Document and Entity Information - USD ($) $ in Millions	12 Months Ended
Document and Entity Information - USD ($) $ in Millions	Dec. 31, 2016	Mar. 03, 2017	Jun. 30, 2016
Document and Entity Information
Entity Registrant Name	T2 Biosystems, Inc.
Entity Central Index Key	0001492674
Document Type	10-K
Document Period End Date	Dec. 31, 2016
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Public Float			$ 154.2
Entity Common Stock, Shares Outstanding		30,576,110
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	FY

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 73,488	$ 73,662
Accounts receivable	327	369
Prepaid expenses and other current assets	820	838
Inventories, net	803	683
Total current assets	75,438	75,552
Property and equipment, net	13,589	10,655
Restricted cash	260	260
Other assets	281	358
Total assets	89,568	86,825
Current liabilities:
Accounts payable	962	1,228
Accrued expenses and other current liabilities	4,908	4,162
Current portion of notes payable	1,269	4,449
Deferred revenue	2,445	2,146
Current portion of lease incentives	301	268
Total current liabilities	9,885	12,253
Notes payable, net of current portion	39,504	26,121
Lease incentives, net of current portion	792	1,076
Other liabilities	49	436
Commitments and contingencies (see Note 13)
Stockholders' equity:
Preferred stock, $0.001 par value; 10,000,000 shares authorized; no shares issued and outstanding at December 31, 2016 and December 31, 2015
Common stock, $0.001 par value; 200,000,000 shares authorized; 30,482,712 and 24,175,381 shares issued and outstanding at December 31, 2016	30	24
Additional paid-in capital	242,997	195,800
Accumulated deficit	(203,689)	(148,885)
Total stockholders' equity	39,338	46,939
Total liabilities and stockholders' equity	$ 89,568	$ 86,825

Consolidated Balance Sheet (Parentheticals) - $ / shares	Dec. 31, 2016	Dec. 31, 2015
Consolidated Balance Sheets
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized	10,000,000	10,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	30,482,712	24,175,381
Common stock, shares outstanding	30,482,712	24,175,381

Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Revenue:
Product revenue	$ 1,747	$ 599
Research revenue	2,333	2,214	$ 119
Total revenue	4,080	2,813	119
Costs and expenses:
Cost of product revenue	6,872	1,740
Research and development	24,009	25,362	19,782
Selling, general and administrative	24,077	19,094	11,018
Total costs and expenses	54,958	46,196	30,800
Loss from operations	(50,878)	(43,383)	(30,681)
Interest expense, net	(4,098)	(1,967)	(721)
Other income, net	172	60	12
Net loss and comprehensive loss	(54,804)	(45,290)	(31,390)
Comprehensive loss	(54,804)	(45,290)	(31,390)
Accretion of redeemable convertible preferred stock to redemption value			(4,570)
Net loss applicable to common stockholders	$ (54,804)	$ (45,290)	$ (35,960)
Net loss per share applicable to common stockholders — basic and diluted	$ (2.11)	$ (2.21)	$ (4.15)
Weighted-average number of common shares used in computing net loss per share — basic and diluted	26,015,751	20,501,748	8,674,931

Consolidated Statements of Redeemable Convertible Preferred Stock and Stockholders Equity (Deficit) - USD ($) $ in Thousands	Series A-1	Series A-2	Series B	Series C	Series D	Series E	Common Stock	Additional Paid-in Capital	Accumulated Deficit	Total
Balance at Dec. 31, 2013	$ 874	$ 7,724	$ 15,464	$ 19,100	$ 27,357	$ 42,294
Balance (in shares) at Dec. 31, 2013	282,849	1,703,959	3,249,877	4,055,125	5,054,945	6,930,967
Increase (Decrease) in Redeemable Convertible Preferred Stock
Accretion of redeemable convertible preferred stock to redemption value	$ 26	$ 240	$ 520	$ 722	$ 1,115	$ 1,947
Conversion of redeemable convertible preferred stock into common stock	$ (900)	$ (7,964)	$ (15,984)	$ (19,822)	$ (28,472)	$ (44,241)
Conversion of redeemable convertible preferred stock into common stock (in shares)	(282,849)	(1,703,959)	(3,249,877)	(4,055,125)	(5,054,945)	(6,930,967)
Balance at Dec. 31, 2013							$ 1		$ (89,544)	$ (89,543)
Balance (in shares) at Dec. 31, 2013							1,411,986
Increase (Decrease) in Stockholders' Equity
Accretion of redeemable convertible preferred stock to redemption value								$ (880)	(3,690)	(4,570)
Stock-based compensation expense								1,653		1,653
Conversion of redeemable convertible preferred stock into common stock							$ 13	96,341	21,029	117,383
Conversion of redeemable convertible preferred stock into common stock (in shares)							12,516,298
Issuance of common stock upon net settlement of warrants to purchase redeemable convertible preferred stock								1,226		1,226
Issuance of common stock upon net settlement of warrants to purchase redeemable convertible preferred stock (in shares)							68,700
Exercise of stock options								153		153
Exercise of stock options (in shares)							64,661
Issuance of common stock							$ 6	58,083		58,089
Issuance of common stock (in shares)							5,980,000
Net loss									(31,390)	(31,390)
Balance at Dec. 31, 2014							$ 20	156,576	(103,595)	53,001
Balance (in shares) at Dec. 31, 2014							20,041,645
Increase (Decrease) in Stockholders' Equity
Stock-based compensation expense								4,168		4,168
Issuance of common stock from exercise of stock options and employee stock purchase plan								1,804		1,804
Issuance of common stock from exercises of stock options and employee stock purchase plan (in shares)							442,687
Issuance of common stock							$ 4	33,252		33,256
Issuance of common stock (in shares)							3,691,049
Net loss									(45,290)	(45,290)
Balance at Dec. 31, 2015							$ 24	195,800	(148,885)	$ 46,939
Balance (in shares) at Dec. 31, 2015							24,175,381			24,175,381
Increase (Decrease) in Stockholders' Equity
Stock-based compensation expense								4,848		$ 4,848
Offering costs on issuance of common stock from secondary public offering								(215)		(215)
Issuance of common stock from exercise of stock options and employee stock purchase plan								1,018		1,018
Issuance of common stock from exercises of stock options and employee stock purchase plan (in shares)							251,990
Issuance of common stock							$ 6	39,717		39,723
Issuance of common stock (in shares)							6,055,341
Issuance of warrants								1,829		1,829
Net loss									(54,804)	(54,804)
Balance at Dec. 31, 2016							$ 30	$ 242,997	$ (203,689)	$ 39,338
Balance (in shares) at Dec. 31, 2016							30,482,712			30,482,712

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Operating activities
Net loss	$ (54,804)	$ (45,290)	$ (31,390)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	2,280	1,465	691
Stock-based compensation expense	4,848	4,168	1,653
Noncash interest expense	564	354	112
Loss on extinguishment of debt	112
Change in fair value of warrants			1
Deferred rent	(250)	(119)	5
Changes in operating assets and liabilities:
Accounts receivable	42	(168)	(201)
Prepaid expenses and other assets	68	190	(1,217)
Inventories, net	(120)	(568)	(115)
Accounts payable	(61)	177	(208)
Accrued expenses and other liabilities	580	260	2,405
Deferred revenue	299	2,066	80
Net cash used in operating activities	(46,442)	(37,465)	(28,184)
Investing activities
Purchases and manufacture of property and equipment	(5,487)	(7,974)	(2,084)
Decrease in restricted cash		80
Net cash used in investing activities	(5,487)	(7,894)	(2,084)
Financing activities
Proceeds from issuance of common stock in public offering, net of offering costs	(385)	33,677	58,089
Proceeds from issuance of common stock and stock options exercises, net	1,018	1,804	153
Proceeds from private investment in public equity	39,723
Proceeds from notes payable, net of issuance costs	43,803	10,000	19,714
Repayments of notes payable	(32,404)	(309)	(4,037)
Net cash provided by financing activities	51,755	45,172	73,919
Net (decrease) increase in cash and cash equivalents	(174)	(187)	43,651
Cash and cash equivalents at beginning of period	73,662	73,849	30,198
Cash and cash equivalents at end of period	73,488	73,662	73,849
Supplemental disclosures of cash flow information
Cash paid for interest	2,732	1,506	515
Supplemental disclosures of noncash investing and financing activities
Accrued property and equipment	$ 82	247	128
Leasehold improvements paid by landlord		1,268	121
Public offering costs unpaid at year end		$ 420
Accretion of Series A-1, A-2, B, C, D and E redeemable convertible preferred stock to redemption value			4,570
Conversion of redeemable and convertible preferred stock to common stock			117,383
Conversion of preferred warrants to common stock			$ 1,226

Nature of Business	12 Months Ended
Nature of Business	Dec. 31, 2016
Nature of Business
Nature of Business	T2 Biosystems, Inc. Notes to Consolidated Financial Statements 1. Nature of Business T2 Biosystems, Inc. (the “Company”) was incorporated on April 27, 2006 as a Delaware corporation with operations based in Lexington, Massachusetts. The Company is an in vitro diagnostics company that has developed an innovative and proprietary technology platform that offers a rapid, sensitive and simple alternative to existing diagnostic methodologies. The Company is using its T2 Magnetic Resonance technology, or T2MR, to develop a broad set of applications aimed at lowering mortality rates, improving patient outcomes and reducing the cost of healthcare by helping medical professionals make targeted treatment decisions earlier. T2MR enables rapid detection of pathogens, biomarkers and other abnormalities in a variety of unpurified patient sample types, including whole blood, plasma, serum, saliva, sputum and urine, and can detect cellular targets at limits of detection as low as one colony forming unit per milliliter, or CFU/mL. The Company’s initial development efforts target sepsis and Lyme disease, which are areas of significant unmet medical need in which existing therapies could be more effective with improved diagnostics. On September 22, 2014, the Company received market clearance from the U.S. Food and Drug Administration (“FDA”) for its first two products, the T2Dx Instrument (the “T2Dx”) and T2Candida Panel (“T2Candida”). The Company has devoted substantially all of its efforts to research and development, business planning, recruiting management and technical staff, acquiring operating assets, raising capital, and, most recently, the commercialization and improvement of its existing products. Liquidity At December 31, 2016, the Company has cash and cash equivalents of $73.5 million and an accumulated deficit of $203.7 million. The future success of the Company is dependent on its ability to successfully commercialize its products, obtain regulatory clearance for and successfully launch its future product candidates, obtain additional capital and ultimately attain profitable operations. Historically, the Company has funded its operations primarily through its August 2014 initial public offering, its December 2015 secondary public offering, its September 2016 private investment in public equity (“PIPE”) financing, private placements of redeemable convertible preferred stock, and through debt financing arrangements. The Company is subject to a number of risks similar to other newly commercial life science companies, including, but not limited to commercially launching the Company’s products, development and market acceptance of the Company’s product candidates, development by its competitors of new technological innovations, protection of proprietary technology, and raising additional capital. Having obtained clearance from the FDA and a CE mark in Europe to market the T2Dx and T2Candida, the Company has incurred significant commercialization expenses related to product sales, marketing, manufacturing and distribution. In addition, the Company anticipates costs and expenses to increase as the Company continues to develop other product candidates, improve existing products and maintain, expand and protect its intellectual property portfolio. The Company may seek to fund its operations through public equity or private equity or debt financings, as well as other sources. However, the Company may be unable to raise additional funds or enter into such other arrangements when needed on favorable terms or at all. The Company’s failure to raise capital or enter into such other arrangements if and when needed would have a negative impact on the Company’s business, results of operations and financial condition and the Company’s ability to develop, commercialize and drive adoption of the T2Dx, T2Candida, its product candidate, T2Bacteria, and future T2MR-based diagnostics.. Management believes that its existing cash and cash equivalents at December 31, 2016, together with the additional remaining liquidity of up to $1.3 million available under an Equipment Lease Credit Facility (the “Credit Facility”) entered into in October 2015 to help the Company meet its capital equipment needs (Note 6), will be sufficient to allow the Company to fund its current operating plan for at least the next 12 months from the date of issuance of these consolidated financial statements. For more information, refer to the section titled “Liquidity and Capital Resources” in Item 7, Management’s Discussion and Analysis of Financial Condition and Results of Operations, and in Item 1a, Risk Factors, for additional risks associated with our capital needs.

Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2016

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Basis of Presentation and Consolidation

The Company’s financial statements have been prepared in conformity with generally accepted accounting principles in the United States of America (“GAAP”). Any reference in these notes to applicable guidance is meant to refer to the authoritative United States generally accepted accounting principles as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates (“ASU”) of the Financial Accounting Standards Board (“FASB”). The Company’s consolidated financial statements include the accounts of the Company and its wholly-owned subsidiary, T2 Biosystems Securities Corporation. All intercompany balances and transactions have been eliminated.

Use of Estimates

The preparation of the Company’s consolidated financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the consolidated financial statements and accompanying notes. The Company utilizes certain estimates in the determination of the fair value of its stock options, deferred tax valuation allowances, revenue recognition, to record expenses relating to research and development contracts, accrued expenses, and to classify the value of instrument raw material and work-in-process inventory between inventory and property and equipment. The Company bases its estimates on historical experience and other market‑specific or other relevant assumptions that it believes to be reasonable under the circumstances. Actual results could differ from such estimates.

Segment Information

Operating segments are defined as components of an enterprise about which separate discrete information is available for evaluation by the chief operating decision maker, or decision‑making group, in deciding how to allocate resources and in assessing performance. The Company’s chief operating decision maker is the Chief Executive Officer. The Company views its operations and manages its business in one operating segment, which is the business of developing and, upon regulatory clearance, launching commercially its diagnostic products aimed at lowering mortality rates, improving patient outcomes and reducing the cost of healthcare by helping medical professionals make targeted treatment decisions earlier.

Off‑Balance Sheet Risk and Concentrations of Credit Risk

The Company has no significant off-balance sheet risks, such as foreign exchange contracts, option contracts, or other foreign hedging arrangements. Cash and cash equivalents are financial instruments that potentially subject the Company to concentrations of credit risk. At December 31, 2016 and 2015, substantially all of the Company’s cash was deposited in accounts at one financial institution, with a significant amount invested in money market funds that are invested in short-term U.S. government agency securities. The Company maintains its cash deposits, which at times may exceed the federally insured limits, with a large financial institution and, accordingly, the Company believes such funds are subject to minimal credit risk.

For the year ended December 31, 2016, the Company derived approximately 45% of its total revenue from one customer and 10% of its total revenue from a second customer. For the year ended December 31, 2015, the Company derived approximately 50% of its total revenue from one customer and 25% of its total revenue from a second customer. For the year ended December 31, 2014, the Company derived all of its revenue from a single customer.

Cash Equivalents

Cash equivalents include all highly liquid investments maturing within 90 days from the date of purchase. Cash equivalents consist of money market funds invested in short-term U.S. government agency securities as of December 31, 2016 and 2015.

Accounts Receivable

The Company’s accounts receivable consists of amounts due from commercial customers and from research and development arrangements with partners. At each reporting period, management reviews all outstanding balances to determine if the facts and circumstances of each customer relationship indicate the need for a reserve. The Company does not require collateral and did not have an allowance for doubtful accounts at December 31, 2016 or 2015.

Inventories

Inventories are stated at the lower of cost or market. The Company determines the cost of its inventories, which includes amounts related to materials, direct labor, and manufacturing overhead, on a first-in, first-out basis. The Company performs an assessment of the recoverability of capitalized inventory during each reporting period, and writes down any excess and obsolete inventories to their realizable value in the period in which the impairment is first identified. Shipping and handling costs incurred for inventory purchases are capitalized and recorded upon sale in cost of product revenues in the consolidated statements of operations and comprehensive loss or are included in the value of T2-owned instruments and components, a component of property and equipment, net, and depreciated.

The Company capitalizes inventories in preparation for sales of products when the related product candidates are considered to have a high likelihood of regulatory clearance, which for the T2Dx Instrument and T2Candida Panel was upon the achievement of regulatory clearance, and the related costs are expected to be recoverable through sales of the inventories. In addition, the Company capitalizes inventories related to the manufacture of instruments that have a high likelihood of regulatory clearance, which for the T2Dx Instrument was upon the achievement of regulatory clearance, and will be retained as the Company’s assets, upon determination that the instrument has alternative future uses. In determining whether or not to capitalize such inventories, the Company evaluates, among other factors, information regarding the product candidate’s status of regulatory submissions and communications with regulatory authorities, the outlook for commercial sales and alternative future uses of the product candidate. Costs associated with development products prior to satisfying the inventory capitalization criteria are charged to research and development expense as incurred.

The Company classifies inventories related to instruments that are Company-owned, as a component of property and equipment. Raw material and work-in-process inventories that are expected to be used to produce Company-owned instruments, based on our business model and forecast, are also classified as property and equipment. Company-owned instruments are instruments that are manufactured and placed with customers in connection with reagent rental agreements, or are used for internal purposes.

The components of inventory consist of the following (in thousands):


	December 31,		December 31,
	2016		2015
Raw materials	$	389	$	203
Work-in-process		351		287
Finished goods		63		193
Total inventories, net	$	803	$	683

Fair Value Measurements

The Company is required to disclose information on all assets and liabilities reported at fair value that enables an assessment of the inputs used in determining the reported fair values. ASC 820, Fair Value Measurements and Disclosures (“ASC 820”), establishes a hierarchy of inputs used in measuring fair value that maximizes the use of observable inputs and minimizes the use of unobservable inputs by requiring that the observable inputs be used when available.

Observable inputs are inputs that market participants would use in pricing the asset or liability based on market data obtained from sources independent of the Company. Unobservable inputs are inputs that reflect the Company’s assumptions about the inputs that market participants would use in pricing the asset or liability, and are developed based on the best information available in the circumstances. The fair value hierarchy applies only to the valuation inputs used in determining the reported fair value of the investments and is not a measure of the investment credit quality. The hierarchy defines three levels of valuation inputs:

Level 1 — Quoted unadjusted prices for identical instruments in active markets.

Level 2 — Quoted prices for similar instruments in active markets, quoted prices for identical or similar instruments in markets that are not active, and model‑derived valuations in which all observable inputs and significant value drivers are observable in active markets.

Level 3 — Model derived valuations in which one or more significant inputs or significant value drivers are unobservable, including assumptions developed by the Company.

The fair value hierarchy prioritizes valuation inputs based on the observable nature of those inputs. Assets and liabilities measured at fair value are classified in their entirety based on the lowest level of input that is significant to the fair value measurement. The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability (See Note 3).

Financial instruments measured at fair value on a recurring basis include cash, money market funds and restricted cash (See Note 3).

For certain financial instruments, including accounts payable and accrued expenses, the carrying amounts approximate their fair values as of December 31, 2016 and 2015 because of their short-term nature. At December 31, 2016 and 2015, the carrying value of the Company’s debt approximated fair value, which was determined using Level 3 inputs, using market quotes from brokers and is based on current rates offered for similar debt (Note 6).

Property and Equipment

Property and equipment are recorded at cost and depreciated over their estimated useful lives using the straight‑line method. Property and equipment includes raw materials, work-in-process and finished instruments that are Company-owned or expected to remain Company-owned when placed in service. Company-owned instruments are instruments that are manufactured and placed with customers in connection with reagent rental agreements, or are used for internal purposes. Repairs and maintenance costs are expensed as incurred, whereas major improvements are capitalized as additions to property and equipment.

Revenue Recognition

The Company generates revenue from product sales, which includes the sale of instruments, consumable diagnostic tests and related services, and research and development agreements with third parties. The Company recognizes revenue in accordance with FASB ASC Topic 605, Revenue Recognition (“ASC 605”). Accordingly, the Company recognizes revenue when all of the following criteria have been met:

i.Persuasive evidence of an arrangement exists

ii.Delivery has occurred or services have been rendered

iii.The seller’s price to the buyer is fixed or determinable

iv.Collectability is reasonably assured

If any of the above criteria have not been met, the Company defers revenue until such time each of the criteria have been satisfied.

Product revenue is generated by the sale of instruments and consumable diagnostic tests predominantly through its direct sales force in the United States, and distributors in geographic regions outside the United States. The Company does not offer product return or exchange rights (other than those relating to defective goods under warranty) or price protection allowances to its customers, including its distributors. Payment terms granted to distributors are the same as those granted to end-user customers and payments are not dependent upon the distributors’ receipt of payment from their end-user customers. The Company either sells instruments to customers and international distributors, or retains title and places the instrument at the customer site pursuant to a reagent rental agreement. When the instrument is directly purchased by a customer, the Company recognizes revenue when all applicable revenue recognition criteria are met. When the instrument is placed under a reagent rental agreement, the Company’s customers generally agree to fixed term agreements, which can be extended, certain of which may include minimum purchase commitments and/or incremental charges on each consumable diagnostic test purchased, which varies based on the volume of test cartridges purchased. Revenue from the sale of consumable diagnostic tests, which includes the incremental charge, is recognized upon delivery as a component of product revenue in the Company’s consolidated statements of operations and comprehensive loss.

Direct sales of instruments include warranty, maintenance and technical support services for one year following the installation of the purchased instrument (“Maintenance Services”). After the completion of the initial Maintenance Services period, customers have the option to renew the Maintenance Services for additional one year periods in exchange for additional consideration. In addition, the Company may provide training to customers. The Company defers revenue from the initial sale of the instrument equal to the relative fair value of the other deliverables, including one year of Maintenance Services, and recognizes the amounts ratably over the service delivery period.

The Company warrants that consumable diagnostic tests will be free from defects, when handled according to product specifications, for the stated life of the product. To fulfill valid warranty claims, the Company either provides a credit to its customers on future orders or provides replacement product. Accordingly, the Company defers revenue associated with the estimated defect rates of the consumable diagnostic tests.

The Company does not offer rights of return for instruments or consumable diagnostic tests.

Shipping and handling costs incurred associated with products sold to customers are recorded as a cost of product revenue in the consolidated statement of operations and comprehensive loss. Shipping and handling costs billed to customers in connection with a product sale are recorded as a component of product revenue in the consolidated statements of operations and comprehensive loss.

For multiple-element arrangements, the Company identifies the deliverables included within each agreement and evaluates which deliverables represent separate units of accounting. The determination that multiple elements in an arrangement meet the criteria for separate units of accounting requires the Company’s management to exercise judgment. The Company accounts for those components as separate elements when the following criteria are met: (1) the delivered items have value to the customer on a stand-alone basis; and, (2) if there is a general right of return relative to the delivered items, delivery or performance of the undelivered items is considered probable and within its control.

The consideration received is allocated among the separate units of accounting based on a selling price hierarchy. The selling price hierarchy is based on: (1) vendor specific objective evidence (“VSOE”), if available; (2) third party evidence of selling price if VSOE is not available; or (3) best estimated selling price (“BESP”) if neither VSOE nor third party evidence is available. The Company generally expects that it will not be able to establish selling price using third-party evidence due to the nature of our products and the markets in which the Company competes, and, as such, the Company typically will determine selling price using VSOE or BESP.

When the Company establishes selling price using BESP, consideration is given to both market and Company-specific factors, including the cost to produce the deliverable and the anticipated margin on that deliverable, as well as the characteristics of markets in which the deliverable is sold.

Revenue earned from activities performed pursuant to research and development agreements is reported as research revenue in the consolidated statements of operations and comprehensive loss, using the proportional performance method as the work is completed, limited to payments earned, and the related costs are expensed as incurred as research and development expense. The timing of receipt of cash from the Company’s research and development agreements generally differs from when revenue is recognized.

Product Recall

In July 2016, the Company initiated a voluntary recall and replacement of its T2Candida cartridges at certain customer sites because T2Candida was experiencing higher than normal invalid test rates as the T2Candida cartridges aged. As of June 30, 2016, as a result of this voluntary recall, the Company deferred revenue totaling $149,000 and recorded additional costs of product revenue of $41,000 related to returned products, which are no longer usable. As of December 31, 2016, the Company had approximately $37,000 of deferred revenue and $3,000 of warranty reserve remaining, both related to this voluntary recall. The impact of the voluntary recall on T2Candida cartridges in inventory was not material to the consolidated financial statements.

Cost of Product Revenue

Cost of product revenue includes the cost of materials, direct labor and manufacturing overhead costs used in the manufacture of consumable diagnostic tests sold to customers and related license and royalty fees. Cost of product revenue also includes depreciation on revenue generating T2Dx that have been placed with customers under reagent rental agreements; costs of materials, direct labor and manufacturing overhead costs on the T2Dx sold to customers; and other costs such as customer support costs, royalties and license fees, warranty and repair and maintenance expense on the T2Dx that have been placed with customers under reagent rental agreements.

Research and Development Costs

Costs incurred in the research and development of the Company’s product candidates are expensed as incurred. Research and development expenses consist of costs incurred in performing research and development activities, including activities associated with performing services under research revenue arrangements, and include salaries and benefits, stock compensation, research‑related facility and overhead costs, laboratory supplies, equipment and contract services.

Impairment of Long Lived Assets

The Company reviews long‑lived assets, including capitalized T2 owned instruments and components, for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable. During this review, the Company reevaluates the significant assumptions used in determining the original cost and estimated lives of long‑lived assets. Although the assumptions may vary from asset to asset, they generally include operating results, changes in the use of the asset, cash flows and other indicators of value. Management then determines whether the remaining useful life continues to be appropriate or whether there has been an impairment of long‑lived assets based primarily upon whether expected future undiscounted cash flows are sufficient to support the assets’ recovery. If impairment exists, the Company would adjust the carrying value of the asset to fair value, generally determined by a discounted cash flow analysis. No impairment charges have been recorded in any of the periods presented.

Comprehensive Loss

Comprehensive loss is defined as the change in equity of a business enterprise during a period from transactions and other events and circumstances from non‑owner sources. Comprehensive loss consists of net loss and other comprehensive loss, which includes certain changes in equity that are excluded from net loss. The Company’s comprehensive loss equals reported net loss for all periods presented.

Stock-Based Compensation

The Company has a stock‑based compensation plan which is more fully described in Note 9. The Company records stock‑based compensation for options granted to employees and to members of the board of directors for their services on the board of directors, based on the grant date fair value of awards issued, and the expense is recorded on a straight‑line basis over the applicable service period, which is generally four years. The Company accounts for non‑employee stock‑based compensation arrangements based upon the fair value of the consideration received or the equity instruments issued, whichever is more reliably measurable. The measurement date for non‑employee awards is generally the date that the performance of services required for the non‑employee award is complete. Stock‑based compensation costs for non‑employee awards is recognized as services are provided, which is generally the vesting period, on a straight‑line basis.

The Company records the expense for stock option grants to performance-based milestone vesting using the accelerated attribution method over the remaining service period when management determines that achievement of the milestone is probable. Management evaluates when the achievement of a performance-based milestone is probable based on the relative satisfaction of the performance conditions as of the reporting date.

The Company expenses restricted stock awards based on the fair value of the award on the date of issuance, on a straight‑line basis over the associated service period of the award.

The Company uses the Black‑Scholes‑Merton option pricing model to determine the fair value of stock options. The use of the Black‑Scholes‑Merton option‑pricing model requires management to make assumptions with respect to the expected term of the option, the expected volatility of the common stock consistent with the expected life of the option, risk‑free interest rates and expected dividend yields of the common stock. The expected term was determined according to the simplified method, which is the average of the vesting tranche dates and the contractual term. Due to the lack of company specific historical and implied volatility data resulting from our limited public market trading history, we have based our estimate of expected volatility primarily on the historical volatility of a group of similar companies that are publicly traded. For these analyses, companies with comparable characteristics are selected, including enterprise value and position within the industry, and with historical share price information sufficient to meet the expected life of the stock‑based awards. The Company computes the historical volatility data using the daily closing prices for the selected companies’ shares during the equivalent period of the calculated expected term of its stock‑based awards. The risk‑free interest rate is determined by reference to U.S. Treasury zero‑coupon issues with remaining maturities similar to the expected term of the options. The Company has not paid, and does not anticipate paying, cash dividends on shares of common stock; therefore, the expected dividend yield is assumed to be zero. The Company is required to estimate forfeitures at the time of grant and revise those estimates in subsequent periods if actual forfeitures differ from those estimates.

Income Taxes

The Company provides for income taxes using the liability method. The Company provides deferred tax assets and liabilities for the expected future tax consequences of temporary differences between the Company’s financial statement carrying amounts and the tax basis of assets and liabilities using enacted tax rates expected to be in effect in the years in which the differences are expected to reverse. A valuation allowance is provided to reduce the deferred tax assets to the amount that will more likely than not be realized.

The Company applies ASC 740 Income Taxes (“ASC 740”) in accounting for uncertainty in income taxes. The Company does not have any material uncertain tax positions for which reserves would be required. The Company will recognize interest and penalties related to uncertain tax positions, if any, in income tax expense.

Guarantees

As permitted under Delaware law, the Company indemnifies its officers and directors for certain events or occurrences while the officer or director is, or was, serving at the Company’s request in such capacity. The term of the indemnification is for the officer’s or director’s lifetime. The maximum potential amount of future payments the Company could be required to make is unlimited; however, the Company has directors’ and officers’ insurance coverage that limits its exposure and enables it to recover a portion of any future amounts paid.

The Company leases office, laboratory and manufacturing space under noncancelable operating leases. The Company has standard indemnification arrangements under the leases that require it to indemnify the landlord against all costs, expenses, fines, suits, claims, demands, liabilities, and actions directly resulting from any breach, violation or nonperformance of any covenant or condition of the Company’s leases.

In the ordinary course of business, the Company enters into indemnification agreements with certain suppliers and business partners where the Company has certain indemnification obligations limited to the costs, expenses, fines, suits, claims, demands, liabilities and actions directly resulting from the Company’s gross negligence or willful misconduct, and in certain instances, breaches, violations or nonperformance of covenants or conditions under the agreements.

As of December 31, 2016 and 2015, the Company had not experienced any material losses related to these indemnification obligations, and no material claims with respect thereto were outstanding. The Company does not expect significant claims related to these indemnification obligations and, consequently, concluded that the fair value of these obligations is negligible, and no related reserves were established.

Net Loss Per Share

Basic net loss per share is calculated by dividing net loss applicable to common stockholders by the weighted‑average number of shares outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is calculated by adjusting the weighted‑average number of 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, redeemable convertible preferred stock, and warrants to purchase redeemable convertible preferred stock, which were outstanding prior to the Company’s IPO, and stock options and unvested restricted stock are considered to be common stock equivalents, but have been excluded from the calculation of diluted net loss per share, as their effect, including the related impact to the numerator of the fair value adjustment of the warrants and the impact to the denominator of the warrant shares, would be anti‑dilutive for all periods presented. Therefore, basic and diluted net loss per share applicable to common stockholders were the same for all periods presented.

Recent Accounting Standards

From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies and adopted by the Company as of the specified effective date. Unless otherwise discussed, the Company believes that the impact of recently issued standards that are not yet effective will not have a material impact on its financial position or results of operations upon adoption.

Accounting Standards Adopted

In 2014, the FASB issued ASU 2014-15, Presentation of Financial Statements – Going Concern (“ASU 2014-15”). ASU 2014-15 provides new guidance on (1) management’s responsibility in evaluating whether or not there is substantial doubt about a company’s ability to continue as a going concern within one year from the date the financial statements are issued each reporting period and (2) related financial statement disclosures. The Company adopted the guidance prescribed by ASU 2014-15 as of December 31, 2016 and the Company concluded that there was not a substantial doubt about its ability to continue as a going concern. The Company faces certain risks and uncertainties, as described in Note 1, “Nature of Business,” that could affect this analysis in the future.

In April 2015, the FASB issued ASU No. 2015-03, Simplifying the Presentation of Debt Issuance Costs (“ASU 2015-03”). This standard amends existing guidance to require the presentation of debt issuance costs in the balance sheet as a deduction from the carrying amount of the related debt liability instead of a deferred charge. It is effective for annual reporting periods beginning after December 15, 2015, but early adoption is permitted. Adoption of ASU 2015-03 is applied retrospectively. The Company adopted ASU 2015-03 as of January 1, 2016, which resulted in a balance sheet reclassification of issuance costs of $22,000 recorded in prepaid expenses and other current assets and $102,000 in other assets to a reduction in the current portion of notes payable and notes payable, net of current portion as of December 31, 2015, respectively. The Company’s adoption of this standard did not have an impact on its consolidated results of operations or cash flows for the calendar year ended December 31, 2016.

Accounting Standards Issued, Not Adopted

In August 2016, the FASB issued ASU 2016-15, Statement of Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments ("ASC 2016-15"), which provides guidance on the classification of certain specific cash flow issues including debt prepayment or extinguishment costs, settlement of certain debt instruments, contingent consideration payments made after a business combination, proceeds from the settlement of certain insurance claims and distributions received from equity method investees. The standard requires the use of a retrospective approach to all periods presented, but may be applied prospectively if retrospective application would be impracticable. The guidance is effective for public entities for fiscal years beginning after December 15, 2017, and interim periods within those years, and early application is permitted. The Company is currently evaluating the impact of its pending adoption of ASU 2016-15 on the Company’s consolidated financial statements.

In March 2016, the FASB released ASU No. 2016-09 Improvements to Employee Share-Based Payment Accounting (“ASU 2016-09”) which is intended to simplify income tax accounting for excess tax benefits, accounting for forfeitures, and employer statutory withholding. Under the current guidance, excess tax benefits that result from an award vesting or settling are recognized in additional paid-in capital in the period that they reduce cash taxes payable. This requires the provision to be computed on a with and without option basis and may result in net operating loss and credit carryforwards on the balance sheet being less than what is available on the tax return. Under the new guidance, the income tax effects of awards will be recognized as a component of income tax expense when the awards vest or are settled (regardless if cash taxes are reduced). For interim reporting purposes, companies will account for excess tax benefits and tax deficiencies as discrete items in the period during which they occurred. The guidance is effective for public entities for fiscal years beginning after December 15, 2016, and interim periods within those years. Early adoption is permitted, however all of the guidance included in the update must be applied when adopted. The Company must use a modified retrospective transition method for adopting and record the cumulative effect of all unrecognized benefits and any change in valuation allowances at the end of the prior tax period as an adjustment to retained earnings. The Company has not elected to early adopt ASU 2016-09 and is evaluating the new guidance and the expected effect on the Company’s consolidated financial statements.

In March 2016, the FASB issued ASU No. 2016-06, Derivatives and Hedging (Topic 815): Contingent Put and Call Options in Debt Instruments (“ASU 2016-06”), which applies to all issuers of or investors in debt instruments with embedded call or put options. ASU 2016-06 clarifies the requirements for assessing whether contingent call or put options that can accelerate the payment of principal on debt instruments are clearly and closely related to their debt hosts. Entities performing the assessment under the guidance of ASU 2016-06 are required to assess the embedded call or put options solely in accordance with the four-step decision process. In addition, ASU 2016-06 clarifies what steps are required when assessing whether the economic characteristics and risks of call or put options are clearly and closely related to the economic characteristics and risks of their debt hosts. ASU 2016-06 is effective for financial statements issued for fiscal years beginning after December 15, 2016 and interim periods within those fiscal years using the modified retrospective method for existing debt instruments. The Company is evaluating the new guidance and the expected effect on the Company’s consolidated financial statements.

In February 2016, the FASB issued ASU No. 2016-02, Leases (“ASU 2016-02”), which applies to all leases. Under ASU 2016-02, a right-of-use asset and lease obligation will be recorded for all leases, whether operating or financing leases, while the statement of operations will reflect lease expense for operating leases and amortization and interest expense for financing leases. ASU 2016-02 is effective for fiscal years beginning after December 15, 2018 and interim periods within those years, which is the year ended December 31, 2019 for the Company. Entities are required to use a modified retrospective approach of adoption for leases that exist or are entered into after the beginning of the earliest comparative period in the financial statements. Full retrospective application is prohibited. The Company is evaluating the new guidance and the expected effect on the Company’s consolidated financial statements.

In July 2015, the FASB issued ASU No. 2015-11, Inventory (Topic 330): Simplifying the Measurement of Inventory (“ASU 2015-11”). The standard simplifies the subsequent measurement of inventory by requiring inventory to be measured at the lower of cost and net realizable value for entities using the first-in-first out method of valuing inventory. ASU 2015-11 eliminates other measures required by current guidance to determine net realizable value. ASU 2015-11 is effective for fiscal years beginning after December 15, 2016 and interim periods within those fiscal years and early adoption is permitted. The Company has not adopted ASU 2015-11 and does not expect the new guidance to have a material effect on its consolidated financial statements.

In June 2014, the FASB issued amended guidance, ASU No. 2014-09, Revenue from Contracts with Customers (“ASU 2014-09”), which is applicable to revenue recognition that will now be effective for the Company for the year ending December 31, 2018, as a result of the deferral of the effective date adopted by the FASB in July 2015. The new guidance must be adopted using either a full retrospective approach for all periods presented or a modified retrospective approach. Early adoption prior to the original adoption date of ASU 2014-09 is not permitted. The new guidance applies a more principles-based approach to revenue recognition. The Company currently anticipates adoption of the new standard effective January 1, 2018 under the full retrospective method. The Company’s revenue is primarily comprised of product sales and research services, and the Company is in the process of determining the impact of the new standard on its financial statements.

Fair Value Measurements

12 Months Ended

Dec. 31, 2016

Fair Value Measurements

Fair Value Measurements

3. Fair Value Measurements

The Company measures the following financial assets at fair value on a recurring basis. There were no transfers between levels of the fair value hierarchy during any of the periods presented. The following tables set forth the Company’s financial assets and liabilities carried at fair value categorized using the lowest level of input applicable to each financial instrument as of December 31, 2016 and 2015 (in thousands):


			Quoted Prices
			in Active		Significant
			Markets for		Other		Significant
	Balance at		Identical		Observable		Unobservable
	December 31,		Assets		Inputs		Inputs
	2016		(Level 1)		(Level 2)		(Level 3)
Assets:
Cash	$	16,887	$	16,887	$	—	$	—
Money market funds		56,601		56,601		—		—
Restricted cash		260		260		—		—
	$	73,748	$	73,748	$	—	$	—


			Quoted Prices
			in Active		Significant
			Markets for		Other		Significant
	Balance at		Identical		Observable		Unobservable
	December 31,		Assets		Inputs		Inputs
	2015		(Level 1)		(Level 2)		(Level 3)
Assets:
Cash	$	1,520	$	1,520	$	—	$	—
Money market funds		72,142		72,142		—		—
Restricted cash		260		260		—		—
	$	73,922	$	73,922	$	—	$	—

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Supplemental Balance Sheet Information

12 Months Ended

Dec. 31, 2016

Supplemental Balance Sheet Information

Supplemental Balance Sheet Information

5. Supplemental Balance Sheet Information

Property and Equipment

Property and equipment consists of the following (in thousands)


	Estimated Useful	December 31,		December 31,
	Life (Years)	2016		2015
Office and computer equipment	3	$	409	$	395
Software	3		708		632
Laboratory equipment	5		4,516		4,112
Furniture	5-7		200		187
Manufacturing equipment	5		897		577
Manufacturing tooling and molds	0.5		154		71
T2-owned instruments and components	5		9,119		4,960
Leasehold improvements	Lesser of useful life or lease term		3,353		3,332
Construction in progress	n/a		1,299		1,196
			20,655		15,462
Less accumulated depreciation and amortization			(7,066)		(4,807)
Property and equipment, net		$	13,589	$	10,655

Construction in progress is primarily comprised of equipment and leasehold improvement construction projects that have not been placed in service. T2-owned instruments and components is comprised of raw materials and work-in-process inventory that are expected to be used or used to produce Company-owned instruments, based on our business model and forecast, and completed instruments that will be used for internal research and development or reagent rental agreements with customers. Completed T2-owned instruments are placed in service once installation procedures are completed and are depreciated over five years. The Company has approximately $5.7 million of T2-owned instruments at customer and clinical locations as of December 31, 2016. Depreciation expense for T2-owned instruments placed at customer sites pursuant to reagent rental agreements is recorded as a component of cost of product revenue and totaled $599,000 and $105,000 for the years ended December 31, 2016 and December 31, 2015, respectively. Depreciation expense for T2-owned instruments used for internal research and development is recorded as a component of research and development expense.

Depreciation and amortization expense of $2.3 million, $1.5 million and $691,000 was charged to operations for the years ended December 31, 2016, 2015 and 2014, respectively.

Accrued Expenses

Accrued expenses consist of the following (in thousands):


	December 31,		December 31,
	2016		2015
Accrued payroll and compensation	$	2,479	$	2,418
Accrued research and development expenses		846		458
Accrued professional services		884		542
Other accrued expenses		699		744
Total accrued expenses	$	4,908	$	4,162

Notes Payable

12 Months Ended

Dec. 31, 2016

Debt

Notes Payable

6. Notes Payable

Future principal payments on the notes payable as of December 31, 2016 are as follows (in thousands):


Year ended December 31,
2017	$	1,286
2018		1,485
2019		1,015
2020		5,723
2021		22,893
Thereafter		17,171
Total before unamortized discount and issuance costs		49,573
Less: paid-in-kind interest		(5,782)
Less: unamortized discount and issuance costs		(3,018)
Total notes payable	$	40,773

In 2016, the Company adopted, and retroactively implemented ASU No. 2015-03, "Simplifying the Presentation of Debt Issuance Costs." Under this new guidance, the Company is required to present debt issuance costs as a direct deduction from the related debt liability on our consolidated balance sheet. The cumulative effect of the change as of December 31, 2015 was $22,000 recorded in prepaid expenses and other current assets and $102,000 in other assets to a reduction in the current portion of notes payable and notes payable, net of current portion.

Term Loan Agreement

In December 2016, the Company entered into a Term Loan Agreement (the “Term Loan Agreement”) with CRG Servicing LLC (“CRG”). The Company initially borrowed $40.0 million pursuant to the Term Loan Agreement and may borrow up to an additional $10.0 million at any time through and including July 27, 2018, provided that, among other conditions, the Company receives 510(k) clearance for the marketing of T2BacteriaTM by the U.S. Food and Drug Administration (“FDA”) on or before April 30, 2018 (the “Approval Milestone”). The Term Loan Agreement has a six-year term with three years (through December 30, 2019) of interest-only payments, which period shall be extended to four years (through December 30, 2020) if the Company achieves the Approval Milestone, after which quarterly principal and interest payments will be due through the December 30, 2022 maturity date. Interest on the amounts borrowed under the Term Loan Agreement accrues at an annual fixed rate of (a) prior to the Approval Milestone, 12.50%, 4.0% of which may be deferred during the interest-only period by adding such amount to the aggregate principal loan amount and (b) following the Approval Milestone, 11.50%, 3.5% of which may be deferred during the interest-only period by adding such amount to the aggregate principal loan amount. In addition, if the Company achieves certain financial performance metrics, the loan will convert to interest-only until the December 30, 2022 maturity, at which time all unpaid principal and accrued unpaid interest will be due and payable. The Company is required to pay CRG a financing fee based on the loan principal amount drawn. The Company is also required to pay a final payment fee of 8% of the principal outstanding upon repayment.

The Company may prepay all or a portion of the outstanding principal and accrued unpaid interest under the Term Loan Agreement at any time upon prior notice subject to a certain prepayment fee during the first five years of the term and no prepayment fee thereafter. As security for its obligations under the Term Loan Agreement the Company entered into a security agreement with CRG whereby the Company granted a lien on substantially all of its assets, including intellectual property. The Loan Agreement also contains customary affirmative and negative covenants for a credit facility of this size and type. The Loan Agreement also requires the Company to achieve certain revenue targets, whereby the Company is required to pay double the amount of any shortfall as an acceleration of principal payments. The Loan Agreement includes a subjective acceleration clause whereby an event of default, including a material adverse change in the business, operations, or conditions (financial or otherwise), could result in the acceleration of the obligations under the Loan Agreement. Under certain circumstances, a default interest rate of an additional 4.00% per annum will apply at the election of CRG on all outstanding obligations during the occurrence and continuance of an event of default. CRG has not exercised its right under this clause, as there have been no such events. The Company believes the likelihood of CRG exercising this right is remote.

The Company assessed the terms and features of the Term Loan Agreement in order to identify any potential embedded features that would require bifurcation or any beneficial conversion features. As part of this analysis, the Company assessed the economic characteristics and risks of the Term Loan Agreement, including put and call features. The Company determined that the features of the Term Loan Agreement are either clearly and closely associated with a debt host and do not require bifurcation as a derivative liability, or the fair value of the feature is immaterial. Included in these features are principal payment acceleration clauses triggered by a developmental milestone. Should the Company’s assessment of this milestone change, there could be a non-cash charge in operations. The Company will continue to reassess the features to determine if they require separate accounting on a quarterly basis.

In December 2016, pursuant to the Term Loan Agreement, the Company made an initial draw of $39.2 million, net of financing fees. The Company used approximately $28.0 million of the initial proceeds to repay approximately $27.5 million of outstanding debt pursuant to the Loan and Security Agreement and to repay approximately $479,000 of outstanding debt pursuant to the Promissory Note. Upon the repayment of all amounts owed by the Company under these agreements, all commitments were terminated and all security interests granted by the Company were released.

In connection with the Term Loan Agreement entered into in December 2016, the Company issued to CRG four separate warrants to purchase a total of 528,958 shares of the Company’s common stock. The warrants are exercisable any time prior to December 30, 2026 at a price of $8.06 per share, with typical provisions for termination upon a change of control or a sale of all or substantially all of the assets of the Company. The warrants are classified within shareholders’ equity, and the proceeds were allocated between the debt and warrants based on their relative fair value. The fair value of the warrants was determined by the Black Scholes Merton option pricing model. The fair value of the warrants at December 30, 2016 was $1.8 million.

Equipment Lease Credit Facility

In October 2015, the Company signed the $10.0 million Credit Facility (the “Credit Facility”) with Essex Capital Corporation (“Essex”) to fund capital equipment needs. As one of the conditions of the Term Loan Agreement, the Credit Facility is capped at a maximum of $5.0 million. Under the Credit Facility, Essex will fund capital equipment purchases presented by the Company. The Company will repay the amounts borrowed in 36 equal monthly installments from the date of the amount funded. At the end of the 36 month lease term, the Company has the option to (a) repurchase the leased equipment at the lesser of fair market value or 10% of the original equipment value, (b) extend the applicable lease for a specified period of time, which will not be less than one year, or (c) return the leased equipment to the Lessor.

In April 2016 and June 2016, the Company completed the first two draws under the Credit Facility of $2.1 million and $2.5 million, respectively. The Company will make monthly payments of $67,000 under the first draw and $79,000 under the second draw. The borrowings under the Credit Facility are treated as capital leases. The amortization of the assets conveyed under the Credit Facility is included as a component of depreciation expense.

Loan and Security Agreement

On July 11, 2014, the Company entered into a loan and security agreement (“Loan and Security Agreement”) with two lenders to borrow up to $30.0 million for operations. The Loan and Security Agreement allows the Company to borrow amounts in two tranches, up to $20.0 million (drawn in amounts not less than $10.0 million upon closing and the remainder drawn in amounts not less than $5.0 million draws) for tranche A and up to $10.0 million for tranche B. The Company borrowed a total of $29.7 million under the Loan and Security Agreement, net of issuance costs. In December 2016, the Company used approximately $27.5 million of the proceeds from the Term Loan agreement to repay the outstanding debt pursuant to the Loan and Security Agreement. Upon the repayment of all amounts owed by the Company under the Loan and Security Agreement, all commitments were terminated and all security interests granted by the Company were released.

The amounts borrowed under the Loan and Security Agreement were collateralized by substantially all of the assets of the Company and bear interest at the one-month LIBOR plus 7.05%. The Company was required to pay interest only payments on the amounts borrowed under the Loan and Security Agreement through July 31, 2016. After the interest-only period, the Company was repaying the amounts borrowed in equal monthly installments until the maturity date. The Loan and Security Agreement required payment of a final fee of 4.75% of the aggregate original principal of amounts borrowed, which the Company accrued over the term of the Loan and Security Agreement. In addition, amounts borrowed could have been prepaid at the option of the Company in denominations of not less than $1.0 million, and any amounts prepaid were subject to a prepayment premium of 1.0% if prepaid prior to the second anniversary of the borrowing date and 0.5% if prepaid prior to the maturity date and after the second anniversary of the borrowing date. The effective interest rate for the Loan and Security Agreement, including final fee interest and non-cash interest, was 9.7%. The Loan and Security Agreement did not include any financial covenants, but did contain a subjective acceleration clause whereby upon an event of default, which includes a material adverse change in the business, operations, or conditions of the Company or a material impairment of the prospect of repayment of any portion of the obligations, the lender could accelerate the Company’s repayment obligations. In the event of default, the lender had first priority to substantially all of the Company’s assets.

The Company assessed the terms and features of the Loan and Security Agreement in order to identify any potential embedded features that would require bifurcation or any beneficial conversion features. As part of this analysis, the Company assessed the economic characteristics and risks of the Loan and Security Agreement, including put and call features. The Company determined that all features of the Loan and Security Agreement were clearly and closely associated with a debt host and do not require bifurcation as a derivative liability, or the fair value of the feature is immaterial.

The Company borrowed the full $20.0 million available under tranche A by December 31, 2014. In May 2015, the Company entered into an amendment to the Loan and Security Agreement whereby the availability to draw up to $10.0 million for tranche B was extended from June 30, 2015 to December 31, 2015. Commencing July 1, 2015, the Company incurred a fee equal to 1.0% per annum of any undrawn amounts under tranche B. This fee was payable on the date tranche B was drawn or upon the expiration of the draw period. The Company paid the $50,000 fee upon drawing the remaining $10.0 million under tranche B on December 28, 2015.

Promissory Note

In May 2011, the Company entered into a promissory agreement (the “Promissory Note”) with a separate lender to borrow up to $1.7 million for the purchase of laboratory equipment and office equipment through December 2013. The Company borrowed a total of $1.4 million under the Promissory Note. The Company paid interest only on the borrowings through December 2013 and was required to make equal monthly payments of principal and interest through the maturity date. In December 2016, the Company used approximately $479,000 of the proceeds from the Term Loan agreement to repay the outstanding debt pursuant to the Promissory Note. Upon the repayment of all amounts owed by the Company under the Promissory Note, all commitments were terminated and all security interests granted by the Company were released.

The amounts borrowed were collateralized by the associated equipment and bear interest at 6.5%. The Promissory Note included financial covenants that required the Company to maintain a minimum cash balance of $300,000. In addition, the Promissory Note contained a subjective acceleration clause whereby an event of default and immediate acceleration of the borrowing occurs if there was a material adverse change in the business, operations, or condition of the Company or a material impairment of the prospect of repayment of any portion of the obligations. In the event of default, the lender had first priority on the laboratory equipment and office equipment purchased with the proceeds.

Interest Expense, Net

Interest expense for the years ended December 31, 2016, 2015 and 2014 was $4.1 million, $2.0 million, and $741,000, respectively. Interest expense for the years ended December 31, 2016, 2015, and 2014 included non-cash interest of $564,000, $354,000, and $112,000, respectively, related to the amortization of debt discounts and deferred financing costs under each of the above agreements. Interest expense for the year ended December 31, 2016 also included a non-cash charge for the extinguishment of debt of $112,000.

Redeemable Convertible Preferred Stock	12 Months Ended
Redeemable Convertible Preferred Stock	Dec. 31, 2016
Redeemable Convertible Preferred Stock.
Redeemable Convertible Preferred Stock	7. Redeemable Convertible Preferred Stock Upon closing of the IPO on August 12, 2014, all of the outstanding shares of the Company’s redeemable convertible preferred stock were converted into 12,516,298 shares of its common stock. As the preferred stock was redeemable, the Company accreted the shares to the redemption values over the period from issuance to the redemption date. The accretion amounts are recorded as an increase to the carrying value of the preferred stock with a corresponding charge to additional paid in capital or accumulated deficit. On the conversion date, the redeemable convertible preferred stock had a balance of $117.4 million, which was recorded in temporary equity. Upon conversion into common stock, this balance was reclassified as stockholders’ equity (deficit), reducing accumulated deficit by $21.0 million, with the residual amount of $96.3 million recorded as common stock (par value) and additional paid-in capital. The amount recorded as a reduction in accumulated deficit reflects the value of redeemable convertible preferred stock dividends and issuance costs accreted through the conversion date. As of August 12, 2014, the Company does not have any redeemable convertible preferred stock issued or outstanding. Prior to the IPO, the holders of the Company’s redeemable convertible preferred stock had certain voting, dividend, and redemption rights, as well as liquidation preferences and conversion privileges. All rights, preferences, and privileges associated with the redeemable convertible preferred stock were terminated at the time of the Company’s IPO in conjunction with the conversion of all outstanding shares of redeemable convertible preferred stock into shares of common stock.

Stockholders' Equity (Deficit)	12 Months Ended
Stockholders' Equity (Deficit)	Dec. 31, 2016
Stockholders' Equity
Stockholders' Equity	8. Stockholders’ Equity Common Stock Each share of common stock is entitled to one vote. The holders of common stock are also entitled to receive dividends whenever funds are legally available and when declared by the board of directors, subject to the prior rights of holders of all classes of stock outstanding. As of December 31, 2016, a total of 4,042,627 shares and 357,798 shares of common stock were reserved for issuance upon (i) the exercise of outstanding stock options and (ii) the issuance of stock awards under the Company’s 2014 Incentive Award Plan and 2014 Employee Stock Purchase Plan, respectively. Private Investment in Public Equity Financing On September 21, 2016, Canon U.S.A., Inc. (“Canon”) became a related party when the Company sold 6,055,341 shares of its common stock (the “Canon Shares”) to Canon at $6.56 per share, the closing price on this date, for an aggregate cash purchase price of $39.7 million. As of September 21, 2016, the Canon Shares represented 19.9% of the outstanding shares of common stock of the Company. In connection with the sale of the Canon Shares, the Company agreed to grant Canon certain board designation rights, including the right to initially appoint a Class I director to the Company’s board of directors. On or before March 21, 2017, the Company has agreed to use its best efforts to prepare and file with the Securities and Exchange Commission (the “SEC”) a registration statement on Form S-3 for purposes of registering the resale of the Canon Shares, or if the Company is not eligible for the use of Form S-3 at that time, on or before June 21, 2017, the Company has agreed to prepare and file a registration statement on Form S-1, or on an alternative form that permits the resale of the Canon Shares, with the SEC.

- Definition

The entire disclosure for shareholders' equity comprised of portions attributable to the parent entity and noncontrolling interest, including other comprehensive income. Includes, but is not limited to, balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings, accumulated balance for each classification of other comprehensive income and amount of comprehensive income.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(d),(e))
-URI http://asc.fasb.org/extlink&oid=26873400&loc=d3e23780-122690

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21484-112644

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 310
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SAB TOPIC 4.E)
-URI http://asc.fasb.org/extlink&oid=27010918&loc=d3e74512-122707

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21488-112644

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.29-31)
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section S99
-Paragraph 4
-Subparagraph (SAB TOPIC 4.C)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187143-122770

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21506-112644

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.3-04)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187085-122770

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 30
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6405834&loc=d3e23285-112656

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21475-112644

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Preferred Stock
-URI http://asc.fasb.org/extlink&oid=6521494

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21463-112644

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21564-112644

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
-Section E

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
-Section C

+ Details

Stock Based Compensation

12 Months Ended

Dec. 31, 2016

Stock Based Compensation

Stock-Based Compensation

9. Stock-Based Compensation

Stock Incentive Plans

2006 Stock Incentive Plan

The Company’s 2006 Stock Option Plan (the “2006 Plan”) was established for granting stock incentive awards to directors, officers, employees and consultants to the Company. Upon closing of the Company’s IPO in August 2014, the Company ceased granting stock incentive awards under the 2006 Plan. The 2006 Plan provided for the grant of incentive and non-qualified stock options and restricted stock grants as determined by the Board of Directors. Under the 2006 Plan, stock options were generally granted with exercise prices equal to or greater than the fair value of the common stock as determined by the board of directors, expired no later than 10 years from the date of grant, and vest over various periods not exceeding 4 years.

2014 Stock Incentive Plan

The Company’s 2014 Plan (the “2014 Plan” and, together with the 2006 Plan, the “Stock Incentive Plans”) provides for the issuance of shares of common stock in the form of stock options, awards of restricted stock, awards of restricted stock unit awards, performance awards, dividend equivalent awards, stock payment awards and stock appreciation rights to directors, officers, employees and consultants of the Company. Since the establishment of the 2014 Plan, the Company has only granted stock options. Generally, stock options are granted with exercise prices equal to or greater than the fair value of the common stock on the date of grant, expire no later than 10 years from the date of grant, and vest over various periods not exceeding 4 years.

The number of shares reserved for future issuance under the 2014 Plan is the sum of (1) 823,529, (2) any shares that were granted under the 2006 Plan which are forfeited, lapse unexercised or are settled in cash subsequent to the effective date of the 2014 Plan and (3) an annual increase on the first day of each calendar year beginning January 1, 2015 and ending on January 1, 2024, equal to the lesser of (A) 4% of the shares outstanding on the final day of the immediately preceding calendar year and (B) such smaller number of shares determined by the Board of Directors. As of December 31, 2016 there were 223,397 shares available for future grant under the Plan.

Stock Options

During the years ended December 31, 2016, 2015, and 2014, the Company granted options with an aggregate fair value of $7.0 million and $10.1 million, and $6.0 million, respectively, which are being amortized into compensation expense over the vesting period of the options as the services are being provided.

The following is a summary of option activity under the Plan (in thousands, except share and per share amounts):


				Weighted-Average
		Weighted-Average		Remaining
	Number of	Exercise Price Per		Contractual Term	Aggregate Intrinsic
	Shares	Share		(In years)	Value
Outstanding at December 31, 2015	3,484,298	$	8.79	7.64	$	14,620
Granted	1,489,384		8.35
Exercised	(165,803)		2.84			930
Forfeited	(664,303)		11.55
Canceled	(100,949)		17.38
Outstanding at December 31, 2016	4,042,627		8.20	7.05		4,091
Exercisable at December 31, 2016	2,251,925		6.77	5.61		3,922
Vested or expected to vest at December 31, 2016	3,845,455		8.12	6.95		4,084

Included in the stock options granted during the year ended December 31, 2016 are 166,066 options to purchase common stock granted to certain executive officers of the Company that vest upon the achievement of certain performance conditions, which include the attainment of specified operating result and regulatory targets, by December 31, 2017. Included in the stock options forfeited during the year ended December 31, 2016 are 20,000 options to purchase common stock upon the achievement of certain performance conditions. There are 146,066 performance based options included in the outstanding balance at December 31, 2016. The Company will continually evaluate the probability of achievement of each performance condition and will commence recognition of stock-based compensation expense on these awards in the period the achievement of each performance condition is deemed probable, including a catch-up adjustment from the grant date.

The weighted‑average fair values of options granted in the years ended December 31, 2016, 2015, and 2014 were $4.68, $8.42, and $7.59 per share, respectively, and were calculated using the following estimated assumptions:


	Year ended
	December 31,
	2016		2015
Weighted-average risk-free interest rate	1.42	%	1.69	%
Expected dividend yield	0.00	%	0.00	%
Expected volatility	61	%	56	%
Expected terms	6.0	years	6.0	years

The total fair values of stock options that vested during the years ended December 31, 2016, 2015, and 2014 were $4.9 million, $4.0 million, and $1.2 million, respectively.

As of December 31, 2016, there was $8.8 million of total unrecognized compensation cost related to non‑vested stock options granted under the Stock Incentive Plans. Total unrecognized compensation cost will be adjusted for future changes in the estimated forfeiture rate. The Company expects to recognize that cost over a remaining weighted‑average period of 2.54 years as of December 31, 2016.

Restricted Stock Units

During the year ended December 31, 2016 the Company awarded shares of restricted stock units to certain employees at no cost to them, which cannot be sold, assigned, transferred or pledged during the restriction period. The restricted stock and restricted stock units vest through the passage of time, assuming continued employment. Restricted stock units are not included in issued and outstanding common stock until the shares are vested and released. The fair value of the award at the time of the grant is expensed on a straight line basis. The granted restricted stock units had an aggregate fair value of $1.4 million, which are being amortized into compensation expense over the vesting period of the options as the services are being provided.

The following is a summary of restricted stock unit activity under the Plan (in thousands, except share and per share amounts):



		Weighted-Average
	Number of	Grant Date Fair
	Shares	Value
Nonvested at December 31, 2015	—	$	—
Granted	272,195		5.83
Exercised	—		—
Forfeited	—		—
Canceled	—		—
Nonvested at December 31, 2016	272,195		5.83

There was no vesting of restricted stock units during the year ended December 31, 2016.

As of December 31, 2016, there was $1.4 million of total unrecognized compensation cost related to non‑vested stock options granted under the Stock Incentive Plans. Total unrecognized compensation cost will be adjusted for future changes in the estimated forfeiture rate. The Company expects to recognize that cost over a remaining weighted‑average period of 1.92 years as of December 31, 2016.

Employee Stock Purchase Plan

The 2014 Employee Stock Purchase Plan (the “2014 ESPP”) period is semi-annual and allows participants to purchase the Company’s common stock at 85% of the lower of (i) the market value per share of common stock on the first day of the offering period or (ii) the market value per share of the common stock on the purchase date. Each participant can purchase up to a maximum of $25,000 per calendar year in fair market value. The first plan period began on August 7, 2014. Stock-based compensation expense from the 2014 ESPP for the years ended December 31, 2016, 2015 and 2014 was approximately $253,000, $233,000 and $103,000, respectively.

The fair value of the purchase rights granted under this plan was estimated on the date of grant that uses the following weighted-average assumptions, which were derived in a manner similar to those discussed in Note 2 relative to stock options:


	Year ended
	December 31,
	2016		2015
Weighted-average risk-free interest rate	0.50	%	0.19	%
Expected dividend yield	0.00	%	0.00	%
Expected volatility	67	%	57	%
Expected terms	0.5	years	0.5	years

The 2014 ESPP provides initially for the granting of up to 220,588 shares of the Company’s common stock to eligible employees. In addition, on the first day of each calendar year beginning January 1, 2015 and ending on January 1, 2024, the number of common shares available under the Plan shall be increased by the number of shares equal to the lesser of (1) 1% of the common shares outstanding on the final day of the immediately preceding calendar year and (2) such smaller number of common shares as determined by the Board of Directors. At December 31, 2016, there were 134,401 shares available under the 2014 ESPP.

Stock‑Based Compensation Expense

The following table summarizes the stock-based compensation expense for stock options granted to employees and non-employees, as well as stock-compensation expense for the 2014 ESPP that was recorded in the Company’s results of operations for the years presented (in thousands):


	Year ended
	December 31,
	2016		2015		2014
Cost of product revenue	$	123	$	—	$	—
Research and development		1,127		1,213		501
Selling, general and administrative		3,480		2,840		1,152
Total stock-based compensation expense	$	4,730	$	4,053	$	1,653

For the years ended December 31, 2016 and December 31, 2015, $118,000 and $115,000 of stock-based compensation expense was capitalized, respectively, as part of inventory or T2 instruments and components.

Warrants	12 Months Ended
Warrants	Dec. 31, 2016
Warrants.
Warrants	10. Warrants In connection with the Term Loan Agreement entered into in December 2016, the Company issued to CRG four separate warrants to purchase a total of 528,958 shares of the Company’s common stock. The warrants are exercisable any time prior to December 30, 2026 at a price of $8.06 per share, with typical provisions for termination upon a change of control or a sale of all or substantially all of the assets of the Company. The warrants are classified within shareholders’ equity, and the proceeds were allocated between the debt and warrants based on their relative fair value. The fair value of the warrants was determined by the Black‑Scholes‑Merton option pricing model. The fair value of the warrants at date of issuance was $1.8 million. Prior to the completion of the IPO, the Company had outstanding warrants to purchase 250,727 shares of various classes of redeemable convertible preferred stock. The warrants were recorded as a liability and changes in the fair value of the warrants were recorded as a component of other income (expense), net. In connection with the closing of the Company’s IPO, all of the Company’s outstanding warrants to purchase convertible preferred stock automatically converted into 68,700 shares of common stock, resulting in the net settlement of the liability to purchase redeemable securities to common stock (par value) and additional paid-in capital as of August 12, 2014.

Net Loss Per Share

12 Months Ended

Dec. 31, 2016

Net Loss Per Share

Net Loss Per Share

11. Net Loss Per Share

The following table presents the calculation of basic and diluted net loss per share applicable to common stockholders (in thousands, except share and per share data):


	Year ended
	December 31,
	2016		2015		2014
Numerator:
Net loss	$	(54,804)	$	(45,290)	$	(31,390)
Accretion of redeemable convertible preferred stock to redemption value		—		—		(4,570)
Net loss applicable to common stockholders	$	(54,804)	$	(45,290)	$	(35,960)
Denominator:
Weighted-average number of common shares outstanding — basic and diluted		26,015,751		20,501,748		8,674,931
Net loss per share applicable to common stockholders — basic and diluted	$	(2.11)	$	(2.21)	$	(4.15)

The following shares were excluded from the calculation of diluted net loss per share applicable to common stockholders, prior to the application of the treasury stock method, because their effect would have been anti‑dilutive for the periods presented:


	Year ended
	December 31,
	2016	2015	2014
Options to purchase common shares	4,042,627	3,484,298	2,911,146
Restricted stock units	272,195	—	—
Warrants to purchase common stock	528,958	—	—
Total	4,843,780	3,484,298	2,911,146

Income Taxes

12 Months Ended

Dec. 31, 2016

Income Taxes

Income Taxes

12. Income Taxes

The reconciliation of the U.S. federal statutory rate to the Company’s effective tax rate is as follows:


	Year Ended December 31,
	2016		2015		2014
Tax at statutory rates	35.0	%	35.0	%	35.0	%
State income taxes	5.2		6.6		5.1
Permanent differences	(1.2)		(1.3)		(0.8)
Research and development credits	1.3		1.5		1.9
Change in valuation allowance	(40.3)		(41.8)		(41.2)
Effective tax rate	0.0	%	0.0	%	0.0	%

The significant components of the Company’s deferred tax asset consist of the following at December 31, 2016 and 2015 (in thousands):


	December 31,
	2016		2015
Deferred tax assets:
Net operating loss carryforwards	$	69,411	$	49,417
Tax credits		5,269		4,107
Other temporary differences		1,636		1,623
Start-up expenditures		5,088		5,288
Stock option expenses		2,779		1,649
Total deferred tax assets		84,183		62,084
Deferred tax asset valuation allowance		(83,924)		(61,813)
Net deferred tax assets		259		271
Deferred tax liabilities:
Prepaid expenses		(259)		(271)
Net deferred taxes	$	—	$	—

In 2016 and 2015, the Company did not record a benefit for income taxes related to its operating losses incurred. ASC 740 requires a valuation allowance to reduce the deferred tax assets reported if, based on the weight of available evidence, it is more likely than not that some portion or all of the deferred tax assets will not be realized. Based upon the level of historical U.S. losses and future projections over the period in which the net deferred tax assets are deductible, at this time, management believes it is more likely than not that the Company will not realize the benefits of these deductible differences, and as a result the Company continues to maintain a valuation allowance for the full amount of the 2016 deferred tax assets. The valuation allowance increased $22.1 million, $18.9 million and $12.7 million for the years ended December 31, 2016, 2015 and 2014, respectively, primarily related to each year’s taxable loss.

As of December 31, 2016, the Company had federal and state net operating losses of $174.9 million and $162.1 million, respectively, which are available to offset future taxable income, if any, through 2036. Included in the federal and state net operating losses are deductions attributable to excess tax benefits from the exercise of stock options of $626,000 and $2.9 million, respectively. The tax benefits attributable to these deductions are credited directly to additional paid-in capital when realized. The Company also had federal and state research and development tax credits of $3.5 million and $2.8 million, respectively, which expire at various dates through 2036. Under the provisions of the Internal Revenue Code, the net operating loss and tax credit carryforwards are subject to review and possible adjustment by the Internal Revenue Service and state tax authorities. Net operating loss and tax credit carryforwards may become subject to an annual limitation in the event of certain cumulative changes in the ownership interest of significant stockholders over a three year period in excess of 50%, as defined under Sections 382 and 383 of the Internal Revenue Code, respectively, as well as similar state provisions. This could limit the amount of tax attributes that can be utilized annually to offset future taxable income or tax liabilities. The amount of the annual limitation is determined based on the value of the Company immediately prior to the ownership change. Subsequent ownership changes may further affect the limitation in future years. The Company has completed several financings since its inception which may have resulted in a change in control as defined by Sections 382 and 383 of the Internal Revenue Code, or could result in a change in control in the future. The Company has not conducted an assessment to determine whether there may have been a Section 382 or 383 ownership change.

The Company has no unrecognized tax benefits. Interest and penalty charges, if any, related to uncertain tax positions would be classified as income tax expenses in the accompanying consolidated statements of operations. At December 31, 2016 and 2015, the Company had no accrued interest or penalties related to uncertain tax positions.

The Company files income tax returns in the U.S. federal tax jurisdiction and various state jurisdictions. Since the Company is in a loss carryforward position, the Company is generally subject to examination by the U.S. federal, state and local income tax authorities for all tax years in which a loss carryforward is available. The Company does not have any international operations as of December 31, 2016. The statute of limitations for assessment by federal and state tax jurisdictions in which the Company has business operations is open for tax years ending December 31, 2013, 2014, and 2015. The tax years under examination vary by jurisdiction.

Commitments and Contingencies

12 Months Ended

Dec. 31, 2016

Commitments and Contingencies.

Commitments and Contingencies

13. Commitments and Contingencies

Operating Leases

In August 2010, the Company entered into a five-year, non-cancelable operating lease for office and laboratory space at its headquarters in Lexington, MA. The lease commenced on January 1, 2011, with the Company providing a security deposit of $400,000. In accordance with the operating lease agreement, the Company reduced its security deposit to $240,000 in May 2015, which is recorded as restricted cash in the consolidated balance sheets. In July 2014, the Company amendment the lease to expand the office and laboratory space leased. In May 2015, the Company entered into an amendment to this lease to extend the term from December 31, 2015 to December 31, 2017. In March 2017, the Company entered into an amendment to extend the term from December 31, 2017 to December 31, 2021. The rent expense, inclusive of the escalating rent payments, is recognized on a straight-line basis over the lease term.

In May, 2013, the Company entered into a two-year operating lease for additional office, laboratory and manufacturing space in Wilmington, MA. The Company entered into an amendment in September 2015 to extend this lease term through December 31, 2017.

In November, 2014 the Company entered into an agreement to rent additional office space in Lexington, MA. The term of the agreement is two years, commencing December 2014. In April 2015, the Company entered into an amendment to extend the term of this agreement. The amendment extends the agreement term from December 31, 2016 to December 31, 2017. In connection with this agreement, the Company paid a security deposit totaling $50,000, which is recorded as a component of prepaid assets in the consolidated balance sheets. In May 2015, the Company entered into an amendment to a lease to expand existing manufacturing facilities in Lexington, MA. The lease amendment term is June 1, 2015 to December 31, 2017.

In November, 2014, the Company entered into a lease for additional laboratory space in Lexington, MA. The lease term commenced April 1, 2015 and extends for six years. The rent expense, inclusive of the escalating rent payments, is recognized on a straight-line basis over the lease term. As an incentive to enter into the lease, the landlord paid approximately $1.4 million of the $2.2 million space build-out costs. The incentive is recorded as a component of lease incentives on the consolidated balance sheets and is amortized as a reduction in rent expense on a straight-line basis over the term of the lease. In connection with this lease agreement, the Company paid a security deposit of $281,000, which is recorded as a component of other assets in the consolidated balance sheets.

Future minimum non-cancelable lease payments under the Company’s operating leases as of December 31, 2016 are as follows (in thousands):


Year ending December 31,
2017	$	2,079
2018		404
2019		414
2020		425
2021		107
Thereafter		—
	$	3,429

The future minimum noncancelable lease payments will increase to $2.1 million in 2017, $1.7 million in 2018, $1.8 million in 2019, $1.9 million in 2020 and $1.6 million in 2021 as a result of the lease amendment entered into on March 7, 2017 for office and laboratory space at the Company’s headquarters in Lexington, MA.

Rent expense for the years ended December 31, 2016, 2015, and 2014 was $1.8 million, $1.6 million, and $950,000, respectively.

License Agreement

In 2006, the Company entered into a license agreement with a third party, pursuant to which the third party granted the Company an exclusive, worldwide, sublicenseable license under certain patent rights to make, use, import and commercialize products and processes for diagnostic, industrial and research and development purposes. The Company agreed to pay an annual license fee ranging from $5,000 to $25,000 for the royalty‑bearing license to certain patents. For the years ended December 31, 2016, 2015 and 2014, the Company incurred $31,000, $34,000 and $345,000, respectively, for regulatory milestones, license fees and reimbursed patent costs under the agreement. The Company also issued a total of 84,678 shares of common stock pursuant to the agreement in 2006 and 2007, which were recorded at fair value at the date of issuance. Regulatory milestones totaling $300,000 became due during the year ended December 31, 2014, as the Company received FDA marketing clearance and European CE Mark for the T2Dx and T2Candida. The Company is required to pay royalties on net sales of products and processes that are covered by patent rights licensed under the agreement at a percentage ranging in the low single digits, subject to reductions and offsets in certain circumstances, as well as a royalty on net sales of products that the Company sublicenses at a low double‑digit percentage of specified gross revenue. Royalties that became due under this agreement for the years ended December 31, 2016 and 2015 were immaterial.

401(k) Savings Plan	12 Months Ended
401(k) Savings Plan	Dec. 31, 2016
401(k) Savings Plan
401(k) Savings Plan	14. 401(k) Savings Plan In March, 2008, the Company established a retirement savings plan under Section 401(k) of the Internal Revenue Code (the “401(k) Plan”). The 401(k) Plan covers substantially all employees of the Company who meet minimum age and service requirements, and allows participants to defer a portion of their annual compensation on a pretax basis. Company contributions to the 401(k) Plan may be made at the discretion of the board of directors. Company contributions to the 401(k) Plan were $237,000 for the year ended December 31, 2016. No contributions were made in the years ended December 31, 2015 and 2014.

Co-Development Agreements	12 Months Ended
Co-Development Agreements	Dec. 31, 2016
Co-Development Agreements
Co-Development Agreements	15. Co-Development Agreements Canon US Life Sciences On September 21, 2016, Canon became a related party when the Company sold the Canon Shares for an aggregate cash purchase price of $39.7 million, which represented 19.9% of the outstanding shares of common stock of the Company. On February 3, 2015, the Company entered into a Co-Development Partnership Agreement (the “Co-Development Agreement”) with Canon U.S. Life Sciences, Inc. (“Canon US Life Sciences”) to develop a diagnostic test panel to rapidly detect Lyme disease. Under the terms of the Co-Development Agreement, the Company received an upfront payment of $2.0 million from Canon US Life Sciences and the agreement includes an additional $6.5 million of consideration upon achieving certain development and regulatory milestones for total aggregate payments of up to $8.5 million. In October 2015, the Company achieved a specified technical requirement and received $1.5 million related to the achievement of the milestone. The Company is eligible to receive an additional $5.0 million under the arrangement, in two milestone payments of $2.0 million and $3.0 million, related to the achievement of additional development and regulatory milestones. All payments under the Co-Development Agreement are non-refundable once received. The Company will retain exclusive worldwide commercialization rights of any products developed under the Co-Development Agreement, including sales, marketing and distribution and Canon US Life Sciences will not receive any commercial right and will be entitled to only receive royalty payments on the sales of all products developed under the Co-Development Agreement. Either party may terminate the Co-Development Agreement upon the occurrence of a material breach by the other party (subject to a cure period). The Company evaluated the deliverables under the Co-Development Agreement and determined that the Co-Development Agreement included one unit of accounting, the research and development services, as the joint research and development committee deliverable was deemed to be de minimus. The Company is recognizing revenue for research and development services as a component of research revenue in the consolidated financial statements as the services are delivered using the proportional performance method of accounting, limited to payments earned. Costs incurred to deliver the services under the Co-Development Agreement are recorded as research and development expense in the consolidated financial statements. The Company recorded revenue of $1.8 million and $1.4 million for the years ended December 31, 2016 and 2015, respectively, under the Co-Development Agreement, and expects to record revenue over the next two years, provided development and regulatory milestones are achieved. Allergan Sales, LLC On November 1, 2016, the Company entered into a Co-Development, Collaboration and Co-Marketing Agreement (the “Allergan Agreement”) with Allergan Sales, LLC (“Allergan Sales”) to develop (1) a direct detection diagnostic test panel that adds one additional bacteria species to the existing T2Bacteria product candidate (the “T2Bacteria II Panel”), and (2) a direct detection diagnostic test panel for testing drug resistance directly in whole blood (the “T2GNR Panel” and, together with the T2Bacteria II Panel, the “Developed Products”). In addition, both the Company and Allergan Sales will participate in a joint research and development committee and Allergan Sales will receive the right to cooperatively market the T2Candida, T2Bacteria, and the Developed Products under the Allergan Agreement to certain agreed-upon customers. Under the terms of the Allergan Agreement, the Company received an upfront payment of $2.0 million from Allergan Sales and will receive additional milestone payments upon achieving certain developmental milestones for total aggregate payments of up to $4.0 million. All payments under the Allergan Agreement are non-refundable once received. The Company will retain exclusive worldwide commercialization rights of any products developed under the Allergan Agreement, including distribution, subject to Allergan Sales’ right to co-market the Developed Products. Allergan Sales, at its election, may co-market T2Candida, T2Bacteria and the Developed Products worldwide to certain agreed-upon customers and will receive royalty based on its sales for a period of time. The Company evaluated the deliverables under the Allergan Agreement and determined that the Allergan Agreement included two units of accounting, the research and development services for the T2Bacteria II Panel and the research and development services for the T2GNR Panel, as the joint research and development committee and right to cooperatively market deliverables were deemed to be de minimus. The Company is recognizing revenue for research and development services as a component of research revenue in the consolidated financial statements as the services are delivered using the proportional performance method of accounting, limited to payments earned. Costs incurred to deliver the services under the Allergan Agreement are recorded as research and development expense in the consolidated financial statements. The Company did not record any revenue for the year ended December 31, 2016 under the Allergan Agreement and expects to record revenue over the next two years, provided development and regulatory milestones are achieved.

Quarterly Financial Data (unaudited)

12 Months Ended

Dec. 31, 2016

Quarterly Financial Data (unaudited)

Quarterly Financial Data (unaudited)

16. Quarterly Financial Data (unaudited)


	Year ended December 31, 2016
	(In thousands, except per share data)
	First Quarter		Second Quarter		Third Quarter		Fourth Quarter
Revenue:
Product revenue	$	437	$	151	$	580	$	579
Research revenue		659		839		504		331
Total revenue	$	1,096	$	990	$	1,084	$	910
Costs and expenses:
Cost of product revenue		1,026		1,781		1,894		2,171
Research and development		6,589		6,369		5,200		5,851
Selling, general and administrative		6,204		6,143		5,935		5,795
Total costs and expenses		13,819		14,293		13,029		13,817
Loss from operations	$	(12,723)	$	(13,303)	$	(11,945)	$	(12,907)
Net loss	$	(13,426)	$	(14,046)	$	(12,783)	$	(14,549)
Net loss applicable to common shareholders	$	(13,426)	$	(14,046)	$	(12,783)	$	(14,549)
Per share data:
Net loss per common share—basic and diluted	$	(0.55)	$	(0.58)	$	(0.51)	$	(0.48)

	Year ended December 31, 2015
	(In thousands, except per share data)
	First Quarter		Second Quarter		Third Quarter		Fourth Quarter
Revenue:
Product revenue	$	11	$	—	$	245	$	343
Research revenue		178		564		804		668
Total revenue	$	189	$	564	$	1,049	$	1,011
Costs and expenses:
Cost of product revenue		1		—		829		910
Research and development		5,869		6,651		6,204		6,638
Selling, general and administrative		4,468		4,437		5,181		5,008
Total costs and expenses		10,338		11,088		12,214		12,556
Loss from operations	$	(10,149)	$	(10,524)	$	(11,165)	$	(11,545)
Net loss	$	(10,619)	$	(10,995)	$	(11,644)	$	(12,032)
Net loss applicable to common shareholders	$	(10,619)	$	(10,995)	$	(11,644)	$	(12,032)
Per share data:
Net loss per common share—basic and diluted	$	(0.53)	$	(0.54)	$	(0.57)	$	(0.56)

Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2016

Summary of Significant Accounting Policies

Basis of Presentation and Consolidation

Use of Estimates

Segment Information

Off Balance Sheet Risk and Concentrations of Credit Risk

Off‑Balance Sheet Risk and Concentrations of Credit Risk

Cash Equivalents

Accounts Receivable

Inventories

The components of inventory consist of the following (in thousands):


	December 31,		December 31,
	2016		2015
Raw materials	$	389	$	203
Work-in-process		351		287
Finished goods		63		193
Total inventories, net	$	803	$	683

Fair Value Measurements

Level 1 — Quoted unadjusted prices for identical instruments in active markets.

Level 3 — Model derived valuations in which one or more significant inputs or significant value drivers are unobservable, including assumptions developed by the Company.

Financial instruments measured at fair value on a recurring basis include cash, money market funds and restricted cash (See Note 3).

Property and Equipment

Revenue Recognition

i.Persuasive evidence of an arrangement exists

ii.Delivery has occurred or services have been rendered

iii.The seller’s price to the buyer is fixed or determinable

iv.Collectability is reasonably assured

If any of the above criteria have not been met, the Company defers revenue until such time each of the criteria have been satisfied.

The Company does not offer rights of return for instruments or consumable diagnostic tests.

Product Recall

Cost of Product Revenue

Research and Development Costs

Impairment of Long Lived Assets

Comprehensive Loss

Stock Based Compensation

Stock-Based Compensation

The Company expenses restricted stock awards based on the fair value of the award on the date of issuance, on a straight‑line basis over the associated service period of the award.

Income Taxes

Guarantees

Net Loss Per Share

Recent Accounting Standards

Accounting Standards Adopted

Accounting Standards Issued, Not Adopted

Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2016

Summary of Significant Accounting Policies

Schedule of inventory

The components of inventory consist of the following (in thousands):


	December 31,		December 31,
	2016		2015
Raw materials	$	389	$	203
Work-in-process		351		287
Finished goods		63		193
Total inventories, net	$	803	$	683

Fair Value Measurements (Tables)

12 Months Ended

Dec. 31, 2016

Fair Value Measurements

Schedule of financial assets and liabilities at fair value on a recurring basis

The following tables set forth the Company’s financial assets and liabilities carried at fair value categorized using the lowest level of input applicable to each financial instrument as of December 31, 2016 and 2015 (in thousands):


			Quoted Prices
			in Active		Significant
			Markets for		Other		Significant
	Balance at		Identical		Observable		Unobservable
	December 31,		Assets		Inputs		Inputs
	2016		(Level 1)		(Level 2)		(Level 3)
Assets:
Cash	$	16,887	$	16,887	$	—	$	—
Money market funds		56,601		56,601		—		—
Restricted cash		260		260		—		—
	$	73,748	$	73,748	$	—	$	—


			Quoted Prices
			in Active		Significant
			Markets for		Other		Significant
	Balance at		Identical		Observable		Unobservable
	December 31,		Assets		Inputs		Inputs
	2015		(Level 1)		(Level 2)		(Level 3)
Assets:
Cash	$	1,520	$	1,520	$	—	$	—
Money market funds		72,142		72,142		—		—
Restricted cash		260		260		—		—
	$	73,922	$	73,922	$	—	$	—

Supplemental Balance Sheet Information (Tables)

12 Months Ended

Dec. 31, 2016

Supplemental Balance Sheet Information.

Schedule of property and equipment

Property and equipment consists of the following (in thousands)


	Estimated Useful	December 31,		December 31,
	Life (Years)	2016		2015
Office and computer equipment	3	$	409	$	395
Software	3		708		632
Laboratory equipment	5		4,516		4,112
Furniture	5-7		200		187
Manufacturing equipment	5		897		577
Manufacturing tooling and molds	0.5		154		71
T2-owned instruments and components	5		9,119		4,960
Leasehold improvements	Lesser of useful life or lease term		3,353		3,332
Construction in progress	n/a		1,299		1,196
			20,655		15,462
Less accumulated depreciation and amortization			(7,066)		(4,807)
Property and equipment, net		$	13,589	$	10,655

Components of accrued expenses

Accrued expenses consist of the following (in thousands):


	December 31,		December 31,
	2016		2015
Accrued payroll and compensation	$	2,479	$	2,418
Accrued research and development expenses		846		458
Accrued professional services		884		542
Other accrued expenses		699		744
Total accrued expenses	$	4,908	$	4,162

Notes Payable (Tables)

12 Months Ended

Dec. 31, 2016

Debt

Summary of future principal payments on the notes payable

Future principal payments on the notes payable as of December 31, 2016 are as follows (in thousands):


Year ended December 31,
2017	$	1,286
2018		1,485
2019		1,015
2020		5,723
2021		22,893
Thereafter		17,171
Total before unamortized discount and issuance costs		49,573
Less: paid-in-kind interest		(5,782)
Less: unamortized discount and issuance costs		(3,018)
Total notes payable	$	40,773

Share Based Compensation (Tables)

12 Months Ended

Dec. 31, 2016

Stock Based Compensation

Summary of stock option activity

The following is a summary of option activity under the Plan (in thousands, except share and per share amounts):


				Weighted-Average
		Weighted-Average		Remaining
	Number of	Exercise Price Per		Contractual Term	Aggregate Intrinsic
	Shares	Share		(In years)	Value
Outstanding at December 31, 2015	3,484,298	$	8.79	7.64	$	14,620
Granted	1,489,384		8.35
Exercised	(165,803)		2.84			930
Forfeited	(664,303)		11.55
Canceled	(100,949)		17.38
Outstanding at December 31, 2016	4,042,627		8.20	7.05		4,091
Exercisable at December 31, 2016	2,251,925		6.77	5.61		3,922
Vested or expected to vest at December 31, 2016	3,845,455		8.12	6.95		4,084

Schedule of estimated assumptions used to calculate weighted-average fair value of options granted


	Year ended
	December 31,
	2016		2015
Weighted-average risk-free interest rate	1.42	%	1.69	%
Expected dividend yield	0.00	%	0.00	%
Expected volatility	61	%	56	%
Expected terms	6.0	years	6.0	years

Summary of restricted stock unit activity

The following is a summary of restricted stock unit activity under the Plan (in thousands, except share and per share amounts):



		Weighted-Average
	Number of	Grant Date Fair
	Shares	Value
Nonvested at December 31, 2015	—	$	—
Granted	272,195		5.83
Exercised	—		—
Forfeited	—		—
Canceled	—		—
Nonvested at December 31, 2016	272,195		5.83

Schedule of estimated assumptions used to calculate weighted-average fair value of the purchase rights granted


	Year ended
	December 31,
	2016		2015
Weighted-average risk-free interest rate	0.50	%	0.19	%
Expected dividend yield	0.00	%	0.00	%
Expected volatility	67	%	57	%
Expected terms	0.5	years	0.5	years

Summary of stock-based compensation expense for stock options granted that was recorded in the Company's results of operations


	Year ended
	December 31,
	2016		2015		2014
Cost of product revenue	$	123	$	—	$	—
Research and development		1,127		1,213		501
Selling, general and administrative		3,480		2,840		1,152
Total stock-based compensation expense	$	4,730	$	4,053	$	1,653

Net Loss Per Share (Tables)

12 Months Ended

Dec. 31, 2016

Net Loss Per Share

Schedule of basic and diluted net loss per share applicable to common stockholders

The following table presents the calculation of basic and diluted net loss per share applicable to common stockholders (in thousands, except share and per share data):


	Year ended
	December 31,
	2016		2015		2014
Numerator:
Net loss	$	(54,804)	$	(45,290)	$	(31,390)
Accretion of redeemable convertible preferred stock to redemption value		—		—		(4,570)
Net loss applicable to common stockholders	$	(54,804)	$	(45,290)	$	(35,960)
Denominator:
Weighted-average number of common shares outstanding — basic and diluted		26,015,751		20,501,748		8,674,931
Net loss per share applicable to common stockholders — basic and diluted	$	(2.11)	$	(2.21)	$	(4.15)

Schedule of shares excluded from the calculation where the inclusion would be anti-dilutive


	Year ended
	December 31,
	2016	2015	2014
Options to purchase common shares	4,042,627	3,484,298	2,911,146
Restricted stock units	272,195	—	—
Warrants to purchase common stock	528,958	—	—
Total	4,843,780	3,484,298	2,911,146

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2016

Income Taxes

Schedule of reconciliation of the U.S. federal statutory rate to the Company?s effective tax rate


	Year Ended December 31,
	2016		2015		2014
Tax at statutory rates	35.0	%	35.0	%	35.0	%
State income taxes	5.2		6.6		5.1
Permanent differences	(1.2)		(1.3)		(0.8)
Research and development credits	1.3		1.5		1.9
Change in valuation allowance	(40.3)		(41.8)		(41.2)
Effective tax rate	0.0	%	0.0	%	0.0	%

Schedule of Deferred Tax Assets

The significant components of the Company’s deferred tax asset consist of the following at December 31, 2016 and 2015 (in thousands):


	December 31,
	2016		2015
Deferred tax assets:
Net operating loss carryforwards	$	69,411	$	49,417
Tax credits		5,269		4,107
Other temporary differences		1,636		1,623
Start-up expenditures		5,088		5,288
Stock option expenses		2,779		1,649
Total deferred tax assets		84,183		62,084
Deferred tax asset valuation allowance		(83,924)		(61,813)
Net deferred tax assets		259		271
Deferred tax liabilities:
Prepaid expenses		(259)		(271)
Net deferred taxes	$	—	$	—

Commitments and Contingencies (Tables)

12 Months Ended

Dec. 31, 2016

Commitments and Contingencies.

Schedule of future minimum lease payments under the Company?s operating leases

Future minimum non-cancelable lease payments under the Company’s operating leases as of December 31, 2016 are as follows (in thousands):


Year ending December 31,
2017	$	2,079
2018		404
2019		414
2020		425
2021		107
Thereafter		—
	$	3,429

Quarterly Financial Data (unaudited) (Tables)

12 Months Ended

Dec. 31, 2016

Quarterly Financial Data (unaudited)

Schedule of quarterly financial information


	Year ended December 31, 2016
	(In thousands, except per share data)
	First Quarter		Second Quarter		Third Quarter		Fourth Quarter
Revenue:
Product revenue	$	437	$	151	$	580	$	579
Research revenue		659		839		504		331
Total revenue	$	1,096	$	990	$	1,084	$	910
Costs and expenses:
Cost of product revenue		1,026		1,781		1,894		2,171
Research and development		6,589		6,369		5,200		5,851
Selling, general and administrative		6,204		6,143		5,935		5,795
Total costs and expenses		13,819		14,293		13,029		13,817
Loss from operations	$	(12,723)	$	(13,303)	$	(11,945)	$	(12,907)
Net loss	$	(13,426)	$	(14,046)	$	(12,783)	$	(14,549)
Net loss applicable to common shareholders	$	(13,426)	$	(14,046)	$	(12,783)	$	(14,549)
Per share data:
Net loss per common share—basic and diluted	$	(0.55)	$	(0.58)	$	(0.51)	$	(0.48)

	Year ended December 31, 2015
	(In thousands, except per share data)
	First Quarter		Second Quarter		Third Quarter		Fourth Quarter
Revenue:
Product revenue	$	11	$	—	$	245	$	343
Research revenue		178		564		804		668
Total revenue	$	189	$	564	$	1,049	$	1,011
Costs and expenses:
Cost of product revenue		1		—		829		910
Research and development		5,869		6,651		6,204		6,638
Selling, general and administrative		4,468		4,437		5,181		5,008
Total costs and expenses		10,338		11,088		12,214		12,556
Loss from operations	$	(10,149)	$	(10,524)	$	(11,165)	$	(11,545)
Net loss	$	(10,619)	$	(10,995)	$	(11,644)	$	(12,032)
Net loss applicable to common shareholders	$	(10,619)	$	(10,995)	$	(11,644)	$	(12,032)
Per share data:
Net loss per common share—basic and diluted	$	(0.53)	$	(0.54)	$	(0.57)	$	(0.56)

Nature of Business (Details) - USD ($) $ in Thousands	12 Months Ended
Nature of Business (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Cash and cash equivalents	$ 73,488	$ 73,662	$ 73,849	$ 30,198
Accumulated deficit	$ (203,689)	$ (148,885)
Period over which cash resources will be sufficient to allow Company to fund current operating plan	12 months
Equipment Lease Credit Facility
Remaining borrowing capacity	$ 1,300

Summary of Significant Accounting Policies (Details)	12 Months Ended
Summary of Significant Accounting Policies (Details)	Dec. 31, 2016 segment	Dec. 31, 2015 item	Dec. 31, 2014 item
Segment Information
Number of operating segments \| segment	1
Off Balance Sheet Risk and Concentrations of Credit Risk
Number of financial institutions in which cash was deposited \| item		1	1

Summary of Significant Accounting Policies (Credit Risk) (Details)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Customer One
Off Balance Sheet Risk and Concentrations of Credit Risk
Total revenue (as a percent)	45.00%	50.00%
Customer Two
Off Balance Sheet Risk and Concentrations of Credit Risk
Total revenue (as a percent)	10.00%	25.00%

Summary of Significant Accounting Policies (Inventory) (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Inventory
Raw materials	$ 389	$ 203
Work-in-process	351	287
Finished goods	63	193
Total inventories, net	$ 803	$ 683

Summary of Significant Accounting Policies Product Service (Details) - USD ($)	3 Months Ended							6 Months Ended	12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Mar. 31, 2015	Jun. 30, 2016	Dec. 31, 2016	Dec. 31, 2015
Product information
Deferred revenue	$ 2,445,000				$ 2,146,000				$ 2,445,000	$ 2,146,000
Cost of product revenue	2,171,000	$ 1,894,000	$ 1,781,000	$ 1,026,000	$ 910,000	$ 829,000	$ 1,000		$ 6,872,000	$ 1,740,000
Instruments
Product information
Maintenance Services period (in years)									1 year
Additional period for Maintenance Service option (in years)									1 year
T2Candida
Product information
Deferred revenue	37,000		$ 149,000					$ 149,000	$ 37,000
Cost of product revenue								$ 41,000
Remaining warranty reserve	$ 3,000								$ 3,000

Summary of Significant Accounting Policies (Impairment, Stock Based Comp) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Impairment of Long Lived Assets
Impairment charges	$ 0	$ 0	$ 0
Stock Based Compensation
Vesting period	4 years
Expected dividend yield	0.00%

Summary of Significant Accounting Policies Recent Accounting Pronouncements (Details) - USD ($)	Dec. 31, 2016	Dec. 31, 2015
New Accounting Pronouncements or Change in Accounting Principle
Prepaid expenses and other current assets	$ 820,000	$ 838,000
Other assets	281,000	358,000
Current portion of notes payable	1,269,000	4,449,000
Notes payable, net of current portion	39,504,000	26,121,000
ASU 2015-03 \| Scenario, Adjustment
New Accounting Pronouncements or Change in Accounting Principle
Prepaid expenses and other current assets	(22,000)
Current portion of notes payable	$ (22,000)
New Accounting Pronouncement, Early Adoption, Effect \| ASU 2015-03
New Accounting Pronouncements or Change in Accounting Principle
Other assets		(102,000)
Notes payable, net of current portion		$ (102,000)

Fair Value Measurements (Table) (Details) - Recurring - Total - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Assets:
Restricted cash	$ 260	$ 260
Total assets	73,748	73,922
Cash
Assets:
Cash and cash equivalents	16,887	1,520
Money market funds
Assets:
Cash and cash equivalents	56,601	72,142
Level I
Assets:
Restricted cash	260	260
Total assets	73,748	73,922
Level I \| Cash
Assets:
Cash and cash equivalents	16,887	1,520
Level I \| Money market funds
Assets:
Cash and cash equivalents	$ 56,601	$ 72,142

Supplemental Balance Sheet Information - Property and Equipment - (Details) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Property and Equipment
Property and equipment, gross	$ 20,655,000	$ 15,462,000
Accumulated depreciation and amortization	(7,066,000)	(4,807,000)
Property and equipment, net	13,589,000	10,655,000
Office and computer equipment
Property and Equipment
Property and equipment, gross	$ 409,000	395,000
Estimated useful lives (Years)	3 years
Software
Property and Equipment
Property and equipment, gross	$ 708,000	632,000
Estimated useful lives (Years)	3 years
Laboratory equipment
Property and Equipment
Property and equipment, gross	$ 4,516,000	4,112,000
Estimated useful lives (Years)	5 years
Furniture
Property and Equipment
Property and equipment, gross	$ 200,000	187,000
Furniture \| Minimum
Property and Equipment
Estimated useful lives (Years)	5 years
Furniture \| Maximum
Property and Equipment
Estimated useful lives (Years)	7 years
Manufacturing equipment
Property and Equipment
Property and equipment, gross	$ 897,000	577,000
Estimated useful lives (Years)	5 years
Manufacturing tooling and molds
Property and Equipment
Property and equipment, gross	$ 154,000	71,000
Estimated useful lives (Years)	6 months
T2-owned instruments and components
Property and Equipment
Property and equipment, gross	$ 9,119,000	4,960,000
Estimated useful lives (Years)	5 years
Leasehold improvements
Property and Equipment
Property and equipment, gross	$ 3,353,000	3,332,000
Construction in progress
Property and Equipment
Property and equipment, gross	1,299,000	1,196,000
T2 Owned Instruments in Service
Property and Equipment
Property and equipment, gross	$ 5,700,000
Estimated useful lives (Years)	5 years
Depreciation expense recorded as a component of cost of product revenue	$ 599,000	$ 105,000

Supplemental Balance Sheet Information - Accrued Expenses (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Accrued expenses
Accrued payroll and compensation	$ 2,479	$ 2,418
Accrued research and development expenses	846	458
Accrued professional services	884	542
Other accrued expenses	699	744
Total accrued expenses	$ 4,908	$ 4,162

Notes Payable - Future principal payments on notes payable (Details) $ in Thousands	Dec. 31, 2016 USD ($)
Future principal payments on the notes payable
2017	$ 1,286
2018	1,485
2019	1,015
2020	5,723
2021	22,893
Thereafter	17,171
Total before unamortized discount and issuance costs	49,573
Less: paid-in-kind interest	(5,782)
Less: unamortized discount and issuance costs	(3,018)
Total notes payable	$ 40,773

Notes Payable (ASU 2015-03) (Details) - USD ($)	Dec. 31, 2016	Dec. 31, 2015
Debt Instrument
Prepaid expenses and other current assets	$ 820,000	$ 838,000
Other assets	281,000	358,000
Current portion of notes payable	1,269,000	4,449,000
Notes payable, net of current portion	39,504,000	26,121,000
New Accounting Pronouncement, Early Adoption, Effect \| ASU 2015-03
Debt Instrument
Other assets		(102,000)
Notes payable, net of current portion		$ (102,000)
Scenario, Adjustment \| ASU 2015-03
Debt Instrument
Prepaid expenses and other current assets	(22,000)
Current portion of notes payable	$ (22,000)

Notes Payable - Term Loan (Details)	1 Months Ended	12 Months Ended			30 Months Ended
Notes Payable - Term Loan (Details)	Dec. 31, 2016 USD ($) item $ / shares shares	Dec. 31, 2016 USD ($) $ / shares shares	Dec. 31, 2015 USD ($)	Dec. 31, 2014 USD ($)	Dec. 31, 2016 USD ($) $ / shares shares	Dec. 30, 2016 USD ($)	Jul. 11, 2014 USD ($)	May 31, 2011 USD ($)
Debt Instrument
Proceeds from notes payable, net of issuance costs		$ 43,803,000	$ 10,000,000	$ 19,714,000
Repayments of notes payable		$ 32,404,000	$ 309,000	$ 4,037,000
Term Loan Agreement
Debt Instrument
Proceeds from issuance of debt	$ 40,000,000
Increase in additional borrowing capacity	$ 10,000,000
Debt term	6 years
Debt term of interest only payments	3 years
Debt extended term of interest only payments	4 years
Final fee as a percentage of the principal outstanding	8.00%	8.00%			8.00%
Prepayment fee term	5 years
Prepayment fee after first five years of the term	$ 0	$ 0			$ 0
Additional interest rate, event of default (as a percent)	4.00%	4.00%			4.00%
Proceeds from notes payable, net of issuance costs	$ 39,200,000
Portion of proceeds used for debt repayment	$ 28,000,000
Term Loan Agreement \| Prior to Approval Milestone
Debt Instrument
Annual fixed rate (as a percent)	12.50%	12.50%			12.50%
Deferred interest rate (as a percent)	4.00%
Term Loan Agreement \| Following Approval Milestone
Debt Instrument
Annual fixed rate (as a percent)	11.50%	11.50%			11.50%
Deferred interest rate (as a percent)	3.50%
Term Loan Agreement \| Common Stock Warrant
Debt Instrument
Number of separate warrants \| item	4
Number of shares issuable for warrants outstanding \| shares	528,958	528,958			528,958
Exercise price (in dollars per share) \| $ / shares	$ 8.06	$ 8.06			$ 8.06
Fair market value of warrants	$ 1,800,000	$ 1,800,000			$ 1,800,000	$ 1,800,000
Loan and Security Agreement
Debt Instrument
Maximum borrowings available							$ 30,000,000
Proceeds from notes payable, net of issuance costs					$ 29,700,000
Repayments of notes payable	27,500,000
Promissory Note
Debt Instrument
Maximum borrowings available								$ 1,700,000
Annual fixed rate (as a percent)								6.50%
Repayments of notes payable	$ 479,000

Notes Payable (Equipment Lease) (Details) - Equipment Lease Credit Facility	1 Months Ended
	Jun. 30, 2016 USD ($) item	Apr. 30, 2016 USD ($)	Oct. 31, 2015 USD ($)
Capital lease obligation
Maximum borrowings available			$ 10,000,000
Maximum capped amount			$ 5,000,000
Debt term			36 months
Repurchase price as percentage of original equipment value that the equipment under lease may be repurchased by lessee			10.00%
Number of draws \| item	2
Minimum
Capital lease obligation
Renewal term (in years)			1 year
First Draw
Capital lease obligation
Amount of draw		$ 2,100,000
Amount of monthly payment		$ 67,000
Second Draw
Capital lease obligation
Amount of draw	$ 2,500,000
Amount of monthly payment	$ 79,000

Notes Payable - Loan and Security Agreement (Details)			1 Months Ended	12 Months Ended			18 Months Ended	30 Months Ended
Notes Payable - Loan and Security Agreement (Details)	Dec. 28, 2015 USD ($)	Jul. 11, 2014 USD ($) tranche Lender	Dec. 31, 2016 USD ($)	Dec. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Dec. 31, 2014 USD ($)	Dec. 31, 2016	Dec. 31, 2016 USD ($)	May 31, 2015 USD ($)
Debt Instrument
Proceeds from notes payable, net of issuance costs				$ 43,803,000	$ 10,000,000	$ 19,714,000
Repayments of notes payable				$ 32,404,000	$ 309,000	4,037,000
Loan and Security Agreement
Debt Instrument
Number of lenders \| Lender		2
Maximum borrowings available		$ 30,000,000
Number of tranches \| tranche		2
Final fee as a percentage of original principal amount of amounts borrowed		4.75%
Minimum amount of denomination for prepayment of borrowings		$ 1,000,000
Effective interest rate (as a percent)			9.70%	9.70%			9.70%	9.70%
Proceeds from notes payable, net of issuance costs								$ 29,700,000
Repayments of notes payable			$ 27,500,000
Loan and Security Agreement \| Prior to second anniversary and after first anniversary of borrowing date
Debt Instrument
Prepayment premium (as a percent)		1.00%
Loan and Security Agreement \| Prior to maturity date and after second anniversary of borrowing date
Debt Instrument
Prepayment premium (as a percent)		0.50%
Loan and Security Agreement \| One-month LIBOR
Debt Instrument
Basis spread (as a percent)		7.05%
Loan and Security Agreement \| Tranche A
Debt Instrument
Maximum borrowings available		$ 20,000,000
Minimum amount of draw upon closing		10,000,000
Minimum amount of draw after closing		5,000,000
Proceeds from issuance of debt						$ 20,000,000
Loan and Security Agreement \| Tranche B
Debt Instrument
Maximum borrowings available		$ 10,000,000							$ 10,000,000
Proceeds from issuance of debt	$ 10,000,000
Commitment fee on undrawn principal (as a percent)							1.00%
Fee Amount	$ 50,000

Notes Payable - Promissory Note (Details) - USD ($)	1 Months Ended	12 Months Ended			68 Months Ended
Notes Payable - Promissory Note (Details) - USD ($)	Dec. 31, 2016	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2016	May 31, 2011
Debt Instrument
Repayments of notes payable		$ 32,404,000	$ 309,000	$ 4,037,000
Promissory Note
Debt Instrument
Maximum borrowings available						$ 1,700,000
Stated interest rate (as a percent)						6.50%
Minimum cash balance						$ 300,000
Proceeds received on borrowings					$ 1,400,000
Repayments of notes payable	$ 479,000

Notes Payable (Interest Expense) (Details) - USD ($)	12 Months Ended
Notes Payable (Interest Expense) (Details) - USD ($)	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Interest expense
Interest expense	$ 4,100,000	$ 2,000,000	$ 741,000
Non-cash interest	564,000	$ 354,000	$ 112,000
Extinguishment of debt	$ 112,000

Redeemable Convertible Preferred Stock (Details) - USD ($) $ in Thousands		12 Months Ended
	Aug. 12, 2014	Dec. 31, 2014
Conversion of convertible preferred stock into common stock	$ 117,400
Conversion of redeemable convertible preferred stock into common stock		$ 117,383
Common Stock
Conversion of redeemable convertible preferred stock into common stock (in shares)	12,516,298	12,516,298
Conversion of redeemable convertible preferred stock into common stock		$ 13
Accumulated Deficit
Conversion of redeemable convertible preferred stock into common stock	$ 21,000	21,029
Additional Paid-in Capital
Conversion of redeemable convertible preferred stock into common stock	$ 96,300	$ 96,341

Stockholders' Equity (Details)	12 Months Ended
Stockholders' Equity (Details)	Dec. 31, 2016 item shares
IPO
Number of voting rights per share of common stock \| item	1
2014 Incentive Award Plan
IPO
Common stock were reserved for issuance	4,042,627
2014 Employee Stock Purchase Plan
IPO
Common stock were reserved for issuance	357,798

Stockholders' Equity - Private Investment (Details) - USD ($) $ / shares in Units, $ in Thousands		12 Months Ended
	Sep. 21, 2016	Dec. 31, 2016
Stock Purchase Agreement
Proceeds from private investment in public equity		$ 39,723
Stock sale agreement \| Private Placement
Stock Purchase Agreement
Number of shares sold	6,055,341
Sale price of stock (in dollars per share)	$ 6.56
Proceeds from private investment in public equity	$ 39,700
Ownership percentage (as a percent)	19.90%

Stock Based Compensation (Stock Options) (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Share-Based Compensation
Vesting period	4 years
Stock Options
Share-Based Compensation
Aggregate fair value of options granted	$ 7,000	$ 10,100	$ 6,000
Number of Shares
Outstanding, beginning of the period (in shares)	3,484,298
Granted (in shares)	1,489,384
Exercised (in shares)	(165,803)
Forfeited (in shares)	(664,303)
Canceled (in shares)	(100,949)
Outstanding, end of the period (in shares)	4,042,627	3,484,298
Exercisable (in shares)	2,251,925
Vested or expected to vest (in shares)	3,845,455
Weighted Average Exercise Price Per Share
Outstanding, beginning of the period (in dollars per share)	$ 8.79
Granted (in dollars per share)	8.35
Exercised (in dollars per share)	2.84
Forfeited (in dollars per share)	11.55
Cancelled (in dollars per share)	17.38
Outstanding, end of the period (in dollars per share)	8.20	$ 8.79
Exercisable (in dollars per share)	6.77
Vested or expected to vest (in dollars per share)	$ 8.12
Weighted-Average Remaining Contractual Term (in years)
Outstanding (in years)	7 years 18 days	7 years 7 months 21 days
Exercisable (in years)	5 years 7 months 10 days
Vested or expected to vest (in years)	6 years 11 months 12 days
Aggregate Intrinsic Value
Outstanding, beginning of the period	$ 14,620
Exercised	930
Outstanding, end of the period	4,091	$ 14,620
Exercisable	3,922
Vested or expected to vest	$ 4,084
Weighted-average fair values of options
Weighted average fair value of options granted (in dollars per share)	$ 4.68	$ 8.42	$ 7.59
Fair value assumptions
Weighted-average risk-free interest rate	1.42%	1.69%
Expected dividend yield	0.00%	0.00%
Expected volatility	61.00%	56.00%
Expected terms	6 years	6 years
Stock options
Fair value of stock options vested	$ 4,900	$ 4,000	$ 1,200
Unrecognized compensation cost
Total unrecognized compensation costs related to non-vested stock options	$ 8,800
Remaining weighted-average period that unrecognized compensation costs are expected to be recognized	2 years 6 months 15 days
Performance-based awards
Number of Shares
Granted (in shares)	166,066
Forfeited (in shares)	(20,000)
Outstanding, end of the period (in shares)	146,066
2006 Stock Incentive Plan \| Maximum \| Stock Options
Share-Based Compensation
Expiration Period	10 years
Vesting period	4 years
2014 Stock Incentive Plan \| Stock Options
Share-Based Compensation
Common stock were reserved for issuance	823,529
Percentage of common shares outstanding	4.00%
Shares available for grant	223,397
2014 Stock Incentive Plan \| Maximum \| Stock Options
Share-Based Compensation
Expiration Period	10 years
Vesting period	4 years

Stock Based Compensation (Restricted Stock) (Details) - Restricted Stock Units $ / shares in Units, $ in Millions	12 Months Ended
	Dec. 31, 2016 USD ($) $ / shares shares
Share-Based Compensation
Aggregate fair value of restricted stock units granted (in dollars) \| $	$ 1.4
Number of Shares
Nonvested at beginning of period (in shares)
Granted (in shares)	272,195
Nonvested at end of period (in shares)	272,195
Weighted-Average Grant Date Fair Value
Nonvested at beginning of period (in dollars per share) \| $ / shares
Granted (in dollars per share) \| $ / shares	5.83
Nonvested at end of period (in dollars per share) \| $ / shares	$ 5.83
Restricted Stock Units
Vested (in shares)	0
Unrecognized compensation cost
Unrecognized compensation cost (in dollars) \| $	$ 1.4
Remaining weighted-average period that unrecognized compensation costs are expected to be recognized	1 year 11 months 1 day

Stock Based Compensation (Employee Stock Purchase Plan) (Details) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Share-Based Compensation
Stock-based compensation expense	$ 4,730,000	$ 4,053,000	$ 1,653,000
Employee Stock Purchase Plan
Share-Based Compensation
Percentage of full share price paid in purchase of common stock	85.00%
Maximum amount of annual employee common stock purchases	$ 25,000
Stock-based compensation expense	$ 253,000	$ 233,000	$ 103,000
Fair value assumptions
Weighted-average risk-free interest rate	0.50%	0.19%
Expected dividend yield	0.00%	0.00%
Expected volatility	67.00%	57.00%
Expected terms	6 months	6 months
Employee Stock Purchase Plan
Shares available for authorization	220,588
Percentage of common shares outstanding	1.00%
Shares available for grant	134,401

Stock Based Compensation (Stock Based Compensation Expense) (Details) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Stock-based compensation expense
Stock-based compensation expense	$ 4,730,000	$ 4,053,000	$ 1,653,000
T2 Owned Instruments in Service
Stock-based compensation expense
Stock-based compensation expense	118,000	115,000
Cost of product revenue
Stock-based compensation expense
Stock-based compensation expense	123,000
Research and development
Stock-based compensation expense
Stock-based compensation expense	1,127,000	1,213,000	501,000
Selling, general and administrative
Stock-based compensation expense
Stock-based compensation expense	$ 3,480,000	$ 2,840,000	$ 1,152,000

Warrants (Details) $ / shares in Units, $ in Millions		1 Months Ended	12 Months Ended
Warrants (Details) $ / shares in Units, $ in Millions	Aug. 12, 2014 shares	Dec. 31, 2016 USD ($) item $ / shares shares	Dec. 31, 2014 shares	Dec. 30, 2016 USD ($)	Aug. 11, 2014 shares
Common Stock
Warrants
Issuance of common stock upon net settlement of warrants to purchase redeemable convertible preferred stock (in shares)			68,700
Common Stock \| IPO
Warrants
Issuance of common stock upon net settlement of warrants to purchase redeemable convertible preferred stock (in shares)	68,700
Common Stock Warrant \| Term Loan Agreement
Warrants
Number of separate warrants \| item		4
Number of shares issuable for warrants outstanding		528,958
Exercise price (in dollars per share) \| $ / shares		$ 8.06
Fair market value of warrants \| $		$ 1.8		$ 1.8
Preferred Stock Warrant
Warrants
Number of shares issuable for warrants outstanding					250,727

Net Loss Per Share (Calc of Basic and Diluted) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Numerator:
Net loss	$ (14,549)	$ (12,783)	$ (14,046)	$ (13,426)	$ (12,032)	$ (11,644)	$ (10,995)	$ (10,619)	$ (54,804)	$ (45,290)	$ (31,390)
Accretion of redeemable convertible preferred stock to redemption value											(4,570)
Net loss applicable to common stockholders	$ (14,549)	$ (12,783)	$ (14,046)	$ (13,426)	$ (12,032)	$ (11,644)	$ (10,995)	$ (10,619)	$ (54,804)	$ (45,290)	$ (35,960)
Denominator:
Weighted-average number of common shares outstanding - basic and diluted									26,015,751	20,501,748	8,674,931
Net loss per common share - basic and diluted (in dollars per share)	$ (0.48)	$ (0.51)	$ (0.58)	$ (0.55)	$ (0.56)	$ (0.57)	$ (0.54)	$ (0.53)	$ (2.11)	$ (2.21)	$ (4.15)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References + Details

Net Loss Per Share (Antidiluted) (Details) - shares	12 Months Ended
Net Loss Per Share (Antidiluted) (Details) - shares	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Stock Options
Antidilutive Securities
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)	4,042,627	3,484,298	2,911,146
Restricted Stock Units
Antidilutive Securities
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)	272,195
Warrants
Antidilutive Securities
Anti-dilutive securities excluded from the computation of diluted net loss per share (in shares)	528,958

Income Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Effective Income Tax Rate Reconciliation, Percent.
Tax at statutory rates	35.00%	35.00%	35.00%
State income taxes	5.20%	6.60%	5.10%
Permanent differences	(1.20%)	(1.30%)	(0.80%)
Research and development credits	1.30%	1.50%	1.90%
Change in valuation allowance	(40.30%)	(41.80%)	(41.20%)
Effective tax rate	0.00%	0.00%	0.00%
Deferred tax assets:
Net operating loss carryforwards	$ 69,411	$ 49,417
Tax credits	5,269	4,107
Other temporary differences	1,636	1,623
Startup expenditures	5,088	5,288
Stock option expenses	2,779	1,649
Total deferred tax assets	84,183	62,084
Deferred tax asset valuation allowance	(83,924)	(61,813)
Net deferred tax assets	259	271
Deferred tax liabilities:
Prepaid expenses	$ (259)	$ (271)

Income Taxes (NOL and Credit) (Details)	12 Months Ended
Income Taxes (NOL and Credit) (Details)	Dec. 31, 2016 USD ($)
Federal
Net operating losses	$ 174,900,000
Tax benefits from the exercise of stock options	626,000
State
Net operating losses	162,100,000
Tax benefits from the exercise of stock options	2,900,000
Research and Development. \| Federal
Credit carryforward	3,500,000
Research and Development. \| State
Credit carryforward	$ 2,800,000

Income Taxes (Unrecognized) (Details) - USD ($)	Dec. 31, 2016	Dec. 31, 2015
Income Taxes
Unrecognized tax benefits	$ 0
Accrued interest or penalties related to uncertain tax positions	$ 0	$ 0

Commitments and Contingencies (Details) - USD ($)	1 Months Ended
Commitments and Contingencies (Details) - USD ($)	Nov. 30, 2014	May 31, 2013	Aug. 31, 2010	May 31, 2015	Jan. 01, 2011
Operating lease entered into August 2010 \| Office and laboratory space
Leases
Term of lease			5 years
Security deposit				$ 240,000	$ 400,000
Operating lease entered into May 2013 \| Office, laboratory and manufacturing space
Leases
Term of lease		2 years
Operating lease entered into November 2014 \| Laboratory Space
Leases
Term of lease	6 years
Security deposit	$ 281,000
Space build-out costs paid	1,400,000
Space build-out costs to be paid by landlord	$ 2,200,000
License Agreement \| Operating lease entered into November 2014 \| Office Space
Leases
Term of lease	2 years
Security deposit	$ 50,000

Commitments and Contingencies (Future Minimum Lease Payments) (Details) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Mar. 07, 2017
Future minimum lease payments
2017	$ 2,079,000			$ 2,100,000
2018	404,000			1,700,000
2019	414,000			1,800,000
2020	425,000			1,900,000
2021	107,000			$ 1,600,000
Total	3,429,000
Rent
Rent expenses	$ 1,800,000	$ 1,600,000	$ 950,000

Commitments and Contingencies (License Agreement) (Details) - License Agreement - USD ($)	12 Months Ended			24 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2007	Dec. 31, 2006
License Agreement
Payment of license fees and reimbursed patent costs	$ 31,000	$ 34,000	$ 345,000
Shares issued				84,678
Amount receivable for achievement of regulatory milestones			$ 300,000
Minimum
License Agreement
Annual license fee payable					$ 5,000
Maximum
License Agreement
Annual license fee payable					$ 25,000

Co-Development Agreements (Details) $ in Thousands					3 Months Ended								12 Months Ended
Co-Development Agreements (Details) $ in Thousands	Nov. 01, 2016 USD ($) item	Sep. 21, 2016 USD ($)	Oct. 31, 2015 USD ($)	Feb. 03, 2015 USD ($) item	Dec. 31, 2016 USD ($) item	Sep. 30, 2016 USD ($)	Jun. 30, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)	Sep. 30, 2015 USD ($)	Jun. 30, 2015 USD ($)	Mar. 31, 2015 USD ($)	Dec. 31, 2016 USD ($) item	Dec. 31, 2015 USD ($)	Dec. 31, 2014 USD ($)
Co-Development Agreements
Proceeds from private investment in public equity													$ 39,723
Revenues					$ 910	$ 1,084	$ 990	$ 1,096	$ 1,011	$ 1,049	$ 564	$ 189	4,080	$ 2,813	$ 119
Investor \| Stock sale agreement \| Canon U.S. Life Sciences Inc.
Co-Development Agreements
Proceeds from private investment in public equity		$ 39,700
Ownership percentage (as a percent)		19.90%
Co Development Partnership Agreement \| Canon U.S. Life Sciences Inc.
Co-Development Agreements
Upfront payment				$ 2,000
Additional consideration receivable upon achievement of certain development and regulatory milestones				6,500
Aggregate consideration receivable				$ 8,500
Proceeds received for achievement of milestone			$ 1,500
Consideration eligible to receive upon achievement of specified technical requirement related to the achievement of the milestone					$ 5,000								$ 5,000
Number of milestone payments \| item					2								2
Additional consideration receivable upon achievement of development and regulatory milestones, payment one					$ 2,000								$ 2,000
Additional consideration receivable upon achievement of development and regulatory milestones, payment two					$ 3,000								3,000
Number of units \| item				1
Revenues													$ 1,800	$ 1,400
Co-Development, Collaboration and Co-Marketing Agreement \| Allergan Sales, LLC
Co-Development Agreements
Upfront payment	$ 2,000
Number of units \| item	2
Number of additional bacteria species added to existing product candidate \| item	1
Period entity expects to record revenue													2 years
Maximum \| Co-Development, Collaboration and Co-Marketing Agreement \| Allergan Sales, LLC
Co-Development Agreements
Additional consideration receivable upon achievement of certain development and regulatory milestones	$ 4,000

Quarterly Financial Data (unaudited) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Revenue:
Product revenue	$ 579	$ 580	$ 151	$ 437	$ 343	$ 245		$ 11	$ 1,747	$ 599
Research revenue	331	504	839	659	668	804	$ 564	178	2,333	2,214	$ 119
Total revenue	910	1,084	990	1,096	1,011	1,049	564	189	4,080	2,813	119
Costs and expenses:
Cost of product revenue	2,171	1,894	1,781	1,026	910	829		1	6,872	1,740
Research and development	5,851	5,200	6,369	6,589	6,638	6,204	6,651	5,869	24,009	25,362	19,782
Selling, general and administrative	5,795	5,935	6,143	6,204	5,008	5,181	4,437	4,468	24,077	19,094	11,018
Total costs and expenses	13,817	13,029	14,293	13,819	12,556	12,214	11,088	10,338	54,958	46,196	30,800
Loss from operations	(12,907)	(11,945)	(13,303)	(12,723)	(11,545)	(11,165)	(10,524)	(10,149)	(50,878)	(43,383)	(30,681)
Net loss	(14,549)	(12,783)	(14,046)	(13,426)	(12,032)	(11,644)	(10,995)	(10,619)	(54,804)	(45,290)	(31,390)
Net loss applicable to common shareholders	$ (14,549)	$ (12,783)	$ (14,046)	$ (13,426)	$ (12,032)	$ (11,644)	$ (10,995)	$ (10,619)	$ (54,804)	$ (45,290)	$ (35,960)
Per share data:
Net loss per common share - basic and diluted (in dollars per share)	$ (0.48)	$ (0.51)	$ (0.58)	$ (0.55)	$ (0.56)	$ (0.57)	$ (0.54)	$ (0.53)	$ (2.11)	$ (2.21)	$ (4.15)

Restricted Cash	12 Months Ended
Restricted Cash	Dec. 31, 2016
Restricted Cash
Restricted cash	4. Restricted Cash The Company is required to maintain a security deposit for its operating lease agreement for the duration of the lease agreement and for its credit cards as long as they are in place. At both December 31, 2016 and 2015, the Company had certificates of deposit for $260,000, which represented collateral as security deposits for its operating lease agreement for its facility and its credit card.

Restricted Cash (Details) - USD ($)	Dec. 31, 2016	Dec. 31, 2015
Certificates of deposit
Restricted cash
Security deposit	$ 260,000	$ 260,000

Fair Value Measurements (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Fair Value Measurements
Transfers of assets from level 1 to 2	$ 0	$ 0

401(k) Savings Plan (Details) - USD ($)	12 Months Ended
401(k) Savings Plan (Details) - USD ($)	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
401(k) Savings Plan
Contributions to 401 (k) plan at the discretion of the board	$ 237,000	$ 0	$ 0