $14.08 per share to $2.87 per share.

As of September 30, 2015, there are 323,078 warrant shares outstanding with a weighted average exercise price of $9.78 per share. The Comerica and TriplePoint warrants have the same “piggyback” registration rights as holders of registrable securities under the investors' rights agreement. Such rights will expire upon the earlier of (i) five years after our IPO and (ii) as to any holder, at such time as all registrable securities held by such holder may be sold without restriction under Rule 144.

Contractual Obligations and Commitments

For the nine months ended September 30, 2015, there were no significant changes to our contractual obligations from those disclosed in our audited financial statements as of December 31, 2014. The following is a summary of our contractual obligations as of September 30, 2015 (in thousands):

	Total		Less than 1 year		1-3 years		3-5 years		More than 5 years
Deferred payment obligations(1)	$	14,719	$	1,990	$	7,729	$	5,000	$	—
Operating lease obligations(2)	3,935		1,057		2,018		860		—
Purchase obligations(3)	261		261		—		—		—
Notes payable(4)	10,040		10,040		—		—		—
Total contractual obligations	$	28,955	$	13,348	$	9,747	$	5,860	$	—

(1) The deferred payment obligations are based upon the gross deferred amounts outstanding for instruments purchased from Gen-Probe as of September 30, 2015 as disclosed in the notes to our unaudited financial statements included elsewhere in this Form 10-Q. Such amounts are recorded at their aggregate present value of $4.1 million on the Balance Sheet as of September 30, 2015. The timing of when these payments are due reflects our current estimates of repayment. We do not believe that future revisions of estimates will have a significant impact on the timing of payments. Additionally, amounts due beyond one year represent the two separate $5.0 million lump-sum payments payable to Gen-Probe in accordance with the amendment to our licensing agreement discussed in "Results of Operations". Such amounts are recorded at their aggregate present value of $7.7 million on the Balance Sheet as of September 30, 2015.

(2) Our operating lease obligations represent the contractual payments due for the lease of our corporate office in Warren, NJ, our laboratory in Warren, NJ and our facility in San Diego, CA.

(3) Our purchase obligations represent the total cost of instruments and supplies which we are committed to purchase from Gen-Probe as well as additional obligations due under other agreements entered into in the normal course of business. In accordance with the supply agreement with Gen-Probe, our purchases of Atlas instruments are defined in rolling quarterly forecasts, and these forecasts become binding commitments for approximately nine months of Atlas instrument purchases at any given time. Our obligation to purchase supplies from Gen-Probe is defined in an annual purchase order submitted in the third quarter of each year.

(4) Such amounts include total principal repayments of $10.0 million and final payment fees of $0.04 million, of which approximately $3.0 million is due within one year from the Balance Sheet date. The remaining amounts are shown as being due in less than one year as our loan agreements contain material adverse change clauses which allow the lenders to call the debt based on subjective factors regarding our business and performance.

29

Amounts which are or may become payable as interest are excluded from the table, but are estimated to approximate $0.2 million during the remainder of 2015.

Off-Balance Sheet Arrangements

We did not have during the periods presented, and we do not currently have, any off-balance sheet arrangements, as defined under the rules and regulations of the Securities and Exchange Commission.

30

Critical Accounting Policies and Significant Estimates

We have prepared our financial statements in accordance with U.S. generally accepted accounting principles. Our preparation of these financial statements requires us to make estimates, assumptions and judgments that affect the reported amounts of assets, liabilities, expenses and related disclosures at the date of the financial statements, as well as revenue and expenses recorded during the reporting periods. We evaluate our estimates and judgments on an ongoing basis. We base our estimates on historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results could therefore differ materially from these estimates under different assumptions or conditions.

There have been no material changes to our critical accounting policies from those described in “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our Annual Report on Form 10-K.

31

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

As of September 30, 2015, our cash and cash equivalents of $6.9 million were primarily held in money market deposit accounts. Our primary exposure to market risk for our cash and cash equivalents is interest income sensitivity, which is affected by changes in the general level of U.S interest rates. However, because of the short-term nature of the instruments in our portfolio, a sudden change in the interest rates associated with these instruments is not expected to have a material impact on our financial condition or results of operations.

As of September 30, 2015, we had $30.9 million of marketable securities classified as held-to-maturity on our balance sheet which had a fair value of $39.0 million. As our intention is to hold these investments through maturity, any interest rate fluctuation changing the fair value of such marketable securities would only be realized if the Company sold the investments prior to maturity.

As of September 30, 2015, we had $10.0 million of variable interest-rate debt outstanding under the Amendment to the loan and security agreement with Comerica. Considering the amounts outstanding and the term of the loan and security agreement, we do not believe a 1.0% increase in the interest rate would have a material impact on our financial condition or results of operations.

We do not have any foreign currency or other derivative financial instruments.

ITEM 4. CONTROLS AND PROCEDURES

a) Conclusion Regarding the Effectiveness of Disclosure Controls and Procedures.

We maintain disclosure controls and procedures (as defined in Rules 13a-15(e) or 15d-15(e) under the Securities Exchange Act of 1934, as amended, or the Exchange Act) that are designed to ensure that information required to be disclosed in the reports that we file or submit under the Exchange Act is (1) recorded, processed, summarized, and reported within the time periods specified in the SEC’s rules and forms and (2) accumulated and communicated to our management, including our principal executive officer and principal financial officer, as appropriate, to allow timely decisions regarding required disclosure. In designing and evaluating the disclosure controls and procedures, management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objectives. In addition, the design of disclosure controls and procedures must reflect the fact that there are resource constraints and that management is required to apply judgment in evaluating the benefits of possible controls and procedures relative to their costs.

We continue the process of reviewing and documenting our disclosure controls and procedures, including our internal controls and procedures for financial reporting, and may from time to time make changes aimed at enhancing their effectiveness and to ensure that our systems evolve with our business.

Our management, with the participation of the principal executive officer and principal financial officer, has evaluated the effectiveness of the design and operation of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”)) as of the end of the period covered by this quarterly report. Based on this evaluation, the principal executive officer and principal financial officer concluded that these disclosure controls and procedures are effective at the reasonable assurance level.

b) Changes in Internal Control Over Financial Reporting.

There was no change in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) identified in connection with the evaluation of our internal control performed during the last fiscal quarter that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

PART II – OTHER INFORMATION

Item 1. LEGAL PROCEEDINGS

We may periodically become subject to legal proceedings and claims arising in connection with our business. Except as set forth below, we are not currently involved in any legal proceedings, nor are any claims pending against us.

32

A putative securities class action originally captioned Ding v. Roka Bioscience, Inc., Case No. 3:14-cv-8020, was filed against Roka and certain of its officers and directors in the United States District Court for the District of New Jersey on December 24, 2014, on behalf of a putative class of persons and entities who had purchased or otherwise acquired Roka securities pursuant or traceable to the Registration Statement for the Company’s initial public offering (the “IPO”). The original putative class period ran from July 17 through November 6, 2014.  The original complaint asserted claims under the Securities Act of 1933 and contended that the IPO Registration Statement was false and misleading, or omitted allegedly material information, in connection with the Company’s statements about its placement of Atlas instruments and its expectations of future growth and increased market share, and the Company’s alleged failure to disclose “known trends and uncertainties about the Company’s sales.”  The alleged misrepresentations and omissions purportedly came to light when Roka issued its third-quarter 2014 earnings release on November 6, 2014.

Pursuant to the Private Securities Litigation Reform Act of 1995, two applicants filed motions on February 23, 2015 for appointment as lead plaintiff.  On March 23, 2015, the applicant with the smaller loss agreed not to oppose the application for lead plaintiff filed by the applicant with the larger loss. The court appointed Stanley Yedlowski as lead plaintiff and The Rosen Law Firm as lead counsel on April 21, 2015. The lead plaintiff then filed an amended complaint, captioned Stanley Yedlowski v. Roka Bioscience, Inc., Case No. 14-cv-8020, on June 23, 2015. The amended complaint pleads Securities Act claims on behalf of persons and entities who purchased or otherwise acquired Roka securities pursuant or traceable to the IPO Registration Statement during an extended putative class period, running from July 17, 2014 through March 26, 2015. The amended complaint alleges that the Registration Statement was false or misleading in that it failed to disclose that our customers purportedly were experiencing false positives and other usage issues with the Listeria assays apparently arising from the customers’ employees’ inability to follow our Listeria assay workflow.  The amended complaint further alleges that the full extent of the purported misstatements and omissions was not revealed until March 26, 2015.  Defendants filed a motion on August 25, 2015 to dismiss the amended complaint, and plaintiffs filed an opposition to that motion on October 9, 2015. The parties have agreed to attempt to resolve the case through mediation in December 2015.

We believe that the claims in the securities class action are without merit and, if the mediation is unsuccessful, we intend to defend the litigation vigorously, and expect to incur costs associated with defending the securities class action. We have various insurance policies related to the risk associated with our business, including directors’ and officers’ liability insurance policies. However, there is no assurance that we will be successful in our defense of the securities class action, and there is no assurance that our insurance coverage will be sufficient or that our insurance carriers will cover all claims or litigation costs. At this early stage of the litigation, we cannot accurately predict the ultimate outcome of this matter. Due to the inherent uncertainties of litigation, we cannot reasonably predict the timing or outcomes, or estimate the amount of loss, if any, or their effect, if any, on our financial statements.

Item 1A. RISK FACTORS

In addition to the other information set forth in this report, you should carefully consider the factors discussed in Part I, “Item 1A. Risk Factors” in our Annual Report on Form 10-K for the year ended December 31, 2014, which could materially affect our business, financial condition or future results. The risks described in our Annual Report on Form 10-K may not be the only risks facing the Company. Additional risks and uncertainties not currently known to the Company or that the Company currently deems to be immaterial also may materially adversely affect the Company’s business, financial condition and/or operating results.

There were no material changes to the risk factors previously disclosed in our Annual Report on Form 10-K filed with the Securities and Exchange Commission on March 27, 2015.

33

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

Unregistered Sale of Equity Securities

Not applicable.

Use of Proceeds

On July 16, 2014, our registration statement on Form S-1 (File No. 333-196135) was declared effective by the Securities and Exchange Commission for our initial public offering pursuant to which we sold an aggregate of 5,000,000 shares of our common stock at a price to the public of $12.00 per share. BofA Merrill Lynch and Leerink Partners acted as joint book-running managers for the offering. Cowen and Company and Wedbush PacGrow Life Sciences acted as co-managers. On July 22, 2014, we closed the sale of 5,000,000 shares, resulting in net proceeds to us of $53.2 million after deducting underwriting discounts and commissions and other offering expenses of $2.6 million. No payments were made by us to directors, officers or persons owning ten percent or more of our common stock or to their associates, or to our affiliates. As of September 30, 2015, we have used $16.6 million of the net proceeds from our initial public offering, of which $8.0 million was paid to Gen-Probe pursuant to the terms of the second amendment to our license agreement with Gen-Probe and the remaining $8.6 million was used in operating activities including the commercialization of our Atlas Detection Assays and ongoing research and development activities. We have invested the balance of the net proceeds from the offering in cash equivalents and marketable securities in accordance with our investment policy. There has been no material change in the planned use of proceeds from our initial public offering as described in our final prospectus filed with the Securities and Exchange Commission on July 17, 2014 pursuant to Rule 424(b).

Issuer Repurchases of Equity Securities

In connection with the vesting of restricted stock in the three months ended September 30, 2015, certain of our employees elected to have shares withheld and transferred back to us in order to cover their income taxes payable as allowed under our equity compensation plans.

Shares of common stock so withheld and transferred back to the Company during the three months ended September 30, 2015 were as follows:

	Issuer Purchases of Equity Securities
Period:	Total Number of Shares Purchased	Average Price Paid per Share		Total Number of Shares Purchased as Part of Publicly Announced Plans or Programs	(a) Maximum Dollar Value of Shares that May Yet be Purchased Under the Program ($ in thousands)
July 1-July 31	451	$	2.62	—	—
August 1-August 31	451	$	2.89	—	—
September 1-September 31	451	$	2.73	—	—

ITEM 6. EXHIBITS

The exhibits filed as part of this Quarterly Report on Form 10-Q are set forth on the Exhibit Index, which is incorporated herein by reference.

34

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 on the date set forth below by the undersigned thereunto duly authorized.

		ROKA BIOSCIENCE, INC.
Date:	November 11, 2015	By: /s/ Paul G. Thomas
		Paul G. Thomas
		President and Chief Executive Officer (Principal Executive Officer)
Date:	November 11, 2015	By: /s/ Steven T. Sobieski
		Steven T. Sobieski
		Senior Vice President and Chief Financial Officer (Principal Financial and Accounting Officer)

35

Exhibit Index

Exhibit No.
10.1+	Controlled Equity OfferingSM Sales Agreement, dated October 30, 2015, by and between Roka Bioscience, Inc. and Cantor Fitzgerald & Co. (incorporated by reference to Exhibit 1.1 to the Company’s current report on Form 8-K filed with the Securities and Exchange Commission on October 30, 2015).
31.1*	Certification of Principal Executive Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
31.2*	Certification of Principal Executive Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
32.1**	Certification of Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
101*	Interactive Data Files regarding (a) our Condensed Balance Sheets as of September 30, 2015 and December 31, 2014 (b) our Condensed Statements of Operations and Comprehensive Loss for the Three Months and Nine Months Ended September 30, 2015 and 2014, (c) our Condensed Statements of Cash Flows for the Nine Months Ended September 30, 2015 and 2014 and (d) the Notes to such Condensed Financial Statements.

*	Filed herewith
+	Incorporated by reference
**	Furnished herewith

36

EX-31.1

Exhibit 31.1

CERTIFICATIONS

I, Paul G. Thomas, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Roka Bioscience, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant and have:

(a)   designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant is made known to us particularly during the period in which this report is being prepared;

(b) (paragraph omitted pursuant to SEC Release Nos. 33-8238/34-47986 and 33-8392/34-49313);

(c) evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d) disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

(a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

(b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: November 11, 2015

/s/ Paul G. Thomas

Paul G. Thomas

President and Chief Executive Officer

(Principal Executive Officer)

EX-31.2

Exhibit 31.2

CERTIFICATIONS

I, Steven T. Sobieski, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Roka Bioscience, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant and have:

(a)   designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant is made known to us particularly during the period in which this report is being prepared;

(b) (paragraph omitted pursuant to SEC Release Nos. 33-8238/34-47986 and 33-8392/34-49313);

(c) evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

(d) disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5. The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

(a) all significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

(b) any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: November 11, 2015

/s/ Steven T. Sobieski

Steven T. Sobieski

Senior Vice President and Chief Financial Officer

(Principal Financial and Accounting Officer)

EX-32.1

Exhibit 32.1

CERTIFICATION PURSUANT TO 18 U.S.C. SECTION 1350, AS ADOPTED PURSUANT TO

SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

Each of the undersigned officers of Roka Bioscience, Inc. (the “Company”) hereby certifies to his knowledge that the Company’s Quarterly Report on Form 10-Q for the period ended September 30, 2015 (the “Report”), as filed with the Securities and Exchange Commission on the date hereof, fully complies with the requirements of Section 13(a) or 15(d), as applicable, of the Securities Exchange Act of 1934, as amended, and that the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: November 11, 2015

/s/ Paul G. Thomas

Paul G. Thomas

President and Chief Executive Officer

(Principal Executive Officer)

Date: November 11, 2015

/s/ Steven T. Sobieski

Steven T. Sobieski

Senior Vice President and Chief Financial Officer

(Principal Financial and Accounting Officer)

XML

Cash and Cash Equivalents - Narrative (Details)	Sep. 30, 2015 financial_institution
Cash and Cash Equivalents [Member] | Credit Concentration Risk [Member]
Concentration Risk [Line Items]
Number of financial institutions	1

XML

Fair Value Measurements - Narrative (Details)	Sep. 30, 2015 shares
Class of Warrant or Right [Line Items]
Convertible preferred stock warrants outstanding (in shares)	323,078
Convertible Preferred Stock Warrants [Member]
Class of Warrant or Right [Line Items]
Convertible preferred stock warrants outstanding (in shares)	0

XML

Accrued Expenses and Other Current Liabilities - Summary of Accrued Expenses (Details) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Payables and Accruals [Abstract]
Employee related	$ 2,016	$ 1,116
Professional services	296	235
Other	411	774
Total accrued expenses and other current liabilities	$ 2,723	$ 2,125

XML

Fair Value Measurements - Summary of the Changes in the Convertible Preferred Stock Warrant Liability (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2014 USD ($)
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Balance at beginning of period	$ 212
Change in fair value of warrants	1,017	[1]
Reclassification to equity	(1,364)	[2]
Balance at end of period	0
Prior Period Adjustment [Member]
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Prior period fair value adjustment	700
Series E Warrants [Member]
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Increase in Series E warrant shares	$ 135

[1] Amount includes $0.7 million of prior period fair value adjustments.

[2] The warrants were re-measured to fair value and reclassified to additional paid-in capital upon the completion of the Company's initial public offering.

XML

Intangible Assets - Narrative (Details) - USD ($)			1 Months Ended		12 Months Ended
	Jan. 01, 2020	Jan. 01, 2018	Jul. 31, 2014	Jun. 30, 2014	Dec. 31, 2014
Technology-Based Intangible Assets [Member]
Finite-Lived Intangible Assets [Line Items]
Intangible technology asset			$ 26,600,000
Royalty Reduction [Member] | Common Stock [Member]
Finite-Lived Intangible Assets [Line Items]
Issuance of common stock for royalty reduction (in shares)			865,063		865,063
Gen Probe [Member]
Finite-Lived Intangible Assets [Line Items]
Option agreement period				2 years
License agreement option payment				$ 2,500,000
Share price (in USD per share)			$ 10.51
Cash payment for royalties			$ 8,000,000
Gen Probe [Member] | Scenario, Forecast [Member]
Finite-Lived Intangible Assets [Line Items]
Cash payment for royalties	$ 5,000,000.0	$ 5,000,000.0

XML

Stock-Based Compensation (Tables)

9 Months Ended

Sep. 30, 2015

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Schedule of Stock Compensation Expense

The Company recognized stock compensation expense as follows (amounts in thousands):

	For the Three Months Ended   September 30,				For the Nine Months Ended September 30,
	2015		2014		2015		2014
Stock options	$	209	$	41	$	584	$	174
Restricted stock	$	300	$	200	$	1,016	$	591

Summary of Range of Assumptions Utilized for Stock Options Granted

The following ranges of assumptions were utilized for stock options granted during the periods indicated:

	For the Nine Months Ended September 30,
	2015	2014
Expected life in years	5.8-6.3	5.9-6.0
Interest rate	1.06%-1.80%	2.01%-2.04%
Volatility	75% - 90%	60%
Dividend yield	—	—

XML

Stock-Based Compensation - Narrative (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2015 USD ($) shares	Sep. 30, 2014 USD ($) shares	Jul. 22, 2014 shares	Jun. 13, 2013 shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Maximum contractual term of restricted stock granted	10 years
Contractual term of restricted stock vested	4 years
Dividend yield	0.00%	0.00%
2009 Equity Incentive Plan [Member] | Employee Stock Option [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options granted (in shares)		4,000
Stock options granted, value | $		$ 20
2009 Equity Incentive Plan [Member] | Restricted Stock [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted stocks granted in the period (in shares)		0
2009 Equity Incentive Plan [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options and restricted shares granted (in shares)				2,028,850
2014 Equity Incentive Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Period between share increases	10 years
Percent of increase	0.03
2014 Equity Incentive Plan [Member] | Employee Stock Option [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options granted (in shares)	940,000
Stock options granted, value | $	$ 2,700
2014 Equity Incentive Plan [Member] | Restricted Stock [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted stocks granted in the period (in shares)	375,000
Stock options granted, value | $	$ 1,600
2014 Equity Incentive Plan [Member] | Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options and restricted shares granted (in shares)			1,086,956

XML

Summary of Significant Accounting Policies (Tables)

9 Months Ended

Sep. 30, 2015

Accounting Policies [Abstract]

Schedule of Changes as a Result of New Accounting Principle

There were no cumulative changes to the Statement of Operations and Comprehensive Loss or the Statement of Convertible Preferred Stock and Stockholders’ Equity (Deficit); changes to the Balance Sheet as of December 31, 2014 as a result of this new accounting principle are noted below (amounts in thousands):

	As of December 31, 2014
	Adjusted	As previously reported	Change
Other assets	262	308	(46	)
Total assets	103,779	103,825	(46	)
Notes payable, current	9,910	9,956	(46	)
Total current liabilities	13,864	13,910	(46	)
Total liabilities	24,704	24,750	(46	)
Total liabilities and stockholders' equity	103,779	103,825	(46	)

XML

Deferred Payments - Summary of Amounts Deferred under Supply Agreement (Details) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Current
Deferred payments, gross	$ 1,990	$ 1,079
Imputed interest	(330)	(384)
Deferred payments, net	1,660	695
Long-term
Deferred payments, gross	2,729	3,683
Imputed interest	(226)	(464)
Deferred payments, net	$ 2,503	$ 3,219

XML

Inventories - Summary of Net Inventories (Details) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Inventory Disclosure [Abstract]
Raw materials	$ 1,744	$ 1,914
Work in process	0	11
Finished goods	2,622	3,005
Inventory, net	$ 4,366	$ 4,930

XML

Summary of Significant Accounting Policies - Narrative (Details)	1 Months Ended
	Jul. 31, 2014
Convertible Preferred Stock [Member]
Summary Of Significant Accounting Policies [Line Items]
Reverse stock split of common stock	11.04:1 reverse stock split
Reverse stock split, conversion ratio	11.04
Series B, Series C and Series E Convertible Preferred Stock [Member]
Summary Of Significant Accounting Policies [Line Items]
Reverse stock split, conversion ratio	0.0906
Series D Convertible Preferred Stock [Member]
Summary Of Significant Accounting Policies [Line Items]
Reverse stock split, conversion ratio	0.0937

XML

Commitments and Contingencies - Narrative (Details)		9 Months Ended
	Feb. 23, 2015 Applicant	Sep. 30, 2015 USD ($)
Commitment And Contingencies [Line Items]
Number of applicants to be appointed as lead plaintiff	2
Gen Probe [Member]
Commitment And Contingencies [Line Items]
Additional milestone payments | $		$ 6,000,000.0

XML

Net Loss Per Share - Schedule of Basic and Diluted Net Loss per Share Applicable to Common Stockholders (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended		12 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014	Dec. 31, 2014
Earnings Per Share [Abstract]
Net loss applicable to common shareholders (thousands)	$ (8,491)	$ (9,083)	$ (26,592)	$ (24,799)	$ (32,230)
Basic and diluted weighted average common shares outstanding (in shares)	17,303,490	14,153,715	17,262,033	5,188,516
Basic and diluted loss per share (in USD per share)	$ (0.49)	$ (0.64)	$ (1.54)	$ (4.78)

XML

Intangible Assets - Summary of Intangibles (Details) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Goodwill and Intangible Assets Disclosure [Abstract]
Intangible asset, gross	$ 28,259	$ 28,259
Accumulated amortization	(4,914)	(2,103)
Intangible assets, net	$ 23,345	$ 26,156

XML

Cash and Cash Equivalents

9 Months Ended

Sep. 30, 2015

Cash and Cash Equivalents [Abstract]

Cash and Cash Equivalents

CASH AND CASH EQUIVALENTS

The Company’s entire balance of Cash and cash equivalents as of September 30, 2015 was held in demand accounts with one financial institution, which subjects the Company to significant concentrations of credit risk.

XML

Net Loss Per Share - Schedule of Calculation of Weighted Average Shares Outstanding, Event of Not Incurring Loss (Details) - shares	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Earnings Per Share [Abstract]
Basic weighted average shares outstanding (in shares)	17,303,490	14,153,715	17,262,033	5,188,516
Dilutive effect of unvested restricted stock (in shares)	0	301,846	71,860	262,861
Basic weighted average shares outstanding had the Company not incurred a loss (in shares)	17,303,490	14,455,561	17,333,893	5,451,377
Dilutive effect of Convertible Preferred Stock (in shares)	0	1,939,212	0	7,642,775
Dilutive effect of warrants (in shares)	0	208	0	69
Dilutive effect of stock options (in shares)	78,284	339,272	97,444	363,792
Diluted weighted average shares outstanding had the Company not incurred a loss (in shares)	17,381,774	16,734,253	17,431,337	13,458,013

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Property and Equipment - Schedule of Property and Equipment (Details) - USD ($) $ in Thousands		Sep. 30, 2015	Dec. 31, 2014
Property, Plant and Equipment [Line Items]
Property and Equipment, Gross		$ 19,765	$ 19,776
Less: Accumulated depreciation		(9,241)	(7,590)
Property and Equipment, Net		10,524	12,186
Instruments with Customers [Member]
Property, Plant and Equipment [Line Items]
Property and Equipment, Gross		4,589	3,875
Instruments for Placement [Member]
Property, Plant and Equipment [Line Items]
Property and Equipment, Gross	[1]	5,314	6,204
Manufacturing Equipment [Member]
Property, Plant and Equipment [Line Items]
Property and Equipment, Gross		2,779	2,753
Laboratory Equipment [Member]
Property, Plant and Equipment [Line Items]
Property and Equipment, Gross		3,026	2,953
Computers and Office Equipment [Member]
Property, Plant and Equipment [Line Items]
Property and Equipment, Gross		1,480	1,469
Leasehold Improvements [Member]
Property, Plant and Equipment [Line Items]
Property and Equipment, Gross		1,435	1,380
Software [Member]
Property, Plant and Equipment [Line Items]
Property and Equipment, Gross		$ 1,142	$ 1,142

[1] The Company does not depreciate Atlas instruments prior to the instruments being placed with customers.

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Intangible Assets (Tables)

9 Months Ended

Sep. 30, 2015

Goodwill and Intangible Assets Disclosure [Abstract]

Summary of Intangible Assets

The following table summarizes the Company's intangible asset as of the periods presented (amounts in thousands):

	September 30, 2015		December 31, 2014
Intangible asset, gross	28,259		28,259
Accumulated amortization	(4,914	)	(2,103	)
Intangible asset, net	23,345		26,156

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Property and Equipment (Tables)

9 Months Ended

Sep. 30, 2015

Property, Plant and Equipment [Abstract]

Schedule of Property and Equipment

The following table provides details of the Company’s property and equipment (amounts in thousands):

	As of September 30,			As of December 31,
	2015			2014
Atlas instruments placed with customers	$	4,589		$	3,875
Atlas instruments intended for placement(1)	5,314			6,204
Manufacturing equipment	2,779			2,753
Laboratory equipment	3,026			2,953
Computer and office equipment	1,480			1,469
Leasehold improvements	1,435			1,380
Software	1,142			1,142
Total property and equipment	$	19,765		$	19,776
Less: Accumulated depreciation	(9,241		)	(7,590		)
Total	$	10,524		$	12,186

Schedule of Expenses for Depreciation of Property and Equipment

Expenses for depreciation of property and equipment were incurred as follows (amounts in thousands):

	For the Three Months Ended September 30,				For the Nine Months Ended September 30,
	2015		2014		2015		2014
Depreciation expense	$	548	$	623	$	1,732	$	1,867

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Convertible Preferred Stock and Stockholders' Equity - Narrative (Details) - $ / shares		9 Months Ended	12 Months Ended
	Jul. 22, 2014	Sep. 30, 2015	Dec. 31, 2014
Temporary Equity [Line Items]
Registration rights, expiration term	5 years
Percentage of registrable securities		51.00%
Total stock, shares authorized (in shares)	520,000,000
Common stock, shares authorized (in shares)	500,000,000	500,000,000	500,000,000
Common stock, par or stated value per share (in USD per share)	$ 0.001	$ 0.001	$ 0.001
Preferred stock, shares authorized (in shares)	20,000,000
Preferred stock, par or stated value per share (in USD per share)	$ 0.001
Common Stock [Member]
Temporary Equity [Line Items]
Conversion of convertible preferred stock into Common Stock (in shares)	10,494,557		10,494,557

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Property and Equipment - Narrative (Details) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Property, Plant and Equipment [Line Items]
Cost of equipment on lease or held for lease, net of accumulated depreciation	$ 10,524	$ 12,186
Accumulated depreciation	9,241	7,590
Atlas Instrument [Member] | Equipment [Member]
Property, Plant and Equipment [Line Items]
Cost of equipment on lease or held for lease, net of accumulated depreciation	8,200	8,900
Accumulated depreciation	$ 1,700	$ 1,200

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Accrued Expenses and Other Current Liabilities (Tables)

9 Months Ended

Sep. 30, 2015

Payables and Accruals [Abstract]

Summary of Accrued Expenses

The following table provides details of the Company’s accrued expenses (amounts in thousands):

	As of September 30,		As of December 31,
	2015		2014
Employee related	$	2,016	$	1,116
Professional services	296		235
Other	411		774
Total accrued expenses and other current liabilities	$	2,723	$	2,125

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Deferred Payments (Tables)

9 Months Ended

Sep. 30, 2015

Other Liabilities Disclosure [Abstract]

Summary of Amounts Deferred under Supply Agreement

The following table summarizes the amounts deferred under this agreement (amounts in thousands):

	As of September 30,			As of December 31,
	2015			2014
Current
Deferred payments, gross	$	1,990		$	1,079
Imputed interest	(330		)	(384		)
Deferred payments, net	$	1,660		$	695
Long-term
Deferred payments, gross	$	2,729		$	3,683
Imputed interest	(226		)	(464		)
Deferred payments, net	$	2,503		$	3,219

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Summary of Significant Accounting Policies

9 Months Ended

Sep. 30, 2015

Accounting Policies [Abstract]

Summary of Significant Accounting Policies

SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Basis of Presentation

The accompanying unaudited condensed financial statements of Roka Bioscience, Inc. have been prepared by the Company in accordance with United States generally accepted accounting principles (“U.S. GAAP”) for interim financial reporting, which do not conform in all respects to the requirements of U.S. GAAP for annual financial statements. The information included in this quarterly report on Form 10-Q should be read in conjunction with the Company’s audited financial statements included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2014 filed with the SEC on March 27, 2015 (the “2014 Form 10-K”). Accordingly, these condensed notes to the unaudited financial statements should be read in conjunction with the 2014 audited financial statements and notes thereto prepared in accordance with U.S. GAAP. The unaudited financial statements have been prepared using accounting policies that are consistent with the policies used in preparing the Company’s audited financial statements for the year ended December 31, 2014. The condensed Balance Sheet as of December 31, 2014 was derived from the Company’s audited financial statements, but does not include all disclosures required by accounting principles generally accepted in the United States. The unaudited financial statements reflect all normal and recurring adjustments necessary, if any, for a fair statement of the Company’s financial position and results of operations for the interim periods presented. The results of operations for the three and nine months ended September 30, 2015 are not necessarily indicative of the results to be expected for the year ending December 31, 2015 or for any other future annual or interim period. There have been no changes in the significant accounting policies from those included in the 2014 Form 10-K. However, in order to further clarify the Company's policy with respect to impairment of long-lived assets, below please find a description of such policy.

Impairment of Long-Lived Assets

The Company’s long-lived assets are primarily comprised of intangible assets and property, plant and equipment. The Company evaluates its finite-lived intangible assets and property, plant and equipment, for impairment whenever events or changes in circumstances indicate the carrying value of an asset or group of assets is not recoverable. If these circumstances exist, recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset group to future undiscounted cash flows expected to be generated by the asset group. If the Company’s estimated undiscounted future cash flows are below the asset group’s carrying value, the Company may recognize an impairment charge measured by its fair value.

Common A and Common B Reverse Stock Split

In July 2014, the Company’s board of directors authorized and the Company’s shareholders approved an 11.04:1 reverse stock split of the Company’s Common A and Common B shares, effective on July 3, 2014. In addition, effective on the date of the reverse stock split, the conversion ratio of Convertible Preferred Stock was adjusted by a factor of 11.04 and consequently, each share of Series B, Series C and Series E became convertible into approximately 0.0906 shares of Common Stock and each share of Series D became convertible into approximately 0.0937 shares of Common Stock. As stated in Note 1, all shares of Common A, Common B and Convertible Preferred Stock converted into Common Stock upon the completion of the Company's IPO. The Company’s historical share and per share information have been retroactively adjusted to give effect to this reverse split and corresponding change in conversion ratio.

New Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (“FASB”) or other standard setting bodies and adopted by the Company as of the specified effective date.

In July 2015, the FASB issued ASU No. 2015-11, Simplifying the Measurement of Inventory. This standard amends existing guidance and requires entities to measure most inventory at the lower of cost and net realizable value. This standard is effective for annual reporting periods beginning after December 15, 2016, and early adoption is permitted. This standard is to be applied on a prospective basis and upon adoption, entities must disclose the nature of and reason for the accounting change. The Company is currently in the process of evaluating the impact this new guidance will have on its financial statements.

In April 2015, the FASB issued ASU No. 2015-05, Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Fees Paid in a Cloud Computing Arrangement. This standard provides guidance to customers about whether a cloud computing arrangement includes a software license. If a cloud computing arrangement includes a software license, then the customer should account for the software license element of the arrangement consistent with the acquisition of other software licenses. If a cloud computing arrangement does not include a software license, the customer should account for the arrangement as a service contract. This amendment is effective for annual periods, including interim periods within those annual periods, beginning after December 15, 2015, and early adoption is permitted. The Company has evaluated this new guidance and determined it will not have an impact on the Company's financial statements.

In August 2014, the FASB issued ASU No. 2014-15, Presentation of Financial Statements—Going Concern (Subtopic 205-40): Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern, which is intended to define management’s responsibility to evaluate whether there is substantial doubt about an organization’s ability to continue as a going concern and to provide related footnote disclosures. This ASU provides guidance to an organization’s management, with principles and definitions that are intended to reduce diversity in the timing and content of disclosures that are commonly provided by organizations today in the financial statement footnotes. The amendments are effective for annual periods ending after December 15, 2016, and interim periods within annual periods beginning after December 15, 2016, and early adoption is permitted. The Company does not believe this new guidance will have a material impact on its financial statements.

In May 2014, the FASB issued ASU 2014-09, Revenue from Contracts with Customers. This standard outlines a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers and supersedes most current revenue recognition guidance. ASU 2014-09 provides companies with two implementation methods. Companies can choose to apply the standard retrospectively to each prior reporting period presented (full retrospective application) or retrospectively with the cumulative effect of initially applying the standard as an adjustment to the opening balance of retained earnings of the annual reporting period that includes the date of initial application (modified retrospective application). This ASU is effective for annual periods ending after December 15, 2016, and interim periods within annual periods beginning after December 15, 2016. In August 2015, the FASB issued ASU 2015-14, Revenue from Contracts with Customers - Deferral of the Effective Date. This ASU defers the effective date of Update 2014-09 for all entities by one year, requiring the guidance in ASU 2014-09 to be applied for annual reporting periods beginning after December 15, 2017, including interim reporting periods within that reporting period. Additionally, this ASU permits earlier application only as of annual reporting periods beginning after December 15, 2016, including interim reporting periods within that reporting period. The Company is currently in the process of evaluating the impact this new guidance will have on its financial statements.

Adoption of New Accounting Principle

In April 2015, the FASB issued Accounting Standards Update (“ASU”) No. 2015-03, Interest - Imputation of Interest: Simplifying the Presentation of Debt Issuance Costs which is intended to simplify the accounting for and presentation of debt issuance costs. This ASU requires debt issuance costs to no longer be capitalized as an asset on the balance sheet and amortized as a deferred charge, and instead be treated as a direct deduction from the face amount of the note. This guidance is effective for annual reporting periods beginning after December 15, 2015, including interim periods within that reporting period, and early application is permitted. The Company adopted the new guidance beginning in the interim period ended June 30, 2015 and has applied the guidance to its financial statements on a retrospective basis, wherein the balance sheet of each individual period presented has been adjusted to reflect the period-specific effects of applying the new guidance. The application of this new guidance did not have a material impact on the Company's financial statements. There were no cumulative changes to the Statement of Operations and Comprehensive Loss or the Statement of Convertible Preferred Stock and Stockholders’ Equity (Deficit); changes to the Balance Sheet as of December 31, 2014 as a result of this new accounting principle are noted below (amounts in thousands):

	As of December 31, 2014
	Adjusted	As previously reported	Change
Other assets	262	308	(46	)
Total assets	103,779	103,825	(46	)
Notes payable, current	9,910	9,956	(46	)
Total current liabilities	13,864	13,910	(46	)
Total liabilities	24,704	24,750	(46	)
Total liabilities and stockholders' equity	103,779	103,825	(46	)

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Fair Value Measurements (Tables)

9 Months Ended

Sep. 30, 2015

Fair Value Disclosures [Abstract]

Summary of Fair Value Information for Cash Held in Money Market Deposit Accounts and Marketable Securities

The following table summarizes the fair value information for the Company’s cash held in money market deposit accounts and its marketable securities at September 30, 2015 and December 31, 2014 (amounts in thousands):

			Fair value measurements using:
	Carrying Value		Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)	Significant Unobservable Inputs (Level 3)
Financial Assets and Liabilities Carried at Fair Value
As of September 30, 2015
Financial Assets:
Money market deposit accounts	$	4,547	$	4,547	—	—
As of December 31, 2014
Financial Assets:
Money market deposit accounts	$	5,741	$	5,741	—	—
Financial Assets Carried at Amortized Cost
As of September 30, 2015
Short-term marketable securities	$	30,946	$	5,004	25,932	—
As of December 31, 2014
Short-term marketable securities	$	36,231	$	10,081	26,116	—
Long-term marketable securities	$	13,366	$	2,001	11,337	—

Summary of the Changes in the Convertible Preferred Stock Warrant Liability

The table below provides a summary of the changes in the Convertible preferred stock warrant liability during the nine months ended September 30, 2014 (amounts in thousands):

	For the Nine Months Ended September 30, 2014
Balance at beginning of period	$	212
Increase in Series E warrant shares	135
Change in fair value of warrants(1)	1,017
Reclassification to equity(2)	$	(1,364	)
Balance at end of period	$	—

(1) Amount includes $0.7 million of prior period fair value adjustments.

(2) The warrants were re-measured to fair value and reclassified to additional paid-in capital upon the completion of the Company's initial public offering.

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Marketable Securities - Summary of the Fair Value of Held-to-Maturity Marketable Securities (Details) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Short-term marketable securities [Member]
Schedule of Held-to-maturity Securities [Line Items]
Debt securities, Short-term, Amortized Cost	$ 30,946	$ 36,231
Gross Unrealized Holding Gains	3	2
Gross Unrealized Holding Losses	(13)	(36)
Debt securities, Short-term, Aggregate Fair Value	$ 30,936	36,197
Long-term marketable securities [Member]
Schedule of Held-to-maturity Securities [Line Items]
Debt securities, Long-term, Amortized Cost		13,366
Gross Unrealized Holding Gains		4
Gross Unrealized Holding Losses		(32)
Debt securities, Long-term, Aggregate Fair Value		$ 13,338

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Fair Value Measurements - Summary of Fair Value Information for Cash Held in Money Market Deposit Accounts and Marketable Securities (Details) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Financial Liabilities:
Short-term marketable securities	$ 30,946	$ 36,231
Long-term marketable securities	0	13,366
Debt Securities [Member]
Financial Liabilities:
Short-term marketable securities	30,946	36,231
Long-term marketable securities		13,366
Money Market Deposit Accounts [Member]
Financial Assets:
Money market deposit accounts	4,547	5,741
Quoted Prices in Active Markets (Level 1) [Member] | Debt Securities [Member]
Financial Liabilities:
Short-term marketable securities	5,004	10,081
Long-term marketable securities		2,001
Quoted Prices in Active Markets (Level 1) [Member] | Money Market Deposit Accounts [Member]
Financial Assets:
Money market deposit accounts	4,547	5,741
Significant Other Observable Inputs (Level 2) [Member] | Debt Securities [Member]
Financial Liabilities:
Short-term marketable securities	25,932	26,116
Long-term marketable securities		11,337
Significant Other Observable Inputs (Level 2) [Member] | Money Market Deposit Accounts [Member]
Financial Assets:
Money market deposit accounts	0	0
Significant Unobservable Inputs (Level 3) [Member] | Debt Securities [Member]
Financial Liabilities:
Short-term marketable securities	0	0
Long-term marketable securities		0
Significant Unobservable Inputs (Level 3) [Member] | Money Market Deposit Accounts [Member]
Financial Assets:
Money market deposit accounts	$ 0	$ 0

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Condensed Balance Sheets (unaudited) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Current Assets:
Cash and cash equivalents	$ 6,949	$ 7,503
Short-term marketable securities	30,946	36,231
Trade accounts receivable, net of $0 allowance for doubtful accounts	681	670
Inventories	4,366	4,930
Prepaid expenses and other current assets	1,975	2,115
Total current assets	44,917	51,449
Long-term marketable securities	0	13,366
Property and equipment, net	10,524	12,186
Intangible assets, net	23,345	26,156
Goodwill	360	360
Other assets	264	262
Total assets	79,410	103,779
Current Liabilities:
Accounts payable	413	1,134
Short-term deferred payments	1,660	695
Notes payable, current	9,811	9,910
Accrued expenses and other current liabilities	2,723	2,125
Total current liabilities	14,607	13,864
Deferred payments	10,187	10,457
Deferred tax liabilities	49	49
Other long-term liabilities	321	334
Total liabilities	$ 25,164	$ 24,704
Commitments and Contingencies (See Note 11)
Common stock, $0.001 par value: 500,000,000 shares of Common Stock authorized; 18,050,024 shares issued and 18,045,058 shares outstanding, respectively at September 30, 2015; 17,660,432 shares issued and 17,658,373 shares outstanding at December 31, 2014	$ 18	$ 18
Additional paid-in capital	213,846	212,069
Treasury stock, at cost: 6,319 shares at September 30, 2015 and 2,059 shares at December 31, 2014	(22)	(8)
Accumulated deficit	(159,596)	(133,004)
Total liabilities and stockholders’ equity	54,246	79,075
Total liabilities and stockholders' equity	$ 79,410	$ 103,779

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Property and Equipment - Schedule of Expenses for Depreciation of Property and Equipment (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Property, Plant and Equipment [Abstract]
Depreciation expense	$ 548	$ 623	$ 1,732	$ 1,867

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Condensed Statements of Cash Flows (unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014
Cash flows from operating activities
Net loss	$ (26,592)	$ (24,799)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	4,543	2,690
Change in fair value of financial instruments	0	785
Loss on disposal of property and equipment	0	98
Provisions for inventory	374	991
Share-based compensation expense	1,600	765
Non-cash interest expense	1,138	800
Changes in operating assets and liabilities:
Accounts receivable	(154)	(549)
Inventories	189	(2,005)
Prepaid expenses and other assets	607	492
Accounts payable and accrued expenses	0	(397)
Deferred taxes	0	3,135
Other liabilities	(12)	(2)
Net cash used in operating activities	(18,307)	(17,996)
Cash flows from investing activities
Purchases of property and equipment	(165)	(199)
Proceeds from sale of property and equipment	71	60
Purchase of marketable securities	(9,856)	0
Proceeds from maturities of marketable securities	28,040	0
Payment pursuant to amended license agreement and option exercise	0	(10,500)
Net cash provided by (used in) investing activities	18,090	(10,639)
Cash flows from financing activities
Net proceeds from issuance of convertible preferred stock and warrants	0	(99)
Net proceeds from issuance of debt and warrants	4,950	5,000
Principal repayments	(5,350)	0
Proceeds from exercise of stock options	77	270
Restricted shares withheld for taxes	(14)	0
Proceeds from issuance of common stock, net of issuance costs	0	53,585
Net cash provided by financing activities	(337)	58,756
Net change in cash and cash equivalents	(554)	30,121
Cash and cash equivalents, beginning of period	7,503	32,728
Cash and cash equivalents, end of period	$ 6,949	$ 62,849

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Stock-Based Compensation - Summary of Range of Assumptions Utilized for Stock Options Granted (Details)	9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Volatility		60.00%
Dividend yield	0.00%	0.00%
Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected life in years	5 years 9 months 7 days	5 years 10 months 24 days
Interest rate	1.06%	2.01%
Volatility	75.00%
Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected life in years	6 years 3 months 15 days	6 years
Interest rate	1.80%	2.04%
Volatility	90.00%

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Segment Information (Tables)

9 Months Ended

Sep. 30, 2015

Segment Reporting [Abstract]

Schedule of Revenue by Major Customers by Reporting Segments [Table Text Block]

These customers accounted for revenues as follows (amounts in thousands):

	Nine Months Ended September 30,
	2015	2014
Customer A	1,040	648
Customer B	889	1,086
Customer C	623	631
Customer D	463	411

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Net Loss Per Share

9 Months Ended

Sep. 30, 2015

Earnings Per Share [Abstract]

Net Loss per Share

NET LOSS PER SHARE

Basic net loss per share is calculated by dividing net loss applicable to common stockholders by the weighted-average shares outstanding during the period, without consideration for common stock equivalents. The weighted-average common shares outstanding excludes unvested restricted stock which although such shares are legally issued and outstanding, are not required to share in losses of the Company and are therefore excluded from the net loss per share calculation. Diluted net loss per share is calculated by adjusting the weighted-average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury-stock method. For purposes of the diluted net loss per share calculation, Convertible Preferred Stock, stock options and warrants are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive. Therefore, basic and diluted net loss per share applicable to common stockholders were the same for all periods presented. Prior to the IPO, the Company had two classes of common stock outstanding, and in connection with the IPO, the two classes were converted into a new class of Common Stock. The tables in this footnote are retroactively adjusted to show the results as if only the new class of Common Stock was outstanding for the entirety of each of the respective periods.

	For the Three Months Ended September 30,						For the Nine Months Ended September 30,
	2015			2014			2015			2014
Net loss applicable to common shareholders (thousands)	$	(8,491	)	$	(9,083	)	$	(26,592	)	$	(24,799	)
Basic and diluted weighted average common shares outstanding	17,303,490			14,153,715			17,262,033			5,188,516
Basic and diluted loss per share	$	(0.49	)	$	(0.64	)	$	(1.54	)	$	(4.78	)

As the Company incurred a loss for the three and nine months endedSeptember 30, 2015 and 2014, all unvested restricted stock awards were excluded from the calculation of basic net loss per share and all potential Common Stock shares issuable for Convertible Preferred Stock, stock options and warrants were excluded from the calculation of diluted net loss per share, as the effect of including them would have been anti-dilutive. Had the Company not incurred a loss, the dilutive effect of the unvested restricted stock awards on basic weighted average common shares outstanding and the dilutive effect of potential Common Stock shares issuable for Convertible Preferred Stock, stock options and warrants on the weighted-average number of Common Stock shares outstanding would have been as follows:

	For the Three Months Ended September 30,		For the Nine Months Ended September 30,
	2015	2014	2015	2014
Basic weighted average shares outstanding	17,303,490	14,153,715	17,262,033	5,188,516
Dilutive effect of unvested restricted stock	—	301,846	71,860	262,861
Basic weighted average shares outstanding had the Company not incurred a loss	17,303,490	14,455,561	17,333,893	5,451,377
Dilutive effect of Convertible Preferred Stock	—	1,939,212	—	7,642,775
Dilutive effect of warrants	—	208	—	69
Dilutive effect of stock options	78,284	339,272	97,444	363,792
Diluted weighted average shares outstanding had the Company not incurred a loss	17,381,774	16,734,253	17,431,337	13,458,013

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Business Overview - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands		9 Months Ended		12 Months Ended
	Jul. 22, 2014	Sep. 30, 2015	Sep. 30, 2014	Dec. 31, 2014
Subsidiary, Sale of Stock [Line Items]
Proceeds from issuance of common stock, net of issuance costs		$ 0	$ 53,585
Common Class A and Class B [Member]
Subsidiary, Sale of Stock [Line Items]
Common stock, conversion basis	1:1
IPO [Member]
Subsidiary, Sale of Stock [Line Items]
Proceeds from issuance of common stock, net of issuance costs	$ 53,200
Common Stock [Member] | IPO [Member]
Subsidiary, Sale of Stock [Line Items]
Issuance of common stock from initial public offering, net of underwriters’ discounts and issuance costs (in shares)	5,000,000			5,000,000
IPO, price per share (in USD per share)	$ 12.00

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Summary of Significant Accounting Policies (Policies)

9 Months Ended

Sep. 30, 2015

Accounting Policies [Abstract]

Basis of Presentation

Basis of Presentation

The accompanying unaudited condensed financial statements of Roka Bioscience, Inc. have been prepared by the Company in accordance with United States generally accepted accounting principles (“U.S. GAAP”) for interim financial reporting, which do not conform in all respects to the requirements of U.S. GAAP for annual financial statements. The information included in this quarterly report on Form 10-Q should be read in conjunction with the Company’s audited financial statements included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2014 filed with the SEC on March 27, 2015 (the “2014 Form 10-K”). Accordingly, these condensed notes to the unaudited financial statements should be read in conjunction with the 2014 audited financial statements and notes thereto prepared in accordance with U.S. GAAP. The unaudited financial statements have been prepared using accounting policies that are consistent with the policies used in preparing the Company’s audited financial statements for the year ended December 31, 2014. The condensed Balance Sheet as of December 31, 2014 was derived from the Company’s audited financial statements, but does not include all disclosures required by accounting principles generally accepted in the United States. The unaudited financial statements reflect all normal and recurring adjustments necessary, if any, for a fair statement of the Company’s financial position and results of operations for the interim periods presented. The results of operations for the three and nine months ended September 30, 2015 are not necessarily indicative of the results to be expected for the year ending December 31, 2015 or for any other future annual or interim period. There have been no changes in the significant accounting policies from those included in the 2014 Form 10-K.

Impairment of Long-Lived Assets

Impairment of Long-Lived Assets

The Company’s long-lived assets are primarily comprised of intangible assets and property, plant and equipment. The Company evaluates its finite-lived intangible assets and property, plant and equipment, for impairment whenever events or changes in circumstances indicate the carrying value of an asset or group of assets is not recoverable. If these circumstances exist, recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset group to future undiscounted cash flows expected to be generated by the asset group. If the Company’s estimated undiscounted future cash flows are below the asset group’s carrying value, the Company may recognize an impairment charge measured by its fair value.

New Accounting Pronouncements

New Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (“FASB”) or other standard setting bodies and adopted by the Company as of the specified effective date.

In July 2015, the FASB issued ASU No. 2015-11, Simplifying the Measurement of Inventory. This standard amends existing guidance and requires entities to measure most inventory at the lower of cost and net realizable value. This standard is effective for annual reporting periods beginning after December 15, 2016, and early adoption is permitted. This standard is to be applied on a prospective basis and upon adoption, entities must disclose the nature of and reason for the accounting change. The Company is currently in the process of evaluating the impact this new guidance will have on its financial statements.

In April 2015, the FASB issued ASU No. 2015-05, Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Fees Paid in a Cloud Computing Arrangement. This standard provides guidance to customers about whether a cloud computing arrangement includes a software license. If a cloud computing arrangement includes a software license, then the customer should account for the software license element of the arrangement consistent with the acquisition of other software licenses. If a cloud computing arrangement does not include a software license, the customer should account for the arrangement as a service contract. This amendment is effective for annual periods, including interim periods within those annual periods, beginning after December 15, 2015, and early adoption is permitted. The Company has evaluated this new guidance and determined it will not have an impact on the Company's financial statements.

In August 2014, the FASB issued ASU No. 2014-15, Presentation of Financial Statements—Going Concern (Subtopic 205-40): Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern, which is intended to define management’s responsibility to evaluate whether there is substantial doubt about an organization’s ability to continue as a going concern and to provide related footnote disclosures. This ASU provides guidance to an organization’s management, with principles and definitions that are intended to reduce diversity in the timing and content of disclosures that are commonly provided by organizations today in the financial statement footnotes. The amendments are effective for annual periods ending after December 15, 2016, and interim periods within annual periods beginning after December 15, 2016, and early adoption is permitted. The Company does not believe this new guidance will have a material impact on its financial statements.

In May 2014, the FASB issued ASU 2014-09, Revenue from Contracts with Customers. This standard outlines a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers and supersedes most current revenue recognition guidance. ASU 2014-09 provides companies with two implementation methods. Companies can choose to apply the standard retrospectively to each prior reporting period presented (full retrospective application) or retrospectively with the cumulative effect of initially applying the standard as an adjustment to the opening balance of retained earnings of the annual reporting period that includes the date of initial application (modified retrospective application). This ASU is effective for annual periods ending after December 15, 2016, and interim periods within annual periods beginning after December 15, 2016. In August 2015, the FASB issued ASU 2015-14, Revenue from Contracts with Customers - Deferral of the Effective Date. This ASU defers the effective date of Update 2014-09 for all entities by one year, requiring the guidance in ASU 2014-09 to be applied for annual reporting periods beginning after December 15, 2017, including interim reporting periods within that reporting period. Additionally, this ASU permits earlier application only as of annual reporting periods beginning after December 15, 2016, including interim reporting periods within that reporting period. The Company is currently in the process of evaluating the impact this new guidance will have on its financial statements.

Debt Issuance Costs

In April 2015, the FASB issued Accounting Standards Update (“ASU”) No. 2015-03, Interest - Imputation of Interest: Simplifying the Presentation of Debt Issuance Costs which is intended to simplify the accounting for and presentation of debt issuance costs. This ASU requires debt issuance costs to no longer be capitalized as an asset on the balance sheet and amortized as a deferred charge, and instead be treated as a direct deduction from the face amount of the note. This guidance is effective for annual reporting periods beginning after December 15, 2015, including interim periods within that reporting period, and early application is permitted. The Company adopted the new guidance beginning in the interim period ended June 30, 2015 and has applied the guidance to its financial statements on a retrospective basis, wherein the balance sheet of each individual period presented has been adjusted to reflect the period-specific effects of applying the new guidance. The application of this new guidance did not have a material impact on the Company's financial statements.

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Business Overview

9 Months Ended

Sep. 30, 2015

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Business Overview

BUSINESS OVERVIEW

Business

Roka Bioscience, Inc. (“Roka” or “the Company”) is focused on the development and commercialization of molecular assay technologies for the detection of foodborne pathogens. The Company was established in September 2009 through the acquisition of industrial testing assets and technology from Gen-Probe Incorporated, which was subsequently acquired by Hologic, Inc. (herein referred to as “Gen-Probe”).

The Company has limited capital resources, has experienced negative cash flows from operations and has incurred net losses since inception. The Company expects to continue to experience negative cash flows from operations and incur net losses in the near term as it devotes substantially all of its efforts on commercialization of its products and continued product development. The Company’s business is subject to significant risks and its ability to successfully develop, manufacture and commercialize proprietary products is dependent upon many factors which include, but are not limited to, risks and uncertainties associated with the supply of molecular diagnostic instruments (“Atlas instruments”) and materials, product development, manufacturing scale-up, attracting and retaining key personnel, customer acceptance as well as competition.

On July 22, 2014, the Company completed an initial public offering ("IPO") in which it sold 5,000,000 shares of common stock at $12.00 per share, before underwriting discounts. The Company received $53.2 million of net proceeds from the offering after deducting underwriting discounts, commissions and offering expenses. In connection with the closing of the IPO, all shares of the Company’s Class A common stock (“Common A”) and Class B common stock (“Common B”) were converted into a new class of common stock ("Common Stock") on a 1:1 basis and all shares of Series B Convertible Preferred Stock (“Series B”), Series C Convertible Preferred Stock (“Series C”), Series D Convertible Preferred Stock (“Series D”) and Series E Convertible Preferred Stock (“Series E”), collectively referred to as “Convertible Preferred Stock”, were converted into Common Stock at their respective conversion ratios.

The Company will need to raise additional capital through the sale of equity and/or debt securities in the future. There is no assurance that the Company will be able to raise needed capital under acceptable terms, if at all. The sale of additional equity may dilute existing shareholders and newly issued shares may contain senior rights and preferences compared to currently outstanding common stock. Issued debt securities may contain covenants and limit the Company’s ability to pay dividends or make other distributions to stockholders. In addition, the Company’s debt agreement contains certain clauses which allow the lenders to require repayment of the debt based on subjective factors regarding the Company’s business and performance if considered a material adverse change by the lender.

Concentration of Suppliers

The Company relies on single source suppliers, including Gen-Probe, for certain components and materials used in its products, including its Atlas Detection Assays. Since the Company’s contracts with these suppliers, including Gen-Probe, do not commit the suppliers to carry inventory or to make available any minimum quantities, the Company may be unable to obtain adequate supplies in a timely manner or on commercially reasonable terms.  If the Company loses such suppliers, or its suppliers encounter financial hardships, the Company may not be able to identify or enter into agreements with alternative suppliers on a timely basis on acceptable terms, if at all. Transitioning to a new supplier could be time consuming, may be expensive, may result in an interruption in the Company’s operations and could affect the performance specifications of the Company’s products. If the Company should encounter delays or difficulties in securing the quality and quantity of materials required for its products, the Company’s ability to manufacture its products would be interrupted which could adversely affect sales.

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Condensed Balance Sheets (unaudited) (Parenthetical) - USD ($)	Sep. 30, 2015	Dec. 31, 2014
Statement of Financial Position [Abstract]
Allowance for doubtful accounts	$ 0	$ 0
Common stock par value (in USD per share)	$ 0.001	$ 0.001
Common stock, shares authorized (in shares)	500,000,000	500,000,000
Common stock, shares issued (in shares)	18,077,197	17,660,432
Common stock, shares outstanding (in shares)	18,070,878	17,658,373
Treasury stock (in shares)	6,319	2,059

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Commitments and Contingencies

9 Months Ended

Sep. 30, 2015

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

COMMITMENTS AND CONTINGENCIES

Operating Leases

The Company has not entered into any new operating leases or amended any existing operating leases during the nine months ended September 30, 2015.

Commitments

During the nine months ended September 30, 2015, there have been no significant changes to the Company’s commitments as disclosed in the Company’s most recent audited financial statements.

Contingent liabilities

In addition to the commitments disclosed in the Company’s most recent audited financial statements, the amendment to the license agreement with Gen-Probe detailed in Note 9 provides for additional milestone payments of up to $6.0 million which will further reduce the royalty rate paid. Such payments are required to be made upon meeting certain revenue milestones or may be made at the election of the Company prior to meeting the revenue milestones.

Legal Matters

The Company may periodically become subject to legal proceedings and claims arising in connection with its business. Except as set forth below, the Company is not currently involved in any legal proceedings, nor are any claims pending against the Company.

A putative securities class action originally captioned Ding v. Roka Bioscience, Inc., Case No. 3:14-cv-8020, was filed against the Company and certain of its officers and directors in the United States District Court for the District of New Jersey on December 24, 2014, on behalf of a putative class of persons and entities who had purchased or otherwise acquired securities pursuant or traceable to the Registration Statement for the Company’s IPO. The original putative class period ran from July 17 through November 6, 2014.  The original complaint asserted claims under the Securities Act of 1933 and contended that the IPO Registration Statement was false and misleading, or omitted allegedly material information, in connection with the Company’s statements about its placement of Atlas instruments and its expectations of future growth and increased market share, and the Company’s alleged failure to disclose “known trends and uncertainties about the Company’s sales.”  The alleged misrepresentations and omissions purportedly came to light when the Company issued its third-quarter 2014 earnings release on November 6, 2014.

Pursuant to the Private Securities Litigation Reform Act of 1995, two applicants filed motions on February 23, 2015 for appointment as lead plaintiff.  On March 23, 2015, the applicant with the smaller loss agreed not to oppose the application for lead plaintiff filed by the applicant with the larger loss. The court appointed Stanley Yedlowski as lead plaintiff and The Rosen Law Firm as lead counsel on April 21, 2015. The lead plaintiff then filed an amended complaint, captioned Stanley Yedlowski v. Roka Bioscience, Inc., Case No. 14-cv-8020, on June 23, 2015. The amended complaint pleads Securities Act claims on behalf of persons and entities who purchased or otherwise acquired Roka securities pursuant or traceable to the IPO Registration Statement during an extended putative class period, running from July 17, 2014 through March 26, 2015. The amended complaint alleges that the Registration Statement was false or misleading in that it failed to disclose that the Company’s customers purportedly were experiencing false positives and other usage issues with the Company’s Listeria assays apparently arising from the customers’ employees’ inability to follow the Company’s Listeria assay workflow. The amended complaint alleges that the full extent of the purported misstatements and omissions was not revealed until March 26, 2015. Defendants filed a motion on August 25, 2015 to dismiss the amended complaint, and plaintiffs filed an opposition to that motion on October 9, 2015. The parties have agreed to attempt to resolve the case through mediation in December 2015.

The Company believes that the claims in the securities class action are without merit and, if the mediation is unsuccessful, the Company intends to defend the litigation vigorously, and expects to incur costs associated with defending the securities class action. The Company has various insurance policies related to the risks associated with its business, including directors’ and officers’ liability insurance policies. However, there is no assurance that the Company will be successful in its defense of the securities class action, and there is no assurance that the insurance coverage will be sufficient or that the insurance carriers will cover all claims or litigation costs. At this early stage of the litigation, the Company cannot accurately predict the ultimate outcome of this matter. Due to the inherent uncertainties of litigation, the Company cannot reasonably predict the timing or outcomes, or estimate the amount of loss, if any, or their effect, if any, on its financial statements.

The Company sells its products in various jurisdictions and is subject to federal, state and local taxes including, where applicable, sales and use tax. While the Company believes that it has properly paid or accrued for all such taxes based on its interpretation of applicable law, tax laws are complex and interpretations differ. Periodically, the Company may be audited by taxing authorities, and it is possible that additional assessments may be made in the future.

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Document and Entity Information - shares	9 Months Ended
	Sep. 30, 2015	Nov. 09, 2015
Document And Entity Information [Abstract]
Document type	10-Q
Amendment Flag	false
Document Period End Date	Sep. 30, 2015
Document Fiscal Year Focus	2015
Document Fiscal Period Focus	Q3
Trading Symbol	ROKA
Entity Registrant Name	ROKA BIOSCIENCE, INC.
Entity Central Index Key	0001472343
Current Fiscal Year End Date	--12-31
Entity Filer Category	Smaller Reporting Company
Entity Common Stock, Shares Outstanding		18,069,968

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Fair Value Measurements

9 Months Ended

Sep. 30, 2015

Fair Value Disclosures [Abstract]

Fair Value Measurements

FAIR VALUE MEASUREMENTS

The Company’s financial instruments consist of cash and cash equivalents, marketable securities, trade accounts receivable, accounts payable, short-term deferred payments, deferred payments, notes payable, accrued expenses and Convertible Preferred Stock Warrants. The carrying amounts of cash and cash equivalents, trade accounts receivable, accounts payable, short-term deferred payments and accrued expenses approximate their fair values because of the short-term nature of the instruments, or, in the case of the deferred payments and notes payable, because the interest rates the Company believes it could obtain for similar borrowings is similar to its existing interest rates.  The carrying amount of the Company's marketable securities is the amortized cost basis based upon their held-to-maturity classification.

The following table summarizes the fair value information for the Company’s cash held in money market deposit accounts and its marketable securities at September 30, 2015 and December 31, 2014 (amounts in thousands):

			Fair value measurements using:
	Carrying Value		Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)	Significant Unobservable Inputs (Level 3)
Financial Assets and Liabilities Carried at Fair Value
As of September 30, 2015
Financial Assets:
Money market deposit accounts	$	4,547	$	4,547	—	—
As of December 31, 2014
Financial Assets:
Money market deposit accounts	$	5,741	$	5,741	—	—
Financial Assets Carried at Amortized Cost
As of September 30, 2015
Short-term marketable securities	$	30,946	$	5,004	25,932	—
As of December 31, 2014
Short-term marketable securities	$	36,231	$	10,081	26,116	—
Long-term marketable securities	$	13,366	$	2,001	11,337	—

A portion of the Company’s cash and cash equivalents are held in money market deposit accounts and a portion of the Company's short-term marketable securities are United States treasury bills, each of which are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices.

The Company's short-term marketable securities and long-term marketable securities not classified within Level 1 of the fair value hierarchy are comprised of commercial paper, U.S. government-related debt, and corporate debt securities, all of which are classified as  Level 2 within the fair value hierarchy. The Company estimates the fair values of these marketable securities by taking into consideration valuations obtained from its investment manager, which utilizes industry standard valuation models, including both income and market-based approaches, for which all significant inputs are observable, either directly or indirectly, to estimate fair value. There have been no transfers between levels during the reporting period.

There were no convertible preferred stock warrants outstanding during the nine months ended September 30, 2015. In conjunction with the closing of the Company’s IPO, the warrants exercisable for shares of Preferred Stock were automatically converted into warrants exercisable for shares of its Common Stock, resulting in the reclassification of the related convertible preferred stock warrant liability to Additional paid-in capital as the warrants to purchase shares of common stock met the criteria for equity classification. Per ASC 820, Fair Value Measurements and Disclosures, (“ASC 820”) the Convertible Preferred Stock Warrants which were outstanding during the nine months ended September 30, 2014 were revalued to their fair value, using the Black-Scholes option-pricing model, at September 30, 2014 and the change in fair value is reflected in the Statement of Operations and Comprehensive Loss. The table below provides a summary of the changes in the Convertible preferred stock warrant liability during the nine months ended September 30, 2014 (amounts in thousands):

	For the Nine Months Ended September 30, 2014
Balance at beginning of period	$	212
Increase in Series E warrant shares	135
Change in fair value of warrants(1)	1,017
Reclassification to equity(2)	$	(1,364	)
Balance at end of period	$	—

(1) Amount includes $0.7 million of prior period fair value adjustments.

(2) The warrants were re-measured to fair value and reclassified to additional paid-in capital upon the completion of the Company's initial public offering.

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Condensed Statements of Operations and Comprehensive Loss (unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Income Statement [Abstract]
Revenue	$ 1,508	$ 1,483	$ 4,484	$ 3,701
Operating expenses:
Cost of revenue	1,672	2,578	5,391	5,416
Research and development	2,058	1,922	5,823	5,991
Selling, general and administrative	4,924	4,618	15,453	14,214
Amortization of intangible assets	937	738	2,811	822
Total operating expenses	9,591	9,856	29,478	26,443
Loss from operations	(8,083)	(8,373)	(24,994)	(22,742)
Other income (expense):
Change in fair value of financial instruments	0	(223)	0	(785)
Interest income (expense), net	(404)	(476)	(1,588)	(1,244)
Loss before income taxes	(8,487)	(9,072)	(26,582)	(24,771)
Income tax provision (benefit)	4	11	10	28
Net loss and comprehensive loss	$ (8,491)	$ (9,083)	$ (26,592)	$ (24,799)
Net Loss per Common Share:
Basic and diluted (in USD per share)	$ (0.49)	$ (0.64)	$ (1.54)	$ (4.78)
Weighted average common shares outstanding used in computing net loss per common share:
Basic and diluted (in shares)	17,303,490	14,153,715	17,262,033	5,188,516

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Property and Equipment

9 Months Ended

Sep. 30, 2015

Property, Plant and Equipment [Abstract]

Property and Equipment

PROPERTY AND EQUIPMENT

The following table provides details of the Company’s property and equipment (amounts in thousands):

	As of September 30,			As of December 31,
	2015			2014
Atlas instruments placed with customers	$	4,589		$	3,875
Atlas instruments intended for placement(1)	5,314			6,204
Manufacturing equipment	2,779			2,753
Laboratory equipment	3,026			2,953
Computer and office equipment	1,480			1,469
Leasehold improvements	1,435			1,380
Software	1,142			1,142
Total property and equipment	$	19,765		$	19,776
Less: Accumulated depreciation	(9,241		)	(7,590		)
Total	$	10,524		$	12,186

(1) The Company does not depreciate Atlas instruments prior to the instruments being placed with customers.

As of September 30, 2015 and December 31, 2014, the cost of Atlas instruments, which represents equipment on lease or held for lease, was $8.2 million and $8.9 million, respectively, net of accumulated depreciation of $1.7 million and $1.2 million, respectively.

Expenses for depreciation of property and equipment were incurred as follows (amounts in thousands):

	For the Three Months Ended September 30,				For the Nine Months Ended September 30,
	2015		2014		2015		2014
Depreciation expense	$	548	$	623	$	1,732	$	1,867

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Inventories

9 Months Ended

Sep. 30, 2015

Inventory Disclosure [Abstract]

Inventories

INVENTORIES

The following table provides details of the Company’s net inventories (amounts in thousands):

	As of September 30,		As of December 31,
	2015		2014
Raw materials	$	1,744	$	1,914
Work in process	—		11
Finished goods	2,622		3,005
	$	4,366	$	4,930

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Segment Information

9 Months Ended

Sep. 30, 2015

Segment Reporting [Abstract]

Segment Information

SEGMENT INFORMATION

The Company operates in a single reportable segment. During each of the nine months endedSeptember 30, 2015, and the nine months endedSeptember 30, 2014, the Company had four customers which each generated more than 10% of the Company’s revenues. These customers accounted for revenues as follows (amounts in thousands):

	Nine Months Ended September 30,
	2015	2014
Customer A	1,040	648
Customer B	889	1,086
Customer C	623	631
Customer D	463	411

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Convertible Preferred Stock and Stockholders' Equity

9 Months Ended

Sep. 30, 2015

Equity [Abstract]

Convertible Preferred Stock and Stockholders' Equity

CONVERTIBLE PREFERRED STOCK AND STOCKHOLDERS’ EQUITY

Registration rights

Prior to the IPO, the Company had multiple classes of preferred stock for which shares were authorized, issued and outstanding. At the closing of the Company's IPO, all shares of Convertible Preferred Stock converted into 10,494,557 shares of Common Stock. The holders of these shares have demand, short-form and piggyback registration rights under the terms of an investor rights agreement between such holders and the Company which will expire upon the earlier of (i) five years after the Company's IPO and (ii) as to a holder, at such time as all registrable securities held by such holder may be sold without restriction under Rule 144. Upon request of holders of at least 51% of the registrable securities, the Company is required to file a registration statement under the Securities Act covering the registration of such shares, subject to terms and conditions set forth in the agreement.

Authorized stock

In connection with the seventh amended and restated certificate of incorporation effective on July 22, 2014, the total authorized shares of stock was changed to 520,000,000 of which 500,000,000 shares are designated as common stock with a par value of $0.001 per share and 20,000,000 shares are designated as "blank check" preferred stock with a par value of $0.001 per share.

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Deferred Payments

9 Months Ended

Sep. 30, 2015

Other Liabilities Disclosure [Abstract]

Deferred Payments

DEFERRED PAYMENTS

Gen-Probe supply agreement

In May 2011, the Company entered into a supply agreement with Gen-Probe to purchase Atlas instruments. Pursuant to the terms of the agreement, the Company can defer up to one half of the purchase price for up to 54 months from the date of delivery. The deferred amounts do not bear interest, and the Company has recorded the imputed interest component as a reduction of the deferred payment and as a reduction of the asset cost. The supply agreement provides for variable repayment terms based on a percentage of net sales as defined in the agreement, and the Company has estimated its net sales in determining amounts due for the 54 month term. The following table summarizes the amounts deferred under this agreement (amounts in thousands):

	As of September 30,			As of December 31,
	2015			2014
Current
Deferred payments, gross	$	1,990		$	1,079
Imputed interest	(330		)	(384		)
Deferred payments, net	$	1,660		$	695
Long-term
Deferred payments, gross	$	2,729		$	3,683
Imputed interest	(226		)	(464		)
Deferred payments, net	$	2,503		$	3,219

The Company estimated the interest rate implicit in the extended payment terms by considering the rate at which it could obtain financing of a similar nature from other sources at the date of each transaction, as well as prevailing rates for similar debt instruments of issuers with similar credit ratings. The estimated effective interest rate used ranges from 9.9% to 11.2%.

In the three and nine months ended September 30, 2015, the Company recorded approximately $0.1 million and $0.3 million, respectively, and in the three and nine months ended September 30, 2014, the Company recorded approximately $0.1 million and $0.3 million, respectively as non-cash interest expense related to the deferred payments pursuant to the supply agreement with Gen-Probe.

Gen-Probe license amendment

The amendment to the license agreement with Gen-Probe detailed in Note 7 includes a $5.0 million payment due on January 1, 2018 and a $5.0 million payment due on January 1, 2020. Under the terms of the amendment, no interest payments are required and no interest rate is stated. The Company determined that imputed interest must be calculated and recognized in accordance with ASC-835, and the payments are recorded in Deferred payments on the Balance Sheet at their present value based upon a 7.6% interest rate for the payment due on January 1, 2018 and a 9.0% interest rate for the payment due on January 1, 2020. The difference between the present value and the amount payable is accreted to Deferred payments over the respective term with a corresponding charge to Interest expense.

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Warrants - Narrative (Details) $ / shares in Units, $ in Thousands		1 Months Ended
	Jul. 22, 2014 $ / shares shares	Nov. 30, 2013 USD ($) $ / shares shares	Sep. 30, 2015 $ / shares shares	May. 29, 2015 shares	Mar. 31, 2014 USD ($) shares
Class of Warrant or Right [Line Items]
Warrants outstanding to purchase shares (in shares)			323,078
Warrants outstanding share exercise price (in USD per share) | $ / shares			$ 9.78
Common Stock [Member]
Class of Warrant or Right [Line Items]
Warrants outstanding share exercise price (in USD per share) | $ / shares	$ 14.08
Additional warrant issued (in shares)				52,265
Number of shares for warrants exercisable (in shares)	31,968			10,656
Comerica Loan [Member]
Class of Warrant or Right [Line Items]
Warrants issued as payments | $		$ 30
TriplePoint Loan [Member]
Class of Warrant or Right [Line Items]
Warrants issued as payments | $		$ 60
Series B Warrants [Member]
Class of Warrant or Right [Line Items]
Warrants outstanding to purchase shares (in shares)	2,480,000
Warrants outstanding share exercise price (in USD per share) | $ / shares	$ 1.00
Warrants conversion ratio	0.0906
Series E Warrants [Member]
Class of Warrant or Right [Line Items]
Warrants outstanding to purchase shares (in shares)		352,941
Warrants outstanding share exercise price (in USD per share) | $ / shares		$ 1.2751
Warrants conversion ratio	0.0906
Series E Warrants [Member] | TriplePoint Loan [Member] | Second Tranche [Member]
Class of Warrant or Right [Line Items]
Additional warrant issued (in shares)					156,863
Additional issues shares value | $					$ 100

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Intangible Assets

9 Months Ended

Sep. 30, 2015

Goodwill and Intangible Assets Disclosure [Abstract]

Intangible Assets

INTANGIBLE ASSETS

In June 2014, the Company entered into an amendment to its license agreement with Gen-Probe. Under the amendment, the Company obtained a two-year option to reduce the royalty rate it pays to Gen-Probe in exchange for an option payment of $2.5 million. Upon completion of its IPO in July 2014, the Company exercised its option and issued to Gen-Probe 865,063 shares of common stock valued at $10.51 per share on the issuance date and made a cash payment of $8.0 million. The Company is required to make additional cash payments of $5.0 million on January 1, 2018 and $5.0 million on January 1, 2020.

The aggregate cash and stock payments made to Gen-Probe along with the present value of the two $5.0 million payments described above were recorded as a $26.6 million addition to the Company's intangible technology asset in Intangible assets on the Balance Sheet and will be amortized on a straight-line basis through December 31, 2021, the end of the estimated remaining life of the technology asset. See Note 9 for further details on the additional required future cash payments described above.

Pursuant to the terms of the license agreement amendment, the Company committed to additional future contingent payments, as described in Note 11 below. If made, such additional payments will further reduce the royalty rate the Company pays to Gen-Probe, and will be recorded as additions to the Company's intangible technology asset upon payment and amortized over the estimated remaining life of the technology asset.

The Company assesses its intangible and other long-lived assets for impairment whenever events or other changes in circumstances suggest that the carrying value of an asset group may not be recoverable based on its undiscounted future cash flows. If the Company’s estimated undiscounted future cash flows are below the asset group’s carrying value, the Company may recognize an impairment charge measured by its fair value.

During the third quarter of 2015, the Company prepared revised projections for revenue and expenses, which indicated continued cash flow losses for the Company, and as a result, the Company determined a triggering event had occurred. The Company completed an assessment of the asset group including the intangible asset for recoverability. The recoverability assessment was based upon probability-weighted cash flow estimates resulting from updated revenue and expense projections and an appropriate terminal value. Based on the impairment assessment, the Company determined that the asset group including the intangible asset was not impaired.

The following table summarizes the Company's intangible asset as of the periods presented (amounts in thousands):

	September 30, 2015		December 31, 2014
Intangible asset, gross	28,259		28,259
Accumulated amortization	(4,914	)	(2,103	)
Intangible asset, net	23,345		26,156

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Accrued Expenses and Other Current Liabilities

9 Months Ended

Sep. 30, 2015

Payables and Accruals [Abstract]

Accrued Expenses and Other Current Liabilities

ACCRUED EXPENSES AND OTHER CURRENT LIABILITIES

The following table provides details of the Company’s accrued expenses (amounts in thousands):

	As of September 30,		As of December 31,
	2015		2014
Employee related	$	2,016	$	1,116
Professional services	296		235
Other	411		774
Total accrued expenses and other current liabilities	$	2,723	$	2,125

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Notes Payable

9 Months Ended

Sep. 30, 2015

Debt Disclosure [Abstract]

Notes Payable

NOTES PAYABLE

In November 2013, the Company entered into two loan and security agreements. One agreement was entered into with Comerica Bank (“Comerica”) and another agreement was entered into with TriplePoint Capital LLC (“TriplePoint”). Upon closing of the two agreements, the Company borrowed $5.0 million under the loan and security agreement with Comerica (the “Comerica Loan”). In March 2014, the Company borrowed $5.0 million under the loan and security agreement with TriplePoint (the “TriplePoint Loan”).

In May 2015, the Company paid off the remaining amounts outstanding and due under the TriplePoint Loan, which consisted of $4.6 million in principal and a $0.4 million final payment fee, and simultaneously amended the Comerica Loan (the “Comerica Amendment”). The Comerica Amendment increased the borrowing under the Comerica Loan to $10.0 million and extended the interest-only period until December 31, 2015. Beginning January 1, 2016, the Company will make monthly payments which will consist of accrued interest and equal principal payments in accordance with a 30-month amortization schedule. The interest rate under the Comerica Amendment remains the same as under the original Comerica Loan, which accrues interest at Comerica’s Prime Referenced Rate (as defined in the loan agreement with Comerica) plus 3.15%, subject to a floor of the daily adjusting LIBOR rate plus 2.5%. As of September 30, 2015, and since inception, the rate was 6.4%.

If the Company has at least $30.0 million in cash and marketable securities as of December 31, 2015, the Company has the option to extend the interest-only period through March 31, 2016. If such interest-only election is made, the interest rate will increase by 0.25%. Additionally, the Company will then make monthly payments which will consist of accrued interest and equal principal payments in accordance with a 22-month amortization schedule.

In connection with the Comerica Loan and the Comerica Amendment, the Company recorded a liability for the note of $9.8 million, net of expenses paid to Comerica, the value of the warrants issued to Comerica and the incremental value due to the amendment of the original Comerica warrant at the time of the repricing. The difference between the liability recorded and the face value of the note will be accreted to Notes payable over the term of the loan with a corresponding charge to Interest expense.

Pursuant to the Comerica Amendment, the Company is required to maintain at least $5.0 million of unrestricted cash and/or marketable securities with Comerica at all times. As of September 30, 2015 and during the period since the Company entered into the Comerica Amendment, the Company has been in compliance with this requirement. Additionally, the Comerica Loan contains various covenants that limit the Company’s ability to engage in specified types of transactions, including limiting the Company’s ability to; sell, transfer, lease or dispose of certain assets; engage in certain mergers and consolidations; incur debt or encumber or permit liens on certain assets, make certain restricted payments, including paying dividends on, or repurchasing or making distributions with respect to, the Company’s Common Stock; and enter into certain transactions with affiliates.

In connection with the closing of the loan and security agreements in November 2013, the Company issued warrants to Comerica and TriplePoint, see Note 15 for further details. In connection with the Comerica Amendment, the Company issued an additional warrant to Comerica to purchase up to an aggregate of 52,265 shares of Common Stock at $2.87 per share and modified the exercise price of the original warrant granted to Comerica under the Comerica Loan from $14.08 per share to $2.87 per share. The value of the new warrant and the incremental value due to the amendment of the original Comerica warrant were recorded as a reduction to Notes payable with a corresponding offset to Additional paid-in capital.

In connection with the repayment of the TriplePoint Loan, the Company recorded approximately $0.2 million of Interest expense as the difference between the amount recorded in the Company's financial records and the amount paid.

As of September 30, 2015, the entire balance of $9.8 million has been classified as Notes payable, current on the Balance Sheet, although only $3.0 million is due within one year. The remaining $6.8 million has also been classified as Notes payable, current because the Comerica Loan agreement contains a material adverse change clause which allows Comerica to require repayment of the debt based on subjective factors regarding the Company’s business and performance.

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Segment Information - Schedule of Revenue by Major Customers (Details) - Customer Concentration Risk [Member] - Revenue [Member] - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014
Customer A [Member]
Revenue from External Customer [Line Items]
Revenues	$ 1,040	$ 648
Customers B [Member]
Revenue from External Customer [Line Items]
Revenues	889	1,086
Customer C [Member]
Revenue from External Customer [Line Items]
Revenues	623	631
Customer D [Member]
Revenue from External Customer [Line Items]
Revenues	$ 463	$ 411

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Segment Information - Narrative (Details)	9 Months Ended
	Sep. 30, 2015 Segment Customer	Sep. 30, 2014 Customer
Revenue, Major Customer [Line Items]
Number of reportable segments | Segment	1
Revenue [Member]
Revenue, Major Customer [Line Items]
Number of customers accounted for more than 10% of revenues	4	4
Concentration risk percentage	10.00%	10.00%

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Net Loss Per Share (Tables)

9 Months Ended

Sep. 30, 2015

Earnings Per Share [Abstract]

Schedule of Basic and Diluted Net Loss per Share Applicable to Common Stockholders

The tables in this footnote are retroactively adjusted to show the results as if only the new class of Common Stock was outstanding for the entirety of each of the respective periods.

	For the Three Months Ended September 30,						For the Nine Months Ended September 30,
	2015			2014			2015			2014
Net loss applicable to common shareholders (thousands)	$	(8,491	)	$	(9,083	)	$	(26,592	)	$	(24,799	)
Basic and diluted weighted average common shares outstanding	17,303,490			14,153,715			17,262,033			5,188,516
Basic and diluted loss per share	$	(0.49	)	$	(0.64	)	$	(1.54	)	$	(4.78	)

Schedule of Calculation of Weighted Average Shares Outstanding, Event of Not Incurring Loss

Had the Company not incurred a loss, the dilutive effect of the unvested restricted stock awards on basic weighted average common shares outstanding and the dilutive effect of potential Common Stock shares issuable for Convertible Preferred Stock, stock options and warrants on the weighted-average number of Common Stock shares outstanding would have been as follows:

	For the Three Months Ended September 30,		For the Nine Months Ended September 30,
	2015	2014	2015	2014
Basic weighted average shares outstanding	17,303,490	14,153,715	17,262,033	5,188,516
Dilutive effect of unvested restricted stock	—	301,846	71,860	262,861
Basic weighted average shares outstanding had the Company not incurred a loss	17,303,490	14,455,561	17,333,893	5,451,377
Dilutive effect of Convertible Preferred Stock	—	1,939,212	—	7,642,775
Dilutive effect of warrants	—	208	—	69
Dilutive effect of stock options	78,284	339,272	97,444	363,792
Diluted weighted average shares outstanding had the Company not incurred a loss	17,381,774	16,734,253	17,431,337	13,458,013

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Notes Payable - Narrative (Details)			1 Months Ended	9 Months Ended
	Dec. 31, 2015 USD ($)	May. 29, 2015 USD ($) $ / shares shares	Nov. 30, 2013 USD ($) agreement	Sep. 30, 2015 USD ($) $ / shares	Sep. 30, 2014 USD ($)	Dec. 31, 2014 USD ($)	Jul. 22, 2014 $ / shares
Line of Credit Facility [Line Items]
Number of loan and security agreements | agreement			2
Principal amount repaid				$ 5,350,000	$ 0
Notes payable				$ 9,811,000		$ 9,910,000
Warrants outstanding share exercise price (in USD per share) | $ / shares				$ 9.78
Current notes payable				$ 3,000,000
Convertible Preferred Stock Series E [Member]
Line of Credit Facility [Line Items]
Warrants outstanding share exercise price (in USD per share) | $ / shares		$ 2.87
Common Stock [Member]
Line of Credit Facility [Line Items]
Additional warrant issued (in shares) | shares		52,265
Warrants outstanding share exercise price (in USD per share) | $ / shares							$ 14.08
Scenario, Forecast [Member]
Line of Credit Facility [Line Items]
Amortization period	22 months
Cash and marketable securities	$ 30,000,000
Interest rate increase	0.25%
Comerica Loan [Member]
Line of Credit Facility [Line Items]
Debt face amount				10,000,000.0
Cash and marketable securities				5,000,000
TriplePoint Loan [Member]
Line of Credit Facility [Line Items]
Principal amount repaid		$ 4,600,000
Final payment fee		400,000
Debt Instrument, Subjective Change Clause [Member]
Line of Credit Facility [Line Items]
Current notes payable				$ 6,800,000
Comerica Loan [Member]
Line of Credit Facility [Line Items]
Amounts borrowed			$ 5,000,000
Amortization period				30 months
Interest rate at period end				6.40%
Net of expenses paid to Comerica		9,800,000
Comerica Loan [Member] | London Interbank Offered Rate (LIBOR) [Member]
Line of Credit Facility [Line Items]
Minimum interest rate			2.50%
Additional minimum interest rate			3.15%
TriplePoint Loan [Member]
Line of Credit Facility [Line Items]
Amounts borrowed			$ 5,000,000
Interest expense		$ 200,000

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Warrants

9 Months Ended

Sep. 30, 2015

Warrants and Rights Note Disclosure [Abstract]

Warrants

WARRANTS

As of September 30, 2015, there were 323,078 warrant shares outstanding with a weighted average exercise price of $9.78 per share. See Note 12 for a summary of the changes in the Convertible preferred stock warrant liability for the nine months ended September 30, 2014.

Warrants Issued prior to IPO

Immediately prior to the Company's IPO, the Company had Series B Warrants outstanding which allowed their holders to purchase 2,480,000 shares of Series B at an exercise price of $1.00 per share. In connection with the IPO, the warrants converted into warrants to purchase Common Stock at their conversion rate of approximately 0.0906 common warrant shares to one Series B warrant share. Such warrants expire in September 2016, whereupon any warrants that remain unexercised will be exercised automatically in whole in a cashless exercise resulting in an issuance, to the holders of the warrants, the number of shares with a value equal to the intrinsic value of the warrants at the time of expiry.

In connection with the closing of the loan and security agreements in November 2013 discussed in Note 10, the Company issued warrants to Comerica and TriplePoint to purchase up to an aggregate of 352,941 shares of Series E with an exercise price of $1.28. Upon issuance, the Company recorded liabilities of approximately $0.03 million and $0.06 million for the warrants issued to Comerica and TriplePoint, respectively. The initial fair value of the warrant issued to Comerica of approximately $0.03 million was deemed a discount on the debt issued by Comerica and is being accreted to interest expense over the term of the Comerica Loan. The initial fair value of the warrants issued to TriplePoint of approximately $0.06 million were capitalized in Other assets on the Balance Sheet as part of debt issuance costs and were amortized to Interest expense. In connection with the borrowings made under the TriplePoint Loan in March 2014, one of the TriplePoint warrants became exercisable for an additional 156,863 shares of Series E. The related fair value of approximately $0.1 million was deemed a discount on the debt issued by TriplePoint and was accreted to interest expense over the term of the TriplePoint Loan through the early payoff in May 2015, at which time the remaining discount was charged to interest expense. In connection with the IPO, the Series E warrants converted into warrants to purchase common stock at their conversion rate of approximately 0.0906 common warrant shares to one Series E warrant share and as a result became exercisable for 31,968 shares of Common Stock with an exercise price of $14.08.

Warrants Issued Subsequent to IPO

In connection with the Comerica Amendment on May 29, 2015, the Company issued an additional warrant to Comerica to purchase up to an aggregate of 52,265 shares of Common Stock at $2.87 per share and modified the exercise price of the original warrant granted to Comerica to purchase up to an aggregate of 10,656 shares of common stock from $14.08 per share to $2.87 per share.

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Marketable Securities (Tables)

9 Months Ended

Sep. 30, 2015

Investments, Debt and Equity Securities [Abstract]

Summary of the Fair Value of Held-to-Maturity Marketable Securities

As of September 30, 2015 and December 31, 2014, the fair value of held-to-maturity marketable securities by type of security was as follows (amounts in thousands):

	Amortized Cost	Gross Unrealized Holding Gains	Gross Unrealized Holding Losses		Aggregate Fair Value
September 30, 2015
Short-term marketable securities
Debt securities	30,946	3	(13	)	30,936
December 31, 2014
Short-term marketable securities
Debt securities	36,231	2	(36	)	36,197
Long-term marketable securities
Debt securities	13,366	4	(32	)	13,338

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Deferred Payments - Narrative (Details) - USD ($)			1 Months Ended		3 Months Ended		9 Months Ended
	Jan. 01, 2020	Jan. 01, 2018	Jul. 31, 2014	May. 31, 2011	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Other Liabilities [Line Items]
Non-cash interest expense related to the deferred payments					$ 100,000	$ 100,000	$ 300,000	$ 300,000
Gen Probe [Member] | January 1, 2018 [Member]
Other Liabilities [Line Items]
Royalty payment, present value interest rate							7.60%
Gen Probe [Member] | January 1, 2020 [Member]
Other Liabilities [Line Items]
Royalty payment, present value interest rate							9.00%
Gen Probe [Member] | Scenario, Forecast [Member]
Other Liabilities [Line Items]
Royalty payment	$ 5,000,000.0	$ 5,000,000.0
Minimum [Member]
Other Liabilities [Line Items]
Debt instrument effective percentage					9.90%		9.90%
Maximum [Member]
Other Liabilities [Line Items]
Debt instrument effective percentage					11.20%		11.20%
Gen Probe [Member]
Other Liabilities [Line Items]
Royalty payment			$ 8,000,000
Gen Probe [Member] | Scenario, Forecast [Member]
Other Liabilities [Line Items]
Royalty payment	$ 5,000,000.0	$ 5,000,000.0
Atlas Instrument [Member] | Gen Probe [Member]
Other Liabilities [Line Items]
Deferred payment period				54 months
Atlas Instrument [Member] | Gen Probe [Member] | Maximum [Member]
Other Liabilities [Line Items]
Deferred purchase price, percentage				50.00%

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Marketable Securities - Narrative (Details)	9 Months Ended
	Sep. 30, 2015
Short-term marketable securities [Member]
Schedule of Held-to-maturity Securities [Line Items]
Marketable securities, maturity period	1 year
Long-term marketable securities [Member] | Minimum [Member]
Schedule of Held-to-maturity Securities [Line Items]
Marketable securities, maturity period	1 year
Long-term marketable securities [Member] | Maximum [Member]
Schedule of Held-to-maturity Securities [Line Items]
Marketable securities, maturity period	5 years

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Condensed Statement of Convertible Preferred Stock and Stockholders' Equity (Deficit) (unaudited) - USD ($) $ in Thousands	Total	Preferred Stock [Member]	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Deficit [Member]	IPO [Member]	IPO [Member] Common Stock [Member]	IPO [Member] Additional Paid-in Capital [Member]	Royalty Reduction [Member]	Royalty Reduction [Member] Common Stock [Member]	Royalty Reduction [Member] Additional Paid-in Capital [Member]	Treasury Stock [Member]
Beginning Balance (in shares) at Dec. 31, 2013		114,737,351	1,185,065
Beginning Balance at Dec. 31, 2013	$ (81,344)	$ 127,797	$ 8	$ 19,422	$ (100,774)							$ 0
Series E convertible preferred stock issuance costs	0	$ (99)
Stock-based compensation expense	1,019			1,019
Issuance of common stock from initial public offering, net of underwriters’ discounts and issuance costs (in shares)							5,000,000
Issuance of common stock from initial public offering, net of underwriters’ discounts and issuance costs						$ 53,214	$ 5	$ 53,209
Conversion of convertible preferred stock into Common Stock (in shares)		(114,737,351)	10,494,557
Conversion of convertible preferred stock into Common Stock	127,698	$ (127,698)	$ 4	127,694
Issuance of Warrants for Common Stock	1,364			1,364
Issuance of common stock upon exercise of option in amended license agreement (in shares)										865,063
Issuance of common stock upon exercise of option in amended license agreement									$ 9,092	$ 1	$ 9,091
Issuance of restricted shares to employees, net of shares withheld for taxes (in shares)			(2,059)
Issuance of restricted shares to employees, net of shares withheld for taxes	(8)											(8)
Exercise of options for Common Stock (in shares)			115,747
Exercise of options for Common Stock	270			270
Net loss	(32,230)				(32,230)
Ending Balance (in shares) at Dec. 31, 2014		0	17,658,373
Ending Balance at Dec. 31, 2014	79,075	$ 0	$ 18	212,069	(133,004)							(8)
Stock-based compensation expense	1,600			1,600
Issuance of Warrants for Common Stock	100			100
Issuance of restricted shares to employees, net of shares withheld for taxes (in shares)			370,766
Issuance of restricted shares to employees, net of shares withheld for taxes	(14)											(14)
Exercise of options for Common Stock (in shares)			41,739
Exercise of options for Common Stock	77			77
Net loss	(26,592)				(26,592)
Ending Balance (in shares) at Sep. 30, 2015		0	18,070,878
Ending Balance at Sep. 30, 2015	$ 54,246	$ 0	$ 18	$ 213,846	$ (159,596)							$ (22)

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Marketable Securities

9 Months Ended

Sep. 30, 2015

Investments, Debt and Equity Securities [Abstract]

Marketable Securities

MARKETABLE SECURITIES

As of September 30, 2015 and December 31, 2014, the fair value of held-to-maturity marketable securities by type of security was as follows (amounts in thousands):

	Amortized Cost	Gross Unrealized Holding Gains	Gross Unrealized Holding Losses		Aggregate Fair Value
September 30, 2015
Short-term marketable securities
Debt securities	30,946	3	(13	)	30,936
December 31, 2014
Short-term marketable securities
Debt securities	36,231	2	(36	)	36,197
Long-term marketable securities
Debt securities	13,366	4	(32	)	13,338

Marketable securities held by the Company consist of United States treasury bills, commercial paper, U.S. government-related debt, and corporate debt securities. All short-term marketable securities held by the Company mature within one year and all long-term marketable securities mature after one year but in less than five years from the respective balance sheet date.

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Stock-Based Compensation - Schedule of Stock Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock options	$ 209	$ 41	$ 584
Restricted stock	$ 300	$ 200	$ 1,016

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Inventories (Tables)

9 Months Ended

Sep. 30, 2015

Inventory Disclosure [Abstract]

Summary of Net Inventories

The following table provides details of the Company’s net inventories (amounts in thousands):

	As of September 30,		As of December 31,
	2015		2014
Raw materials	$	1,744	$	1,914
Work in process	—		11
Finished goods	2,622		3,005
	$	4,366	$	4,930

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Summary of Significant Accounting Policies - Schedule of Changes as a Result of New Accounting Principle (Details) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Other assets	$ 264	$ 262
Total assets	79,410	103,779
Notes payable, current	9,811	9,910
Total current liabilities	14,607	13,864
Total liabilities	25,164	24,704
Total liabilities and stockholders' equity	$ 79,410	103,779
Adjusted [Member]
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Other assets		262
Total assets		103,779
Notes payable, current		9,910
Total current liabilities		13,864
Total liabilities		24,704
Total liabilities and stockholders' equity		103,779
As Previously Reported [Member]
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Other assets		308
Total assets		103,825
Notes payable, current		9,956
Total current liabilities		13,910
Total liabilities		24,750
Total liabilities and stockholders' equity		103,825
Change [Member]
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Other assets		(46)
Total assets		(46)
Notes payable, current		(46)
Total current liabilities		(46)
Total liabilities		(46)
Total liabilities and stockholders' equity		$ (46)

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Stock-Based Compensation

9 Months Ended

Sep. 30, 2015

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Stock-Based Compensation

STOCK-BASED COMPENSATION

Effective upon the closing of the IPO, the Company adopted the Roka Bioscience, Inc. 2014 Equity Incentive Plan (the "2014 Plan"). The 2014 Plan initially made available 1,086,956 shares to be granted to employees, officers, directors, consultants, advisors or other individual service providers of the Company. The number of shares of Common Stock available for issuance under the 2014 Plan shall automatically increase on January 1st of each year for a period of ten years commencing on January 1, 2015 and ending on (and including) January 1, 2024, in an amount equal to 3% of the total number of shares of Common Stock outstanding on December 31st of the preceding calendar year.

Under the Roka Bioscience, Inc. 2009 Equity Incentive Plan (the “2009 Plan”), as amended on June 13, 2013, incentive and non-qualified stock options and restricted stock may be granted for up to a maximum of 2,028,850 shares to employees, consultants and directors of the Company. Effective upon adoption of the 2014 Plan, the Company does not intend to issue additional shares under the 2009 Plan.

Stock options and shares of restricted stock granted under the 2009 Plan and the 2014 Plan have a maximum contractual term of ten years from the date of grant and generally vest over four years. For stock options, the exercise price may not be less than the fair value of the stock on the grant date.

The Company recognized stock compensation expense as follows (amounts in thousands):

	For the Three Months Ended   September 30,				For the Nine Months Ended September 30,
	2015		2014		2015		2014
Stock options	$	209	$	41	$	584	$	174
Restricted stock	$	300	$	200	$	1,016	$	591

Under the 2014 Plan, the Company granted approximately 940,000 stock options and approximately 375,000 shares of restricted stock during the nine months ended September 30, 2015, valued at approximately $2.7 million and $1.6 million, respectively. Under the 2009 Plan, the Company granted approximately 4,000 stock options valued at approximately $0.02 million and no shares of restricted stock during the nine months ended September 30, 2014.

The Company determines the fair value of stock option awards at the date of grant using a Black-Scholes valuation model. This model requires the Company to make assumptions and judgments on the expected volatility, dividend yield, the risk-free interest rate and the expected term of the stock options. The following ranges of assumptions were utilized for stock options granted during the periods indicated:

	For the Nine Months Ended September 30,
	2015	2014
Expected life in years	5.8-6.3	5.9-6.0
Interest rate	1.06%-1.80%	2.01%-2.04%
Volatility	75% - 90%	60%
Dividend yield	—	—

The Company estimates the expected life of its employee stock options using the “simplified” method, whereby the expected life equals the arithmetic average of the vesting term and the original contractual term of the option due to its lack of sufficient historical data. The risk-free interest rates are based on the U.S. Treasury yield curve in effect at the time of grant for periods corresponding with the expected life of the option. The expected stock price volatility rates are based on average historical volatilities of the common stock of the Company and a group of public companies in similar industries. The Company has no history or expectations of paying dividends on its Common Stock and therefore uses a zero percent dividend yield in the Black-Scholes option pricing model.