Sequenom (SQNM) 10-Q 5 May 16 2016 Q1 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	3 Months Ended
	Mar. 31, 2016	Apr. 25, 2016
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Mar. 31, 2016
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	Q1
Entity Registrant Name	SEQUENOM INC
Entity Central Index Key	1,076,481
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		119,216,003

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Assets
Cash and cash equivalents	$ 45,249	$ 50,344
Marketable securities, available-for-sale	20,808	25,826
Accounts receivable, net	6,950	6,421
Inventories	2,994	2,417
Prepaid expenses and other current assets	2,960	2,943
Total current assets	78,961	87,951
Property, equipment and leasehold improvements, net	7,651	10,059
Goodwill	10,007	10,007
Intangible assets, net	7,297	8,087
Other assets	700	624
Total assets	104,616	116,728
Liabilities and stockholders’ deficit
Accounts payable	7,078	5,234
Accrued expenses	12,523	15,368
Long-term debt and obligations, current portion	311	316
Other current liabilities	578	589
Total current liabilities	20,490	21,507
Long-term debt and obligations, less current portion	5,212	5,294
Convertible senior notes, net of issuance costs	127,438	127,079
Other long-term liabilities	1,404	1,246
Total liabilities	$ 154,544	$ 155,126
Commitments and contingencies
Stockholders’ deficit:
Convertible preferred stock, par value $0.001; 5,000 shares authorized, no shares issued or outstanding at March 31, 2016 and December 31, 2015	$ 0	$ 0
Common stock, par value $0.001; 185,000 shares authorized, 119,216 and 118,568 shares issued and outstanding at March 31, 2016 and December 31, 2015, respectively	119	119
Additional paid-in capital	992,915	990,999
Accumulated other comprehensive income	115	112
Accumulated deficit	(1,043,077)	(1,029,628)
Total stockholders’ deficit	(49,928)	(38,398)
Total liabilities and stockholders’ deficit	$ 104,616	$ 116,728

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Mar. 31, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Convertible senior notes interest rate	5.00%	5.00%
Convertible preferred stock, par value	$ 0.001	$ 0.001
Preferred stock, shares authorized	5,000,000	5,000,000
Convertible preferred stock, shares issued	0	0
Convertible preferred stock, shares outstanding	0	0
Common stock, par value	$ 0.001	$ 0.001
Common stock, shares authorized	185,000,000	185,000,000
Common stock, shares issued	119,216,003	118,567,676
Common stock, shares outstanding	119,216,003	118,567,676

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations and Comprehensive (Loss) Income - USD ($) shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Revenues:
Diagnostic services, net	$ 25,410	$ 35,703
License	2,160	2,102
Total revenues	27,570	37,805
Costs and expenses:
Cost of revenues	16,804	19,306
Selling and marketing	8,510	8,486
Research and development	4,901	5,869
General and administrative	7,854	8,676
Restructuring costs	859	0
Total costs and expenses	38,928	42,337
Gain on pooled patents agreement	0	21,000
Operating (loss) income	(11,358)	16,468
Interest expense	(2,057)	(1,994)
Interest income	38	11
Other income (expense), net	23	(125)
(Loss) income before income taxes	(13,354)	14,360
Income tax expense	(95)	(76)
Net (loss) income	$ (13,449)	$ 14,284
Net (loss) income per common share, basic
Net (loss) income per basic share (in dollars per share)	$ (0.11)	$ 0.12
Weighted average number of shares outstanding, basic	118,859	117,737
Net (loss) income per common share, diluted
Net (loss) income per diluted share (in dollars per share)	$ (0.11)	$ 0.11
Weighted average number of shares outstanding, diluted	118,859	146,642
Statements of Comprehensive (Loss) Income
Net (loss) income	$ (13,449)	$ 14,284
Other comprehensive (loss) income:
Unrealized net gain on available-for-sale securities, net of taxes	3	38
Foreign currency translation adjustment	0	28
Total other comprehensive income	3	66
Comprehensive (loss) income	$ (13,446)	$ 14,350

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Operating activities
Net (loss) income	$ (13,449)	$ 14,284
Adjustments to reconcile net (loss) income to net cash used in operating activities:
Share-based compensation	1,694	1,542
Depreciation and amortization	2,175	2,892
Other non-cash items	343	236
Gain on pooled patents agreement	0	(21,000)
Changes in operating assets and liabilities:
Accounts receivable	(529)	1,468
Inventories	(148)	1,737
Prepaid expenses and other assets	761	578
Accounts payable and accrued expenses	(1,066)	(7,715)
Other liabilities	146	(1,220)
Net cash used in operating activities	(10,073)	(7,198)
Investing activities
Purchases of property, equipment and leasehold improvements	(200)	(289)
Purchases of marketable securities	(9,967)	(10,007)
Maturities and sales of marketable securities	15,009	10,052
Proceeds from pooled patents agreement	0	6,000
Net cash provided by investing activities	4,842	5,756
Financing activities
Payments on term loan and capital lease obligations	(87)	(1,909)
Proceeds from common stock issued under employee stock plans	223	177
Net cash provided by (used in) financing activities	136	(1,732)
Effect of exchange rate changes on cash and cash equivalents	0	(45)
Net decrease in cash and cash equivalents	(5,095)	(3,219)
Cash and cash equivalents at beginning of period	50,344	63,309
Cash and cash equivalents at end of period	$ 45,249	$ 60,090

Summary of Significant Accounti

Summary of Significant Accounting Policies	3 Months Ended
	Mar. 31, 2016
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	The Company and a Summary of Its Significant Accounting Policies The Company Sequenom, Inc., and its wholly owned subsidiary Sequenom Center for Molecular Medicine LLC, doing business as Sequenom Laboratories (collectively the “Company”), is a pioneering genetic testing company dedicated to women’s health through the development of innovative products and services. The Company serves patients and physicians by providing early patient management information. The Company develops and commercializes innovative molecular diagnostics testing services that serve the women’s health market and is developing products and services for the oncology market. Basis of Presentation and Consolidation The accompanying unaudited condensed consolidated financial statements of Sequenom, Inc. should be read in conjunction with the audited consolidated financial statements and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015 , as filed with the Securities and Exchange Commission. The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles, or GAAP, for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, the interim statements do not include all of the information and notes required by GAAP for complete financial statements. The accompanying condensed consolidated financial statements, which include all wholly owned subsidiaries, reflect all adjustments, consisting of normal recurring adjustments that are, in the opinion of management, necessary for a fair statement of the results for the interim periods presented. The preparation of financial statements requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosures of contingent assets and liabilities. Interim results are not necessarily indicative of results for a full year or any other period(s). Segment and Geographic Information The Company evaluates segment reporting in accordance with Accounting Standards Codification, or ASC, 280 during each reporting period, including evaluating the reporting package reviewed by the Company’s Chief Operating Decision Maker, or CODM. As of March 31, 2016 , the Company concluded it operates in a single operating segment and a single reporting unit as a provider of innovative diagnostic testing services based on the financial information available and that is evaluated regularly by the CODM in deciding how to allocate resources and in assessing performance. The Company currently derives its diagnostic services revenue from domestic and international customers by providing testing services in its laboratory located in San Diego, California. During the three months ended March 31, 2016 and 2015 , 5.4% and 4.4% of diagnostic services revenue was recognized from international customers, respectively. The Company also generates license revenue through the Company’s Pooled Patents Agreement, or Pooled Patents Agreement, with Illumina, Inc., or Illumina, discussed in further detail below. The Company has limited visibility into the revenue reported by Illumina to the Company. For the portion of the Company’s license revenue recognized from the Pooled Patents Agreement that is derived from Illumina partners or licensees, the Company does not have the ability to determine whether the license revenue was derived from domestic or international sources. Use of Estimates The preparation of financial statements in conformity with GAAP requires that management make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. An example of the Company’s significant accounting estimates that may involve a higher degree of judgment and complexity than others include revenue recognition. Actual results could differ materially from those estimates and assumptions. Revenue Recognition The Company generates revenue from diagnostic services from providing laboratory-developed tests, or LDTs, primarily for the detection of specific fetal abnormalities or other genetic conditions, as well as through the Pooled Patents Agreement and others who have licensed the Company’s technology. Revenue is recognized when persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the price is fixed or determinable, and collectability is reasonably assured. The Company assesses whether the fee is fixed or determinable based on the nature of the fee charged for the services delivered, whether there are existing contractual arrangements, and historical payment patterns. In determining when to record revenue, the Company evaluates collectability and considers whether there is sufficient history to reliably estimate a payor’s payment patterns. Revenue is deferred for fees received before earned. Diagnostic services revenue is derived from providing testing services in the Company’s laboratory, which are reimbursed through arrangements with third-party payors and amounts patients self-pay or through contractual arrangements (client bill). Diagnostic services revenue for third-party payors is recognized upon cash collection until a reliable estimate of the amount that would be ultimately collected from such payor for the test and the above criteria have been met, at which time revenue is recognized on an accrual basis. Third-party payors include commercial payors, such as health insurance companies, health maintenance organizations and government payors, such as Medicare and Medicaid in the United States. Client bill revenue is primarily recognized on an accrual basis and includes laboratories and customers with whom the Company has a contractual agreement where they will pay for the test upon delivery of the test results to the ordering physicians. The Company generally bills third-party payors upon delivery of a test result to the ordering physician following completion of a test. Patients have responsibility for out-of-pocket costs for amounts not covered by their insurance carrier and the Company bills the patient directly for these amounts in the form of co-pays and deductibles in accordance with their insurance carrier and health plans. Revenue from patients, through co-payments or through cash based service offerings, are recognized on a cash basis. Some payors may not cover the test as ordered by the physician under their reimbursement policies. Consequently, the Company pursues reimbursement on a case-by-case basis. From time to time, the Company receives requests for refunds of payments, generally due to overpayments made by third-party payors. Upon becoming aware of a refund request, the Company establishes an accrued liability for tests covered by the refund request until such time as the Company determines whether or not a refund is due. License arrangements with third-party partners may involve multiple elements and the Company evaluates the agreements to determine whether each deliverable represents a separate unit of accounting. A deliverable constitutes a separate unit of accounting when it has stand-alone value to the customer. Items are considered to have stand-alone value when they are sold separately by any vendor or when the customer could resell the item on a stand-alone basis. Consideration is allocated at the inception of the contract to all deliverables based on their relative selling price. The relative selling price for each deliverable is determined using vendor specific objective evidence, or VSOE, of selling price or third-party evidence of selling price if VSOE does not exist. If neither VSOE nor third-party evidence exists, the Company uses its best estimate of the selling price for the deliverable. Such amounts are recognized as revenue when each unit is delivered. If the delivered element does not have stand-alone value without one of the undelivered elements in the arrangement, the elements are combined and accounted for as a single unit of accounting. Such amounts are recognized as revenue when the last deliverable of the combined units is delivered. Recurring revenue generated under license or royalty arrangements, including the Pooled Patents Agreement with Illumina, is recognized in the period reported by the partner or licensee and when the revenue recognition criteria have been met. Pooled Patents Agreement In December 2014, the Company entered into the Pooled Patents Agreement with Illumina. Pursuant to the Pooled Patents Agreement, a patent pool was established that is global in nature and combines the noninvasive prenatal testing, or NIPT, patents controlled by the Company and Illumina. Under the Pooled Patents Agreement, both the Company and its sublicensees and Illumina and its sublicensees pay a per-test fee into the pool for NIPT tests, which is then shared between the Company and Illumina. The Company recognizes license revenue in the period reported by its partners and Illumina and in certain cases this can result in a delay in recognizing revenue up to one quarter from the period in which the test was performed. As of March 31, 2016 , there were 46 licensees to the patent pool, including Illumina’s affiliate, Verinata Health, Inc., or Verinata, and Sequenom Laboratories. Cost of Revenues Cost of revenues include the cost of materials, direct labor (including laboratory and service personnel), equipment and infrastructure expenses associated with processing blood and other samples, quality control analyses, shipping charges to transport samples, and license and test fees, including those owed to Illumina as specified in the Pooled Patents Agreement. Infrastructure expenses include allocated facility occupancy and information technology costs. Costs associated with performing testing services are recorded as tests are processed. Costs recorded for sample processing and shipping charges represent the cost of all the tests processed during the period regardless of whether revenue is recognized with respect to that test. Royalties for licensed technology calculated on a per test basis or as a percentage of product revenue and fixed annual payments relating to the launch and commercialization of LDTs are recorded as license fees in cost of revenues at the time product revenue is recognized or in accordance with other contractual obligations. Concentration of Risks Financial instruments, which potentially are a concentration of credit risk, consist primarily of cash equivalents, marketable securities, and accounts receivable. The exposure to credit loss is limited by placing cash, cash equivalents and marketable securities with U.S. financial institutions. Additionally, the Company has established guidelines regarding diversification of investments and their maturities, which are designed to maintain principal and maximize liquidity. Credit risk with respect to accounts receivable is limited due to the Company’s large and diverse customer base. The Company considers ordering physicians and client laboratories to be its customers. For the three months ended March 31, 2015 , one customer represented more than 10% of total revenue, accounting for $5.6 million , or 14.8% , of total revenue during that period. No single customer accounted for over 10% of total revenue for the three months ended March 31, 2016 . Additionally, hundreds of third-party payors have reimbursed the Company for one or more of its tests. At a third-party payor level, no single payor represented more than 10% of total revenue for the three months ended March 31, 2016 or 2015 . The Company requires raw materials and devices of appropriate quality and reliability, which meet applicable regulatory requirements, that currently are available from a limited number of sources and in certain cases a single source of supply. Consequently, in the event that supplies are delayed or interrupted for any reason, it could impair the Company’s ability to develop and produce services, which could have a material adverse effect on the Company’s business, financial condition and results of operations. Net (Loss) Income Per Share Basic net (loss) income per share is computed by dividing net (loss) income by the weighted-average number of common shares outstanding during the period. Diluted net income per share reflects the net income, plus interest charges during the period applicable to the Company’s convertible senior notes, divided by the weighted-average number of common shares and potentially dilutive common shares from outstanding stock options, restricted shares, employee stock purchases, warrants and convertible senior notes. Potential dilutive common shares were calculated using the treasury stock method and represent incremental shares issuable upon exercise of the Company’s outstanding stock options, unvested restricted stock and warrants. Potential dilutive common shares for convertible senior notes were calculated using the if-converted method. For periods in which the Company incurs a loss, the interest charges during the period are not added back to net loss and the potentially dilutive shares are not considered in the calculation of net loss per share as their effect would be anti-dilutive. A summary of information used to compute basic and diluted net earnings per share is shown below (in thousands, except per share data): Three Months Ended March 31, 2016 March 31, 2015 Net (loss) income for basic earnings per share $ (13,449 ) $ 14,284 Interest on convertible senior notes — 1,884 Net (loss) income for diluted earnings per share $ (13,449 ) $ 16,168 Weighted-average common shares outstanding 118,859 117,737 Dilutive effect of common share equivalents — 28,905 Shares used in calculating diluted earnings per share 118,859 146,642 Net (loss) income per basic share $ (0.11 ) $ 0.12 Net (loss) income per diluted share $ (0.11 ) $ 0.11 Common stock equivalents that could potentially reduce net income per common share in the future that were not included in the determination of diluted net (loss) income per common share, as their effects were antidilutive, are as follows (in thousands): Three Months Ended March 31, 2016 March 31, 2015 Shares underlying Convertible Senior Notes 28,088 — Options to purchase common stock 14,436 9,032 Restricted stock units not yet vested and released 5,816 41 Warrants to purchase common stock 200 200 Total 48,540 9,273 Recent Accounting Pronouncements In May 2014, the Financial Accounting Standards Board, or FASB, issued Accounting Standard Update, or ASU, No. 2014-09, Revenue from Contracts with Customers (Topic 606). The ASU creates a single source of revenue guidance for companies in all industries. The new standard provides guidance for all revenue arising from contracts with customers and affects all entities that enter into contracts to provide goods or services to their customers, unless the contracts are within the scope of other accounting standards. It also provides a model for the measurement and recognition of gains and losses on the sale of certain nonfinancial assets. This guidance, as amended, must be adopted using either a full retrospective approach for all periods presented or a modified retrospective approach and will be effective for fiscal years beginning after December 15, 2017, which will be the Company’s fiscal year 2018. The Company is currently assessing the impact this guidance will have on its consolidated financial statements. In February 2015, the FASB issued ASU 2016-02, Leases (Topic 842), which amends the FASB Accounting Standards Codification and creates Topic 842, “Leases.” The new topic supersedes Topic 840, “Leases,” and increases transparency and comparability among organizations by recognizing lease assets and lease liabilities on the balance sheet and requires disclosures of key information about leasing arrangements. The guidance is effective for reporting periods beginning after December 15, 2018. ASU 2016-02 mandates a modified retrospective transition method. The Company is currently assessing the impact this guidance will have on its consolidated financial statements. In April 2015, the FASB issued ASU No. 2015-03, Interest - Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs . The ASU is the result of the FASB’s simplification initiative intended to improve GAAP by reducing costs and complexity while maintaining or enhancing the usefulness of related financial statement information. The ASU specifies that debt issuance costs related to a note shall be reported in the balance sheet as a direct reduction from the face amount of the note. The ASU became effective for interim and annual periods on January 1, 2016. The ASU required the Company to reclassify its capitalized debt issuance costs previously recorded as assets on the condensed consolidated balance sheets. As a result of the ASU, the Company reclassified debt issuance costs of $1.0 million from “other current assets and prepaid expenses” and $1.0 million from “other assets” to “long-term debt and obligations, less current portion” as of December 31, 2015. As of March 31, 2016, $1.8 million of debt issuance costs were recorded as a direct reduction of the long-term debt amounts. The ASU had no effect on the Company’s results of operations or liquidity. In July 2015, the FASB issued ASU No. 2015-11, Inventory (Topic 330): Simplifying the Measurement of Inventory , which simplifies the subsequent measurement of inventory. It replaces the current lower of cost or market test with a lower of cost or net realizable value test. The standard is effective for public entities for annual reporting periods beginning after December 15, 2016, and interim periods therein. Early adoption is permitted and the new guidance must be applied prospectively. The Company does not expect the ASU to have a material impact on its financial statements upon adoption. In March 2016, the FASB issued ASU 2016-09, Compensation—Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting . The ASU includes provisions intended to simplify various aspects related to how share-based payments are accounted for and presented in the financial statements, including the income tax consequences, classification of awards as either equity or liabilities, and classification on the statement of cash flows. Specifically, the ASU allows entities to withhold an amount up to the employees’ maximum individual tax rate in the relevant jurisdiction without resulting in liability classification of the award and allowing forfeitures to be either estimated, as required today, or recognized when they occur. The new guidance will be effective for public entities in fiscal years beginning after December 15, 2016, with early adoption permitted. The Company expects the guidance could impact its accounting and reporting and is currently assessing the impact this guidance will have on its consolidated financial statements.

Supplementary Financial Informa

Supplementary Financial Information	3 Months Ended
	Mar. 31, 2016
Other Financial Information [Abstract]
Supplementary Financial Information	Supplementary Financial Information Marketable Securities, Available-for-sale (in thousands): March 31, 2016 Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Estimated Fair Value U.S. treasury securities $ 20,201 $ 5 $ (1 ) $ 20,205 Certificates of deposit 102 — — 102 Mutual funds 312 198 (9 ) 501 Total marketable securities $ 20,615 $ 203 $ (10 ) $ 20,808 December 31, 2015 Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Estimated Fair Value U.S. treasury securities $ 25,238 $ — $ (24 ) $ 25,214 Certificates of deposit 97 — — 97 Mutual funds 312 203 — 515 Total marketable securities $ 25,647 $ 203 $ (24 ) $ 25,826 As of March 31, 2016 and December 31, 2015 , gross unrealized losses on marketable securities were insignificant. There were no impairments considered other-than-temporary for the periods presented, as the Company has the intent and ability to hold the securities for a period of time sufficient to allow for recovery in the market value. As of March 31, 2016 , all marketable securities were due within fifteen months. Inventories (in thousands): March 31, 2016 December 31, 2015 Raw materials $ 2,759 $ 2,145 Work in process 235 272 Total $ 2,994 $ 2,417 Prepaid Expenses and Other Current Assets (in thousands): March 31, 2016 December 31, 2015 Prepaid expenses $ 1,630 $ 2,550 Assets held-for-sale, net 1,281 — Other 49 393 Total $ 2,960 $ 2,943 Property, Equipment and Leasehold Improvements (in thousands): March 31, 2016 December 31, 2015 Building and improvements $ 4,273 $ 8,673 Laboratory equipment 33,372 33,796 Leasehold improvements 8,116 6,411 Office furniture and equipment 16,330 16,448 62,091 65,328 Less accumulated depreciation (54,440 ) (55,269 ) Total $ 7,651 $ 10,059 Depreciation expense for the three months ended March 31, 2016 and 2015, was $1.4 million and $2.1 million , respectively. Depreciation of assets under capital leases is included in depreciation expense. Accrued Expenses (in thousands): March 31, 2016 December 31, 2015 Accrued royalties, licenses, and collaboration payments $ 4,496 $ 5,046 Accrued compensation and related taxes 4,689 5,349 Accrued professional and consulting fees 1,173 468 Accrued interest 24 1,649 Other 2,141 2,856 Total $ 12,523 $ 15,368

Long-Term Obligations

Long-Term Obligations	3 Months Ended
	Mar. 31, 2016
Debt Disclosure [Abstract]
Long-Term Obligations	Long-Term Obligations Long-Term Obligations (in thousands, except percentages): March 31, 2016 December 31, 2015 5.0% Convertible Senior Notes due October 2017 ($45,000) and January 2018 ($85,000), interest payable semi-annually in April and October $ 130,000 $ 130,000 Unamortized debt discount on Convertible Senior Notes due January 2018 (764 ) (867 ) Unamortized debt issuance costs on Convertible Senior Notes due October 2017 and January 2018 (1,798 ) (2,054 ) Obligation for building and improvements, effective interest rate of 5.2% as of March 31, 2016 and December 31, 2015, expiring October 2026 5,523 5,597 Capital lease liabilities, expired January 2016 — 13 Total long-term obligations 132,961 132,689 Less current portion (311 ) (316 ) Non-current portion $ 132,650 $ 132,373 Convertible Senior Notes On September 17, 2012 , the Company issued $130 million aggregate principal amount of Convertible Senior Notes, or the 2017 Notes, in a private offering to qualified institutional buyers in reliance on Rule 144A under the Securities Act of 1933, as amended, or the Securities Act. On June 4, 2015, the Company entered into separate privately negotiated agreements with certain holders of the 2017 Notes to exchange in a private placement in reliance on Section 4(a)(2) of the Securities Act $85 million in aggregate principal amount of 2017 Notes for $85 million in aggregate principal amount at maturity of new 5.0% Convertible Exchange Senior Notes due 2018, or the 2018 Notes, of the Company (the “Exchange Transactions”). The 2018 Notes were issued on June 9, 2015. The Company accounted for the Exchange Transactions as a debt modification and not a debt extinguishment under ASC 470-50, as the terms of the 2018 Notes were not substantially different from those of the exchanged 2017 Notes. The Company incurred approximately $1.6 million in fees directly related to the Exchange Transactions which were expensed as incurred during the year ended December 31, 2015. As noted above, the 2018 Notes term was extended for an additional three months and mature January 1, 2018. The extension of the term increased the fair value of the 2018 Notes embedded, unseparated conversion option by approximately $1.1 million , which was recorded as an increase in the debt discount of the convertible senior notes and corresponding increase in additional paid-in capital and will be amortized over the remaining 30 month term of the 2018 Notes using the effective interest rate method. Following the closings of the Exchange Transactions, $45 million in aggregate principal amount of the 2017 Notes remained outstanding, with the terms unchanged. 2017 Notes The 2017 Notes bear interest at a fixed rate of 5.0% per year, payable semiannually in arrears on April 1 and October 1 of each year. The 2017 Notes mature on October 1, 2017 , unless earlier converted, redeemed, or repurchased. The 2017 Notes are convertible at any time prior to the third trading day immediately preceding the maturity date, at the option of the holders, into shares of common stock. The 2017 Notes are convertible into a total of 9.7 million shares of common stock, which was equal to an initial conversion rate of 216.0644 shares of common stock per $1,000 principal amount of the 2017 Notes (equivalent to an initial conversion price of approximately $4.63 per share of common stock), and will be subject to adjustment upon the occurrence of certain events. The maximum conversion rate is 275.4821 shares of common stock per $1,000 principal amount of the 2017 Notes, which would result in a maximum issuance of 12.4 million shares of common stock if all holders converted at the maximum conversion rate. In addition, under certain circumstances the Company, in connection with a make-whole fundamental change (as defined in the indenture governing the 2017 Notes), may be required to increase the conversion rate for holders of the 2017 Notes. As of March 31, 2016 , no change to the conversion rate had occurred on the 2017 Notes. The Company could not redeem the 2017 Notes prior to October 1, 2015 . After October 1, 2015 , the Company may redeem for cash all, but not less than all, of the 2017 Notes if the last reported sale price of the common stock equals or exceeds 140% of the applicable conversion price for at least 20 trading days during the 30 consecutive trading day period ending on the trading day immediately prior to the date on which the notice of the redemption is delivered. The redemption price will equal 100% of the principal amount of the 2017 Notes to be redeemed, plus any accrued and unpaid interest to, but excluding, the redemption date. In addition, if the 2017 Notes are called for redemption, a make-whole fundamental change will be deemed to occur. As a result, in certain circumstances, this would increase the conversion rate for holders who convert their 2017 Notes after a notice of redemption is delivered and on or prior to the close of business on the third business day immediately preceding the relevant redemption date. Upon a fundamental change, subject to certain exceptions, the holders may require that the Company repurchase some or all of their 2017 Notes for cash at a repurchase price equal to 100% of the principal amount of the 2017 Notes being repurchased, plus any accrued and unpaid interest to, but excluding, the fundamental change repurchase date. On September 17, 2012, the Company entered into an indenture with Wells Fargo Bank, National Association, as trustee, relating to the 2017 Notes. The 2017 Notes are senior, unsecured obligations and rank equal in right of payment with existing and future senior, unsecured indebtedness, and will be senior in right of payment to any future indebtedness that is expressly subordinated to the 2017 Notes. The 2017 Notes will be effectively subordinated to existing and future secured indebtedness to the extent of the assets securing such indebtedness and will be structurally subordinated to all indebtedness and other liabilities and commitments of subsidiaries, including trade payables and any guarantees that they may provide with respect to any existing or future indebtedness. 2018 Notes The 2018 Notes bear interest at a fixed rate of 5.0% per year, payable semiannually in arrears on April 1 and October 1 of each year, beginning October 1, 2015 . Interest on the 2018 Notes accrues from April 1, 2015 . The 2018 Notes will mature on January 1, 2018 , unless earlier converted or repurchased. The 2018 Notes are convertible at any time prior to the third trading day immediately preceding the maturity date, at the option of the holders, into shares of the Company’s common stock. Subject to compliance with certain conditions, the Company has the right to mandatorily convert the 2018 Notes if the last reported sales price of the Company’s common stock is equal to or greater than 115% of the applicable conversion price of the 2018 Notes for at least 20 trading days during the 30 consecutive trading day period ending within five trading days immediately prior to the date on which the Company delivers a mandatory conversion notice. The conversion rate is initially 216.0644 shares of common stock per $1,000 principal amount of 2018 Notes (equivalent to an initial conversion price of approximately $4.63 per share of common stock), and will be subject to adjustment upon the occurrence of certain events. In addition, holders of the 2018 Notes who convert their 2018 Notes in connection with a make-whole fundamental change (defined in the indenture governing the 2018 Notes (the “Indenture”)), whose 2018 Notes are converted in connection with a mandatory conversion or who convert their 2018 Notes on a conversion date on which the last reported sales price of the Company’s common stock equals or exceeds the then applicable conversion price are, under certain circumstances, entitled to an increase in the conversion rate. The Company may not redeem the 2018 Notes prior to the maturity date. Upon a fundamental change (defined in the Indenture), subject to certain exceptions, the holders of the 2018 Notes may require that the Company repurchase some or all of their 2018 Notes for cash at a repurchase price equal to 100% of the principal amount of the 2018 Notes being repurchased, plus any accrued and unpaid interest to, but excluding, the fundamental change repurchase date. The 2018 Notes will be the Company’s senior, unsecured obligations and rank equal in right of payment with the Company’s existing and future senior, unsecured indebtedness, including the 2017 Notes, and will be senior in right of payment to any future indebtedness that is expressly subordinated to the 2018 Notes. The 2018 Notes will be effectively subordinated to the Company’s existing and future secured indebtedness to the extent of the assets securing such indebtedness and will be structurally subordinated to all indebtedness and other liabilities and commitments of the Company’s subsidiaries, including trade payables and any guarantees that they may provide with respect to any of the Company’s existing or future indebtedness. Obligation for Building and Improvements In November 2011, the Company entered into a lease agreement for a building in Raleigh-Durham, North Carolina, that was accounted for as a financing lease. The term of the lease and the obligation was initially 15 years through October 2026, including two 5 -year extensions of the lease. Rent payments under the lease were allocated primarily between interest expense and a reduction to the long-term obligation. The Company entered into an agreement to terminate the lease in April 2016 in order to consolidate the North Carolina operations into the San Diego laboratory. Refer to “Note 8 - Other Transactions” for additional details on the lease termination.

Commitments and Contingencies

Commitments and Contingencies	3 Months Ended
	Mar. 31, 2016
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Ariosa Litigation In December 2011, the Company was named as a defendant in a complaint filed by plaintiff Aria Diagnostics, Inc., in the U.S. District Court for the Northern District of California, or District Court, case no. 3:11-cv-06391-SI. Since the complaint was filed, Aria changed its name to Ariosa Diagnostics, Inc., or Ariosa. In the complaint, the plaintiff seeks a judicial declaration that no activities related to the plaintiff’s noninvasive, prenatal test using cell-free DNA circulating in the blood of a pregnant woman do or will infringe any claim of U.S. Patent No. 6,258,540 entitled Noninvasive Prenatal Diagnosis, or the ‘540 Patent, which was exclusively in-licensed from Isis Innovation ltd., or Isis, prior to September 30, 2014, when the Company purchased the patent from Isis. In March 2012, the Company filed an answer to the complaint and asserted counterclaims that Ariosa is infringing the ‘540 Patent and seeking unspecified damages and injunctive relief. The Company’s counterclaims named Isis as a nominal counter-defendant for purposes of subject matter jurisdiction only, but with the purchase of the ‘540 Patent, Isis was dismissed from the lawsuit. In March 2012, Ariosa responded to the Company’s answer and counterclaims and asserted affirmative defenses including invalidity of the ‘540 Patent under U.S. patent laws. In March 2012, the Company filed a motion against Ariosa for preliminary injunctive relief. On July 5, 2012, the District Court denied the Company’s motion for preliminary injunctive relief and on July 16, 2012, the Company filed a Notice of Appeal to the U.S. Court of Appeals for the Federal Circuit, or CAFC, from the order denying the preliminary injunction motion. On August 9, 2013, the CAFC vacated and remanded the District Court’s decision, ruling that the District Court incorrectly interpreted the claims of the ‘540 Patent and improperly balanced factors regarding issuance of a preliminary injunction. On August 16, 2013, Ariosa filed a motion for summary judgment in favor of Ariosa on our counterclaim for patent infringement on the ground that the claims of the ‘540 Patent are invalid because they are not drawn to patent-eligible subject matter under the patent code, Title 35 U.S.C. § 101. On October 16, 2013, the District Court issued its order on the interpretation of the claims of the patent. On October 30, 2013, the District Court issued its order granting Ariosa’s motion for summary judgment, finding that the ‘540 Patent is invalid under Title 35 U.S.C. §101. The Company disagreed with the Order and appealed the decision to the CAFC. The CAFC issued its decision on June 12, 2015 affirming the District Court. On August 13, 2015, the Company filed a petition for en banc rehearing by the CAFC. That petition was denied by the Court of Appeals on December 2, 2015. On March 21, 2016, the Company filed a petition for a writ of certiorari that asks the U.S. Supreme Court to review the appeal and find the claims of the ‘540 Patent directed to patent-eligible subject matter. If that petition is successful, the Company intends to vigorously defend against the judicial declarations sought by Ariosa in its complaint and intends to vigorously pursue the Company’s claims against Ariosa for damages and injunctive relief. However, the Company cannot predict the outcome of this matter. Ariosa Inter Partes Review In addition, Ariosa has sought to invalidate the ‘540 Patent through a petition for inter parties review, or IPR, (Case IPR2012-00022 (MPT)) under 35 U.S.C. section 312 and 37 C.F.R. section 42.108, before the Patent Trial and Appeal Board, or PTAB, of the United States Patent and Trademark Office, or USPTO. Trial of the IPR was held before the PTAB on January 24, 2014. The PTAB issued a Decision in the IPR on September 2, 2014, invalidating some claims but upholding the validity of other claims. Both the Company and Ariosa requested reconsideration of the PTAB decision. Those requests were denied by the PTAB. On April 7, 2015, Ariosa filed a Notice of Appeal to appeal the PTAB decision to the CAFC. Two weeks later, on April 21, 2015, the Company filed a Notice of Appeal for the Company’s cross-appeal of the PTAB decision to the CAFC. Both the Company and Ariosa requested, by joint motion filed on July 17, 2015, a stay of the appeal of the PTAB decision pending resolution of the appeal of the decision from the District Court that the ‘540 patent claimed patent ineligible subject matter. On July 22, 2015, the clerk of the CAFC granted a full stay of proceedings. On January 11, 2016, and in response to a request for an update from the clerk of the CAFC, the Company and Ariosa once again requested by joint motion a full stay of the appeal of the PTAB decision. Natera Litigation In January 2012, the Company was named as a defendant in a complaint filed by plaintiff Natera, a Delaware corporation, in the District Court, case no. 3:12-cv-00132-SI. In the complaint, Natera seeks a judicial declaration that (i) activities related to Natera’s noninvasive, prenatal paternity test do not directly or indirectly infringe any claim of the ‘540 Patent, and (ii) one or more claims of the ‘540 Patent are invalid for failure to comply with the requirements of the patent laws of the U.S. In April 2012, the Company filed an answer to the complaint and asserted counterclaims that Natera and DNA Diagnostics Center, Inc., or DDC, are infringing the ‘540 Patent based on their activities relating to noninvasive prenatal paternity testing and noninvasive prenatal aneuploidy testing and seeking unspecified damages and injunctive relief. The Company’s counterclaims named Isis as a nominal counter-defendant for purposes of subject matter jurisdiction only and the Company has dismissed Isis from the case now that the Company has purchased the ‘540 patent from Isis. On October 16, 2013, the District Court issued its order on the interpretation of the patent claims. Many of the ‘540 Patent claims asserted against Natera are the same claims that were invalidated by the District Court on October 30, 2013 in the litigation involving Ariosa, set forth above, and the Company and Natera stipulated to final judgment on the ‘540 patent claims in this case and appealed the patent invalidity determination to the CAFC, which consolidated the Ariosa, Natera, and Verinata case appeals. On August 13, 2015, the Company filed a petition for en banc rehearing by the CAFC. That petition was denied by the CAFC on December 2, 2015. On March 21, 2016, the Company filed a petition for writ of certiorari petition that asks the U.S. Supreme Court to review the appeal and find the claims of the ‘540 Patent directed to patent-eligible subject matter. If that petition is successful, the Company intends to vigorously defend against the judicial declarations sought by Natera in its complaint and intends to vigorously pursue the Company’s claims against Natera for damages and injunctive relief. However, the Company cannot predict the outcome of this matter. EU Opposition Proceedings On September 29, 2014 and October 1, 2014, two unknown third parties initiated Opposition Proceedings against European Patent EP2183693 B1, entitled “Diagnosing Fetal Chromosomal Aneuploidy Using Genomic Sequencing,” in the European Patent Office. This patent was previously in-licensed by the Company from the Chinese University of Hong Kong, or CUHK, but has since been added to the patent pool under the Pooled Patents Agreement. The Company has rights to this patent under the patent pool but the Company no longer controls efforts to defend this patent in the Opposition Proceedings. Premaitha Litigation Certain litigations were initiated in 2015 and 2016 to enforce the pooled patent rights. On March 13, 2015, Illumina filed a complaint in the High Court of Justice, Chancery Division, United Kingdom, alleging that Premaitha Health PLC, or Premaitha, infringed two European patents in the patent pool: EP0994963 and EP1981995. The Company is named as a plaintiff in this lawsuit because the Company owns the EP0994963 patent by virtue of its purchase of this patent, a counterpart to the U.S. ‘540 patent, from Isis in 2014. On January 7, 2016, Illumina filed a second complaint in the High Court of Justice, Chancery Division, United Kingdom, alleging that Premaitha infringed a third European patent in the patent pool: EP2183693. The Company is not named as a plaintiff in this second lawsuit. The two cases have been consolidated for trial, which is expected to take place sometime after July 1, 2017. Ariosa & TDL Litigation On January 7, 2016, Illumina filed a complaint in the High Court of Justice, Chancery Division, United Kingdom, alleging that Ariosa and The Doctors Laboratory Ltd., or TDL, infringed a European patent in the patent pool: EP0994963. The Company is named as a plaintiff in this lawsuit because the Company owns the EP0994963 patent by virtue of its purchase of this patent, a counterpart to the U.S. ‘540 patent, from Isis in 2014. Trial in this case has not been scheduled. Other In addition, from time to time, the Company may be involved in litigation, claims, investigations and/or proceedings relating to employment, intellectual property and contractual matters as well as claims arising out of its operations in the normal course of business, including claims related to its products, tests, and services, including LDT testing services. These other matters are, in the opinion of management, immaterial with respect to the Company’s consolidated financial position, liquidity, or results of operations or the damage amounts alleged by claimants are not necessarily meaningful indicators of potential liabilities. The Company determines whether it should accrue an estimated loss for a contingency in a particular legal proceeding by assessing whether a loss is deemed probable and whether the amount can be reasonably estimated. Claim estimates that are probable and can be reasonably estimated are reflected as liabilities. Legal proceedings are inherently unpredictable and the matters in which the Company is involved often present complex legal and factual issues. Because of the uncertainties related to the Company’s pending litigations, investigations, inquiries or claims, management is currently unable to predict the ultimate outcome of any litigation, investigation, inquiry or claim, determine whether a liability has been incurred, or make an estimate regarding the possible loss or range of loss that could result from an unfavorable outcome. It is reasonably possible that some of the matters, which are pending or may be asserted, could be decided unfavorably to the Company. An adverse ruling or outcome in any lawsuit involving the Company could materially affect its business, liquidity, consolidated financial position or results of operations, the ability to sell one or more of the Company’s products or could result in additional competition. In view of the unpredictable nature of such matters, the Company cannot provide any assurances regarding the outcome of any litigation, investigation, inquiry or claim to which it is a party or the impact on the Company of an adverse ruling of such matters.

Stock Compensation Plans

Stock Compensation Plans	3 Months Ended
	Mar. 31, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock Compensation Plans	Stock Compensation Plans Equity Incentive Plans The following table summarizes stock option activity of the Company during the three months ended March 31, 2016 (shares in thousands): Shares Subject to Options Weighted-Average Exercise Price per Share As of December 31, 2015 11,408 $ 4.41 Granted 2,716 $ 1.58 Exercised — $ — Forfeitures and cancellations (753 ) $ 4.52 Outstanding at March 31, 2016 13,371 $ 3.83 Options exercisable at March 31, 2016 7,765 $ 5.02 The following table summarizes activity related to restricted stock awards and restricted stock units of the Company during the three months ended March 31, 2016 : Number of Shares Weighted-Average Grant Date Fair Value Outstanding at December 31, 2015 2,443 $ 2.64 Grants and awards 3,212 $ 1.58 Vested and released (298 ) $ 3.32 Forfeitures and cancellations (131 ) $ 2.84 Outstanding at March 31, 2016 5,226 $ 1.97 Issuances of Common Stock In the three months ended March 31, 2016, the Company issued a total of 277,437 shares of common stock under the employee stock purchase plan, or ESPP, resulting in proceeds of $0.4 million . Share-Based Compensation Expense Following are the weighted-average underlying assumptions used to determine the fair value of stock option award grants and for stock purchase rights under the ESPP for the periods indicated: Three Months Ended Stock Option Grants March 31, 2016 March 31, 2015 Risk-free interest rate 1.5 % 1.7 % Volatility 89.5 % 92.1 % Dividend yield — % — % Expected life (years) 6.8 7.2 Weighted-average grant date fair value $ 1.21 $ 2.78 Three Months Ended ESPP Stock Purchase Rights March 31, 2016 March 31, 2015 Risk-free interest rate 0.39 % 0.14 % Volatility 74.6 % 55.7 % Dividend yield — % — % Expected life (years) 0.5 0.5 Weighted-average grant date fair value $ 0.56 $ 1.07

Fair Value Measurements

Fair Value Measurements	3 Months Ended
	Mar. 31, 2016
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements Assets and Liabilities Measured at Fair Value on a Recurring Basis The following tables summarize the fair value hierarchy for assets and liabilities measured at fair value on a recurring basis. As of March 31, 2016 (in thousands) Fair Value Quoted Prices in Active Markets for Identical Assets (Level 1) Significant Other Observable Inputs (Level 2) Cash equivalents: Money market funds $ 37,879 $ 37,879 $ — Total cash equivalents 37,879 37,879 — Marketable securities: U.S. treasury securities 20,205 20,205 — Certificates of deposit 102 — 102 Mutual funds 501 501 — Total marketable securities 20,808 20,706 102 Total $ 58,687 $ 58,585 $ 102 As of December 31, 2015 (in thousands) Fair Value Quoted Prices in Active Markets for Identical Assets (Level 1) Significant Other Observable Inputs (Level 2) Cash equivalents: Money market funds $ 43,815 $ 43,815 $ — Total cash equivalents 43,815 43,815 — Marketable securities: U.S. treasury securities 25,214 25,214 — Certificates of deposit 97 — 97 Mutual funds 515 515 — Total marketable securities 25,826 25,729 97 Total $ 69,641 $ 69,544 $ 97 There were no transfers in or out of Level 1, Level 2, or Level 3 investments during the three months ended March 31, 2016 or the year ended December 31, 2015 . For fair values determined by Level 1 inputs, which utilize quoted prices in active markets for identical assets, the level of judgment required to estimate fair value is relatively low. The value of investments in money market funds, U.S. treasury securities and mutual funds was determined using Level 1 inputs. Fair values determined by Level 2 inputs, utilize data points that are observable such as quoted prices, interest rates and yield curves. Investments in certificates of deposit are valued using Level 2 inputs. Fair Value of Other Financial Instruments The carrying amounts of certain financial instruments, including cash and cash equivalents, accounts payable and accrued expenses, approximate fair value due to their short-term nature. The carrying amounts and fair values of the 2017 Notes and 2018 Notes are as follows (in thousands): March 31, 2016 December 31, 2015 Carrying Amount Fair Value Carrying Amount Fair Value Convertible Senior Notes $ 127,438 $ 84,640 $ 127,079 $ 106,505 At March 31, 2016 and December 31, 2015 , the fair values of the 2017 Notes and the 2018 Notes were based on quoted market prices in an active market for the notes (Level 1). The carrying amounts at March 31, 2016 and December 31, 2015 include unamortized debt issuance costs of $1.8 million and $2.1 million , respectively, and unamortized debt discounts of $0.8 million and $0.9 million , respectively.

Income Taxes

Income Taxes	3 Months Ended
	Mar. 31, 2016
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The Company’s income tax expense is primarily due to tax liabilities resulting from state operations and deferred income tax expense related to amortization of indefinite lived intangibles. The Company’s income tax expense is computed using the asset and liability method, under which deferred tax assets and liabilities are recognized for the expected future tax consequences of temporary differences between the financial reporting and tax bases of assets and liabilities, and for the expected future tax benefit to be derived from tax loss and credit carryforwards. Deferred tax assets and liabilities are determined using the enacted tax rates in effect for the years in which those tax assets are expected to be realized. A valuation allowance is established when it is more likely than not the future realization of all or some of the deferred tax assets will not be achieved. The evaluation of the need for a valuation allowance is performed on a jurisdiction by jurisdiction basis, and includes a review of all available positive and negative evidence. When the Company establishes or reduces the valuation allowance against deferred tax assets, the provision for income taxes will increase or decrease, respectively, in the period such determination is made. As of March 31, 2016 and December 31, 2015 , the Company maintained valuation allowances against its deferred tax assets as the Company concluded it had not met the “more likely than not” threshold. Changes in the valuation allowance when they are recognized in the provision for income taxes may result in a change in the estimated annual effective tax rate.

Other Transactions

Other Transactions	3 Months Ended
	Mar. 31, 2016
Subsequent Events [Abstract]
Other Transactions	Other Transactions Subsequent Events On April 17, 2016, the Company entered into an agreement to terminate the lease for the Company’s laboratory facility in Raleigh-Durham, North Carolina, or the Termination Agreement. The term of the lease was originally scheduled to expire on December 31, 2016, with available extensions through October 2026. The Termination Agreement accelerated the expiration of the lease to April 17, 2016. The Company had previously accounted for the lease as a financing lease and recognized a capital lease liability on its balance sheet with rental payments allocated between interest expense and a reduction to the Company’s capital lease liability. As a result of the transaction, the Company was relieved of the capital lease liability for the building as of April 17, 2016. Additionally, on April 18, 2016, the Company entered into an asset purchase agreement, or APA, pursuant to which the Company sold certain equipment and tenant improvements at the North Carolina facility for a one-time cash payment of $0.7 million . The Company does not anticipate recognizing a gain or loss in the second quarter of 2016 upon the de-recognition of the capital lease obligation and the corresponding tenant improvements and sale of certain equipment and tenant improvements that were included in the APA. Restructuring Costs During the first quarter of 2016 the Company incurred $0.9 million of restructuring costs related to the consolidation of its North Carolina operations and planned reduction in oncology related research and development activities. The restructuring charges primarily consist of one-time employee severance benefits, contract termination costs and other costs associated with the closure of the North Carolina laboratory. The Company may incur additional restructuring charges related to its cost saving initiatives in the second quarter of 2016, however, amounts are expected to be immaterial. As of March 31, 2016, the Company had $0.5 million of unpaid severance benefits in accrued expenses on the condensed consolidated balance sheet which will be paid out during the second quarter of 2016.

Summary of Significant Accoun14

Summary of Significant Accounting Policies (Policies)	3 Months Ended
	Mar. 31, 2016
Accounting Policies [Abstract]
Basis of Presentation and Consolidation	Basis of Presentation and Consolidation The accompanying unaudited condensed consolidated financial statements of Sequenom, Inc. should be read in conjunction with the audited consolidated financial statements and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015 , as filed with the Securities and Exchange Commission. The accompanying condensed consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles, or GAAP, for interim financial information and with the instructions to Form 10-Q and Article 10 of Regulation S-X. Accordingly, the interim statements do not include all of the information and notes required by GAAP for complete financial statements. The accompanying condensed consolidated financial statements, which include all wholly owned subsidiaries, reflect all adjustments, consisting of normal recurring adjustments that are, in the opinion of management, necessary for a fair statement of the results for the interim periods presented. The preparation of financial statements requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosures of contingent assets and liabilities. Interim results are not necessarily indicative of results for a full year or any other period(s).
Segment and Geographical Information	Segment and Geographic Information The Company evaluates segment reporting in accordance with Accounting Standards Codification, or ASC, 280 during each reporting period, including evaluating the reporting package reviewed by the Company’s Chief Operating Decision Maker, or CODM. As of March 31, 2016 , the Company concluded it operates in a single operating segment and a single reporting unit as a provider of innovative diagnostic testing services based on the financial information available and that is evaluated regularly by the CODM in deciding how to allocate resources and in assessing performance. The Company currently derives its diagnostic services revenue from domestic and international customers by providing testing services in its laboratory located in San Diego, California. During the three months ended March 31, 2016 and 2015 , 5.4% and 4.4% of diagnostic services revenue was recognized from international customers, respectively. The Company also generates license revenue through the Company’s Pooled Patents Agreement, or Pooled Patents Agreement, with Illumina, Inc., or Illumina, discussed in further detail below. The Company has limited visibility into the revenue reported by Illumina to the Company. For the portion of the Company’s license revenue recognized from the Pooled Patents Agreement that is derived from Illumina partners or licensees, the Company does not have the ability to determine whether the license revenue was derived from domestic or international sources.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with GAAP requires that management make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. An example of the Company’s significant accounting estimates that may involve a higher degree of judgment and complexity than others include revenue recognition. Actual results could differ materially from those estimates and assumptions.
Revenue Recognition	Revenue Recognition The Company generates revenue from diagnostic services from providing laboratory-developed tests, or LDTs, primarily for the detection of specific fetal abnormalities or other genetic conditions, as well as through the Pooled Patents Agreement and others who have licensed the Company’s technology. Revenue is recognized when persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the price is fixed or determinable, and collectability is reasonably assured. The Company assesses whether the fee is fixed or determinable based on the nature of the fee charged for the services delivered, whether there are existing contractual arrangements, and historical payment patterns. In determining when to record revenue, the Company evaluates collectability and considers whether there is sufficient history to reliably estimate a payor’s payment patterns. Revenue is deferred for fees received before earned. Diagnostic services revenue is derived from providing testing services in the Company’s laboratory, which are reimbursed through arrangements with third-party payors and amounts patients self-pay or through contractual arrangements (client bill). Diagnostic services revenue for third-party payors is recognized upon cash collection until a reliable estimate of the amount that would be ultimately collected from such payor for the test and the above criteria have been met, at which time revenue is recognized on an accrual basis. Third-party payors include commercial payors, such as health insurance companies, health maintenance organizations and government payors, such as Medicare and Medicaid in the United States. Client bill revenue is primarily recognized on an accrual basis and includes laboratories and customers with whom the Company has a contractual agreement where they will pay for the test upon delivery of the test results to the ordering physicians. The Company generally bills third-party payors upon delivery of a test result to the ordering physician following completion of a test. Patients have responsibility for out-of-pocket costs for amounts not covered by their insurance carrier and the Company bills the patient directly for these amounts in the form of co-pays and deductibles in accordance with their insurance carrier and health plans. Revenue from patients, through co-payments or through cash based service offerings, are recognized on a cash basis. Some payors may not cover the test as ordered by the physician under their reimbursement policies. Consequently, the Company pursues reimbursement on a case-by-case basis. From time to time, the Company receives requests for refunds of payments, generally due to overpayments made by third-party payors. Upon becoming aware of a refund request, the Company establishes an accrued liability for tests covered by the refund request until such time as the Company determines whether or not a refund is due. License arrangements with third-party partners may involve multiple elements and the Company evaluates the agreements to determine whether each deliverable represents a separate unit of accounting. A deliverable constitutes a separate unit of accounting when it has stand-alone value to the customer. Items are considered to have stand-alone value when they are sold separately by any vendor or when the customer could resell the item on a stand-alone basis. Consideration is allocated at the inception of the contract to all deliverables based on their relative selling price. The relative selling price for each deliverable is determined using vendor specific objective evidence, or VSOE, of selling price or third-party evidence of selling price if VSOE does not exist. If neither VSOE nor third-party evidence exists, the Company uses its best estimate of the selling price for the deliverable. Such amounts are recognized as revenue when each unit is delivered. If the delivered element does not have stand-alone value without one of the undelivered elements in the arrangement, the elements are combined and accounted for as a single unit of accounting. Such amounts are recognized as revenue when the last deliverable of the combined units is delivered. Recurring revenue generated under license or royalty arrangements, including the Pooled Patents Agreement with Illumina, is recognized in the period reported by the partner or licensee and when the revenue recognition criteria have been met. Pooled Patents Agreement In December 2014, the Company entered into the Pooled Patents Agreement with Illumina. Pursuant to the Pooled Patents Agreement, a patent pool was established that is global in nature and combines the noninvasive prenatal testing, or NIPT, patents controlled by the Company and Illumina. Under the Pooled Patents Agreement, both the Company and its sublicensees and Illumina and its sublicensees pay a per-test fee into the pool for NIPT tests, which is then shared between the Company and Illumina. The Company recognizes license revenue in the period reported by its partners and Illumina and in certain cases this can result in a delay in recognizing revenue up to one quarter from the period in which the test was performed. As of March 31, 2016 , there were 46 licensees to the patent pool, including Illumina’s affiliate, Verinata Health, Inc., or Verinata, and Sequenom Laboratories.
Cost of Revenue	Cost of Revenues Cost of revenues include the cost of materials, direct labor (including laboratory and service personnel), equipment and infrastructure expenses associated with processing blood and other samples, quality control analyses, shipping charges to transport samples, and license and test fees, including those owed to Illumina as specified in the Pooled Patents Agreement. Infrastructure expenses include allocated facility occupancy and information technology costs. Costs associated with performing testing services are recorded as tests are processed. Costs recorded for sample processing and shipping charges represent the cost of all the tests processed during the period regardless of whether revenue is recognized with respect to that test. Royalties for licensed technology calculated on a per test basis or as a percentage of product revenue and fixed annual payments relating to the launch and commercialization of LDTs are recorded as license fees in cost of revenues at the time product revenue is recognized or in accordance with other contractual obligations.
Concentration of Risks	Concentration of Risks Financial instruments, which potentially are a concentration of credit risk, consist primarily of cash equivalents, marketable securities, and accounts receivable. The exposure to credit loss is limited by placing cash, cash equivalents and marketable securities with U.S. financial institutions. Additionally, the Company has established guidelines regarding diversification of investments and their maturities, which are designed to maintain principal and maximize liquidity. Credit risk with respect to accounts receivable is limited due to the Company’s large and diverse customer base. The Company considers ordering physicians and client laboratories to be its customers. For the three months ended March 31, 2015 , one customer represented more than 10% of total revenue, accounting for $5.6 million , or 14.8% , of total revenue during that period. No single customer accounted for over 10% of total revenue for the three months ended March 31, 2016 . Additionally, hundreds of third-party payors have reimbursed the Company for one or more of its tests. At a third-party payor level, no single payor represented more than 10% of total revenue for the three months ended March 31, 2016 or 2015 . The Company requires raw materials and devices of appropriate quality and reliability, which meet applicable regulatory requirements, that currently are available from a limited number of sources and in certain cases a single source of supply. Consequently, in the event that supplies are delayed or interrupted for any reason, it could impair the Company’s ability to develop and produce services, which could have a material adverse effect on the Company’s business, financial condition and results of operations.
Net Income (Loss) Per Share	Net (Loss) Income Per Share Basic net (loss) income per share is computed by dividing net (loss) income by the weighted-average number of common shares outstanding during the period. Diluted net income per share reflects the net income, plus interest charges during the period applicable to the Company’s convertible senior notes, divided by the weighted-average number of common shares and potentially dilutive common shares from outstanding stock options, restricted shares, employee stock purchases, warrants and convertible senior notes. Potential dilutive common shares were calculated using the treasury stock method and represent incremental shares issuable upon exercise of the Company’s outstanding stock options, unvested restricted stock and warrants. Potential dilutive common shares for convertible senior notes were calculated using the if-converted method. For periods in which the Company incurs a loss, the interest charges during the period are not added back to net loss and the potentially dilutive shares are not considered in the calculation of net loss per share as their effect would be anti-dilutive. A summary of information used to compute basic and diluted net earnings per share is shown below (in thousands, except per share data): Three Months Ended March 31, 2016 March 31, 2015 Net (loss) income for basic earnings per share $ (13,449 ) $ 14,284 Interest on convertible senior notes — 1,884 Net (loss) income for diluted earnings per share $ (13,449 ) $ 16,168 Weighted-average common shares outstanding 118,859 117,737 Dilutive effect of common share equivalents — 28,905 Shares used in calculating diluted earnings per share 118,859 146,642 Net (loss) income per basic share $ (0.11 ) $ 0.12 Net (loss) income per diluted share $ (0.11 ) $ 0.11 Common stock equivalents that could potentially reduce net income per common share in the future that were not included in the determination of diluted net (loss) income per common share, as their effects were antidilutive, are as follows (in thousands): Three Months Ended March 31, 2016 March 31, 2015 Shares underlying Convertible Senior Notes 28,088 — Options to purchase common stock 14,436 9,032 Restricted stock units not yet vested and released 5,816 41 Warrants to purchase common stock 200 200 Total 48,540 9,273
Recent Accounting Pronouncements	Recent Accounting Pronouncements In May 2014, the Financial Accounting Standards Board, or FASB, issued Accounting Standard Update, or ASU, No. 2014-09, Revenue from Contracts with Customers (Topic 606). The ASU creates a single source of revenue guidance for companies in all industries. The new standard provides guidance for all revenue arising from contracts with customers and affects all entities that enter into contracts to provide goods or services to their customers, unless the contracts are within the scope of other accounting standards. It also provides a model for the measurement and recognition of gains and losses on the sale of certain nonfinancial assets. This guidance, as amended, must be adopted using either a full retrospective approach for all periods presented or a modified retrospective approach and will be effective for fiscal years beginning after December 15, 2017, which will be the Company’s fiscal year 2018. The Company is currently assessing the impact this guidance will have on its consolidated financial statements. In February 2015, the FASB issued ASU 2016-02, Leases (Topic 842), which amends the FASB Accounting Standards Codification and creates Topic 842, “Leases.” The new topic supersedes Topic 840, “Leases,” and increases transparency and comparability among organizations by recognizing lease assets and lease liabilities on the balance sheet and requires disclosures of key information about leasing arrangements. The guidance is effective for reporting periods beginning after December 15, 2018. ASU 2016-02 mandates a modified retrospective transition method. The Company is currently assessing the impact this guidance will have on its consolidated financial statements. In April 2015, the FASB issued ASU No. 2015-03, Interest - Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs . The ASU is the result of the FASB’s simplification initiative intended to improve GAAP by reducing costs and complexity while maintaining or enhancing the usefulness of related financial statement information. The ASU specifies that debt issuance costs related to a note shall be reported in the balance sheet as a direct reduction from the face amount of the note. The ASU became effective for interim and annual periods on January 1, 2016. The ASU required the Company to reclassify its capitalized debt issuance costs previously recorded as assets on the condensed consolidated balance sheets. As a result of the ASU, the Company reclassified debt issuance costs of $1.0 million from “other current assets and prepaid expenses” and $1.0 million from “other assets” to “long-term debt and obligations, less current portion” as of December 31, 2015. As of March 31, 2016, $1.8 million of debt issuance costs were recorded as a direct reduction of the long-term debt amounts. The ASU had no effect on the Company’s results of operations or liquidity. In July 2015, the FASB issued ASU No. 2015-11, Inventory (Topic 330): Simplifying the Measurement of Inventory , which simplifies the subsequent measurement of inventory. It replaces the current lower of cost or market test with a lower of cost or net realizable value test. The standard is effective for public entities for annual reporting periods beginning after December 15, 2016, and interim periods therein. Early adoption is permitted and the new guidance must be applied prospectively. The Company does not expect the ASU to have a material impact on its financial statements upon adoption. In March 2016, the FASB issued ASU 2016-09, Compensation—Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting . The ASU includes provisions intended to simplify various aspects related to how share-based payments are accounted for and presented in the financial statements, including the income tax consequences, classification of awards as either equity or liabilities, and classification on the statement of cash flows. Specifically, the ASU allows entities to withhold an amount up to the employees’ maximum individual tax rate in the relevant jurisdiction without resulting in liability classification of the award and allowing forfeitures to be either estimated, as required today, or recognized when they occur. The new guidance will be effective for public entities in fiscal years beginning after December 15, 2016, with early adoption permitted. The Company expects the guidance could impact its accounting and reporting and is currently assessing the impact this guidance will have on its consolidated financial statements.

Summary of Significant Accoun15

Summary of Significant Accounting Policies (Tables)	3 Months Ended
	Mar. 31, 2016
Accounting Policies [Abstract]
Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share	For periods in which the Company incurs a loss, the interest charges during the period are not added back to net loss and the potentially dilutive shares are not considered in the calculation of net loss per share as their effect would be anti-dilutive. A summary of information used to compute basic and diluted net earnings per share is shown below (in thousands, except per share data): Three Months Ended March 31, 2016 March 31, 2015 Net (loss) income for basic earnings per share $ (13,449 ) $ 14,284 Interest on convertible senior notes — 1,884 Net (loss) income for diluted earnings per share $ (13,449 ) $ 16,168 Weighted-average common shares outstanding 118,859 117,737 Dilutive effect of common share equivalents — 28,905 Shares used in calculating diluted earnings per share 118,859 146,642 Net (loss) income per basic share $ (0.11 ) $ 0.12 Net (loss) income per diluted share $ (0.11 ) $ 0.11 Common stock equivalents that could potentially reduce net income per common share in the future that were not included in the determination of diluted net (loss) income per common share, as their effects were antidilutive, are as follows (in thousands): Three Months Ended March 31, 2016 March 31, 2015 Shares underlying Convertible Senior Notes 28,088 — Options to purchase common stock 14,436 9,032 Restricted stock units not yet vested and released 5,816 41 Warrants to purchase common stock 200 200 Total 48,540 9,273

Supplementary Financial Infor16

Supplementary Financial Information (Tables)	3 Months Ended
	Mar. 31, 2016
Other Financial Information [Abstract]
Marketable Securities	Marketable Securities, Available-for-sale (in thousands): March 31, 2016 Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Estimated Fair Value U.S. treasury securities $ 20,201 $ 5 $ (1 ) $ 20,205 Certificates of deposit 102 — — 102 Mutual funds 312 198 (9 ) 501 Total marketable securities $ 20,615 $ 203 $ (10 ) $ 20,808 December 31, 2015 Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Estimated Fair Value U.S. treasury securities $ 25,238 $ — $ (24 ) $ 25,214 Certificates of deposit 97 — — 97 Mutual funds 312 203 — 515 Total marketable securities $ 25,647 $ 203 $ (24 ) $ 25,826
Inventories	March 31, 2016 December 31, 2015 Raw materials $ 2,759 $ 2,145 Work in process 235 272 Total $ 2,994 $ 2,417
Schedule of Prepaid Expenses and Other Current Assets	Prepaid Expenses and Other Current Assets (in thousands): March 31, 2016 December 31, 2015 Prepaid expenses $ 1,630 $ 2,550 Assets held-for-sale, net 1,281 — Other 49 393 Total $ 2,960 $ 2,943
Property, Plant and Equipment	Property, Equipment and Leasehold Improvements (in thousands): March 31, 2016 December 31, 2015 Building and improvements $ 4,273 $ 8,673 Laboratory equipment 33,372 33,796 Leasehold improvements 8,116 6,411 Office furniture and equipment 16,330 16,448 62,091 65,328 Less accumulated depreciation (54,440 ) (55,269 ) Total $ 7,651 $ 10,059 Depreciation expense for the three months ended March 31, 2016 and 2015, was $1.4 million and $2.1 million , respectively. Depreciation of assets under capital leases is included in depreciation expense.
Accrued Expenses	Accrued Expenses (in thousands): March 31, 2016 December 31, 2015 Accrued royalties, licenses, and collaboration payments $ 4,496 $ 5,046 Accrued compensation and related taxes 4,689 5,349 Accrued professional and consulting fees 1,173 468 Accrued interest 24 1,649 Other 2,141 2,856 Total $ 12,523 $ 15,368

Long-Term Obligations (Tables)

Long-Term Obligations (Tables)	3 Months Ended
	Mar. 31, 2016
Debt Disclosure [Abstract]
Schedule of Long-term Debt Instruments	Long-Term Obligations Long-Term Obligations (in thousands, except percentages): March 31, 2016 December 31, 2015 5.0% Convertible Senior Notes due October 2017 ($45,000) and January 2018 ($85,000), interest payable semi-annually in April and October $ 130,000 $ 130,000 Unamortized debt discount on Convertible Senior Notes due January 2018 (764 ) (867 ) Unamortized debt issuance costs on Convertible Senior Notes due October 2017 and January 2018 (1,798 ) (2,054 ) Obligation for building and improvements, effective interest rate of 5.2% as of March 31, 2016 and December 31, 2015, expiring October 2026 5,523 5,597 Capital lease liabilities, expired January 2016 — 13 Total long-term obligations 132,961 132,689 Less current portion (311 ) (316 ) Non-current portion $ 132,650 $ 132,373

Stock Compensation Plans (Table

Stock Compensation Plans (Tables)	3 Months Ended
	Mar. 31, 2016
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Schedule of Share-based Compensation, Stock Options, Activity	The following table summarizes stock option activity of the Company during the three months ended March 31, 2016 (shares in thousands): Shares Subject to Options Weighted-Average Exercise Price per Share As of December 31, 2015 11,408 $ 4.41 Granted 2,716 $ 1.58 Exercised — $ — Forfeitures and cancellations (753 ) $ 4.52 Outstanding at March 31, 2016 13,371 $ 3.83 Options exercisable at March 31, 2016 7,765 $ 5.02
Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity	The following table summarizes activity related to restricted stock awards and restricted stock units of the Company during the three months ended March 31, 2016 : Number of Shares Weighted-Average Grant Date Fair Value Outstanding at December 31, 2015 2,443 $ 2.64 Grants and awards 3,212 $ 1.58 Vested and released (298 ) $ 3.32 Forfeitures and cancellations (131 ) $ 2.84 Outstanding at March 31, 2016 5,226 $ 1.97
Equity Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions	Following are the weighted-average underlying assumptions used to determine the fair value of stock option award grants and for stock purchase rights under the ESPP for the periods indicated: Three Months Ended Stock Option Grants March 31, 2016 March 31, 2015 Risk-free interest rate 1.5 % 1.7 % Volatility 89.5 % 92.1 % Dividend yield — % — % Expected life (years) 6.8 7.2 Weighted-average grant date fair value $ 1.21 $ 2.78
Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Schedule of Share-based Payment Award, Employee Stock Purchase Plan, Valuation Assumptions	Three Months Ended ESPP Stock Purchase Rights March 31, 2016 March 31, 2015 Risk-free interest rate 0.39 % 0.14 % Volatility 74.6 % 55.7 % Dividend yield — % — % Expected life (years) 0.5 0.5 Weighted-average grant date fair value $ 0.56 $ 1.07

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	3 Months Ended
	Mar. 31, 2016
Fair Value Disclosures [Abstract]
Summary of fair value for assets measured on recurring basis	The following tables summarize the fair value hierarchy for assets and liabilities measured at fair value on a recurring basis. As of March 31, 2016 (in thousands) Fair Value Quoted Prices in Active Markets for Identical Assets (Level 1) Significant Other Observable Inputs (Level 2) Cash equivalents: Money market funds $ 37,879 $ 37,879 $ — Total cash equivalents 37,879 37,879 — Marketable securities: U.S. treasury securities 20,205 20,205 — Certificates of deposit 102 — 102 Mutual funds 501 501 — Total marketable securities 20,808 20,706 102 Total $ 58,687 $ 58,585 $ 102 As of December 31, 2015 (in thousands) Fair Value Quoted Prices in Active Markets for Identical Assets (Level 1) Significant Other Observable Inputs (Level 2) Cash equivalents: Money market funds $ 43,815 $ 43,815 $ — Total cash equivalents 43,815 43,815 — Marketable securities: U.S. treasury securities 25,214 25,214 — Certificates of deposit 97 — 97 Mutual funds 515 515 — Total marketable securities 25,826 25,729 97 Total $ 69,641 $ 69,544 $ 97
Carrying amounts and fair value of long-term obligations	The carrying amounts and fair values of the 2017 Notes and 2018 Notes are as follows (in thousands): March 31, 2016 December 31, 2015 Carrying Amount Fair Value Carrying Amount Fair Value Convertible Senior Notes $ 127,438 $ 84,640 $ 127,079 $ 106,505

Summary of Significant Accoun20

Summary of Significant Accounting Policies (Narrative) (Details) $ in Thousands	3 Months Ended
	Mar. 31, 2016USD ($)patent	Mar. 31, 2015USD ($)Customers	Dec. 31, 2015USD ($)
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Finite-Lived Patents, Number of Licenses | patent	46
Deferred Finance Costs, Net	$ 1,800		$ 2,100
Revenues	$ 27,570	$ 37,805
Sales Revenue, Net | Customer Concentration Risk
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Concentration risk, number of customers | Customers		0
Sales Revenue, Net | Customer Concentration Risk | Diagnostic Services | International Locations
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Concentration risk percentage	5.40%	4.40%
Third-Party Payor, Customer One | Sales Revenue, Net | Customer Concentration Risk
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Concentration risk percentage		14.80%
Concentration risk, number of customers | Customers		1
Revenues		$ 5,600
Other current assets and prepaid expenses | Accounting Standards Update 2015-03
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Deferred Finance Costs, Net			1,000
Other assets | Accounting Standards Update 2015-03
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Deferred Finance Costs, Net			$ 1,000
Long-term Debt | Accounting Standards Update 2015-03
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Deferred Finance Costs, Net	$ 1,800

Summary of Significant Accoun21

Summary of Significant Accounting Policies (Net Earnings (Loss) Per Share) (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Net (loss) income for basic earnings per share	$ (13,449)	$ 14,284
Interest on convertible senior notes	$ 0	$ 1,884
Net (loss) income for diluted earnings per share	(13,449)	16,168
Weighted-average common shares outstanding	118,859	117,737
Dilutive effect of common share equivalents	0	28,905
Shares used in calculating diluted earnings per share	118,859	146,642
Net (loss) income per basic share (in dollars per share)	$ (0.11)	$ 0.12
Net (loss) income per diluted share (in dollars per share)	$ (0.11)	$ 0.11
Antidilutive securities excluded from computation of earnings per share, amount	48,540	9,273
Shares underlying Senior Convertible Notes
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	28,088	0
Stock Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	14,436	9,032
Restricted Stock Units (RSUs)
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	5,816	41
Warrants to purchase common stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	200	200

Supplementary Financial Infor22

Supplementary Financial Information (Marketable Securities) (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 20,615	$ 25,647
Gross Unrealized Gains	203	203
Gross Unrealized Losses	(10)	(24)
Estimated Fair Value	20,808	25,826
U.S. treasury securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	20,201	25,238
Gross Unrealized Gains	5	0
Gross Unrealized Losses	(1)	(24)
Estimated Fair Value	20,205	25,214
Certificates of deposit
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	102	97
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Estimated Fair Value	102	97
Mutual funds
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	312	312
Gross Unrealized Gains	198	203
Gross Unrealized Losses	(9)	0
Estimated Fair Value	$ 501	$ 515

Supplementary Financial Infor23

Supplementary Financial Information (Schedule of Inventory Table) (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Inventory Disclosure [Abstract]
Raw materials	$ 2,759	$ 2,145
Work in process	235	272
Total	$ 2,994	$ 2,417

Supplementary Financial Infor24

Supplementary Financial Information Prepaid Expenses and Other Current Assets (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Prepaid and Other Assets Disclosure [Abstract]
Prepaid Expense	$ 1,630	$ 2,550
Assets Held-for-sale, Not Part of Disposal Group	1,281	0
Other Assets, Miscellaneous	49	393
Other Assets, Current	$ 2,960	$ 2,943

Supplementary Financial Infor25

Supplementary Financial Information (Property, Plant and Equipment) (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015	Dec. 31, 2015
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	$ 62,091		$ 65,328
Accumulated Depreciation, Depletion and Amortization, Property, Plant, and Equipment	(54,440)		(55,269)
Property, equipment and leasehold improvements, net	7,651		10,059
Depreciation	1,400	$ 2,100
Building and Building Improvements [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	4,273		8,673
Equipment [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	33,372		33,796
Leaseholds and Leasehold Improvements [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	8,116		6,411
Office Equipment [Member]
Property, Plant and Equipment [Line Items]
Property, Plant and Equipment, Gross	$ 16,330		$ 16,448

Supplementary Financial Infor26

Supplementary Financial Information (Accrued Expenses) (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Accrued Expenses [Abstract]
Accrued royalties, licenses, and collaboration payments	$ 4,496	$ 5,046
Accrued compensation and related taxes	4,689	5,349
Accrued professional fees and consulting	1,173	468
Accrued interest	24	1,649
Other	2,141	2,856
Total	$ 12,523	$ 15,368

Long-Term Obligations (Long-Ter

Long-Term Obligations (Long-Term Obligations Schedule) (Details) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015	Dec. 31, 2015	Sep. 17, 2012
Debt Instrument [Line Items]
Accrued interest	$ 24		$ 1,649
Convertible senior notes interest rate	5.00%		5.00%
Unamortized debt discount	$ (800)		$ (900)
Unamortized debt issuance costs on Convertible Senior Notes due October 2017 and January 2018	(1,798)		(2,054)
Long-term debt and capital lease obligations	132,961		132,689
Long-term Debt and Capital Lease Obligations, Current	(311)		(316)
Long-term Debt and Captial Lease Obligations Excluding Current Portion	$ 132,650		$ 132,373
Weighted-average common shares outstanding	118,859	117,737
5% Convertible Senior Notes, Due October 2017
Debt Instrument [Line Items]
Accrued interest	$ 45,000
Senior Notes | 5% Convertible Senior Notes, Due October 2017
Debt Instrument [Line Items]
Convertible senior notes interest rate	5.00%		5.00%	5.00%
Unamortized debt discount	$ (764)		$ (867)
Long-term debt and capital lease obligations	130,000		130,000
Senior Notes | Convertible Exchange Senior Notes, Due January 2018
Debt Instrument [Line Items]
Accrued interest	85,000
Convertible senior notes interest rate				5.00%
Capital Lease Obligations | Financed Capital Lease Obligations, Due October 2026
Debt Instrument [Line Items]
Long-term debt and capital lease obligations	5,523		5,597
Capital Lease Obligations | Capital Lease Obligations, Due January 2016
Debt Instrument [Line Items]
Long-term debt and capital lease obligations	$ 0		$ 13
Debt Instrument, Interest Rate, Effective Percentage	5.20%		5.20%

Long-Term Obligations (Maturiti

Long-Term Obligations (Maturities of Long-term Debt) (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Debt Disclosure [Abstract]
Less unamortized discounts for imputed interest	$ 800	$ 900
Total long-term obligations	$ 132,961	$ 132,689

Long-Term Obligations (Narrativ

Long-Term Obligations (Narrative) (Details) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended
	Nov. 30, 2011option	Mar. 31, 2016USD ($)dshares	Dec. 31, 2015USD ($)	Jun. 30, 2015USD ($)$ / shares	Sep. 17, 2012
Debt Instrument [Line Items]
Total long-term obligations		$ 132,961	$ 132,689
Payments of debt restructuring costs		$ 1,600
Increase in fair value conversion option				$ 1,100
Remaining discount amortization period		30 months
Accrued interest		$ 24	1,649
Convertible senior notes, net of issuance costs		$ 127,438	$ 127,079
Convertible senior notes interest rate		5.00%	5.00%
Capital lease obligation term	15 years
Capital lease obligation, number of extension options | option	2
Capital lease obligation, Extension period	5 years
5% Convertible Senior Notes, Due October 2017
Debt Instrument [Line Items]
Accrued interest		$ 45,000
Convertible Notes Payable
Debt Instrument [Line Items]
Latest convertible date		Oct. 1, 2017
Senior Notes | 5% Convertible Senior Notes, Due October 2017
Debt Instrument [Line Items]
Total long-term obligations		$ 130,000	$ 130,000
Convertible senior notes, net of issuance costs		$ 85,000
Convertible senior notes interest rate		5.00%	5.00%		5.00%
Number of equity instruments | shares		9,722,898
Conversion price | $ / shares				$ 4.63
Earliest call date		Oct. 1, 2015
Stock price trigger, percent of sales must exceed conversion price		140.00%
Stock price trigger, trading days | d		20
Stock price trigger, consecutive trading day period prior to notice of redemption		30 days
Redemption price percentage		100.00%
Senior Notes | Convertible Exchange Senior Notes, Due January 2018
Debt Instrument [Line Items]
Accrued interest		$ 85,000
Convertible senior notes interest rate					5.00%
Conversion price | $ / shares				$ 4.63
Stock price trigger, trading days | d		20
Stock price trigger, consecutive trading day period prior to notice of redemption		30 days
Redemption price percentage		100.00%
Senior Notes | Minimum | 5% Convertible Senior Notes, Due October 2017
Debt Instrument [Line Items]
Conversion ratio		216.0644
Senior Notes | Minimum | Convertible Exchange Senior Notes, Due January 2018
Debt Instrument [Line Items]
Conversion ratio		216.0644
Stock price trigger, percent of sales must exceed conversion price		115.00%
Senior Notes | Maximum | 5% Convertible Senior Notes, Due October 2017
Debt Instrument [Line Items]
Number of equity instruments | shares		12,396,695
Conversion ratio		275.4821

Stock Compensation Plans (Narra

Stock Compensation Plans (Narrative) (Details) - USD ($) $ in Millions	3 Months Ended
	Mar. 31, 2016	Dec. 31, 2015
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common stock, shares issued	119,216,003	118,567,676
Common Stock | Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Common stock, shares issued	277,437
Proceeds from Issuance of Common Stock	$ 0.4

Stock Compensation Plans (Combi

Stock Compensation Plans (Combined Activity) (Details) - Equity Incentive Plan - Stock Options - Common Stock shares in Thousands	3 Months Ended
	Mar. 31, 2016$ / sharesshares
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Outstanding at beginning of period (shares) | shares	11,408
Granted (shares) | shares	2,716
Exercised (shares) | shares	0
Forfeitures and cancelled (shares) | shares	(753)
Outstanding at end of period (shares) | shares	13,371
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price [Roll Forward]
Outstanding at beginning of period (usd per share) | $ / shares	$ 4.41
Granted (usd per share) | $ / shares	1.58
Exercised (usd per share) | $ / shares	0
Forfeited and cancelled (usd per share) | $ / shares	4.52
Outstanding at end of period (usd per share) | $ / shares	$ 3.83
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Options exercisable at end of period, Shares Subject to Options | shares	7,765
Options vested and exercisable at end of period, Weighted Average Exercise Price | $ / shares	$ 5.02

Stock Compensation Plans (Restr

Stock Compensation Plans (Restricted Stock and Restricted Stock Units) (Details) - Restricted Stock - Restricted Stock shares in Thousands	3 Months Ended
	Mar. 31, 2016$ / sharesshares
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]
Oustanding at Beginning of Period (shares) | shares	2,443
Grants and awards (shares) | shares	3,212
Vested and released (shares) | shares	(298)
Forfeitures and cancellations (shares) | shares	(131)
Oustanding at End of Period (shares) | shares	5,226
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Abstract]
Outstanding at December 31, 2015 | $ / shares	$ 2.64
Grants and awards | $ / shares	1.58
Vested and released | $ / shares	3.32
Forfeitures and cancellations | $ / shares	2.84
Outstanding at March 31, 2016 | $ / shares	$ 1.97

Stock Compensation Plans (Weigh

Stock Compensation Plans (Weighted-Average Underlying Assumptions Used) (Details) - Common Stock - $ / shares	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Equity Incentive Plan | Stock Options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	1.50%	1.70%
Volatility	89.50%	92.10%
Dividend yield	0.00%	0.00%
Expected life (years)	6 years 9 months	7 years 2 months 12 days
Weighted-average grant date fair value	$ 1.21	$ 2.78
Employee Stock Purchase Plan | Employee stock purchase rights
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	0.39%	0.14%
Volatility	74.60%	55.70%
Dividend yield	0.00%	0.00%
Expected life (years)	6 months	6 months
Weighted-average grant date fair value	$ 0.56	$ 1.07

Fair Value Measurements (Fair V

Fair Value Measurements (Fair Value, Assets and Liabilities Measured on a Recurring Basis) (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Marketable securities:
Total	$ 58,687	$ 69,641
Quoted Prices in Active Markets for Identical Assets (Level 1)
Marketable securities:
Total	58,585	69,544
Significant Other Observable Inputs (Level 2)
Marketable securities:
Total	102	97
Marketable Securities
Marketable securities:
U.S. treasury securities	20,205	25,214
Certificates of deposit	102	97
Mutual funds	501	515
Total marketable securities	20,808	25,826
Marketable Securities | Quoted Prices in Active Markets for Identical Assets (Level 1)
Marketable securities:
U.S. treasury securities	20,205	25,214
Certificates of deposit	0	0
Mutual funds	501	515
Total marketable securities	20,706	25,729
Marketable Securities | Significant Other Observable Inputs (Level 2)
Marketable securities:
U.S. treasury securities	0	0
Certificates of deposit	102	97
Mutual funds	0	0
Total marketable securities	102	97
Cash Equivalents
Cash equivalents:
Money market funds	37,879	43,815
Total cash equivalents	37,879	43,815
Cash Equivalents | Quoted Prices in Active Markets for Identical Assets (Level 1)
Cash equivalents:
Money market funds	37,879	43,815
Total cash equivalents	37,879	43,815
Cash Equivalents | Significant Other Observable Inputs (Level 2)
Cash equivalents:
Money market funds	0	0
Total cash equivalents	$ 0	$ 0

Fair Value Measurements (Fair35

Fair Value Measurements (Fair Value of Long-term Commitments) (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Unamortized debt issuance costs	$ (1,800)	$ (2,100)
Unamortized debt discounts	(800)	(900)
Carrying (Reported) Amount, Fair Value Disclosure
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Convertible Senior Notes	127,438	127,079
Estimate of Fair Value, Fair Value Disclosure
Fair Value, Balance Sheet Grouping, Financial Statement Captions [Line Items]
Convertible Senior Notes	$ 84,640	$ 106,505

Other Transactions (Details)

Other Transactions (Details) - USD ($) $ in Thousands	Apr. 18, 2016	Mar. 31, 2016	Mar. 31, 2015
Subsequent Event [Line Items]
Restructuring costs		$ 859	$ 0
Severance and retention costs and facility lease costs
Subsequent Event [Line Items]
Restructuring costs		900
Severance and retention costs and facility lease costs | Accrued Liabilities
Subsequent Event [Line Items]
Restructuring reserve		$ 500
Subsequent Event
Subsequent Event [Line Items]
Proceeds from the sale of assets	$ 700