UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

FORM 10-Q

(Mark One)

ý QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended September 30, 2016

OR

¨ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from to

Commission file number 000-30755

CEPHEID

(Exact Name of Registrant as Specified in its Charter)

California	77-0441625
(State or Other Jurisdiction of Incorporation or Organization)	(I.R.S. Employer Identification No.)
904 Caribbean Drive, Sunnyvale, California	94089-1189
(Address of Principal Executive Office)	(Zip Code)

(408) 541-4191

(Registrant’s Telephone Number, Including Area Code)

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

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  ý    No  ¨

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

Large Accelerated Filer	ý	Accelerated Filer	¨
Non-Accelerated Filer	¨  (Do not check if smaller reporting company)	Smaller Reporting Company	¨

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

As of October 27, 2016, there were 73,480,343 shares of the registrant’s common stock outstanding.

REPORT ON FORM 10-Q FOR THE

QUARTER ENDED SEPTEMBER 30, 2016

INDEX

		Page
Part I.	Financial Information
Item 1.	Financial Statements	3
	Condensed Consolidated Balance Sheets as of September 30, 2016 and December 31, 2015	3
	Condensed Consolidated Statements of Operations for the three and nine months ended September 30, 2016 and 2015	4
	Condensed Consolidated Statements of Comprehensive Loss for the three and nine months ended September 30, 2016 and 2015	5
	Condensed Consolidated Statements of Cash Flows for the nine months ended September 30, 2016 and 2015	6
	Notes to Condensed Consolidated Financial Statements	7
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	25
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	38
Item 4.	Controls and Procedures	39
Part II.	Other Information
Item 1.	Legal Proceedings	40
Item 1A	Risk Factors	41
Item 2.	Unregistered Sales of Equity Securities and Use of Proceeds	62
Item 3.	Defaults Upon Senior Securities	62
Item 4.	Mine Safety Disclosures	63
Item 5.	Other Information	63
Item 6.	Exhibits	63
Signatures

Cepheid®, the Cepheid logo, GeneXpert®, Xpert®, and SmartCycler are trademarks of Cepheid.

PART I — FINANCIAL INFORMATION

ITEM 1. FINANCIAL STATEMENTS

CEPHEID

CONDENSED CONSOLIDATED BALANCE SHEETS

(in thousands, except share data)

	September 30,			December 31,
	2016			2015
	(unaudited)
ASSETS
Current assets:
Cash and cash equivalents	$	115,718		$	112,568
Short-term investments	253,457			210,147
Accounts receivable, less allowance for doubtful accounts of $446 as of September 30, 2016 and $383 as of December 31, 2015	81,910			66,550
Inventory, net	155,720			148,690
Prepaid expenses and other current assets	23,056			18,515
Total current assets	629,861			556,470
Property and equipment, net	151,227			127,639
Investments	—			62,175
Other non-current assets	5,632			4,205
Intangible assets, net	20,956			25,241
Goodwill	39,681			39,681
Total assets	$	847,357		$	815,411
LIABILITIES AND SHAREHOLDERS’ EQUITY
Current liabilities:
Accounts payable	$	56,046		$	57,771
Accrued compensation	36,863			39,015
Accrued royalties	4,309			5,469
Accrued and other liabilities	30,919			27,451
Current portion of deferred revenue	18,338			12,778
Total current liabilities	146,475			142,484
Long-term portion of deferred revenue	10,614			5,538
Convertible senior notes, net	289,758			281,627
Other liabilities	19,864			15,779
Total liabilities	466,711			445,428
Commitments and contingencies (Note 8)
Shareholders’ equity:
Preferred stock, no par value; 5,000,000 shares authorized, none issued or outstanding	—			—
Common stock, no par value; 150,000,000 shares authorized, 73,281,941 and 72,415,317 shares issued and outstanding at September 30, 2016 and December 31, 2015, respectively	458,939			449,704
Additional paid-in capital	292,763			263,429
Accumulated other comprehensive loss, net	(1,074		)	(908		)
Accumulated deficit	(369,982		)	(342,242		)
Total shareholders’ equity	380,646			369,983
Total liabilities and shareholders’ equity	$	847,357		$	815,411

The accompanying notes are an integral part of these Condensed Consolidated Financial Statements.

3

CEPHEID

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(in thousands, except per share data)

(unaudited)

	Three Months Ended   September 30,						Nine Months Ended   September 30,
	2016			2015			2016			2015
Revenue	$	158,488		$	126,465		$	449,269		$	391,577
Costs and operating expenses:
Cost of sales	83,390			67,681			229,220			198,259
Collaboration profit sharing	2,915			1,286			4,857			3,879
Research and development	29,912			32,909			93,418			84,987
Sales and marketing	29,302			28,664			87,971			82,678
General and administrative	18,688			15,401			49,161			47,395
Total costs and operating expenses	164,207			145,941			464,627			417,198
Loss from operations	(5,719		)	(19,476		)	(15,358		)	(25,621		)
Other income (expense):
Interest income	873			494			2,332			1,283
Interest expense	(3,856		)	(3,687		)	(11,433		)	(10,937		)
Foreign currency exchange loss and other, net	(1,012		)	(408		)	(1,242		)	(2,848		)
Other expense, net	(3,995		)	(3,601		)	(10,343		)	(12,502		)
Loss before income taxes	(9,714		)	(23,077		)	(25,701		)	(38,123		)
(Provision for) benefit from income taxes	(1,193		)	176			(2,039		)	(602		)
Net loss	$	(10,907	)	$	(22,901	)	$	(27,740	)	$	(38,725	)
Basic net loss per share	$	(0.15	)	$	(0.32	)	$	(0.38	)	$	(0.54	)
Diluted net loss per share	$	(0.15	)	$	(0.32	)	$	(0.38	)	$	(0.54	)
Shares used in computing basic net loss per share	73,158			72,199			72,890			71,777
Shares used in computing diluted net loss per share	73,158			72,199			72,890			71,777

The accompanying notes are an integral part of these Condensed Consolidated Financial Statements.

4

CEPHEID

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS

(in thousands)

(unaudited)

	Three Months Ended   September 30,						Nine Months Ended   September 30,
	2016			2015			2016			2015
Net loss	$	(10,907	)	$	(22,901	)	$	(27,740	)	$	(38,725	)
Other comprehensive loss, before tax:
Change in unrealized gains and losses related to cash flow hedges:
Loss recognized in accumulated other comprehensive loss, net	(1,804		)	(545		)	(1,949		)	(1,596		)
Loss reclassified from accumulated other comprehensive loss, net to the statement of operations	320			369			1,006			414
Change in unrealized gains and losses related to available-for-sale investments:
Gain (loss) recognized in accumulated other comprehensive loss, net	(86		)	(148		)	735			(5		)
Gain (loss) reclassified from accumulated other comprehensive loss, net to the statement of operations	52			—			42			(3		)
Other comprehensive loss, before tax	(1,518		)	(324		)	(166		)	(1,190		)
Income tax benefit (expense) related to items of accumulated other comprehensive loss, net	497			—			—			(100		)
Comprehensive loss	$	(11,928	)	$	(23,225	)	$	(27,906	)	$	(39,815	)

The accompanying notes are an integral part of these Condensed Consolidated Financial Statements.

5

CEPHEID

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(in thousands)

(unaudited)

	Nine Months Ended   September 30,
	2016			2015
Cash flows from operating activities:
Net loss	$	(27,740	)	$	(38,725	)
Adjustments to reconcile net loss to net cash provided by operating activities:
Depreciation and amortization of property and equipment	24,092			20,170
Amortization of intangible assets	4,286			4,814
Unrealized foreign exchange differences	(757		)	2,242
Amortization of debt discount and transaction costs	8,130			7,627
Impairment of acquired intangible assets, licenses, property and equipment	1,286			224
Stock-based compensation expense	29,546			25,752
Excess tax benefits from stock-based compensation expense	—			(53		)
Other non-cash items	634			254
Changes in operating assets and liabilities:
Accounts receivable	(15,360		)	8,426
Inventory, net	(7,243		)	(11,733		)
Prepaid expenses and other current assets	(3,693		)	(9,691		)
Other non-current assets	(57		)	(801		)
Accounts payable and other current and non-current liabilities	3,877			12,297
Accrued compensation	(2,152		)	(511		)
Deferred revenue	10,634			(795		)
Net cash provided by operating activities	25,483			19,497
Cash flows from investing activities:
Capital expenditures	(49,244		)	(29,087		)
Cost of acquisitions, net	—			(3,000		)
Proceeds from sale of equipment and an intangible asset	44			834
Proceeds from sales of marketable securities and investments	86,310			49,173
Proceeds from maturities of marketable securities and investments	177,479			175,272
Purchases of marketable securities and investments	(244,495		)	(198,701		)
Transfer from (to) restricted cash	(2,335		)	1,792
Net cash used in investing activities	(32,241		)	(3,717		)
Cash flows from financing activities:
Net proceeds from the issuance of common shares and exercise of stock options	9,288			26,444
Excess tax benefits from stock-based compensation expense	—			53
Principal payment of notes payable	(128		)	(121		)
Net cash provided by financing activities	9,160			26,376
Effect of foreign exchange rate change on cash and cash equivalents	748			(2,332		)
Net increase in cash and cash equivalents	3,150			39,824
Cash and cash equivalents at beginning of period	112,568			96,663
Cash and cash equivalents at end of period	$	115,718		$	136,487

The accompanying notes are an integral part of these Condensed Consolidated Financial Statements.

6

CEPHEID

NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Unaudited)

1. Organization and Summary of Significant Accounting Policies

Organization and Basis of Presentation

Cepheid (the “Company”) was incorporated in the State of California on March 4, 1996. The Company is a molecular diagnostics company that develops, manufactures, and markets fully-integrated systems for diagnostic testing. The Company’s systems enable fast, sophisticated molecular testing for organisms and genetic-based diseases by automating otherwise complex manual laboratory procedures.

Proposed Transaction with Danaher Corporation

On September 2, 2016, Cepheid entered into a Merger Agreement (the "Merger Agreement") with Danaher Corporation (“Danaher”) pursuant to which Danaher has agreed to acquire Cepheid for $53.00 per share in an all-cash transaction valued at approximately $4.0 billion, inclusive of the Company's net cash (the "Merger"). The transaction is expected to close in the fourth quarter of fiscal 2016, subject to certain conditions, including shareholder approval and other customary closing conditions. Cepheid incurred transaction-related costs of $2.6 million during the three months ended September 30, 2016 in connection with the Merger and expect to incur additional costs related to the Merger during the fourth quarter of fiscal 2016 if the transaction is successfully completed. For additional information related to the Merger and the Merger Agreement, please refer to Cepheid’s Current Report on Form 8-K filed with the Securities and Exchange Commission (“SEC”) on September 6, 2016 and the Definitive Proxy Statement on Schedule 14A filed with the SEC on October 7, 2016. The foregoing description of the Merger Agreement is qualified in its entirety by reference to the full text of the Merger Agreement included as Exhibit 2.1 to Cepheid’s Current Report on Form 8-K filed September 6, 2016. Upon completion of the Merger, shares of Cepheid common stock will cease trading on The Nasdaq Global Select Market.

Other than transaction expenses associated with the proposed Merger of $2.6 million, which were recorded to general and administrative expense in the Condensed Consolidated Statement of Operations, for the three and nine months ended September 30, 2016, the terms of the Merger Agreement did not impact the Company's Condensed Consolidated Financial Statements.

Basis of Presentation

The Condensed Consolidated Balance Sheet at September 30, 2016, the Condensed Consolidated Statements of Operations for the three and nine months ended September 30, 2016 and 2015, the Condensed Consolidated Statements of Comprehensive Loss for the three and nine months ended September 30, 2016 and 2015 and the Condensed Consolidated Statements of Cash Flows for the nine months ended September 30, 2016 and 2015 are unaudited. In the opinion of management, these condensed consolidated financial statements reflect all normal recurring adjustments that management considers necessary for a fair presentation of the Company’s financial position at such dates, and the operating results and cash flows for those periods. The accompanying condensed consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States. However, certain information or footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles (“GAAP”) have been condensed or omitted pursuant to the rules and regulations of the SEC. The results of operations for such periods are not necessarily indicative of the results expected for the remainder of 2016 or for any future period. The Condensed Consolidated Balance Sheet as of December 31, 2015 is derived from audited consolidated financial statements as of that date but does not include all of the information and footnotes required by accounting principles generally accepted in the United States for complete financial statements. These condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and related notes included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2015.

Functional Currency

The U.S. dollar is the functional currency of all of the Company’s subsidiaries. The Company remeasures its foreign subsidiaries’ monetary assets and liabilities to the U.S. dollar and records the net gains or losses resulting from remeasurement in “Foreign currency exchange loss and other, net” in the consolidated statements of operations.

Use of Estimates

7

The preparation of condensed consolidated financial statements in conformity with United States GAAP requires management to make estimates and assumptions that affect the amounts reported in the condensed consolidated financial statements and accompanying notes. We base our estimates on historical experience and on various other assumptions that we believe to be reasonable under the circumstances. Actual results could differ from these estimates.

Cash, Cash Equivalents, Short-Term Investments and Non-Current Investments

Cash and cash equivalents consist of cash on deposit with banks and money market instruments. The Company’s marketable debt securities have been classified and accounted for as available-for-sale. The Company determines the appropriate classification of its investments at the time of purchase and re-evaluates the designations at each balance sheet date. The Company classifies its marketable debt securities as cash equivalents, short-term investments or non-current investments based on each instrument’s underlying effective maturity date. All highly liquid investments with maturities of three months or less at the date of purchase are classified as cash equivalents. Marketable debt securities with effective maturities of 12 months or less are classified as short-term, and marketable debt securities with effective maturities greater than 12 months are classified as non-current. All unrealized gains and losses associated with our investments were reported within accumulated other comprehensive loss, a component of shareholders’ equity. The cost of securities sold is based upon the specific identification method. Interest income includes interest, dividends, amortization of purchase premiums and discounts and realized gains and losses on sales of securities.

The Company assesses whether an other-than-temporary impairment loss on its investments has occurred due to declines in fair value or other market conditions. With respect to the Company’s debt securities, this assessment takes into account the severity and duration of the decline in value, the Company’s intent to sell the security, whether it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis, and whether or not the Company expects to recover the entire amortized cost basis of the security (that is, a credit loss exists).

See Note 3, “Investments”, for information and related disclosures regarding the Company’s investments.

Restricted Cash

Prepaid expense and other current assets included $3.7 million and $2.7 million of restricted cash as of September 30, 2016 and December 31, 2015, respectively and other non-current assets included $3.4 million and $2.1 million of restricted cash as of September 30, 2016 and December 31, 2015, respectively. The majority of this restricted cash is held as security for bank guarantees provided to a foreign customer contract. The Company is required to maintain such guarantees until its contractual obligations are satisfied under the contract.

Concentration of Credit Risks and Other Uncertainties

The carrying amounts for financial instruments consisting of cash and cash equivalents, restricted cash, accounts receivable, accounts payable, and accrued and other liabilities approximate fair value due to their short maturities. Derivative instruments and investments are stated at their estimated fair values, based on quoted market prices for the same or similar instruments. The counterparties to the agreements relating to the Company’s derivative instruments consist of large financial institutions of high credit standing.

The Company’s main financial institution for banking operations held 65% and 66% of the Company’s cash and cash equivalents as of September 30, 2016 and December 31, 2015, respectively.

The Company’s accounts receivable are derived from sales to customers and distributors. The Company performs credit evaluations of its customers’ financial condition. The Company provides reserves for potential credit losses but has not experienced significant losses to date. There was one direct customer whose accounts receivable balance represented 11% of total accounts receivable as of December 31, 2015. No direct customer represented more than 10% of total accounts receivable as of September 30, 2016.

See Note 10, “Segment and Significant Concentrations,” for disclosure regarding total sales to direct customers and single countries.

8

Inventory, net

Inventory is stated at the lower of standard cost (which approximates actual cost) or market value, with cost determined on the first-in-first-out method. The allocation of production overhead to inventory costs is based on normal production capacity. Abnormal amounts of idle facility expense, freight, handling costs, and spoilage are expensed as incurred, and not included in overhead. The Company maintains provisions for excess and obsolete inventory based on management’s estimates of forecasted demand and, where applicable, product expiration.

The components of inventories were as follows (in thousands):

	September 30, 2016		December 31, 2015
Raw Materials	$	44,108	$	39,267
Work in Process	66,097		62,153
Finished Goods	45,515		47,270
Inventory, net	$	155,720	$	148,690

In addition, capitalized stock-based compensation expense of $2.3 million and $2.5 million were included in inventory as of September 30, 2016 and December 31, 2015, respectively.

Revenue Recognition

The Company recognizes revenue from sales when there is persuasive evidence that an arrangement exists, delivery has occurred, the price is fixed or determinable, and collectability is reasonably assured. No right of return exists for the Company’s products except in the case of damaged goods. The Company has not experienced any significant returns of its products. Shipping and handling costs are expensed as incurred and included in cost of sales. In those cases where the Company bills shipping and handling costs to customers, the amounts billed are classified as revenue. The Company sells service contracts for which revenue is deferred and recognized ratably over the contract period.

The Company enters into revenue arrangements that may consist of multiple deliverables of its products and services. In situations with multiple deliverables, revenue is recognized upon the delivery of the separate elements.

For multiple element arrangements, the total consideration for an arrangement is allocated among the separate elements in the arrangement based on a selling price hierarchy. The selling price hierarchy for a deliverable is based on: (1) vendor specific objective evidence (“VSOE”), if available; (2) third party evidence of selling price if VSOE is not available; or (3) an estimated selling price, if neither VSOE nor third party evidence is available. Estimated selling price is the Company's best estimate of the selling price of an element in a transaction. The Company limits the amount of revenue recognized for delivered elements to the amount that is not contingent on the future delivery of products or services or other future performance obligations. For sales that include customer-specified acceptance criteria, revenue is recognized after the acceptance criteria have been met.

The Company may place an instrument at a customer site under a reagent rental agreement ("reagent rental"). Under a reagent rental, the Company retains title to the instrument and earns revenue for the usage of the instrument and related maintenance services through the amount charged for reagents and other disposables. Under a reagent rental, a customer may commit to purchasing minimum quantities of reagents at stated prices over a defined contract term, which is typically between three and five years. Revenue is recognized over the term of a reagent rental as reagents and other disposables are shipped and all other revenue recognition criteria have been met. All revenue recognized from reagent rentals is included in reagent and disposable sales in Note 10, “Segment and Significant Concentrations”.

Revenue includes fees for research and development services earned under grants and collaboration agreements, which are recognized on a contract-specific basis. Revenue and profit under cost-plus service contracts are recognized as costs are incurred plus negotiated fees. For certain contracts, the Company utilizes the proportional performance method of revenue recognition, which requires that the Company estimate the total amount of costs to be expended for a project and recognize revenue equal to the portion of costs incurred to date. The Company exercises judgment when estimating the level of effort required to complete a project. The estimated total costs to complete a project are subject to revision from time-to-time.

9

Earnings Per Share

Basic earnings per share is computed by dividing net income or loss for the period by the weighted average number of common shares outstanding during the period. Diluted net income per share is computed by dividing net income for the period by the weighted average number of common shares outstanding and common equivalent shares from dilutive stock options, employee stock purchases, restricted stock awards, restricted stock units and shares issuable upon a potential conversion of the convertible senior notes, using the treasury stock method. In loss periods, the earnings per share calculation excludes all common equivalent shares because their inclusion would be antidilutive. Antidilutive common equivalent shares totaled 10,439,000 and 9,007,000 for the three months ended September 30, 2016 and 2015, respectively, and 11,361,000 and 8,771,000 for the nine months ended September 30, 2016 and 2015, respectively.

The following summarizes the computation of basic and diluted net loss per share (in thousands, except for per share amounts):

	Three Months Ended September 30,						Nine Months Ended September 30,
	2016			2015			2016			2015
Basic:
Net loss	$	(10,907	)	$	(22,901	)	$	(27,740	)	$	(38,725	)
Basic weighted shares outstanding	73,158			72,199			72,890			71,777
Net loss per share	$	(0.15	)	$	(0.32	)	$	(0.38	)	$	(0.54	)
Diluted:
Net loss	$	(10,907	)	$	(22,901	)	$	(27,740	)	$	(38,725	)
Basic weighted shares outstanding	73,158			72,199			72,890			71,777
Effect of dilutive securities:
Stock options, ESPP, restricted stock units, restricted stock awards and convertible senior notes	—			—			—			—
Diluted weighted shares outstanding	73,158			72,199			72,890			71,777
Net loss per share	$	(0.15	)	$	(0.32	)	$	(0.38	)	$	(0.54	)

Recent Accounting Pronouncements

In August 2016, the Financial Accounting Standards Board (“FASB") issued Accounting Standards Update (“ASU") No. 2016-15, Classification of Certain Cash Receipts and Cash Payments. This ASU addresses how certain cash receipts and cash payments are presented and classified in the statement of cash flows under Topic 230, Statement of Cash flow, and other Topics. The requirements of this ASU are effective for annual reporting periods, and interim periods therein, beginning after December 15, 2017. The Company is currently assessing the impact of this ASU on its financial statements.

In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments. This ASU amends the impairment model to utilize an expected loss methodology in place of the currently used incurred loss methodology, which will result in the more timely recognition of losses. The requirements of this ASU are effective for interim and annual reporting periods beginning after December 15, 2019. The Company is currently assessing the impact of this ASU on its financial statements.

In March 2016, the FASB issued ASU No. 2016-09, Improvements to Employee Share-Based Payment Accounting. This ASU affects entities that issue share-based payment awards to their employees. The ASU is designed to simplify several aspects of accounting for share-based payment award transactions which include – the income tax consequences, classification of awards as either equity or liabilities, classification on the statement of cash flows and forfeiture rate calculations. The ASU is effective for fiscal years and interim periods within those years beginning after December 15, 2016. The Company is currently assessing the impact of this ASU on its financial statements.

10

In March 2016, the FASB issued ASU No. 2016-08, Revenue from Contracts with Customers: Principal versus Agent Considerations, which are intended to improve the operability and understandability of the implementation guidance on principal versus agent considerations. In April 2016, the FASB issued ASU 2016-10, Revenue from Contracts with Customers: Identifying Performance Obligations and Licensing, which clarified the implementation guidance on identifying promised goods or services and on evaluating whether an entity's promise to grant a license of intellectual property involves a right to use the entity's intellectual property (which is satisfied at a point in time) or a right to access the entity's intellectual property (which is satisfied over time). In May 2016, the FASB issued ASU 2016-11, Revenue Recognition and Derivatives and Hedging: Rescission of SEC Guidance Because of Accounting Standards Updates 2014-09 and 2014-16 Pursuant to Staff Announcements at the March 3, 2016 EITF Meeting, which rescinds certain SEC comments upon adoption of ASU 2014-09, including the SEC comments related to consideration given by a vendor to a customer. In May 2016, the FASB also issued ASU 2016-12, Revenue from Contracts with Customers: Narrow Scope Improvements and Practical Expedients, which provides narrow scope improvements and technical expedients on assessing collectability, presentation of sales taxes, evaluating contract modifications and completed contracts at transition and the disclosure requirement for the effect of the accounting change for the period of adoption. Collectively, all of these ASUs are intended to improve and clarify the implementation guidance of ASU No. 2014-09, Revenue from Contracts with Customers, and have the same effective date as the original standard. The Company is currently assessing the potential impact of this new guidance on its financial statements.

In March 2016, the FASB issued ASU No. 2016-06, Derivatives and Hedging: Contingent Put and Call Options in Debt Instruments. The amendments clarify the steps required to assess whether a call or put option meets the criteria for bifurcation as an embedded derivative. The ASU is effective for fiscal years and interim periods within those years beginning after December 15, 2016. The Company does not expect the adoption of this ASU to have a material impact on its financial statements.

In February 2016, the FASB issued ASU No. 2016-02, Leases. Under the new guidance, lessees will be required to recognize a lease liability and a right-of-use asset for all leases (with the exception of short-term leases) at the commencement date. The ASU is effective for fiscal years and interim periods within those years beginning after December 15, 2018. The Company is currently assessing the impact of this ASU on its financial statements.

In November 2015, the FASB issued ASU No. 2015-17, Income Taxes: Balance Sheet Classification of Deferred Taxes, which changes how deferred taxes are classified on the balance sheet. The ASU eliminates the current requirement for organizations to present deferred tax liabilities and assets as current and noncurrent in a classified balance sheet. Instead, organizations will be required to classify all deferred tax assets and liabilities as noncurrent. The Company early-adopted the provisions of this ASU as of December 31, 2015. The provisions have been applied prospectively and prior periods were not retrospectively adjusted, as permitted by the ASU.

In April 2015, the FASB issued ASU No. 2015-03, Interest – Imputation of Interest (Subtopic 835-30): Simplifying the Presentation of Debt Issuance Costs, which amends limited sections within ASC Subtopic 835-30. ASU No. 2015-03 requires an entity to present debt issuance costs in the balance sheet as a direct deduction from the related debt liability rather than an asset. Amortization of the costs will continue to be reported as interest expense. ASU No. 2015-03 is effective for annual reporting periods beginning after December 15, 2015. The Company adopted ASU No. 2015-03 on January 1, 2016, and applied its provisions retrospectively for each period presented. The adoption of ASU No. 2015-03 resulted in the reclassification of approximately $6 million of unamortized debt issuance costs related to the Company's convertible senior notes from other non-current assets to convertible senior notes, net within our condensed consolidated balance sheets as of June 30, 2016 and December 31, 2015. Other than this reclassification, the adoption of ASU No. 2015-03 did not have an impact on the Company's condensed consolidated financial statements.

In May 2014, the FASB issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606), which supersedes the revenue recognition requirements in ASC 605, Revenue Recognition. The core principal of ASU No. 2014-09 is to recognize revenue at an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. The ASU also requires additional disclosure about the nature, amount, timing, and uncertainty of revenue and cash flows arising from customer contracts, including significant judgments, and changes in judgments and assets recognized from costs incurred to obtain or fulfill a contract. The effective date will be the first quarter of fiscal year 2018 using one of two retrospective transition methods. The Company has not yet selected a transition method nor has it determined the potential effects that the adoption of ASU No. 2014-09 will have on its consolidated financial statements.

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2. Fair Value

During the three months ended September 30, 2016, the Company classified all investments, which are not considered cash equivalents as short-term investments as management no longer has the intent to hold such investments until their expected maturity. As a result, the Company reclassified less than $0.1 million of unrealized investment losses to the statement of operations as a component of other income (expense) in the Condensed Consolidated Statements of Operations.

The following table summarizes the fair value hierarchy for the Company’s financial assets (cash, cash equivalents, short-term investments, non-current investments, and foreign currency derivatives) and financial liabilities (foreign currency derivatives) measured at fair value on a recurring basis as of September 30, 2016 and December 31, 2015 (in thousands):

Balance as of September 30, 2016:
	Level 1		Level 2		Level 3		Total
Assets:
Cash and cash equivalents	$	90,126	$	25,592	$	—	$	115,718
Short-term investments:
Asset-backed securities	—		58,975		—		58,975
Corporate debt securities	—		96,125		—		96,125
Commercial paper	—		90,341		—		90,341
Other securities	—		8,016		—		8,016
Total short-term investments	—		253,457		—		253,457
Foreign currency derivatives	—		1,109		—		1,109
Total	$	90,126	$	280,158	$	—	$	370,284
Liabilities:
Foreign currency derivatives	$	—	$	2,612	$	—	$	2,612
Total	$	—	$	2,612	$	—	$	2,612

Balance as of December 31, 2015:
	Level 1		Level 2		Level 3		Total
Assets:
Cash and cash equivalents	$	84,625	$	27,943	$	—	$	112,568
Short-term investments:
Asset-backed securities	—		51,973		—		51,973
Corporate debt securities	—		81,600		—		81,600
Commercial paper	—		48,762		—		48,762
Government agency securities	—		12,684		—		12,684
Other securities	—		15,128		—		15,128
Total short-term investments	—		210,147		—		210,147
Foreign currency derivatives	—		1,431		—		1,431
Investments:
Asset-backed securities	—		11,818		—		11,818
Corporate debt securities	—		36,414		—		36,414
Government agency securities	—		11,944		—		11,944
Other securities	—		1,999		—		1,999
Total investments	—		62,175		—		62,175
Total	$	84,625	$	301,696	$	—	$	386,321
Liabilities:
Foreign currency derivatives	$	—	$	1,298	$	—	$	1,298
Total	$	—	$	1,298	$	—	$	1,298

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The estimated fair values of the Company’s other financial instruments which are not measured at fair value on a recurring basis as of September 30, 2016 and December 31, 2015 were as follows (in thousands):

Balance as of September 30, 2016:
	Level 1		Level 2		Level 3		Total
Liabilities:
Convertible senior notes	$	—	$	355,350	$	—	$	355,350
Total	$	—	$	355,350	$	—	$	355,350

Balance as of December 31, 2015:
	Level 1		Level 2		Level 3		Total
Liabilities:
Convertible senior notes	$	—	$	307,481	$	—	$	307,481
Total	$	—	$	307,481	$	—	$	307,481

The Company utilized levels 1 and 2 to value its financial assets on a recurring basis. Level 1 instruments use quoted prices in active markets for identical assets or liabilities, which include the Company’s cash accounts, short-term deposits, and money market funds as these specific assets are liquid. Level 2 instruments are valued using the market approach, which uses quoted prices in markets that are not active or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities. Level 2 instruments include asset-backed securities, corporate debt securities, commercial paper, government agency securities, and other securities, as similar or identical instruments can be found in active markets.

The Company recorded derivative assets and liabilities at fair value. The Company’s derivatives consist of foreign exchange forward contracts. The Company has elected to use the income approach to value the derivatives, using observable Level 2 market expectations at the measurement date and standard valuation techniques to convert future amounts to a single present amount assuming that participants are motivated, but not compelled to transact.

Level 2 inputs for the valuations are limited to quoted prices for similar assets or liabilities in active markets (specifically foreign currency spot rate and forward points) and inputs other than quoted prices that are observable for the asset or liability (specifically LIBOR rates, credit default spot rates, and company specific LIBOR spread). Mid-market pricing is used as a practical expedient for fair value measurements. The fair value measurement of an asset or liability must reflect the nonperformance risk of the entity and the counterparty. Therefore, the impact of the counterparty’s creditworthiness when in an asset position and the Company’s creditworthiness when in a liability position has also been factored into the fair value measurement of the derivative instruments and did not have a material impact on the fair value of these derivative instruments. Both the counterparty and the Company are expected to continue to perform under the contractual terms of the instruments. The estimated fair value of the convertible senior notes, which have been classified as Level 2 financial instruments, was determined based on the quoted price of the convertible senior notes in an over-the-counter market on September 30, 2016.

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3. Investments

The Company’s marketable securities as of September 30, 2016, were classified as available-for-sale securities, with changes in fair value recognized in Accumulated Other Comprehensive Income ("AOCI"), a component of shareholders’ equity. As discussed in Note 2 of Notes to Condensed Consolidated Financial Statements, the Company classified all investments, which are not considered cash equivalents as short-term investments as management no longer has the intent to hold such investments until their expected maturity.

The following tables summarize available-for-sale marketable securities (in thousands):

Balance as of September 30, 2016:
	Cost			Gross Unrealized Gain			Gross Unrealized Loss		Estimated Fair Value
Short-term investments:
Asset-backed securities	$	58,914		$	61		$	—	$	58,975
Commercial paper	115,902			31			—		115,933
Corporate debt securities	96,017			108			—		96,125
Other securities	8,000			16			—		8,016
Amounts classified as cash equivalents	(25,586		)	(6		)	—		(25,592		)
Total short-term investments	$	253,247		$	210		$	—	$	253,457

Balance as of December 31, 2015:
	Cost			Gross Unrealized Gain		Gross Unrealized Loss			Estimated Fair Value
Short-term investments:
Asset-backed securities	$	52,102		$	—	$	(129	)	$	51,973
Commercial paper	76,711			3		(9		)	76,705
Corporate debt securities	81,777			—		(177		)	81,600
Government agency securities	12,701			—		(17		)	12,684
Other securities	15,122			7		(1		)	15,128
Amounts classified as cash equivalents	(27,943		)	—		—			(27,943		)
Total short-term investments	$	210,470		$	10	$	(333	)	$	210,147
Investments:
Asset-backed securities	$	11,884		$	—	$	(66	)	$	11,818
Corporate debt securities	36,530			3		(119		)	36,414
Government agency securities	11,999			—		(55		)	11,944
Other securities	2,001			—		(2		)	1,999
Total investments	$	62,414		$	3	$	(242	)	$	62,175

Proceeds from the sale of marketable securities were $86.3 million and $49.2 million for the nine months ended September 30, 2016 and 2015, respectively. The Company determines gains and losses from sales of marketable securities based on specific identification of the securities sold. Realized gains and realized and unrealized losses from sales of marketable securities, all of which are reported as a component of other income (expense) in the Condensed Consolidated Statements of Operations, were immaterial for the three and nine months ended September 30, 2016 and 2015.

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As discussed in Note 2 of Notes to Condensed Consolidated Financial Statements, the Company classified all investments, which are not considered cash equivalents as short-term investments as management no longer has the intent to hold such investments until their expected maturity. As a result, the Company recognized less than $0.1 million of unrealized investment losses to the statement of operations as a component of other income (expense) in the Condensed Consolidated Statements of Operations.

The following table summarizes the fair value of the Company’s marketable securities with unrealized losses at December 31, 2015, and the duration of time that such losses had been unrealized (in thousands):

Balance as of December 31, 2015:
	Less Than 12 months					More than 12 months					Total
	Fair Value		Unrealized Loss			Fair Value		Unrealized Loss			Fair Value		Unrealized Loss
Asset-backed securities	$	57,866	$	(192	)	$	5,923	$	(3	)	$	63,789	$	(195	)
Corporate debt securities	101,701		(289		)	8,911		(7		)	110,612		(296		)
Government agency securities	24,628		(72		)	—		—			24,628		(72		)
Commercial Paper	11,374		(9		)	—		—			11,374		(9		)
Other securities	7,496		(3		)	—		—			7,496		(3		)
Total	$	203,065	$	(565	)	$	14,834	$	(10	)	$	217,899	$	(575	)

The Company evaluated marketable securities, which consist of investments in asset-backed securities, corporate debt securities, government agency securities, commercial paper, and other securities as of December 31, 2015, and has determined that there was no indication of other-than-temporary impairments. This determination was based on several factors, including the length of time and extent to which fair value has been less than the cost basis, the financial condition and near-term prospects of the debt issuer, and the Company’s intent and ability to hold the securities for a period of time sufficient to allow for any anticipated recovery in market value.

The following table summarizes the amortized cost and estimated fair value of available-for-sale debt securities at September 30, 2016 and December 31, 2015, by contractual maturity (in thousands):

	September 30, 2016				December 31, 2015
	Amortized Cost		Estimated Fair Value		Amortized Cost		Estimated Fair Value
Mature in one year or less	$	194,917	$	194,997	$	186,311	$	186,118
Mature after one year through three years	75,623		75,750		106,377		106,086
Mature in more than three years	8,293		8,302		8,139		8,061
Total	$	278,833	$	279,049	$	300,827	$	300,265

4. Derivative Financial Instruments

The Company uses derivatives to partially offset its exposure to foreign currency exchange risk. The Company may enter into foreign currency forward contracts to offset some of the foreign exchange risk on expected future cash flows on certain forecasted revenue and expenses and on certain existing assets and liabilities.

To address fluctuations in foreign currency exchange rates, a portion of forecasted foreign currency revenue and expenses of certain of the Company’s subsidiaries are hedged. The Company hedges portions of its forecasted foreign currency exposure associated with revenue, cost of sales, and operating expenses for generally up to twelve months.

The Company may also enter into foreign currency forward contracts to partially offset the foreign currency exchange gains and losses generated by the re-measurement of certain assets and liabilities. However, the Company may choose not to hedge certain foreign currency exchange exposures for a variety of reasons including, but not limited to, accounting considerations and the prohibitive economic cost of hedging particular exposures. The Company does not hold or purchase any currency contracts for trading purposes.

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The Company records all derivatives in the Condensed Consolidated Balance Sheet at fair value. The Company’s accounting treatment of these instruments is based on whether the instruments are designated as hedge or non-hedge instruments. For derivative instruments that are designated and qualify as cash flow hedges, the Company initially records the effective portion of the gain or loss on the derivative instrument in AOCI, a separate component of shareholders’ equity and subsequently reclassifies these amounts into earnings within the same financial statement line item as the hedged item in the period during which the hedged transaction is recognized in earnings. The ineffective portions of cash flow hedges are recorded in foreign currency exchange gain (loss) and other, net.

The Company had a net deferred loss of $1.4 million and net deferred loss of $0.4 million associated with cash flow hedges recorded in AOCI as of September 30, 2016 and December 31, 2015, respectively. Deferred gains and losses associated with cash flow hedges of forecasted foreign currency revenue are recognized as a component of revenues in the same period as the related revenue is recognized, and deferred gains and losses related to cash flow hedges of forecasted expenses are recognized as a component of cost of sales, research and development expense, sales and marketing expense and general and administrative expense in the same period as the related expenses are recognized. The Company’s hedged transactions as of September 30, 2016 are expected to occur within twelve months.

Derivative instruments designated as cash flow hedges must be de-designated as hedges when it is probable that the forecasted hedged transaction will not occur in the initially identified time period or within a subsequent two-month time period. Deferred gains and losses in AOCI associated with such derivative instruments are reclassified immediately into foreign currency exchange loss and other, net. Any subsequent changes in fair value of such derivative instruments are reflected in foreign currency exchange gain (loss) and other, net unless they are re-designated as hedges of other transactions. The Company did not recognize any significant net gains or losses related to the loss of hedge designation on discontinued cash flow hedges during the three and nine months ended September 30, 2016 and 2015.

Gains or losses on derivatives not designated as hedging instruments are recorded in foreign currency exchange gain (loss) and other, net. During the three months ended September 30, 2016 and 2015, the Company recognized a loss of $2.4 million and a gain of $2.3 million, respectively, as a component of foreign currency exchange gain (loss) and other, net, related to derivative instruments not designated as hedging instruments. During the nine months ended September 30, 2016 and 2015, the Company recognized a loss of $2.9 million and a gain of $4.0 million, respectively, as a component of foreign currency exchange gain (loss) and other, net, related to derivative instruments not designated as hedging instruments. These amounts represent the net gain or loss on the derivative contracts and do not include changes in the related exposures or ineffective portion or amounts excluded from the effectiveness testing of cash flow hedges.

The notional principal amounts of the Company’s outstanding derivative instruments designated as cash flow hedges are $91.0 million and $117.6 million as of September 30, 2016 and December 31, 2015, respectively. The notional principal amount of the Company’s outstanding derivative instruments not designated as cash flow hedges was $25.9 million as of December 31, 2015. There was no outstanding derivative instruments not designated as cash flow hedges as of September 30, 2016.

The following tables show the Company’s derivative instruments at gross fair value as reflected in the Condensed Consolidated Balance Sheets as of September 30, 2016 and December 31, 2015, respectively (in thousands):

	September 30, 2016
	Fair Value of Derivatives Designated as Hedge Instruments			Fair Value of Derivatives Not Designated as Hedge Instruments		Total Fair Value
Derivative Assets (a):
Foreign exchange contracts	$	1,109		$	—	$	1,109
Derivative Liabilities (b):
Foreign exchange contracts	(2,612		)	—		(2,612		)

	December 31, 2015
	Fair Value of Derivatives Designated as Hedge Instruments			Fair Value of Derivatives Not Designated as Hedge  Instruments			Total Fair Value
Derivative Assets (a):
Foreign exchange contracts	$	1,390		$	41		$	1,431
Derivative Liabilities (b):
Foreign exchange contracts	(1,250		)	(48		)	(1,298		)

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(a) The fair value of derivative assets is measured using Level 2 fair value inputs and is recorded as prepaid expenses and other current assets in the Condensed Consolidated Balance Sheets.

(b) The fair value of derivative liabilities is measured using Level 2 fair value inputs and is recorded as accrued and other liabilities in the Condensed Consolidated Balance Sheets.

The following tables show the pre-tax effect of the Company’s derivative instruments designated as cash flow hedges in the Condensed Consolidated Statements of Operations for the three and nine month periods ended September 30, 2016 and 2015 (in thousands):

	Three Months Ended September 30,
	Loss Recognized in OCI - Effective Portion						Loss Reclassified from AOCI into Income - Effective Portion						Loss Recognized - Ineffective Portion and Amount Excluded from Effectiveness Testing
	2016			2015			2016 (a)			2015 (b)			Location	2016			2015
Cash flow hedges:
Foreign exchange contracts	$	(1,804	)	$	(545	)	$	(320	)	$	(369	)	Foreign currency exchange loss and other, net	$	(141	)	$	(45	)
Total	$	(1,804	)	$	(545	)	$	(320	)	$	(369	)		$	(141	)	$	(45	)

(a) Includes gains and losses reclassified from AOCI into net loss for the effective portion of cash flow hedges, of which a $0.3 million loss within costs and operating expenses and less than a $0.1 million gain within revenue, were recognized within the Condensed Consolidated Statement of Operations for the three months ended September 30, 2016.

(b) Includes gains and losses reclassified from AOCI into net loss for the effective portion of cash flow hedges, of which a $1.2 million loss within costs and operating expenses and a $1.5 million gain within revenue, were recognized within the Condensed Consolidated Statement of Operations for the three months ended September 30, 2015.

	Nine Months Ended September 30,
	Loss Recognized in OCI- Effective Portion						Loss Reclassified from AOCI into Income - Effective Portion						Loss Recognized - Ineffective Portion and Amount Excluded from Effectiveness Testing
	2016			2015			2016 (a)			2015 (b)			Location	2016			2015
Cash flow hedges:
Foreign exchange contracts	$	(1,949	)	$	(1,596	)	$	(1,006	)	$	(414	)	Foreign currency exchange loss and other, net	$	(491	)	$	(169	)
Total	$	(1,949	)	$	(1,596	)	$	(1,006	)	$	(414	)		$	(491	)	$	(169	)

(a) Includes gains and losses reclassified from AOCI into net income for the effective portion of cash flow hedges, of which a $1.0 million loss within costs and operating expenses and a less than $0.1 million loss within revenue, were recognized within the Condensed Consolidated Statement of Operations for the nine months ended September 30, 2016.

(b) Includes gains and losses reclassified from AOCI into net loss for the effective portion of cash flow hedges, of which a $6.6 million loss within costs and operating expenses and a $6.2 million gain within revenue, were recognized within the Condensed Consolidated Statement of Operations for the nine months ended September 30, 2015.

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5. Intangible Assets

Intangible assets related to licenses are recorded at cost, less accumulated amortization. Intangible assets related to technology and other intangible assets acquired in acquisitions are recorded at fair value at the date of acquisition, less accumulated amortization. Intangible assets are amortized over their estimated useful lives, ranging from 3 to 15 years, on a straight-line basis. Amortization of intangible assets is primarily included in cost of sales, research and development and sales and marketing in the Condensed Consolidated Statements of Operations.

The recorded value and accumulated amortization of major classes of intangible assets were as follows (in thousands):

	Gross Carrying Amount		Accumulated Amortization			Net Carrying Amount
Balance, September 30, 2016
Licenses	$	11,256	$	(7,859	)	$	3,397
Technology acquired in acquisitions	8,613		(8,613		)	—
Customer relationships and other intangible assets acquired in acquisitions	35,849		(18,290		)	17,559
	$	55,718	$	(34,762	)	$	20,956
Balance, December 31, 2015
Licenses	$	11,454	$	(7,280	)	$	4,174
Technology acquired in acquisitions	8,613		(8,613		)	—
Customer relationships and other intangible assets acquired in acquisitions	35,849		(14,782		)	21,067
	$	55,916	$	(30,675	)	$	25,241

Intangible asset amortization expense was $1.4 million and $1.5 million for the three months ended September 30, 2016 and 2015, respectively, and $4.3 million and $4.8 million for the nine months ended September 30, 2016 and 2015, respectively. The following table summarizes the expected future annual amortization expense of intangible assets recorded on the Company’s Condensed Consolidated Balance Sheet as of September 30, 2016, assuming no impairment charges (in thousands):

For the Years Ending December 31,	Amortization Expense
2016 (remaining three months)	$	1,426
2017	5,343
2018	5,260
2019	4,235
2020	3,891
Thereafter	801
Total expected future amortization	$	20,956

6. Income Taxes

Effective December 31, 2015, the Company early-adopted ASU No. 2015-17, Income Taxes: Balance Sheet Classification of Deferred Taxes, which changes how deferred taxes are classified on the balance sheet. The ASU eliminates the current requirement for organizations to present deferred tax liabilities and assets as current and noncurrent in a classified balance sheet. Instead, organizations will be required to classify all deferred tax assets and liabilities as noncurrent. The provisions have been applied on a prospective basis and prior periods were not retrospectively adjusted, as permitted by the ASU.

For the three and nine months ended September 30, 2016, the Company recorded an income tax expense of $1.2 million and $2.0 million, respectively, primarily related to ordinary tax expense of the Company’s foreign subsidiaries. For the three and nine months ended September 30, 2015, the Company recorded an income tax benefit of $0.2 million and tax expense of $0.6 million, respectively, comprised primarily of ordinary foreign tax expense of the Company’s foreign subsidiaries, partially offset by the tax effect of items in accumulated other comprehensive loss, net.

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The Company’s effective tax rate for the three and nine months ended September 30, 2016 and 2015 differs from the statutory federal income tax rate of 34%, primarily due to the impact of operations in foreign jurisdictions, as well as income or loss in the United States federal and state jurisdictions for which no tax expense or benefit is recorded. There is a difference in the effective tax rate for the three and nine months ended September 30, 2016, compared to the three and nine months ended September 30, 2015, which is primarily due to levels of losses in the United States for which no income tax benefit was recorded in relation to income generated in foreign jurisdictions.

The Company utilizes the liability method of accounting for income taxes. Under the liability method, deferred taxes are determined based on the temporary differences between the financial statement and tax bases of assets and liabilities using enacted tax rates. The Company’s position is to record a valuation allowance when it is more likely than not that some of the deferred tax assets will not be realized. Based on all available objective evidence, the Company believes that it is more likely than not that the net United States deferred tax assets will not be fully realized. Accordingly, the Company continues to maintain a full valuation allowance on its United States deferred tax assets and will do so until there is sufficient evidence to support the reversal of all or some portion of this valuation allowance.

The Company or one of its subsidiaries files income tax returns in the United States federal jurisdiction and various state and foreign jurisdictions. The Company’s United States and state income tax return years 1996 through 2015 remain open to examination. In addition, the Company files tax returns in multiple foreign taxing jurisdictions with open tax years ranging from 2010 to 2015.

The Company anticipates that the total unrecognized tax benefits will not significantly change within the next 12 months due to the settlement of audits and the expiration of statutes of limitations.

The Company recognizes interest and penalties related to uncertain tax positions in income tax expense. For the three and nine months ended September 30, 2016 and 2015, the Company did not recognize any significant interest or penalties related to uncertain tax positions, nor had any been accrued for as of September 30, 2016 and December 31, 2015.

7. Convertible Senior Notes

In February 2014, the Company issued $345 million aggregate principal amount of 1.25% convertible senior notes (the “Notes”) due February 1, 2021, unless earlier repurchased by the Company or converted by the holder pursuant to their terms. Interest is payable semiannually in arrears on February 1 and August 1 of each year, commencing on August 1, 2014.

The Notes are governed by an Indenture between the Company, as issuer, and Wells Fargo Bank, National Association, as trustee. The Notes are unsecured and rank: senior in right of payment to the Company’s future indebtedness that is expressly subordinated in right of payment to the Notes; equal in right of payment to the Company’s existing and future indebtedness that is not so subordinated; effectively subordinated in right of payment to any of the Company’s secured indebtedness to the extent of the value of the assets securing such indebtedness; and structurally subordinated to all existing and future indebtedness and other liabilities incurred by the Company’s subsidiaries.

Upon conversion, the Company will pay or deliver, as the case may be, cash, shares of the Company’s common stock or a combination of cash and shares of common stock, at the Company’s election.

The Notes have an initial conversion rate of 15.3616 shares of common stock per $1,000 principal amount of Notes. This represents an initial effective conversion price of approximately $65.10 per share of common stock and approximately 5,300,000 shares upon conversion. Throughout the term of the Notes, the conversion rate may be adjusted upon the occurrence of certain events. Holders of the Notes will not receive any cash payment representing accrued and unpaid interest, if any, upon conversion of a Note, except in limited circumstances. Accrued but unpaid interest will be deemed to be paid by the cash, shares of the Company’s common stock or a combination of cash and shares of the Company’s common stock paid or delivered, as the case may be, to the holder upon conversion of a Note.

Prior to the close of business on the business day immediately preceding August 1, 2020, the Notes will be convertible at the option of holders during certain periods, only upon satisfaction of certain conditions set forth below. On or after August 1, 2020, until the close of business on the second scheduled trading day immediately preceding the maturity date, holders may convert all or any portion of their Notes at the conversion rate at any time regardless of whether the conditions set forth below have been met.

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Holders may convert all or a portion of their Notes prior to the close of business on the business day immediately preceding August 1, 2020, in multiples of $1,000 principal amount, only under the following circumstances:

• during any calendar quarter commencing after the calendar quarter ending on March 31, 2014 (and only during such calendar quarter), if the last reported sale price of the Company’s common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day;

• during the five business day period after any five consecutive trading day period (the “Notes Measurement Period”) in which the “trading price” (as the term is defined in the Indenture) per $1,000 principal amount of notes for each trading day of such Notes Measurement Period was less than 98% of the product of the last reported sale price of the Company’s common stock on such trading day and the conversion rate on each such trading day; or

• upon the occurrence of specified corporate events.

As of September 30, 2016, the Notes were not yet convertible.

Based on market data available for publicly traded, senior, unsecured corporate bonds issued by companies in the same industry and with similar maturity, the Company estimated the implied interest rate of its Notes to be approximately 5.0%, assuming no conversion option. Assumptions used in the estimate represent what market participants would use in pricing the liability component, including market interest rates, credit standing, and yield curves, all of which are defined as Level 2 observable inputs. The estimated implied interest rate was applied to the Notes, which resulted in a fair value of the liability component of $270 million upon issuance, calculated as the present value of implied future payments based on the $345 million aggregate principal amount. The excess of the principal amount of the liability component over its carrying amount (“debt discount”) is amortized to interest expense over the term of the Notes. The $75 million difference between the aggregate principal amount of $345 million and the estimated fair value of the liability component was recorded in additional paid-in capital as the Notes were not considered redeemable.

In accounting for the transaction costs related to the issuance of the Notes, the Company allocated the total amount incurred to the liability and equity components based on their estimated relative fair values. Transaction costs attributable to the liability component, totaling $7.2 million, are being amortized to expense over the term of the Notes, and transaction costs attributable to the equity component, totaling $2.0 million, and were netted with the equity component in shareholders’ equity.

The Notes consist of the following (in thousands):

	September 30, 2016			December 31, 2015
Liability component:
Principal	$	345,000		$	345,000
Less: debt discount, net of amortization and reclassification of debt issuance costs	(55,242		)	(63,373		)
Net carrying amount	$	289,758		$	281,627
Equity component (a)	$	73,013		$	73,013

(a) Recorded in the condensed consolidated balance sheets within additional paid-in capital, net of $2.0 million issuance costs in equity

The following table sets forth total interest expense recognized related to the Notes (in thousands):

	Three Months Ended September 30,				Nine Months Ended September 30,
	2016		2015		2016		2015
1.25% coupon	$	1,078	$	1,078	$	3,234	$	3,234
Amortization of debt issuance costs	203		157		573		435
Amortization of debt discount	2,551		2,427		7,558		7,193
	$	3,832	$	3,662	$	11,365	$	10,862

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As of September 30, 2016 and December 31, 2015, the fair value of the Notes, which was determined based on inputs that are observable in the market or that could be derived from, or corroborated with, observable market data, quoted price of the Notes in an over-the-counter market (Level 2), and carrying value of debt instruments (carrying value excludes the equity component of the Company’s convertible notes classified in equity) were as follows (in thousands):

	September 30, 2016				December 31, 2015
	Fair Value		Carrying Value		Fair Value		Carrying Value
Convertible Senior Notes	$	355,350	$	289,758	$	307,481	$	281,627

In connection with the issuance of the Notes, the Company entered into capped call transactions with certain counterparties affiliated with the initial purchasers and others. The capped call transactions are expected to reduce potential dilution of earnings per share upon conversion of the Notes. Under the capped call transactions, the Company purchased capped call options that in the aggregate relate to the total number of shares of the Company’s common stock underlying the Notes, with an initial strike price of approximately $65.10 per share, which corresponds to the initial conversion price of the Notes and is subject to anti-dilution adjustments substantially similar to those applicable to the conversion rate of the Notes, and have a cap price of approximately $78.61. The cost of the purchased capped calls of $25.1 million was recorded to shareholders’ equity and will not be re-measured.

Based on the closing price of our common stock of $52.69 on September 30, 2016, the if-converted value of the Notes was less than their respective principal amounts.

On September 2, 2016, Cepheid entered into the Merger Agreement with Danaher. At the effective time of the Merger, holders of the Company's $345 million aggregate principal amount of Notes shall have the right to convert such Notes into conversion consideration pursuant to the terms of the indenture under which the Notes were issued. In connection with the closing of the Merger, the capped call transactions will also be settled pursuant to the terms thereof.

8. Commitments, Contingencies and Legal Matters

Purchase Commitments

The following table summarizes the Company’s purchase commitments at September 30, 2016 (in thousands):

Years Ending December 31,	Purchase Commitments
2016 (remaining three months)	$	25,273
2017	3,230
2018	—
2019	—
2020	—
Thereafter	—
Total minimum payments	$	28,503

Purchase commitments include non-cancellable purchase orders or contracts for the purchase of raw materials used in the manufacturing of the Company’s reagents and orders for purchase of systems and system modules.

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Legal Matters

In May 2005, the Company entered into a license agreement with F. Hoffmann-La Roche Ltd. and Roche Molecular Systems, Inc. (“Roche”) that provided the Company with rights under a broad range of Roche patents, including patents relating to the polymerase chain reaction ("PCR") process, reverse transcription-based methods, nucleic acid quantification methods, real-time PCR detection process and composition, and patents relating to methods for detection of viral and cancer targets. A number of the licensed patents expired in the United States prior to the end of August of 2010 and in Europe prior to the end of August of 2011. In August 2010, the Company terminated the Company’s license to United States Patent No. 5,804,375 (the “375 Patent”) and ceased paying United States-related royalties. The Company terminated the entire license agreement in the fourth quarter of 2011. In August 2011, Roche initiated an arbitration proceeding against the Company in the International Chamber of Commerce pursuant to the terms of the terminated agreement. The Company filed an answer challenging arbitral jurisdiction over the issues submitted by Roche and denying that the Company violated any provision of the agreement. A three-member panel was convened to address these issues in confidential proceedings. On July 30, 2013, the panel determined that it had jurisdiction to decide the claims, a determination that the Company appealed to the Swiss Federal Supreme Court. On October 2, 2013, the arbitration panel determined that it would proceed with the arbitration while this appeal was pending. On February 27, 2014 the Swiss Federal Supreme Court upheld the jurisdiction of the arbitration panel to hear the case. On April 22, 2016, the arbitration panel transmitted a partial award holding that the Company was liable for damages for the manufacture and sale of certain accused products starting after the Company terminated the license until September 2015, with the final amount to be determined by audit. The partial award also denied Roche’s requests for an injunction, and allocated certain legal fees and costs between the parties.

Based on its ongoing evaluation of the facts and circumstances of the case, including the partial award, the Company believes that it is probable that this arbitration proceeding could result in a material loss. Accordingly, the Company recorded an estimated charge of $20 million as its best estimate of the potential loss as of December 31, 2014, which amount was included in accrued and other liabilities in the Company’s consolidated balance sheets. Taking into account the partial award, this continues to be the Company's best estimate for this potential loss as of September 30, 2016. Depending on the final ruling of the arbitrators, it is possible that the Company could also be responsible for certain fees, costs and/or interest, if any; however, the Company is unable at this time to determine the likelihood of whether these potential outcomes will occur or estimate their respective potential amounts.

On August 21, 2012 the Company filed a lawsuit against Roche in the United States District Court for the Northern District of California (“the Court”), for a declaratory judgment of (a) invalidity, expiration, and non-infringement of the 375 Patent; and (b) invalidity, unenforceability, expiration and non-infringement of United States Patent No. 6,127,155 (the “155 Patent”). On January 17, 2013, the Court issued an order granting a motion by Roche to stay the suit with respect to the 375 Patent pending resolution of the above noted arbitration proceeding. In the same order, the Court dismissed the Company’s suit with respect to the 155 Patent for lack of subject matter jurisdiction, without considering or ruling on the merits of the Company’s case. The Court left open the possibility that the Company could re-file its case against the 155 Patent in the future. The Company believes that the possibility that these legal proceedings will result in a material adverse effect on the Company’s business is remote.

On July 16, 2014 Roche filed a lawsuit in the Court, alleging that the Company’s Xpert MTB-RIF product infringes United States Patent No. 5,643,723 (the “723 Patent”), which expired on July 1, 2014. On September 15, 2014, the Company filed its answer and counterclaims denying Roche’s allegations of infringement and asking the Court to find the 723 Patent invalid, unenforceable, and not infringed. On November 10, 2014, the Company filed a petition for inter partes review (“IPR”) of the 723 Patent in the United States Patent and Trademark Office (the “USPTO”) and filed a motion with the Court to stay this lawsuit pending the outcome of the IPR. On January 7, 2015, the Court issued an order staying the lawsuit pending the outcome of the IPR. On March 16, 2015, the Company filed a second petition for IPR of an additional claim of the 723 Patent. On June 11, 2015, the USPTO issued a decision declining to institute the first requested IPR. On July 13, 2015, the Company filed a request for reconsideration of the first petition for IPR with respect to certain challenged claims. On September 16, 2015, the USPTO denied the request for reconsideration. On September 17, 2015, the USPTO decided to institute the Company's second petition for IPR. On May 18, 2016, the parties submitted a joint status update to the Court in which Roche stated that it had disclaimed and would not assert the claim the Company had challenged in the second petition for IPR. On May 20, 2016, the Court issued an order lifting the 2015 stay. On July 19, 2016, the Company filed a motion for summary judgment of patent ineligibility as to all asserted claims. The Court is scheduled to conduct an oral hearing on the motion on November 16, 2016, and the Company expects a decision on the motion by the end of 2016. The Company believes that the possibility that these legal proceedings will result in a material loss is remote.

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The Company may be subject to various additional claims, complaints and legal actions that arise from time to time in the normal course of business. Other than as described above, the Company does not believe it is party to any currently pending legal proceedings that will result in a material adverse effect on its business. There can be no assurance that existing or future legal proceedings arising in the ordinary course of business or otherwise will not have a material adverse effect on the Company’s business, consolidated financial position, results of operations or cash flows.

9. Employee Equity Incentive Plans and Stock-Based Compensation Expense

The following table is a summary of the major categories of stock-based compensation expense recognized in accordance with ASC 718, “Compensation—Stock Compensation” (“ASC 718”) for the three and nine months ended September 30, 2016 and 2015 (in thousands):

	Three Months Ended   September 30,				Nine Months Ended   September 30,
	2016		2015		2016		2015
Cost of sales	$	1,784	$	1,128	$	4,882	$	3,177
Research and development	2,765		3,438		7,709		7,913
Sales and marketing	2,207		1,825		6,237		5,018
General and administrative	4,057		3,584		10,878		9,694
Total stock-based compensation expense	$	10,813	$	9,975	$	29,706	$	25,802

The following table summarizes option activity under all plans (in thousands, except weighted average exercise price and weighted average remaining contractual term):

	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term (in years)	Intrinsic Value
Outstanding, December 31, 2015	5,442		$	39.46
Granted	1,282		$	34.54
Exercised	(352	)	$	13.31
Forfeited	(213	)	$	39.47
Outstanding, September 30, 2016	6,159		$	39.90	4.21	$	83,020
Exercisable, September 30, 2016	3,604		$	38.18	3.10	$	53,971
Vested and expected to vest, September 30, 2016	5,984		$	39.85	4.15	$	80,667

The following table summarizes all award activity, which consists of restricted stock awards and restricted stock units (in thousands, except weighted average grant date fair value):

	Shares		Weighted Average Grant Date Fair Value
Outstanding, December 31, 2015	1,000		$	48.44
Granted	669		34.05
Vested	(286	)	48.70
Cancelled	(69	)	45.75
Outstanding, September 30, 2016	1,314		$	41.20

Included in the restricted stock awards and restricted stock units granted during the nine months ended September 30, 2016 are 285,000 performance-based restricted stock units ("PRSUs"), which were granted to certain members of the Company's senior management team that vest upon the achievement of certain performance conditions, the performance period for which is the three-year period from January 1, 2016 to December 31, 2018. The number of PRSUs ultimately earned by each recipient will range from zero to 125% of the target PRSU number awarded to each recipient. Each PRSU will vest as to any earned PRSUs following determination and certification of the level of achievement of specified metrics by the Compensation Committee at the end of the performance period. To the extent earned, each PRSU will be settled by the issuance of one share of Cepheid common stock. Recipients of PRSUs generally must remain employed by Cepheid on a continuous basis through the end of the performance period in order to receive any amount of the PRSUs earned, except that recipients may be entitled to accelerated vesting of PRSUs in the case of the recipient’s death or disability or upon a change in control. In the proposed Merger with Danaher, the PRSUs will be treated as described in the Merger Agreement.

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The following table summarizes the assumptions used in determining the fair value of the Company’s stock options granted to employees and directors and shares purchased by employees under the Company’s 2012 Employee Stock Purchase Plan (“ESPP”):

	Three Months Ended   September 30,						Nine Months Ended   September 30,
	2016			2015			2016			2015
OPTION SHARES:
Expected Term (in years)	4.38			4.49			4.45			4.46
Volatility	0.47			0.36			0.44			0.36
Expected Dividends	—			—			—			—
Risk Free Interest Rates	1.14		%	1.54		%	1.38		%	1.46		%
Estimated Forfeitures	6.01		%	6.14		%	6.01		%	6.14		%
Weighted Average Fair Value Per Share	$	14.24		$	16.91		$	13.12		$	17.93
ESPP SHARES:
Expected Term (in years)	1.24			1.22			1.23			1.22
Volatility	0.52			0.34			0.49			0.34
Expected Dividends	—			—			—			—
Risk Free Interest Rates	0.54		%	0.41		%	0.59		%	0.39		%
Weighted Average Fair Value Per Share	$	13.63		$	16.50		$	10.20		$	16.49

10. Segment and Significant Concentrations

The Company and its wholly owned subsidiaries operate in one business segment.

The following table summarizes total revenue by type (in thousands):

	Three Months Ended September 30,				Nine Months Ended September 30,
	2016		2015		2016		2015
Revenue:
System and other revenue	$	27,496	$	19,749	$	76,618	$	62,823
Reagent and disposable revenue	130,992		106,716		372,651		328,754
Total revenue	$	158,488	$	126,465	$	449,269	$	391,577

The Company currently sells product through its direct sales force and through third-party distributors. No single customer or distributor accounted for more than 10% of total revenue for the three and nine months ended September 30, 2016 and 2015.

The following table summarizes revenue by geographic region (in thousands):

	Three Months Ended September 30,				Nine Months Ended September 30,
	2016		2015		2016		2015
Geographic revenue information:
North America	$	89,122	$	73,627	$	252,714	$	232,119
International	69,366		52,838		196,555		159,458
Total revenue	$	158,488	$	126,465	$	449,269	$	391,577

The Company recognized revenue of $87.2 million and $70.7 million for sales to United States customers for the three months ended September 30, 2016 and 2015, respectively, and $246.1 million and $220.3 million for the nine months ended September 30, 2016 and 2015, respectively.

No single country outside of the United States represented more than 10% of the Company’s total revenue for the three and nine months ended September 30, 2016 and 2015.

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The following table summarizes long-lived assets, excluding intangible assets and goodwill, by geographic region (in thousands):

	September 30, 2016		December 31, 2015
United States	$	129,966	$	108,210
Other regions	21,261		19,429
Total long-lived assets	$	151,227	$	127,639

The Company does not hold a significant amount of long-lived assets in any single country outside of the United States as of September 30, 2016 and December 31, 2015.

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

Forward-Looking Statements

This Quarterly Report on Form 10-Q, including this Management’s Discussion and Analysis of Financial Condition and Results of Operations contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended and Section 21E of the Securities Exchange Act of 1934, as amended that relate to future events or our future financial performance and the September 2, 2016 Agreement and Plan of Merger (the “Merger Agreement”) with Danaher Corporation (“Danaher”), and Copper Merger Sub, Inc., a wholly-owned subsidiary of Danaher and the anticipated timing and benefits of the merger contemplated thereby (the “Merger”). In some cases, you can identify forward-looking statements by terminology such as “may”, “will”, “should”, “expect”, “plan”, “anticipate”, “believe”, “estimate”, “intend”, “potential”, “project” or “continue” or the negative of these terms or other comparable terminology. Forward-looking statements are based upon current expectations that involve risks and uncertainties. Our actual results and the timing of events could differ materially from those anticipated in our forward-looking statements as a result of many factors, including, but not limited to, the following: consistency of product availability and delivery; the effectiveness of our sales personnel and our ability to successfully expand and effectively manage increased sales and marketing operations, including expansion of our direct sales force to address the smaller hospital market and the independent reference laboratory market and expansion of our United States sales organization; sales organization productivity and the productivity and effectiveness of our distributors; speed and extent of test menu expansion and utilization; the success of our cost reduction and gross margin improvement efforts; execution of manufacturing operations; our reliance on a single contract manufacturer; our success in increasing product sales under the High Burden Developing Country (“HBDC”) program; the relative mix of commercial and HBDC sales and the relative mix of instrument and test sales; our success in commercial test and commercial system sales; our ability to sell directly to the smaller hospital market and the independent reference laboratory market; the performance and market acceptance of our new products, including our new point-of-care system, the GeneXpert Omni, our new Honeycomb module and new virology and oncology products; manufacturing costs associated with the ramp-up of new products; test performance in the field; testing volumes for our products; unforeseen supply, development and manufacturing problems; our ability to manage our inventory levels; our ability to scale up manufacturing; our research and development budget; the potential need for intellectual property licenses for tests and other products and the terms of such licenses; the environment for capital spending by hospitals and other customers for our diagnostic systems; lengthy sales cycles in certain markets, including the HBDC program and the smaller hospital market; variability in systems placements and reagent pull-through in our HBDC program and the smaller hospital market; the impact of competitive products and pricing; sufficient customer demand; customer confidence in product availability and available customer budgets; the level of testing at clinical customer sites, including for healthcare associated infections; our ability to consolidate customer demand through volume pricing; our ability to develop new products and complete clinical trials successfully in a timely manner for new products; our ability to obtain regulatory approvals for new products; uncertainties related to the United States Food and Drug Administration (“FDA”) regulatory and international regulatory processes; our ability to respond to changing laws and regulations affecting our industry and changing enforcement practices related thereto; our reliance on distributors in some regions to market, sell and support our products in certain geographic locations; the occurrence of unforeseen expenditures, asset impairments, acquisitions or other transactions; costs of litigation, including settlement costs and including Merger-related litigation; our ability to manage geographically-dispersed operations; the scope and timing of actual United States Postal Service (“USPS”) funding of the Biohazard Detection System (“BDS”) in its current configuration; the rate of environmental testing using the BDS conducted by the USPS, which will affect the amount of consumable products sold; underlying market conditions worldwide; the impact of foreign currency exchange; protection of our intellectual property and proprietary information; risks relating to the Merger Agreement and Merger, including but not limited to: the timing to complete the Merger, failure to receive necessary shareholder approvals, the risk that a condition to completion of the Merger may not be satisfied, the anticipated benefits of the Merger to Danaher and Danaher’s ability to achieve the synergies and value creation projected to be realized following the completion of the Merger, Danaher’s ability to integrate Cepheid’s business with its own promptly and effectively, the diversion of management and workforce time on Merger-related issues, changes in Danaher’s or Cepheid’s businesses, future cash requirements, capital requirements, results of operations, revenues, financial condition and/or cash flow; changes in acquisition-related transaction costs, the amount of fees paid to advisors and the potential payments to Cepheid executive officers in connection with the Merger, operating costs and business disruption that may be greater than expected, the ability to retain and hire key personnel and maintain relationships with customers, providers or other business partners pending completion of the Merger and the risk that lawsuits challenging the proposed Merger may result in adverse rulings that may impair or delay completion of the Merger;and the other risks set forth under “Risk Factors” and elsewhere in this report. We neither undertake, nor assume any obligation to update any of the forward-looking statements after the date of this report or to conform these forward-looking statements to actual results.

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OVERVIEW

We are a molecular diagnostics company that develops, manufactures and markets fully-integrated systems for testing. Our systems enable fast, sophisticated molecular testing for organisms and genetic-based diseases by automating otherwise complex manual laboratory procedures.

On September 2, 2016, we entered into the Merger Agreement with Danaher pursuant to which Danaher has agreed to acquire Cepheid for $53.00 per share in an all-cash transaction valued at approximately $4.0 billion, inclusive of the Company's net cash. The transaction is expected to close in the fourth quarter of fiscal 2016, subject to certain conditions, including shareholder approval and other customary closing conditions. We incurred transaction-related costs of $2.6 million during the three months ended September 30, 2016 in connection with the Merger and expect to incur additional costs related to the Merger during the fourth quarter of fiscal 2016 if the merger is successfully completed. For additional information related to the Merger Agreement, refer to the Definitive Proxy Statement on Schedule 14A filed with the SEC on October 7, 2016.

Our objective is to become the leading supplier of integrated systems and tests for molecular diagnostics. We intend to do this, in part, by extending the reach of our platform deeper into the hospital and reference laboratory markets as well as expanding into the point-of-care market and new geographic markets, and, in part, by extending the breadth of our platform by developing new tests for our systems, such as oncology tests and additional virology tests. Key elements of our strategy to achieve this objective include:

• Provide a fully-integrated molecular testing solution to the Clinical market. We are focusing our investments on selling our systems and tests to the Clinical market and we believe our GeneXpert system and Xpert tests will continue to significantly expand our presence in the Clinical market due to their ability to deliver accurate and fast results, ease of use, flexibility and scalability. Features of the GeneXpert system and Xpert tests include:

• an approach by which the reagents are typically prepackaged in a single vessel (the test cartridge) into which the specimen is added;

• no further user intervention once the Xpert cartridge is loaded into the GeneXpert system;

• all three phases of PCR: 1) sample preparation, 2) amplification and 3) detection, are performed within the single sealed test cartridge automatically;

• a menu of moderate complexity Clinical Laboratory Improvement Amendments ("CLIA") categorized, amplified molecular tests means the GeneXpert system can be operated without the need for highly-trained laboratory technologists. Additionally, we are entering the United States CLIA-waived market, which will enable certain of our tests to be run in point-of-care environments. For example, in December 2015, the FDA granted CLIA waiver for our Xpert Flu+RSV Xpress test for use on our GeneXpert System. The Xpert Flu+RSV Xpress is the first PCR panel test to achieve CLIA waiver, and the first in a series of reference-quality molecular tests that we intend to deliver to the point-of-care market over the next several years;

• commercial availability of systems in a variety of configurations ranging from one to 80 individual test modules, which enables testing in environments ranging from low volume to high volume, near-patient, core or central lab testing, and system capacity that can be expanded in support of growing test volumes by adding additional modules;

• notably, to our knowledge, the only truly scalable real-time PCR system that operates entirely within a closed system architecture, reducing hands-on time, reducing the likelihood of human error and contamination and enabling nested PCR capability, a proven process for maximizing real-time PCR sensitivity and specificity; and

• full random access whereby different tests for different targets may be run simultaneously in different modules in the same GeneXpert system, which increases potential utilization and throughput of the system and also enables on-demand or “STAT” testing, whereby the user can add a new test to the system at any time without regard to the stage of processing of any other test on the system.

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• Continue to develop and market new tests and modules and systems.

• Tests. We plan to capitalize on our strengths in nucleic acid chemistry and molecular biology to continue to develop new tests for our systems and offer our customers the broadest menu of Xpert tests designed to address many of the highest volume molecular test opportunities. Our strategy is to offer a portfolio of Xpert tests spanning healthcare-associated infections, infectious disease, sexual health, virology, oncology and genetic disease. For example, in March 2016, we received clearance from the FDA to market our Xpert Carba-R test for use with bacterial isolates. In June 2016, we received clearance from the FDA for expanded claims for use of rectal swabs with Xpert Carba-R as an aid for infection control for monitoring the spread of carbapenem-non-susceptible organisms in healthcare settings. Also in June 2016, our Xpert HIV-1 Qualitative was awarded WHO prequalification. In September 2016, we received clearance from the FDA for expanded claims for the use of urine samples from symptomatic and asymptomatic men with our Xpert Trichomonas test. Also in September 2016, we announced the launch of Xpert C. difficile BT in countries accepting the CE mark, which expands the results reporting capability of our Xpert C. difficile test to detect the presence of binary toxin-producing C. difficile. Additionally, in October 2016, we launched our Xpert Bladder Cancer Monitor and Xpert Bladder Cancer DX tests, which are now commercially available in Germany and cleared for commercial availability in all countries accepting the CE mark. Our Xpert Xpress Flu/RSV test also achieved CE mark in October 2016 and is now available in all countries accepting the CE mark. We now have a cumulative menu of tests of 27 that have achieved CE mark available internationally and 20 unique tests that are FDA cleared in the United States.

• Modules and Systems. We continue to develop the Honeycomb module (our high-level multiplexing initiative) and we are moving forward with the use of the module in the development of our Xpert Breast Cancer Signature product. The GeneXpert Omni system was originally scheduled for launch in the emerging markets in 2016 and its initial testing has been underway with a number of tests successfully running on the system and the majority of its components fully operational and functioning as expected. However, in the first quarter of 2016, we decided to delay its launch to the third quarter of 2017 so that we could invest additional time to ensure that the detection and amplification module of the system, more specifically the ICORE module, is functioning in a fully robust manner to address both our current and future test menu.

• Market segment expansion. We plan to further extend the reach of our GeneXpert system and menu of Xpert tests to additional markets in 2016 and beyond. Following the clearance of our first CLIA-waived test for Flu+RSV at the end of 2015 and the announcement of our non-exclusive United States distribution agreements with Henry Schein in January 2016 and Medline and McKesson in April 2016, our GeneXpert System and menu of moderately complex Xpert tests, including the CLIA-waived test for Flu+RSV, is now increasingly available to the non-acute laboratory market, including moderately complex physician-office laboratories, women's health facilities, large multi-specialty clinics, urgent care facilities and reference laboratories. Our existing GeneXpert Systems along with our Xpress Xpert tests under development will expand our presence in the United States CLIA waived market. Additionally, Henry Schein, Medline, and McKesson will distribute our CLIA-waived products for the GeneXpert Omni, which is expected to launch outside the United States in late 2017, and which we expect to further expand our presence in the point-of-care market in the years following launch.

• Extend geographic reach. Our European sales and marketing operations are headquartered in France. In addition, as of September 30, 2016, we had direct sales forces in Australia, the Benelux region, Brazil, France, Germany, Hong Kong, India, Italy, South Africa and the United Kingdom, and we have offices in China, Japan and the United Arab Emirates. We expect to continue to expand our international commercial operations capability on both a direct and distributor basis during the remainder of 2016 and in future years.

• Extend High Burden Developing Countries sales programs. We expect to continue to expand our presence in HBDCs to deliver GeneXpert systems and Xpert tests, including virology and Ebola, to HBDCs at a discount to our standard commercial prices. We believe that participation in the HBDC program considerably broadens the geographic reach of our products and increases recognition of the Cepheid brand and product portfolio.

• Obtain additional target rights. We expect to continue to expand our collaborations with academic institutions and commercial organizations to develop and obtain target rights to various infectious disease and oncology targets. In addition, we expect to focus key business development activities on identifying infectious disease and oncology targets held by academic institutions or commercial organizations for potential license or acquisition.

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Products

Our product portfolio consists of tests, reagents and systems for the Clinical and Non-Clinical markets. Our main system is the GeneXpert system, including the Infinity systems, which incorporates sample preparation, nucleic acid extraction and purification, DNA amplification, and detection into a small, self-contained cartridge, enabling fast molecular testing 24 hours a day, 7 days a week, offering medically relevant results when and where they are needed most. We also offer our first generation system, the SmartCycler, which integrates DNA amplification and detection for fast batch or random access analysis in “real-time.”

In the Clinical market, we offer tests for the GeneXpert system in the five following disease franchises: (i) healthcare-associated infections, (ii) critical infectious disease, (iii) sexual health, (iv) virology and (v) oncology and genetics. These tests include U.S. Food and Drug Administration (“FDA”) cleared products, such as IVD medical devices, CE Marked products (“CE IVD”), Research Use Only (“RUO”) tests and Emergency Use Authorization ("EUA") tests. As of September 30, 2016, our Xpert menu includes the following FDA cleared tests, CE IVD approved tests, RUO and EUA tests:

Healthcare Associated Infections (HAI), which includes the following tests for infection control in healthcare facilities:

• Xpert MRSA

• Xpert MRSA/SA Nasal Complete

• Xpert MRSA/SA BC for Blood Culture

• Xpert MRSA/SA SSTI for Skin and Soft Tissue Infections

• Xpert C. difficile

• Xpert C. difficile/epi (FDA only)

• Xpert C. difficile BT (CE IVD only)

• Xpert Carba-R

• Xpert Norovirus

• Xpert Van A for vancomycin resistant enterococci (FDA only)

• Xpert Van A/Van B (CE IVD only)

Critical Infectious Disease (CID), which includes the following tests for critical illness-causing, highly contagious organisms:

• Xpert MTB/RIF

• Xpert EV for Enterovirus

• Xpert Ebola (EUA)

• Xpert Flu

• Xpert Flu/RSV

• Xpert Flu+RSV (CLIA Waived, FDA Only)

Sexual Health, which includes the following tests for pathogens impacting sexual health:

• Xpert CT/NG

• Xpert CT (CE IVD only)

• Xpert Trichomonas

• Xpert HPV (CE IVD only)

• Xpert GBS for Group B Streptococcus

• Xpert GBS for Lim broth (FDA only)

Virology, which includes the following tests for detection of viruses:

• Xpert HIV-1 Viral Load (CE IVD only)

• Xpert HIV-1 Qualitative (CE IVD only)

• Xpert HCV Viral Load (CE IVD only)

Oncology and Genetic Disease, which includes the following tests for oncology and genetic polymorphism:

• Xpert Factor II and Factor V Leiden

• Xpert BCR-ABL Monitor (CE IVD only)

• Xpert BCR-ABL Ultra (CE IVD only)

• Xpert BCR-ABL (RUO, US only)

29

The following tables present certain significant financial measurements for the period indicated (in thousands, except per share data):

	Three Months Ended September 30,										Nine Months Ended September 30,
	2016			2015			$ Change		% Change		2016			2015			$ Change		% Change
Total revenue	$	158,488		$	126,465		$	32,023	25	%	$	449,269		$	391,577		$	57,692	15	%
Gross margin	47%			46%			N/A		1%		49%			49%			N/A		—	%
Net loss	$	(10,907	)	$	(22,901	)	$	11,994	(52	)%	$	(27,740	)	$	(38,725	)	$	10,985	(28	)%
Diluted net loss per share	(0.15		)	(0.32		)	0.17		(53	)%	(0.38		)	(0.54		)	0.16		(30	)%
Non-GAAP Adjusted Results
Total revenue on a constant currency basis	$	159,214		$	124,943		$	34,271	27	%	$	452,698		$	385,470		$	67,228	17	%
Non-GAAP gross margin	49%			48%			N/A		1	%	51%			51%			N/A		—	%
Non-GAAP net income (loss)	$	6,448		$	(9,131	)	$	15,579	(171	)%	$	16,224		$	(1,270	)	$	17,494	(1,377	)%
Non-GAAP diluted net income (loss) per share	0.09			(0.13		)	0.22		(169	)%	0.22			(0.02		)	0.24		(1,200	)%

*Reconciliations of non-GAAP adjusted measures are presented below under "Use of Non-GAAP Measures".

Results of Operations

Comparison of the ThreeandNine Months Ended September 30, 2016 and 2015

Revenue

The following table summarizes total revenue by type (in thousands, except percentages):

	Three Months Ended September 30,								Nine Months Ended September 30,
	2016		2015		$ Change		% Change		2016		2015		$ Change		% Change
Revenue:
System and other revenue	$	27,496	$	19,749	$	7,747	39	%	$	76,618	$	62,823	$	13,795	22	%
Reagent and disposable revenue	130,992		106,716		24,276		23	%	372,651		328,754		43,897		13	%
Total revenue	$	158,488	$	126,465	$	32,023	25	%	$	449,269	$	391,577	$	57,692	15	%
Non-GAAP Adjusted Results
Total revenue on a constant currency basis	$	159,214	$	124,943	$	34,271	27	%	$	452,698	$	385,470	$	67,228	17	%

*Reconciliations of non-GAAP adjusted measures are presented below under "Use of Non-GAAP Measures".

Total revenue increased $32.0 million, or 25%, for the three months ended September 30, 2016, or 27% on a constant currency basis, compared to the same period in the prior year. The increase was primarily attributable to the increase in reagent and disposable revenue of $24.3 million, or 23%, over the same prior year period, driven by an increased volume of reagents sold.

Total revenue increased $57.7 million, or 15%, for the nine months ended September 30, 2016, or 17% on a constant currency basis, compared to the same period in the prior year. The increase was primarily attributable to the increase in reagent and disposable revenue of $43.9 million, or 13%, over the same prior year period, driven by an increased volume of reagents sold.

30

Reagent and disposable revenue

Reagent and disposable revenue increased $24.3 million, or 23%, for the three months ended September 30, 2016 as compared to the same period in the prior year and increased $43.9 million, or 13%, for the nine months ended September 30, 2016 as compared to the same period in the prior year. The increases in revenue were primarily driven by the performance of our CID, sexual health and HAI disease franchises as shown in the table below for the three and nine month periods ended September 30, 2016 and September 30, 2015 (in thousands):

Year-over-Year Changes in Reagent and Disposable Revenue
Three months ended September 30, 2015	$	106,716	Nine months ended September 30, 2015	$	328,754
Increase in:			Increase in:
CID	7,096		CID	24,344
HAI	4,869		Sexual Health	9,753
Sexual Health	4,708		HAI	7,647
Other	7,603		Other	2,153
Total Increase	24,276		Total Increase	43,897
Three months ended September 30, 2016	$	130,992	Nine months ended September 30, 2016	$	372,651

For both the three and nine month periods ending September 30, 2016, the increases in revenue from our three major disease franchises as shown above were attributable to the following factors:

• The increase in revenue from our CID franchise was primarily driven by increases in MTB and Flu test volumes. In particular, the growth in MTB test volumes was driven by our High Burden Developing Countries ("HBDC") program, and a large order from India. The relatively late start of the 2015-2016 flu season also contributed to the increase in the 2016 Flu test volumes compared to the same periods in the prior year.

• The increase in revenue from our HAI disease franchise was primarily driven by higher test volumes of MRSA, C. Diff. and Carba-R tests.

• The increase in revenue from our sexual health disease franchise was primarily driven by an increase in CT/NG test volumes.

• The increase in revenue from other franchises in the three month period ending September 30, 2016 was primarily driven by higher volume of anthrax cartridge sales to the USPS.

For the year ended December 31, 2015, our HAI disease franchise was the largest single contributor to our revenue, accounting for 40% of our total revenue as compared to 42% in 2014 and 46% in 2013. While we expect revenue from our HAI disease franchise will continue to grow on an absolute basis, we expect it will continue to decline as a percentage of total revenue in the foreseeable future as the rate of revenue growth in our CID, sexual health, virology and oncology and genetic disease franchises is expected to outpace the revenue growth in our HAI disease franchise.

System and other revenue

System and other revenue increased $7.7 million, or 39%, for the three months ended September 30, 2016 as compared to the same period in the prior year and $13.8 million, or 22%, for the nine months ended September 30, 2016 as compared to the same period in the prior year. The increases were primarily driven by higher shipment volume to customers participating in the HBDC program and included a large system order delivered to India during the first two quarters of 2016 while we had no such large transactions in 2015.

Our revenue may be subject to seasonal fluctuations driven primarily by the timing and severity of seasonal illnesses such as influenza, respiratory syncytial virus, enteroviruses, and norovirus, which are most prevalent in the first and fourth calendar quarters of the year.

We expect our revenue to continue to increase in the fourth quarter of 2016 primarily driven by an overall increase in sales of our Xpert tests.

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The following table provides a breakdown of our revenue by geographic regions (in thousands, expect percentages):

	Three Months Ended September 30,								Nine Months Ended September 30,
	2016		2015		$ Change		% Change		2016		2015		$ Change		% Change
Geographic revenue information:
North America	$	89,122	$	73,627	$	15,495	21	%	$	252,714	$	232,119	$	20,595	9	%
International	69,366		52,838		16,528		31	%	196,555		159,458		37,097		23	%
Total revenue	$	158,488	$	126,465	$	32,023	25	%	$	449,269	$	391,577	$	57,692	15	%

North American revenue

North American revenue increased $15.5 million, or 21%, for the three months ended September 30, 2016 as compared to the same period in the prior year, and increased $20.6 million, or 9%, for the nine months ended September 30, 2016 as compared to the same period in the prior year, in each case, primarily driven by higher sales of reagents, particularly in the areas of HAI, sexual health and CID and also driven by a higher volume of anthrax cartridge sales to the USPS. The increases in North American revenue from HAI, sexual health and CID were primarily driven by the same factors mentioned in our reagent and disposable revenue discussion.

International Revenue

International revenue increased $16.5 million, or 31%, for the three months ended September 30, 2016 as compared to the same period in the prior year, and increased $37.1 million, or 23%, for the nine months ended September 30, 2016 as compared to the same period in the prior year, in each case, primarily driven by higher system sales and higher sales of reagents, primarily in our CID franchise. The increases in international revenue from systems and from CID were primarily driven by the same factors mentioned in our reagent and disposable revenue discussion.

The recent strengthening of the United States dollar has impacted the relative value of sales transactions that are denominated in foreign currencies. On a constant currency basis, we estimate our revenue would have increased 27% and 17%, respectively, for the three month and nine month periods ended September 30, 2016 compared to the same periods in the prior year. We use foreign currency exchange forward contracts to hedge a portion of our forecasted revenue. We estimate the foreign currency movements relative to the United States dollar negatively impacted net revenue in the three month and nine month periods ended September 30, 2016 by approximately $2.2 million and $9.5 million, respectively, inclusive of net hedge benefits of approximately $1.6 million and $6.4 million, respectively, the majority of which were recorded in revenue in the same periods in the prior year.

We expect foreign currency rates will continue to negatively impact our international revenue. The majority of our foreign currency exchange forward contracts for estimated 2016 revenue were placed after the strengthening of the United States dollar. Therefore, we do not expect to recognize similar hedging gains in revenue in 2016.

Costs and Operating Expenses

The following table illustrates the changes in operating expenses (in thousands, except percentages):

	Three Months Ended September 30,									Nine Months Ended September 30,
	2016		2015		$ Change			% Change		2016		2015		$ Change		% Change
Costs and operating expenses:
Cost of sales	$	83,390	$	67,681	$	15,709		23	%	$	229,220	$	198,259	$	30,961	16	%
Collaboration profit sharing	2,915		1,286		1,629			127	%	4,857		3,879		978		25	%
Research and development	29,912		32,909		(2,997		)	(9	)%	93,418		84,987		8,431		10	%
Sales and marketing	29,302		28,664		638			2	%	87,971		82,678		5,293		6	%
General and administrative	18,688		15,401		3,287			21	%	49,161		47,395		1,766		4	%
Total costs and operating expenses	$	164,207	$	145,941	$	18,266		13	%	$	464,627	$	417,198	$	47,429	11	%

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Cost of Sales and Gross Margin

The following table illustrates the changes in gross margins:

	Three Months Ended September 30,						Nine Months Ended September 30,
	2016		2015		Change		2016		2015		Change
Gross margin	47	%	46	%	1	%	49	%	49	%	—	%
Non-GAAP gross margin	49	%	48	%	1	%	51	%	51	%	—	%

*Reconciliations of non-GAAP adjusted measures are presented below under "Use of Non-GAAP Measures".

Cost of sales consists of raw materials, direct labor and stock-based compensation expense, manufacturing overhead, facility costs and warranty costs. Cost of sales also includes product royalties, amortization of intangible assets related to technology licenses, and intangible assets acquired in business combinations.

Gross margin increased for the three months ended September 30, 2016 compared to the same period in 2015 primarily due to lower product manufacturing costs, partially offset by a less favorable product mix and a $1.2 million impairment charge related to a canceled information technology project recorded during the three months ended September, 2016. Gross margin remained constant for the nine months ended September 30, 2016 compared to the same period in 2015 primarily due to the benefit from lower product manufacturing costs, offset by a higher mix of HBDC pricing revenue, driven by a large system and reagent order delivered to India during the first three quarters of 2016 and the impairment charge related to a canceled information technology project.

We currently expect that our gross margin will be higher during the three months ended December 31, 2016 compared to the gross margin for the three months ended September 30, 2016, primarily due to manufacturing cost improvements and a lower mix of revenue derived from our HBDC customers.

Collaboration Profit Sharing

Collaboration profit sharing represents the amount that we pay to Life Technologies Corporation (acquired by Thermo Fisher Scientific) under our collaboration agreement to develop and manufacture reagents for use in the USPS BDS program. Under the agreement, computed gross margin on anthrax cartridge sales are shared equally between the two parties. Collaboration profit sharing expenses increased $1.6 million, or 127%, for the three months ended September 30, 2016 compared to the same period in the prior year and increased $1.0 million, or 25%, for the nine months ended September 30, 2016 compared to the same period in the prior year, in each case, primarily driven by higher anthrax cartridge sales under the USPS BDS program.

Research and Development Expenses

Research and development expenses consist of salaries and employee-related expenses, including stock-based compensation, clinical trials, research and development materials, facility costs, depreciation, amortization of certain intangible assets, license fees, and milestone payments related to in-licensed products if it is determined that they have no alternative future use.

Research and development expenses decreased $3.0 million, or 9%, for the three months ended September 30, 2016 compared to the same period in the prior year, primarily due to a $2.5 million decrease in clinical trial costs, a $1.6 million decrease in consulting expenses, and $0.7 million decrease in material costs, partially offset by a $1.7 million increase in salaries and employee related expenses, including stock-based compensation expense driven by an approximate 28% increase in research and development headcount as of September 30, 2016 compared to the research and development headcount as of September 30, 2015.

Research and development expenses increased $8.4 million, or 10%, for the nine months ended September 30, 2016 compared to the same period in the prior year, primarily due to a $7.9 million increase in salaries and employee related expenses, including stock-based compensation expense driven by an approximate 29% increase in the average quarterly headcount, and a $3.9 million increase in material costs, partially offset by a $4.2 million decrease in clinical trial costs.

We currently expect our research and development expenses, as a percentage of revenue, for the fourth quarter of 2016 to be comparable to the first three quarters of 2016.

Sales and Marketing Expenses

Sales and marketing expenses consist primarily of salaries and employee-related expenses, including commissions and stock-based compensation, travel, facility-related costs and marketing and promotion expenses.

33

Sales and marketing expenses increased $0.6 million, or 2%, for the three months ended September 30, 2016 compared to the same period in the prior year, primarily due to a $1.3 million increase in salaries and employee related expenses and stock-based compensation expense driven by an approximate 10% increase in sales and marketing headcount as of September 30, 2016 compared to the sales and marketing headcount as of September 30, 2015, as a result of the expansion of our sales force, partially offset by a $0.4 million decrease in travel expenses and a $0.2 million decrease in marketing expense.

Sales and marketing expenses increased $5.3 million, or 6%, for the nine months ended September 30, 2016 compared to the same period in the prior year, primarily due to a $5.0 million increase in salaries and employee related expenses and stock-based compensation expense, driven by an approximate 15% increase in the average quarterly headcount as a result of the expansion of our sales force.

We currently expect our sales and marketing expenses, as a percentage of revenue, to increase in the fourth quarter of 2016 compared to the first three quarters of 2016.

General and Administrative Expenses

General and administrative expenses consist primarily of salaries and employee-related expenses, which include stock-based compensation, travel, facility costs, and legal, accounting and other professional fees.

General and administrative expenses increased $3.3 million, or 21%, for the three months ended September 30, 2016 compared to the same period in the prior year primarily due to $2.6 million of expense directly related to the Merger, and a $0.8 million increase in salaries and employee related expenses and stock-based compensation expense as a result of an approximate 19% increase in general and administrative headcount as of September 30, 2016 compared to the general and administrative headcount as of September 30, 2015, partially offset by lower consulting expenses.

General and administrative expenses increased $1.8 million, or 4%, for the nine months ended September 30, 2016 compared to the same period in the prior year, primarily due to $2.6 million of expense directly related to the Merger, and a $4.1 million increase in salaries and employee related expenses and stock-based compensation expense driven by an approximate 23% increase in the average quarterly headcount, partially offset by a $4.6 million decrease in legal fees primarily as a result of significant expense in preparing for IPRs and arbitration proceedings with respect to Roche in 2015 and lower consulting expense.

We currently expect our general and administrative expenses, as a percentage of revenue, to increase in the fourth quarter of 2016 as compared to the first three quarters of 2016 primarily driven by the additional costs related to the Merger expected to be incurred during the fourth quarter of fiscal 2016.

Other Income (Expense)

The following table illustrates the changes in our other income (expense), net (in thousands, except percentages):

	Three Months Ended September 30,											Nine Months Ended September 30,
	2016			2015			$ Change			% Change		2016			2015			$ Change			% Change
Other income (expense)
Interest income	$	873		$	494		$	379		77	%	$	2,332		$	1,283		$	1,049		82	%
Interest expense	(3,856		)	(3,687		)	(169		)	5	%	(11,433		)	(10,937		)	(496		)	5	%
Foreign currency exchange loss and other, net	(1,012		)	(408		)	(604		)	148	%	(1,242		)	(2,848		)	1,606			(56	)%
Total other expense, net	$	(3,995	)	$	(3,601	)	$	(394	)	11	%	$	(10,343	)	$	(12,502	)	$	2,159		(17	)%

Other income (expense) primarily consists of interest income earned from our cash, cash equivalents, investment balances, interest expense related to senior convertible notes, notes payable balances outstanding during the period and the net effect of foreign currency exchange transactions, including the net effect of non-qualifying derivative activities.

Interest income increased by $0.4 million, or 77%, for the three months ended September 30, 2016 compared to the same period in the prior year, and increased by $1.0 million, or 82%, for the nine months ended September 30, 2016 compared to the same period in the prior year, in each case, primarily due to an increase in yields in our investment portfolio.

34

Interest expense increased $0.2 million, or 5%, for the three months ended September 30, 2016 compared to the same period in the prior year, and increased $0.5 million, or 5%, for the nine months ended September 30, 2016 compared to the same period in the prior year, in each case, primarily due to increased accretion of the convertible note discount into interest expense from the issuance of senior convertible notes in February 2014.

Foreign currency exchange loss and other, net increased by $0.6 million, or 148%, for the three months ended September 30, 2016 compared to the same period in the prior year, primarily due to the strengthening of the United States dollar against the British Pound, partially offset by the strengthening South African Rand against the United States dollar during the three months ended September 30, 2016 compared with the three months ended September 30, 2015 when the Euro and South African Rand weakened considerably against the United States dollar. Foreign currency exchange loss and other, net decreased by $1.6 million, or 56%, for the nine months ended September 30, 2016 compared to the same period in the prior year, primarily due to the strengthening of the United States dollar against the British Pound, partially offset by the strengthening of the Euro and South African Rand against the United States dollar during the nine months ended September 30, 2016 compared with the nine months ended September 30, 2015 when the Euro and South African Rand weakened considerably against the United States dollar.

Use of Non-GAAP Measures

We have supplemented our reported GAAP financial information with total revenue growth on a constant currency basis, which excludes the impacts of foreign exchange and our cash flow hedges. The foreign exchange impact is the translation impact if revenue for the third quarter of fiscal 2016 was translated at exchange rates applicable during the third quarter of fiscal 2015. We also have supplemented our reported GAAP financial information with non-GAAP gross margin, non-GAAP cost of sales, non-GAAP net income (loss) and non-GAAP net income (loss) per share, each of which do not include the impact of our stock-based compensation expense and amortization of purchased intangible assets. In addition, non-GAAP net income (loss) and non-GAAP net income (loss) per share also exclude merger-related expenses and amortization of debt discount and transaction costs. The presentation of this additional information is not meant to be considered in isolation or as a substitute for results prepared in accordance with U.S. GAAP. Our management uses the non-GAAP information internally to evaluate our ongoing business, continuing operational performance and cash requirements, and we believe these non-GAAP measures are useful to investors as they provide a basis for evaluating our cash requirements and additional insight into the underlying operating results and our ongoing performance in the ordinary course of our operations.

These non-GAAP measures may be different from non-GAAP measures used by other companies. In addition, these non-GAAP measures are not based on any comprehensive set of accounting rules or principles. Non-GAAP measures have limitations in that they do not reflect all of the amounts associated with the Company's results of operations as determined in accordance with U.S. GAAP and therefore these measures should only be used to evaluate the Company’s results of operations in conjunction with the corresponding GAAP measures.

Non-GAAP Net Income (Loss) and Non-GAAP Gross Margin

As described above, the Company excludes the following items from non-GAAP gross margin, non-GAAP cost of sales, non-GAAP net income (loss) and non-GAAP net income (loss) per share, where applicable:

Stock-based Compensation Expense. This consists primarily of expenses for stock options and restricted stock under ASC 718. We exclude stock-based compensation expense from its non-GAAP measures primarily because it is a non-cash expense that we do not believe is reflective of ongoing operating results in the period incurred. Further, as we apply ASC 718, we believe that it is useful to investors to understand the impact of the application of ASC 718 on our results of operations.

Amortization of Debt Discount and Transaction Costs. We incur amortization of debt discount and transaction costs in connection with the Convertible Senior Notes issued in February 2014. We exclude these amounts because these expenses are not reflective of ongoing operating results in the period incurred. These amounts arise from our issuance of debt and have no direct correlation to the operation of our business.

Merger-related Expenses. We incurred costs related directly to the Merger and include legal and other advisory services. We exclude these amounts because these expenses are not reflective of ongoing operating results.

Amortization of Purchased Intangible Assets. We incur amortization of purchased intangible assets in connection with acquisitions. We exclude these amounts because these expenses are not reflective of ongoing operating results in the period incurred. These amounts arise from our prior acquisitions and have no direct correlation to the operation of our business.

35

Constant Currency

We present certain revenue information in this release on a constant currency basis that excludes the effect of foreign currency rate fluctuations and hedging transactions. We calculate constant currency revenue growth by (i) translating current quarter or year-to-date revenues to constant currency revenues using the applicable prior period exchange rates and (ii) excluding any gain or loss from foreign currency hedge contracts that are reported in revenue. We believe constant currency revenue growth provides useful supplemental information to investors about the financial performance of our business and enables a more accurate comparison of financial results between periods, by excluding the impact of currency rate fluctuations and hedging transactions. You should be cautioned that the effect of changing foreign currency exchange rates has an actual effect on operating results.

The following table reconciles total revenue growth on a constant currency basis, non-GAAP gross margin, non-GAAP cost of sales, non-GAAP net income (loss) and non-GAAP diluted net income (loss) per share from GAAP financial measures (in thousands, except per share data):

	Three Months Ended September 30,						Nine Months Ended   September 30,
	2016			2015			2016			2015
Total revenue	$	158,488		$	126,465		$	449,269		$	391,577
Foreign currency exchange loss on Q3 '16 revenue using Q3 '15 rates	658			—			3,139			—
Loss (benefit) from cash flow hedges	68			(1,522		)	290			(4,585		)
Total revenue on a constant currency basis	$	159,214		$	124,943		$	452,698		$	386,992
Total revenue growth	25%						15%
Total revenue growth on a constant currency basis	27%						17%
Cost of sales	$	83,390		$	67,681		$	229,220		$	198,259
Stock-based compensation expense	(1,784		)	(1,129		)	(4,882		)	(3,177		)
Amortization of purchased intangible assets	(829		)	(829		)	(2,487		)	(2,877		)
Non-GAAP measure of cost of sales	$	80,777		$	65,723		$	221,851		$	192,205
GAAP gross margin	47%			46%			49%			49%
Non-GAAP gross margin	49%			48%			51%			51%
Net loss	$	(10,907	)	$	(22,901	)	$	(27,740	)	$	(38,725	)
Stock-based compensation expense	10,813			9,975			29,706			25,802
Amortization of debt discount and transaction cost	2,754			2,583			8,131			7,627
Merger-related expenses	2,618			—			2,618			—
Amortization of purchased intangible assets	1,170			1,212			3,509			4,026
Non-GAAP measure of net income (loss)	$	6,448		$	(9,131	)	$	16,224		$	(1,270	)
Diluted net loss per share	$	(0.15	)	$	(0.32	)	$	(0.38	)	$	(0.54	)
Stock-based compensation expense	0.15			0.14			0.40			0.36
Amortization of debt discount and transaction cost	0.04			0.03			0.11			0.10
Merger-related expenses	0.03			—			0.04			—
Amortization of purchased intangible assets	0.02			0.02			0.05			0.06
Non-GAAP measure of net income (loss) per share	$	0.09		$	(0.13	)	$	0.22		$	(0.02	)
Shares used in computing basic and diluted net loss per share	73,158			72,199			72,890			71,777
Shares used in computing Non-GAAP diluted net income (loss) per share	75,125			72,199			74,406			71,777

36

LIQUIDITY AND CAPITAL RESOURCES

Cash and Cash Flow

	Nine Months Ended September 30,
(in thousands)	2016			2015			Change
Net cash provided by operating activities	$	25,483		$	19,497		$	5,986
Net cash used in investing activities	(32,241		)	(3,717		)	(28,524		)
Net cash provided by financing activities	9,160			26,376			(17,216		)

Cash Flows from Operating Activities

Our largest source of operating cash flows is cash collections from customers and our primary cash outflows are purchases of inventory and personnel-related expenses. Net cash provided by operating activities during the first nine months of 2016 increased $6.0 million compared with the first nine months of 2015, primarily due to the following:

• a decrease in net loss of $11.0 million during the first nine months of fiscal 2016 compared with the same period last year,

• a favorable impact of $11.4 million from an increase in deferred revenue during the first nine months of 2016 compared with the first nine months of 2015, primarily due to the timing of product shipments and contracts,

• a favorable impact of $6.0 million from a reduction of the rate of increase in our prepaid expenses and other current assets balance during the first nine months of 2016 compared with the first nine months of 2015, primarily driven by volume and timing of pre-payments and timing of payments of other receivables, and

• a favorable impact of $4.5 million from a reduction of the rate of increase in our net inventory balance, primarily due to reduced volume and timing of purchases, and

• a $3.8 million increase in stock-based compensation expense during the first nine months of 2016 compared with the first nine months of 2015; partially offset by

• an unfavorable impact of $8.4 million from a reduction of the rate of increase in our accounts payable and other current and non-current liabilities balance, primarily driven by timing of payments, and

• an unfavorable impact of a $15.4 million net increase in the accounts receivable balance during the first nine months of 2016, compared to a favorable impact of a $8.4 million net decrease in the accounts receivable balance during the first nine months of 2015. This unfavorable change was primarily due to an overall increase in revenue and the timing of product shipments.

We believe that current cash balances and cash flows from our operations will be sufficient to support our business operations, including our growth initiatives, for the next 12 months and beyond.

Cash Flows from Investing Activities

Our cash flows from investing activities are primarily for capital expenditures and purchases of marketable securities and investments, while cash inflows are primarily proceeds from sales and maturities of marketable securities and investments and proceeds from the sale of equipment and intangible assets. Net cash used in investing activities during the first nine months of 2016 increased $28.5 million compared with the first nine months of 2015, primarily due to the following:

• $20.1 million additional capital expenditures, including the purchase of an additional manufacturing site, leasehold improvements and additional manufacturing capacity; and

• $6.5 million less net proceeds from sales and maturities of investments during the first nine months of 2016 compared with the first nine months of 2015.

Cash Flows from Financing Activities

Net cash provided by financing activities during the first nine months of 2016 decreased $17.2 million compared with the first nine months of 2015, primarily due to a decrease in net proceeds from issuance of common stock and exercise of stock options of $17.2 million during the first nine months of 2016.

Off-Balance-Sheet Arrangements

As of September 30, 2016, we did not have any off-balance-sheet arrangements, as defined in Item 303(a)(4)(ii) of Regulation S-K promulgated under the Securities Act of 1933, as amended.

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Financial Condition Outlook

We plan to continue to make expenditures to expand our manufacturing capacity and to support our activities in sales and marketing and research and development. These expenditures may vary from quarter to quarter, as evidenced by our increased operating expenses for the three months ended September 30, 2016. We plan to continue to support our working capital needs and anticipate that our existing cash resources will enable us to maintain currently planned operations. Based on past performance and current expectations, we believe that our current available sources of funds will be adequate to finance our operations for at least the next year. This expectation is based on our current and long-term operating plan and may change as a result of many factors, including our future capital requirements and our ability to increase revenues and reduce expenses, which depend on a number of factors outside our control, including general global economic conditions. For example, our future cash use will depend on, among other things, market acceptance of our new products, manufacturing costs associated with the ramp-up of new products, the resources we devote to developing and supporting our products, the expansion of our U.S. sales organization, continued progress of our research and development of potential products, our ability to gain FDA clearance for our new products, the need to acquire licenses to new technology or to use our technology in new markets, expansion through acquisitions and the availability of other financing.

If the Merger is not completed in the future, we may seek additional funds to support our strategic business needs and may seek to raise such additional funds through private or public sales of securities, strategic relationships, bank debt, lease financing arrangements, or other available means. If additional funds are raised through the issuance of equity or equity-related securities, shareholders may experience additional dilution, or such equity securities may have rights, preferences, or privileges senior to those of the holders of our common stock. If adequate funds are not available or are not available on acceptable terms to meet our business needs, our business may be harmed.

CRITICAL ACCOUNTING POLICIES, ESTIMATES AND ASSUMPTIONS

The items that we disclosed as our critical accounting policies and estimates in Management’s Discussion and Analysis of Financial Condition and Results of Operation in our 2015 Annual Report on Form 10-K filed with the Securities and Exchange Commission remain unchanged. For a description of those critical accounting policies, please refer to our 2015 Annual Report on Form 10-K.

Recent Accounting Pronouncements

Refer to Note 1, “Organization and Summary of Significant Accounting Policies – Recent Accounting Pronouncements” for a discussion of new and recently adopted accounting guidance.

ITEM 3.    QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISKS

Interest Rate Sensitivity

Our investment portfolio is exposed to market risk from changes in interest rates. The fair market value of fixed rate securities may be adversely impacted by fluctuations in interest rates while income earned on floating rate securities may decline as a result of decreases in interest rates. Under our current policies, we do not use interest rate derivative instruments to manage exposure to interest rate changes. We attempt to ensure the safety and preservation of our invested principal funds by limiting default risk, market risk and reinvestment risk. We mitigate default risk by investing in investment grade securities. We have historically maintained a relatively short average maturity for our investment portfolio, and we believe a hypothetical 100 basis point adverse move in interest rates along the entire interest rate yield curve would change the fair value of our interest sensitive financial instruments by approximately $1.2 million as of September 30, 2016. In addition, if a 100 basis point change in overall interest rates were to occur in 2016, our interest income would not change significantly in relation to amounts we would expect to earn, based on our cash, cash equivalents, and investments as of September 30, 2016.

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Changes in interest rates may also impact gains or losses from the conversion of our outstanding convertible senior notes. In February 2014, we issued $345.0 million in aggregate principal amount of our 1.25% convertible senior notes due 2021. At our election, the notes are convertible into cash, shares of our common stock, or a combination of cash and shares of our common stock in each case under certain circumstances, including trading price conditions related to our common stock. If the trading price of our common stock reaches a price for a sustained period at 130% above the conversion price of $65.10, the notes will become convertible. Upon conversion, we are required to record a gain or loss for the difference between the fair value of the debt to be extinguished and its corresponding net carrying value. The fair value of the debt to be extinguished depends on our then-current incremental borrowing rate. If our incremental borrowing rate at the time of conversion is higher or lower than the implied interest rate of the notes, we will record a gain or loss in our consolidated statement of operations during the period in which the notes are converted. The implicit interest rate for the notes is 5.0%. An incremental borrowing rate that is a hypothetical 100 basis points lower than the implicit interest rate upon conversion of $100 million aggregate principal amount of the notes would result in a loss of approximately $6.0 million.

Foreign Currency Risk

We operate primarily in the United States and a majority of our revenue, cost, expense and capital purchasing activities for the three months ended September 30, 2016 were transacted in United States dollars. As a corporation with international and domestic operations, we are exposed to changes in foreign exchange rates. Our international revenue is predominantly in European countries and South Africa and is denominated in a number of currencies, primarily the Euro, United States dollar, British Pound, South African Rand and Australian dollar. In our international operations, we pay payroll and other expenses in local currencies. Our exposures to foreign currency risks may change over time and could have a material adverse impact on our financial results.

We expect to continue to hedge our foreign currency exposure in the future and may use currency forward contracts, currency options and/or other common derivative financial instruments to reduce foreign currency risk. We performed a sensitivity analysis as of September 30, 2016 based on a model that measures the impact of a hypothetical 10% adverse change in foreign exchange rates to the United States dollar (with all other variables held constant) on our underlying estimated major foreign currency exposures, net of derivative financial instruments. The foreign exchange rates used in the model were based on the spot rates in effect as of September 30, 2016. The sensitivity analysis indicated that a hypothetical 10% adverse movement in foreign exchange rates would have an unfavorable impact on the underlying cash flow exposure, net of our foreign exchange derivative financial instruments, of $2.7 million as of September 30, 2016.

ITEM 4.    CONTROLS AND PROCEDURES

EVALUATION OF DISCLOSURE CONTROLS AND PROCEDURES

Our management, with the participation of our Chief Executive Officer and Chief Financial Officer, evaluated the effectiveness of our disclosure controls and procedures pursuant to Rule 13a-15 under the Securities Exchange Act of 1934, as amended (Exchange Act), as of the end of the period covered by this Quarterly Report on Form 10-Q.

Based on this evaluation, our Chief Executive Officer and Chief Financial Officer concluded that, as of September 30, 2016, our disclosure controls and procedures are designed at a reasonable assurance level and are effective to provide reasonable assurance that information we are required to disclose in reports that we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in the SEC’s rules and forms, and that such information is accumulated and communicated to our management, including our Chief Executive Officer and Chief Financial Officer, as appropriate, to allow timely decisions regarding required disclosures.

CHANGES IN INTERNAL CONTROL OVER FINANCIAL REPORTING

During the quarter ended September 30, 2016, there were no changes in internal control over financial reporting that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

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PART II — OTHER INFORMATION

ITEM 1.    LEGAL PROCEEDINGS

In May 2005, we entered into a license agreement with F. Hoffmann-La Roche Ltd. and Roche Molecular Systems, Inc. (“Roche”) that provided us with rights under a broad range of Roche patents, including patents relating to the PCR process, reverse transcription-based methods, nucleic acid quantification methods, real-time PCR detection process and composition, and patents relating to methods for detection of viral and cancer targets. A number of the licensed patents expired in the United States prior to the end of August of 2010 and in Europe prior to the end of August of 2011. In August 2010, we terminated our license to United States Patent No. 5,804,375 (the “375 Patent”) and ceased paying United States-related royalties. We terminated the entire license agreement in the fourth quarter of 2011. In August 2011, Roche initiated an arbitration proceeding against us in the International Chamber of Commerce pursuant to the terms of the terminated agreement. We filed an answer challenging arbitral jurisdiction over the issues submitted by Roche and denying that we violated any provision of the agreement. A three-member panel was convened to address these issues in confidential proceedings. On July 30, 2013, the panel determined that it had jurisdiction to decide the claims, a determination that we appealed to the Swiss Federal Supreme Court. On October 2, 2013, the arbitration panel determined that it would proceed with the arbitration while this appeal was pending. On February 27, 2014 the Swiss Federal Supreme Court upheld the jurisdiction of the arbitration panel to hear the case. On April 22, 2016, the arbitration panel transmitted a partial award holding that we were liable for damages for the manufacture and sale of certain accused products starting after we terminated the license until September 2015, with the final amount to be determined by audit. The partial award also denied Roche’s requests for an injunction, and allocated certain legal fees and costs between the parties.

Based on our ongoing evaluation of the facts and circumstances of the case, including the partial award, we believe that it is probable that this arbitration proceeding could result in a material loss. Accordingly, we recorded an estimated charge of $20 million as our best estimate of the potential loss as of December 31, 2014, which amount was included in accrued and other liabilities in our consolidated balance sheets. Taking into account the partial award, this continues to be our best estimate for this potential loss as of September 30, 2016. Depending on the final ruling of the arbitrators, it is possible that we could also be responsible for certain fees, costs and/or interest, if any; however, we are unable at this time to determine the likelihood of whether these potential outcomes will occur or estimate their respective potential amounts.

On August 21, 2012, we filed a lawsuit against Roche in the United States District Court for the Northern District of California (“the Court”), for a declaratory judgment of (a) invalidity, expiration and non-infringement of the 375 Patent; and (b) invalidity, unenforceability, expiration and non-infringement of United States Patent No. 6,127,155 (the “155 Patent”). On January 17, 2013, the Court issued an order granting a motion by Roche to stay the suit with respect to the 375 Patent pending resolution of the above noted arbitration proceeding. In the same order, the Court dismissed our suit with respect to the 155 Patent for lack of subject matter jurisdiction, without considering or ruling on the merits of our case. The Court left open the possibility that we could re-file our case against the 155 Patent in the future. We believe that the possibility that these legal proceedings will result in a material adverse effect on our business is remote.

On July 16, 2014, Roche filed a lawsuit in the Court, alleging that our Xpert MTB-RIF product infringes United States Patent No. 5,643,723 (the “723 Patent”), which expired on July 1, 2014. On September 15, 2014, we filed our answer and counterclaims denying Roche’s allegations of infringement and asking the Court to find the 723 Patent invalid, unenforceable and not infringed. On November 10, 2014, we filed a petition for inter partes review (“IPR”) of the 723 Patent in the USPTO and we filed a motion with the Court to stay this lawsuit pending the outcome of the IPR. On January 7, 2015, the Court issued an order staying the lawsuit pending the outcome of the IPR. On March 16, 2015, we filed a second petition for IPR of an additional claim of the 723 Patent. On June 11, 2015, the USPTO issued a decision declining to institute the first requested IPR. On July 13, 2015, we filed a request for reconsideration of the first petition for IPR with respect to certain challenged claims. On September 16, 2015, the USPTO denied the request for reconsideration. On September 17, 2015, the USPTO decided to institute our second petition for IPR. On May 18, 2016, the parties submitted a joint status update to the Court in which Roche stated that it had disclaimed and would not assert the claim we had challenged in the second petition for IPR. On May 20, 2016, the Court issued an order lifting the 2015 stay. On July 19, 2016, we filed a motion for summary judgment of patent ineligibility as to all asserted claims. The Court is scheduled to conduct an oral hearing on the motion on November 16, 2016, and we expect a decision on the motion by the end of 2016. We believe that the possibility that these legal proceedings will result in a material loss is remote.

We may be subject to various additional claims, complaints and legal actions that arise from time to time in the normal course of business. Other than as described above, we do not believe we are party to any currently pending legal proceedings that will result in a material adverse effect on our business. There can be no assurance that existing or future legal proceedings arising in the ordinary course of business or otherwise will not have a material adverse effect on our business, consolidated financial position, results of operations or cash flows.

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ITEM 1A.    RISK FACTORS

You should carefully consider the risks and uncertainties described below, together with all of the other information included in this Report, in considering our business and prospects. The risks and uncertainties described below are not the only ones facing us. Additional risks and uncertainties not presently known to us or that we currently deem immaterial also may impair our business operations. The occurrence of any of the following risks could harm our business, financial condition or results of operations.

Risks Related to the Merger

Our proposed merger with Danaher Corporation may not be completed within the expected timeframe, or at all, and the failure to complete the Merger could adversely affect our business and the market price of our common stock.

On September 2, 2016, we entered into the Merger Agreement with Danaher Corporation and Copper Merger Sub, Inc., a wholly-owned subsidiary of Danaher, pursuant to which Cepheid would become a wholly-owned subsidiary of Danaher if the Merger is completed. The Merger Agreement is subject to closing conditions beyond our control, including the approval requirement that holders of more than 50% of our outstanding common stock adopt the Merger Agreement, and there is no guarantee that these conditions will be satisfied in a timely manner or at all. If any of the conditions to the proposed Merger are not satisfied (or waived by the other party), the Merger might not be completed. In addition, the Merger Agreement may be terminated under specified circumstances. Failure to complete the Merger could adversely affect our business and the market price of our common stock in a number of ways, including:

• if the Merger is not completed, and no other party is willing and able to acquire us at a price of $53.00 per share or higher, on terms acceptable to us, the share price of our common stock is likely to decline;

• we have incurred, and continue to incur, significant expenses for professional services in connection with the proposed Merger, for which we will have received little or no benefit if the Merger is not completed. Many of these fees and costs will be payable even if the merger is not completed and may relate to activities that we would not have undertaken other than to complete the Merger;

• a failed Merger may result in negative publicity and/or give a negative impression of us in the investment community or business community generally; and

• if the Merger Agreement is terminated under specified circumstances, we may be required to pay Danaher a $131,000,000 termination fee.

The announcement and pendency of the Merger could adversely affect our business, financial condition, and results of operations.

The announcement and pendency of our proposed merger with Danaher could disrupt our business and create uncertainty about it, which could have an adverse effect on our business, financial condition, and results of operations, regardless of whether the Merger is completed. These risks to our business, all of which could be exacerbated by a delay in the completion of the Merger, include:

• diversion of significant management time and resources towards the completion of the merger;

• impairment of our ability to attract and retain key personnel;

• difficulties maintaining relationships with employees, customers, and other business partners;

• restrictions on the conduct of our business prior to the completion of the merger, which prevent us from taking specified actions without the prior consent of Danaher, which we might otherwise take in the absence of the Merger Agreement; and

• litigation relating to the Merger and the related costs.

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We may have difficulty attracting, motivating and retaining executives and other key employees in light of the proposed Merger.

Uncertainty among our employees about their future roles after the completion of the proposed merger with Danaher may impair our ability to attract, retain and motivate key personnel. In addition, some of our key employees are entitled to accelerated vesting of outstanding equity awards as a result of the completion of the proposed merger, or to severance payments if they terminate their employment after the proposed merger as a result of specified circumstances, including changes in their duties, positions, compensation and benefits, or their primary office location. These factors may encourage some key employees to consider career changes, distracting them from performing their duties to our company. In addition, distractions for the workforce and management associated with integrating our employees into the Danaher workforce could arise in the time before completion of the Merger. Any of these issues could have an adverse effect on our business operations and financial performance.

Our important business relationships may be disrupted due to uncertainties associated with the Merger, which could adversely affect our business.

Some of the parties with which we do business may be uncertain about their business relationships with us as a result of the proposed Merger. For example, customers, distributors, suppliers, vendors and others may attempt to negotiate changes in their existing business relationships with us or they may consider entering into alternative business relationships with other parties. Some of our customers, distributors, suppliers, vendors and others may have rights to terminate contracts that are triggered upon completion of the proposed merger. These disruptions could have an adverse effect on our businesses, financial condition or results of operations, or the prospects of the combined business. Any delay in completion of the Merger, or termination of the Merger Agreement, could exacerbate these risks and adverse effects.

Various lawsuits that have been filed challenging the proposed Merger may prevent the Merger from being completed.

Lawsuits challenging the proposed Merger have been filed and other similar lawsuits may be filed in the future. An adverse ruling in any such lawsuit may prevent the Merger from being completed.

One of the conditions to completion of the Merger is the absence of any applicable law or any order being in effect that prohibits completion of the Merger. Accordingly, if a plaintiff is successful in obtaining an order enjoining completion of the Merger, then such order may prevent the Merger from being completed, or from being completed within the expected time frame. In addition, we intend to defend the lawsuits vigorously, which may involve considerable expense.

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Risks Related to Our Business

We have a history of operating losses and may not achieve profitability again.

We incurred operating losses in each annual fiscal year since our inception, except for 2011. For the nine months ended September 30, 2016, we had a net loss of $27.7 million, and in 2015 and 2014 we experienced a net loss of $48.5 million and $50.1 million, respectively. As of September 30, 2016, we had an accumulated deficit of approximately $370.0 million. We do not expect to be profitable for fiscal 2016 and our ability to be profitable in the future will depend on our ability to continue to increase our revenue, which is subject to a number of factors including our ability to continue to successfully penetrate the Clinical market, our ability to successfully market the GeneXpert system and develop and market additional Xpert tests, our ability to successfully expand our United States sales organization and international commercial operations and the success of our sales organization in selling our systems and tests, the timing and success of market entry to the point-of-care market and the introduction of the GeneXpert Omni, the acceptance and success of our Xpert tests in the point-of-care market upon launch, our ability to diversify our revenue streams by successfully selling and marketing our existing products while introducing new products and increasing the volume of sales of such new products, the success of our distributor relationships, particularly in expanding our offerings into non-acute care laboratory customers, including moderately complex physician office labs, our ability to secure regulatory approval of additional Xpert tests, our ability to gain FDA regulatory and international regulatory clearance for our new products, our ability to continue to grow sales of Xpert tests, our ability to compete effectively against current and future competitors, the increasing number of competitors in our market that could reduce the average selling price of our products, the continued development of our HBDC program, the amount of products sold through the HBDC program and the extent of global funding for such program, our ability to penetrate new geographic markets, global economic and political conditions and our ability to increase manufacturing throughput. Our ability to be profitable also depends on our expense levels and product gross margin, which are also influenced by a number of factors, including: the mix of revenue from Clinical reagent sales and GeneXpert system sales as opposed to GeneXpert Infinity system sales and sales under our HBDC program, both of which have lower gross margins; the resources we devote to developing and supporting our products; increases in manufacturing costs associated with our operations, including those associated with ramp-up of new products; increases in costs related to our distributor relationships; our ability to improve manufacturing efficiencies; our ability to manage our inventory levels; third-party freight costs; the resources we devote to our research and development of, and compliance with regulatory processes for, potential products; license fees or royalties we may be required to pay; the potential need to acquire licenses to new technology or to use our technology in new markets, which could require us to pay unanticipated license fees and royalties in connection with these licenses; the impact of foreign currency exchange rates; and the prices at which we are able to sell our GeneXpert systems and Xpert tests. Our manufacturing expansion efforts may prove more expensive than we currently anticipate, and we may not succeed in increasing our revenue to offset higher expenses. These expenses or a reduction in the prices at which we are able to sell our products, among other things, may cause our net income and working capital to decrease. For example, our gross margin for the third quarter of 2015 was lower than expected due primarily to a higher proportion of lower-margin HBDC business and less commercial business as well as higher than expected manufacturing expenses associated with the ramp-up to volume of our newest virology tests. If we fail to grow our revenue, manage our expenses and improve our gross margin, we may never achieve profitability again. If we fail to do so, the market price of our common stock will likely decline.

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Our operating results may fluctuate significantly, our customers’ future purchases are difficult to predict and any failure to meet financial expectations may result in a decline in our stock price.

Our quarterly operating results may fluctuate in the future as a result of many factors, such as those described elsewhere in this section, many of which are beyond our control. Because our revenue and operating results are difficult to predict, we believe that period-to-period comparisons of our results of operations are not a good indicator of our future performance. Our operating results may be affected by the inability of some of our customers to consummate anticipated purchases of our products, whether due to adverse economic conditions, changes in internal priorities or, in the case of governmental customers, problems with the appropriations process, concerns over future United States federal government budgetary negotiations, variability and timing of orders and delays in our customer billing, and the impact of foreign currency exchange rates. Additionally, we have experienced, and expect to continue to experience, meaningful variability in connection with our commercial system placements and system placements and reagent pull-through in our HBDC program. This variability may cause our revenue and operating results to fluctuate significantly from quarter to quarter. Additionally, because of the limited visibility into the actual timing of future system placements, our operating results are difficult to forecast from quarter to quarter. Additionally, we expect moderate fluctuations from quarter to quarter in gross margin depending on product, geography and channel mix, including the relative mix of instrument and test sales, as well as the revenue contribution from our HBDC program, which has a lower gross margin than our commercial sales. If revenue declines in a quarter, whether due to a delay in recognizing expected revenue, adverse economic conditions and unexpected costs or otherwise, our results of operations will be harmed because many of our expenses are relatively fixed. In particular, research and development expenses, a portion of our sales and marketing expenses and general and administrative expenses are not significantly affected by variations in revenue. However, if we have an unexpected increase in costs and expenses in a quarter, our quarterly operating results will be affected. For example, for the year ended December 31, 2013, we incurred certain costs and inventory reserve provisions related to our manufacturing scale up and restructuring activities. Additionally, in July 2014, we began to self-insure for a portion of employee health insurance coverage and we estimate the liabilities associated with the risks retained by us, in part, by considering actuarial assumptions which, by their nature, are subject to a high degree of variability. If the number or severity of claims for which we are self-insured increases, or if we are required to accrue or pay additional amounts because the claims prove to be more severe than our original assessments, our operating results may be affected. Additionally, we had higher than expected operating expenses and lower than expected gross margin for the third quarter of 2015, which were primarily driven by a higher proportion of lower-margin HBDC business and less commercial business and higher than expected manufacturing costs associated with the ramp-up to volume of our newest virology tests. If our quarterly operating results fail to meet or exceed the expectations of securities analysts or investors, our stock price could drop suddenly and significantly.

A substantial majority of our revenue is derived from our HAI and CID disease franchises.

We classify our primary revenue generating products into systems and tests and reagents and disposables. Our reagents and disposables revenue can be categorized into the following five disease franchises: Healthcare-Associated Infections (HAI); Critical Infectious Disease (CID); Sexual Health; Virology; and Oncology and Genetic Disease. Historically we have been substantially dependent on revenues from our HAI products. For fiscal 2015, our HAI disease franchise represented approximately 40% of our total revenue and together with our CID disease franchise represented approximately 64% of our total revenue. Further, for fiscal 2016 our tests for MRSA and C. difficile represented the majority of our HAI revenues. While we continue to expand and develop our other disease franchises, we expect that sales of our HAI products will continue to account for a significant portion of our revenue for the foreseeable future and that sales of our HAI tests and CID tests will collectively continue to account for a majority of our revenue for the foreseeable future. Our ability to execute our growth strategy will depend, in part, upon the continued demand for tests in these disease franchises. For example, we note that revenues from our HAI tests have decreased, as a percentage of revenue, each of the past years and growth in our HAI tests has slowed over the past three years. If such trends continue and are not offset by growth of products in other disease franchises, our financial results could be harmed. Additionally, our MRSA tests and C. difficile tests represent a majority of the revenue from our HAI disease franchise and if the sales of these tests slow due to alternative testing solutions or a decrease in the infection rate of MRSA and C. difficile, then our financial results could be harmed. Underperformance of our HAI and CID disease franchises could have a significant adverse impact on our business, financial condition and operating results.

If we are unable to manufacture our products in sufficient quantities and in a timely manner, our operating results will be harmed, our ability to generate revenue could be diminished, and our gross margin may be negatively impacted.

Our revenue and other operating results will depend in large part on our ability to manufacture and assemble our products in sufficient quantities and in a timely manner. In the past, we have experienced lower than expected revenue due to intermittent interruptions in our supply chain, which also negatively impacted the efficiency of our manufacturing operations and our resulting gross margin. In addition, we may incur unexpected expenses in connection with the manufacturing scale-up of new products, which could negatively impact our gross margin. For example, in the third quarter of 2015, higher than expected manufacturing costs associated with new test ramp-up contributed to lower than expected gross margin.

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We recently expanded our existing relationship with a contract manufacturer, which was previously responsible for the manufacture of a significant portion of our GeneXpert systems to now include the complete manufacturing, assembly and testing of our GeneXpert systems. This outsourced manufacturing approach was fully in place as of the end of fiscal 2015. We create estimates in order to schedule production runs with this contract manufacturer. To the extent system orders materially vary from our estimates, we may experience constraints in our systems production and delivery capacity.

Any future interruptions we or our contract manufacturer experience in the manufacturing or shipping of our products in sufficient quantities and on a timely basis could delay our ability to recognize revenue and adversely affect our operating results in a particular quarter, could adversely affect our relationships with our customers, and could erode customer confidence in our product availability. Manufacturing problems can and do arise, as evidenced by our higher than expected manufacturing costs associated with new test ramp-up in the third quarter of 2015, and as demand for our products increases, any such problems could have an increasingly significant impact on our operating results. In the past, we have experienced problems and delays in production that have impacted our product yield and the efficiency of our manufacturing operations and caused delays in our ability to ship finished products, and we, or our contract manufacturer, may experience such delays in the future. We may not be able to react quickly enough to ship products and recognize anticipated revenue for a given period if we experience significant delays in the manufacturing process. In addition, we must maintain sufficient production capacity and inventory in order to minimize such delays, which carry fixed costs that we may not be able to offset if orders slow, which would adversely affect our operating margins.

We have a limited number of suppliers for critical product components, and a contract manufacturer for the manufacture and assembly of our systems, and our reliance on such suppliers and contract manufacturer exposes us to increased risks associated with quality control, production delays and costs.

We depend on a limited number of suppliers for some of the components used in the manufacture of our systems and our disposable reaction tubes and cartridges. We also depend on a single contract manufacturer for the manufacture and final assembly of the entire line of our GeneXpert systems. Strategic purchases of components are necessary for our business, but our reliance on a limited number of suppliers and a single contract manufacturer could expose us to reduced control over product quality and product availability, which could lead to product reliability issues and/or lower revenue and product shortages as a result of manufacturing capacity issues at our suppliers or contract manufacturer, or failure to adequately forecast demand for our components or systems. In addition, we cannot be certain that our suppliers or contract manufacturer will continue to be willing and able to meet our requirements according to existing terms or at all. If alternative suppliers or contract manufacturers are not immediately available, we will have to identify and qualify alternative suppliers or contract manufacturers and we could experience production delays and additional costs. We may not be able to find adequate alternative suppliers or contract manufacturers in a reasonable time period or on commercially acceptable terms, if at all. Shipments of affected products have been limited or delayed as a result of such problems in the past, and similar problems could occur in the future. For example, in the past, we have experienced intermittent interruptions in the supply of Xpert cartridge parts, which negatively impacted our product sales. In addition, some companies continue to experience financial difficulties, partially resulting from continued economic uncertainty. We cannot be assured that our suppliers or contract manufacturer will not be adversely affected by this uncertainty or that they will be able to continue to provide us with the components we need or to manufacture and assemble our systems. If we are unable to obtain the key source supplies for the manufacture of our products or we experience interruptions in the manufacture and assembly of our systems, product shipments may be delayed, which could harm customer relationships and our distributor relationships or force us to curtail operations or temporarily cease production of our products.

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If our direct selling efforts for our products fail, our business expansion plans could suffer and our ability to generate sales will be diminished.

In late 2014, we consolidated our global commercial operations under a single executive, our Executive Vice President, Worldwide Commercial Operations, to emphasize end-to-end accountability, eliminate duplication and clarify decision responsibilities, and reduce organizational complexity. In addition to the re-alignment of our organizational structure, over the past 2 years, we have substantially expanded our United States sales force and redesigned our sales territories. If such expansion efforts are not successful, it could be disruptive to our sales and our ability to generate revenue will be negatively impacted.

Additionally, in 2014 and 2015, we significantly restructured our marketing organization. We appointed the head of our marketing organization in mid-2014 and hired several new leaders in specific market segments during 2015. As a result, our restructured marketing team has a relatively short working history.

If we are unable to successfully scale our sales operations, successfully manage the increase in sales force and the related territory realignment or our marketing organization is unable to support our sales, our ability to expand our business and grow sales could be harmed and our expenses could increase. If the size of our sales force, changes to the organization of our sales force and marketing team or other issues cause our direct selling efforts to fail, our business expansion plans could suffer and our ability to generate sales could be diminished, which would harm our business.

Our sales cycle can be lengthy, which can cause variability and unpredictability in our operating results.

The sales cycles for our systems can be lengthy, particularly during times of uncertain economic and political conditions, which makes it more difficult for us to accurately forecast revenue in a given period, and may cause revenue and operating results to vary significantly from period to period. For example, sales of our products often involve purchasing decisions by large public and private institutions where any purchases can require many levels of approval. Additionally, participants in our HBDC program may be dependent on funding from governmental agencies and/or non-governmental organizations; as a result, such customers’ purchase decisions may not be within their direct control and may be subject to lengthy administrative processes. Accordingly, the sales cycle in our HBDC program is lengthy and unpredictable. As a result, we may expend considerable resources on unsuccessful sales efforts or we may not be able to complete transactions on the schedule anticipated.

If we cannot successfully commercialize our products, our business could be harmed.

If our tests for use on our systems do not continue to gain market acceptance, the launch of our GeneXpert Omni, our new point-of-care diagnostic platform, is not successful or the launch of other new products, including our Honeycomb module, are unsuccessful, we will be unable to generate significant sales growth, which may prevent us from achieving profitability. While we have received FDA clearance for a number of tests, these products may not experience increased sales. Many factors may affect the market acceptance and commercial success of our products, including:

• our ability to fulfill orders;

• the results of clinical trials needed to support any regulatory approvals of our tests;

• our ability to obtain requisite FDA or other regulatory clearances or approvals for tests under development;

• the timing of market entry for various tests for the GeneXpert systems, our new point-of-care diagnostic platform, GeneXpert Omni, and future products, including our Honeycomb module;

• our ability to convince our potential customers of the advantages and economic value of our systems and tests over competing technologies and products;

• the breadth of our test menu relative to competitors;

• changes to policies, procedures or what are considered best practices in clinical diagnostics, including practices for detecting and preventing healthcare-associated infections;

• the extent and success of our marketing and sales efforts;

• the effectiveness of our distribution agreements, particularly in expanding our offerings into non-acute care laboratory customers, including moderately complex physician office labs;

• the functionality of new products that address market requirements and customer demands;

• the pricing of our products;

• the level of reimbursement for our products by third-party payers; and

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• the publicity concerning our systems and tests.

In particular, we believe that the success of our business will depend in large part on our ability to continue to increase sales of our Xpert tests and our ability to successfully introduce additional tests for the Clinical market, including oncology tests, which is a key part of our strategy, and the successful launch of GeneXpert Omni, our new point-of-care diagnostic platform. For example, in April 2016, we announced a delay in the timing of the market launch of our GeneXpert Omni. Any further delay could impact our ability to capitalize on this market opportunity. Similarly, delays in the market launch of our Honeycomb module or other new products could impact our ability to capitalize on those market opportunities. We believe that successfully expanding our business in the Clinical market is critical to our long-term goals and success. We have limited ability to forecast future demand for our products in this market.

The regulatory processes applicable to our products and operations are expensive, time-consuming and uncertain, and may prevent us from obtaining required approvals for the commercialization of some of our products.

In the Clinical market, our products are regulated as medical device products by the FDA and comparable agencies of other countries, for example, the Pharmaceuticals and Medical Devices Agency ("PMDA") of Japan and the China Food and Drug Administration ("CFDA"). In particular, FDA regulations govern activities such as product development, product testing, product labeling, product storage, premarket clearance or approval, manufacturing, advertising, promotion, product sales, reporting of certain product failures and distribution. Some of our products, depending on their intended use, will require premarket approval from the FDA prior to marketing. In general, there are two types of FDA review processes applicable to our products: a premarket approval (“PMA”) and a 510(k) clearance. The PMA review process is much more costly, lengthy and uncertain, and generally takes from six months to one year or longer to complete after a submission. In some cases, the FDA may convene an expert advisory panel to independently review a submission and make a recommendation to approve or deny the submission. The 510(k) review process usually takes approximately three months after a submission, although the review process can sometimes take longer, particularly for novel or first-in-class products. Clinical studies are required to support both PMA and 510(k) submissions in the United States. Similar studies are required in other countries to support regulatory submissions, including for example, submissions to the PMDA in Japan and to the CFDA in China. Certain of our products for use on our GeneXpert and SmartCycler systems, when used for clinical purposes in the United States, may require PMA, and all such tests will most likely, at a minimum, require 510(k) clearance. Products intended for use in point-of-care settings, such as those intended to be used outside of the typical hospital laboratory environment (e.g., a physician office laboratory), require supplemental human factors clinical studies and an additional regulatory submission known as a CLIA waiver application. For example, we are seeking CLIA waiver for use of our next generation Flu/RSV, Flu, and Group A Strep tests on GeneXpert II and IV. CLIA waiver applications may be submitted concurrently with a PMA or 510(k), or sequentially after a PMA or 510(k) review has been completed. Concurrent review of a CLIA waiver application with a PMA or 510(k) takes approximately 210 days from submission. Sequential review of a CLIA waiver application after a PMA approval or 510(k) clearance takes approximately 180 days from submission. Clinical trials are expensive and time-consuming, as are human factors studies required for a CLIA waiver. In addition, the commencement or completion of any clinical trials may be delayed or halted for any number of reasons, including product performance, changes in intended use, changes in medical practice and the opinion of evaluator Institutional Review Boards. Additionally, since 2009, the FDA has significantly increased the scrutiny applied to its oversight of companies subject to its regulations, including PMA and 510(k) submissions, by hiring new investigators and increasing inspections of both domestic and foreign manufacturing facilities. We continue to monitor the FDA Office of In Vitro Diagnostics and Radiological Health ("OIR") and analyze how its decisions will impact the approval or clearance of our products and our ability to improve our systems and tests. The OIR has proposed a new class of devices that would be subject to heightened review processes, following an Institute of Medicine report on the 510(k) regulatory process that was released in late July 2011, but has since deferred any action on this proposal. At any time, actions proposed by the OIR could result in significant changes to the PMA or 510(k) processes, which could complicate the product approval or clearance process. If we fail to adequately respond to the increased scrutiny for the PMA and 510(k) submission processes, our business may be adversely impacted.

In 2014, the FDA issued several important guidance documents on assessing risks and benefits associated with use of a 510(k) approach for PMA products, pre- and post-market balance, expedited PMA, and on oversight of laboratory developed tests. While the overall goal of these guidance documents was to streamline the regulatory process by applying a risk-based approach to the requirements for data collection in the pre- and post-market periods, it is uncertain how the guidance documents will actually be implemented. The oversight of laboratory developed tests would require laboratories that compete with high risk (PMA) tests to go through FDA review. It is unclear if this guidance will be finalized.

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Further, our manufacturing facilities located in Sunnyvale and Lodi, California, Seattle, Washington and Stockholm, Sweden, where we assemble and produce cartridges and other molecular diagnostic kits and reagents, are subject to periodic regulatory inspections by the FDA and other federal and state and foreign regulatory agencies, as are the manufacturing facilities of our contract manufacturer. For example, these facilities are subject to Quality System Regulations (“QSR”) of the FDA and are subject to annual inspection and licensing by the States of California and Washington and European regulatory agencies. If we, or our contract manufacturer, fail to maintain these facilities in accordance with the QSR requirements, state or international quality standards or other regulatory requirements, the manufacture of our systems and tests could be suspended or terminated, and, in the case of a failure by our contract manufacturer, we could be required to find a suitable replacement for the manufacture and supply of our systems, which would prevent us from being able to provide products to our customers in a timely fashion, or at all, and therefore harm our business.

Failure to comply with the applicable regulatory requirements can result in, among other things, warning letters, administrative or judicially imposed sanctions such as injunctions, civil penalties, recall or seizure of products, total or partial suspension of production, refusal to grant PMA for devices, withdrawal of marketing clearances or approvals, or criminal prosecution. For example, on July 27, 2015 Cepheid received a warning letter from the FDA regarding the Xpert Norovirus test describing deficiencies in the production quality system at Cepheid’s Stockholm, Sweden manufacturing facility. We continue to actively work with the FDA on resolution of the deficiencies. The Xpert Norovirus test manufactured in Sweden is not sold or distributed in the United States. As a result, it is our expectation that routine production and sale of the Xpert Norovirus test in the United States will not be affected. International sales of this test are not subject to FDA regulation. Until we successfully resolve the issues raised in the warning letter, the FDA will not approve any Cepheid Class III product. Cepheid has some Class III products currently in development but these are not currently expected to be available until late 2017.

With regard to future products for which we seek 510(k) clearance, PMA, and/or a CLIA waiver (as appropriate) from the FDA, or similar regulatory approvals from foreign regulatory agencies, any failure or material delay to obtain such clearance or approval could harm our business. In addition, it is possible that the current regulatory framework could change or additional regulations could arise at any stage during our product development or marketing, which may adversely affect our ability to obtain or maintain approval of our products and could harm our business. For example, earlier this year, the Department of Health and Human Services announced plans for a Notice of Proposed Rulemaking on Federal Policy for the Protection of Human Subjects (NPRM), which, if enacted in its entirety, could substantially limit the use of leftover, de-identified clinical specimens for pre-clinical and clinical research by requiring informed consent for all clinical specimens. Cepheid and other diagnostic development companies routinely use leftover, de-identified specimens to support pre-clinical and clinical research. A requirement for informed consent on all clinical specimens would substantially increase the cost and potentially limit the accessibility to these types of specimens.

Recently enacted healthcare legislation reforming the United States healthcare system, as well as future reforms, may have a material adverse effect on our financial condition and results of operations.

In 2010, the United States President signed the Patient Protection and Affordable Care Act, as amended by the Health Care and Education Reconciliation Act (collectively, the “PPACA”), which makes changes that are expected to significantly impact the pharmaceutical and medical device industries, including a requirement that medical device manufacturers pay an excise tax (or sales tax) of 2.3% of certain United States medical device revenue. Although the device tax was suspended for two years in January 2016, the medical device excise tax will be reinstated beginning on January 1, 2018, subject to any intervening legislative action. This excise tax will apply to most of our products sold within the United States and will result in decreased profits to us, which will adversely affect our financial condition and results of operations.

Legislative changes have been proposed and adopted since the PPACA was enacted. For example, on August 2, 2011, the United States President signed into law the Budget Control Act of 2011, which, among other things, creates the Joint Select Committee on Deficit Reduction to recommend proposals in spending reductions to Congress. The Joint Select Committee did not achieve a targeted deficit reduction of at least $1.2 trillion for the years 2013 through 2021, triggering the legislation’s automatic reduction to several government programs. This included aggregate reductions to Medicare payments to providers of 2% per fiscal year, which went into effect on April 1, 2013, and will remain in effect through 2024 unless additional congressional action is taken. On January 2, 2013, the American Taxpayer Relief Act of 2012 was signed into law, which, among other things, further reduced Medicare payments to several providers, including hospitals, imaging centers and cancer treatment centers, which could mean that such providers have less available funds to purchase our products.

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The Protecting Access to Medicare Act of 2014 (“PAMA”) will require applicable laboratories to report all private payor reimbursement rates and the volumes for each test it performs. The final rule published in June 2016, requires that Medicare establish reimbursement rates based on the weighted median of private insurance reimbursement rates effective January 1, 2018. The new Medicare rates would be subject to a maximum reduction of 10% a year for the initial three year period and a maximum of 15% a year for the subsequent three year period. There is no limit on the amount of potential rate increases. As a result, some of our customers in the United States may experience lower Medicare reimbursement rates for our products, which may adversely affect our business, financial condition and results of operations.

We expect that additional state and federal health care reform measures may be adopted in the future, any of which could have a material adverse effect on our industry generally and our ability to successfully commercialize our products. The United States government has in the past considered, is currently considering and may in the future consider healthcare policies and proposals intended to curb rising healthcare costs, including those that could significantly affect both private and public reimbursement for healthcare services. For example, the United States government implemented bundled payment mechanisms, such as the Center for Medicare & Medicaid Service’s Comprehensive Joint Replacement program for total hip/total knee arthroplasty procedures, which allows one fixed payment for the procedure and all related healthcare services for a period of 90-days post discharge. Further, state and local governments, as well as a number of foreign governments, are also considering or have adopted similar types of policies. Future significant changes in the healthcare systems in the United States or elsewhere, and current uncertainty about whether and how changes may be implemented, could have a negative impact on the demand for our products. We are unable to predict whether other healthcare policies, including policies stemming from legislation or regulations affecting our business may be proposed or enacted in the future; what effect such policies would have on our business; or the effect ongoing uncertainty about these matters will have on the purchasing decisions of our customers.

Our HBDC program exposes us to increased risks of variability and unpredictable operating results.

Our HBDC program exposes us to risks that are additional and different from the risks associated with our commercial operations, including among other things:

• the participants in our HBDC program are located in less developed countries, exposing us to customers in countries that may have less political, social or economic stability and less developed infrastructure and legal systems;

• the sales cycle in our HBDC program is lengthy and unpredictable, as HBDC program participants are frequently dependent upon governmental agencies and/or non-governmental organizations with additional administrative processes, causing variability and unpredictability in our operating results and timing of cash collection;

• our HBDC program has lower gross margins and, therefore, growth in our HBDC program as a percentage of total revenue negatively impacts our gross margins as a whole; and

• our collaborative partners and other supporters, such as FIND, BMGF, USAID, UNITAID, UNOPS - Global Drug Facility and the World Health Organization, may cease to devote financial resources to or otherwise cease to support our HBDC program, which may result in excess capacity and higher production costs.

Continued unpredictable sales cycles and lower gross margins and/or an adverse development relating to one or more of these risks could negatively impact our business, results of operations and financial condition. Additionally, our HBDC program facilitates the expansion of our commercial operations into additional geographic locations and, to the extent that our HBDC program is ineffective as a result of one or more of these risks, the international expansion of our commercial operations could suffer.

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We may face risks associated with acquisitions of companies, products and technologies and our business could be harmed if we are unable to address these risks.

In order to remain competitive, obtain key competencies, consolidate our supply chain or sales force, acquire complementary products or technologies, or for other reasons, we may seek to acquire additional businesses, products or technologies. Even if we identify an appropriate acquisition or are presented with appropriate opportunities to acquire or make other investments, we may not be successful in negotiating the terms of the acquisition, financing the acquisition, consummating the acquisition or effectively integrating the acquired business, product or technology into our existing business and operations. For example, in 2012, we acquired one of our plastic molders; in 2013, we acquired distributors in two of our international locations; and in 2014, we re-acquired certain product distribution rights and acquired customer relationship assets from a former distributor in the United States. We have limited experience in successfully acquiring and integrating businesses, products and technologies, and even if we are able to consummate an acquisition or other investment, we may not realize the anticipated benefits of such acquisitions or investments, including our recent acquisitions. We may face risks, uncertainties and disruptions, including difficulties in the integration of the operations and services of these acquisitions or any other acquired company, integration of acquired technology with our products, diversion of our management’s attention from other business concerns, the potential loss of key employees or customers of the acquired businesses and impairment charges if future acquisitions are not as successful as we originally anticipate. If we fail to successfully integrate companies, assets, products or technologies that we acquire or if we fail to successfully exploit acquired product distribution rights and maintain acquired relationships with customers, our business could be harmed. Furthermore, we may have to incur debt or issue equity securities to pay for any additional future acquisitions or investments or issue shares of common stock as consideration in the acquisition, the issuance of which could be dilutive to our existing shareholders. In addition, our operating results may suffer because of acquisition-related costs or amortization expenses or charges relating to acquired intangible assets. Furthermore, identifying, contemplating, negotiating or completing an acquisition and integrating an acquired business, product or technology could significantly divert management and employee time and resources.

The current uncertainty in global economic conditions makes it particularly difficult to predict product demand and other related matters and makes it more likely that our actual results could differ materially from expectations.

Our operations and performance depend on global economic conditions, which have been adversely impacted by continued global economic uncertainty, including the implications of the recent "Brexit" vote in the United Kingdom, political instability and military hostilities in multiple geographies, the recent strengthening of the United States dollar compared to foreign currencies, the volatility of the capital markets in the United States and abroad, and monetary and international financial uncertainties. These conditions have and may continue to make it difficult for our customers and potential customers to accurately forecast and plan future business activities, and have caused our customers and potential customers to slow or reduce spending, particularly for systems. Furthermore, during economic uncertainty, our customers have experienced and may continue to experience issues gaining timely access to sufficient credit, which could result in their unwillingness to purchase products or an impairment of their ability to make timely payments to us. If that were to continue to occur, we might experience decreased sales, be required to increase our allowance for doubtful accounts and our days sales outstanding would be negatively impacted. Even with improved global economic conditions, it may take time for our customers to establish new budgets and return to normal purchasing patterns. We cannot predict the recurrence or worsening of any economic slowdown or the sustainability of improved economic conditions, worldwide, in the United States or in our industry. These and other economic factors could have a material adverse effect on demand for our products and on our financial condition and operating results.

If certain of our products fail to obtain an adequate level of reimbursement from third-party payers, our ability to sell products in the Clinical market would be harmed.

Our ability to sell our products in the Clinical market will depend in part on the extent to which reimbursement for tests using our products will be available from government health administration authorities, private health coverage insurers, managed care organizations and other organizations. There are efforts by governmental and third-party payers to contain or reduce the costs of healthcare through various means and the continuous growth of managed care, together with efforts to reform the healthcare delivery system in the United States and Europe, has increased pressure on healthcare providers and participants in the healthcare industry to reduce costs. Consolidation among healthcare providers and other participants in the healthcare industry has resulted in fewer, more powerful healthcare groups, whose purchasing power gives them cost containment leverage. Additionally, third-party payers are increasingly challenging the price of medical products and services. If purchasers or users of our products are not able to obtain adequate reimbursement for the cost of using our products, they may forego or reduce their use. Significant uncertainty exists as to the reimbursement status of newly approved healthcare products and whether adequate third-party coverage will be available.

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The life sciences industry is highly competitive and subject to rapid technological change, if our competitors and potential competitors develop superior products and technologies, our competitive position and results of operations would suffer.

We face intense competition from a number of companies that offer products in our target markets, some of which have substantially greater financial, technical, research and other resources and larger, more established marketing, sales, distribution and service organizations than we do. Moreover, these competitors may offer broader product lines and tactical discounts and have greater name recognition. These competitors include:

• companies developing and marketing sequence detection systems for production of laboratory-developed tests;

• diagnostic companies; and

• companies developing or offering biothreat detection technologies.

Several companies provide systems and reagents for DNA amplification or detection. Life Technologies Corporation (acquired by Thermo Fisher Scientific) and Roche sell systems integrating DNA amplification and detection to the commercial market. Roche, Abbott, Becton Dickinson and Company, Qiagen N.V., Hologic Inc., Luminex Corporation, Meridian Bioscience, Inc., Biofire Diagnostics, Inc. (which was acquired by bioMerieux SA in 2014), and Quidel Corporation sell nucleic acid detection systems, some with separate robotic batch DNA purification systems, and sell reagents to the Clinical market. Other companies, such as Nanosphere Inc. (which was acquired by Luminex Corporation in June 2016), Alere Inc. (which announced an agreement to be acquired by Abbott in February 2016), and GenMark Diagnostics, Inc., offer molecular tests. Additionally, we anticipate that in the future, additional competitors will emerge that offer a broad range of competing products.

In addition, consolidation trends in the pharmaceutical and biotechnology industries, such as Luminex's acquisition of Nanosphere and Abbott’s announced acquisition of Alere, have served to create fewer customer accounts and to concentrate purchasing decisions for some customers. Moreover, customers may believe that consolidated businesses are better able to compete as sole source vendors and therefore, prefer to purchase from such businesses.

The life sciences industry is characterized by rapid and continuous technological innovation. We may need to develop new technologies for our products to remain competitive. For example, we are developing products in oncology, which is a key part of our strategy. If we are unable to successfully develop these products, our business could be harmed.

Additionally, one or more of our current or future competitors could render our present or future products technologically obsolete or uneconomical by introducing new products or reducing the prices of their competing products. In addition, the introduction or announcement of new products by us or others could result in a delay of or decrease in sales of existing products, as we await regulatory approvals and as customers evaluate these new products. We may also encounter other problems in the process of delivering new products to the marketplace such as problems related to design, development or manufacturing of such products or problems related to our distribution agreements or the effectiveness of our sales team, and as a result we may be unsuccessful in selling such products. Our future success depends on our ability to compete effectively against current technologies, as well as to respond effectively to technological advances by developing and marketing products that are competitive in the continually changing technological landscape. If we fail to compete effectively, we could lose sales, and our business will be harmed.

If our products do not perform as expected or the reliability of the technology on which our products are based is questioned, we could experience lost revenue, delayed or reduced market acceptance of our products, increased costs and damage to our reputation.

Our success depends on the market’s confidence that we can provide reliable, high-quality molecular systems and tests. We believe that customers in our target markets are likely to be particularly sensitive to product defects and errors. Our reputation and the public image of our products or technologies may be impaired if our products fail to perform as expected or our products are perceived as difficult to use. Despite testing, defects or errors could occur in our products or technologies. Furthermore, with respect to the USPS BDS program, our products are incorporated into larger systems that are built and delivered by others and we cannot control many aspects of the final system.

In the future, if our products experience a material defect or error, this could result in loss or delay of revenue, delayed market acceptance, damaged reputation, diversion of development resources, legal claims, increased insurance costs or increased service and warranty costs, any of which could harm our business. Such defects or errors could also prompt us to amend certain warning labels or narrow the scope of the use of our products, either of which could hinder our success in the market. Furthermore, any product failure in the overall USPS BDS program, even if it is unrelated to our products, could harm our business. Even after any underlying concerns or problems are resolved, any widespread concerns regarding our technology or any manufacturing defects or performance errors in our products could result in lost revenue, delayed market acceptance, damaged reputation, increased service and warranty costs and claims against us.

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If product liability lawsuits are successfully brought against us, we may face reduced demand for our products and incur significant liabilities.

We face an inherent risk of exposure to product liability claims if our technologies or systems are alleged to have caused harm or do not perform in accordance with specifications, in part because our products are used for sensitive applications. We cannot be certain that we would be able to successfully defend any product liability lawsuit brought against us. Regardless of merit or eventual outcome, product liability claims may result in:

• decreased demand for our products;

• injury to our reputation;

• increased product liability insurance costs;

• costs of related litigation; and

• substantial monetary awards to plaintiffs.

Although we carry product liability insurance, if we become the subject of a successful product liability lawsuit, our insurance may not cover all substantial liabilities, which could harm our business.

If our distributor relationships are not successful, our ability to market and sell our products would be harmed and our financial performance will be adversely affected.

We depend on relationships with distributors for the marketing and sales of our products in the clinical and non-clinical markets in various geographic regions, and we have a limited ability to influence their efforts. We expect to continue to rely substantially on our distributor relationships for sales, which are key to our long-term growth strategy. For example, we recently entered into significant, non-exclusive agreements with Henry Schein, Medline, and McKesson offering our GeneXpert Systems to their non-acute care laboratory customers in the United States and intend to enter into additional distribution agreements to penetrate this market. Relying on distributors for our sales and marketing could harm our business for various reasons, including:

• agreements with distributors may terminate prematurely due to disagreements or may result in litigation between the partners;

• we may not be able to renew existing distributor agreements on acceptable terms;

• our distributors may not devote sufficient resources to the sale of our products;

• our distributors may be unsuccessful in marketing our products; and

• our existing relationships with distributors may preclude us from entering into additional future arrangements with other distributors.

If any of our distribution agreements are terminated or if we elect to distribute products directly, as occurred in October 2014 when we terminated our distribution agreement with the Laboratory Supply Company and transitioned the smaller hospital market from a distributor sales model to a direct sales model, we may incur one-time costs or litigation risk related to such terminations and transitions. Additionally, we will have to invest in alternative distribution agreements or additional sales personnel, which would increase future selling expenses and result in transition risks, such as difficulties maintaining relationships with specific customers and hiring appropriately trained personnel, any of which could result in lower revenue. Further, if we elect to distribute products directly in markets or geographic regions in which we were previously relying on distributors, as a result of termination of our distribution agreement or otherwise, then we would be exposed to similar risks.

As we seek to enter into other distribution arrangements, we may not be able to enter into new distribution agreements on satisfactory terms, or at all. For example, we may desire to enter into additional distribution agreements for our new point-of-care diagnostic platform and may not be able to enter into such agreements on satisfactory terms, or at all. If we fail to enter into acceptable distribution agreements that we deem are necessary or otherwise fail to successfully market our products, including our new point-of-care diagnostic platform, our product sales may decrease or we may be unable to successfully launch our new point-of-care diagnostic platform.

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Guidelines, recommendations and studies published by various organizations may reduce the use of our products.

Professional societies, government agencies, practice management groups, private health/science foundations, research institutions, hospitals and other organizations involved in healthcare issues may publish guidelines, recommendations or studies to the healthcare and patient communities. Recommendations of government agencies or from such other societies, agencies, groups, foundations, institutions, hospitals and other organizations may relate to such matters as usage and cost-effectiveness of our GeneXpert systems and tests, and use of related therapies. Guidelines, recommendations and studies have been published about our products and those of our competitors. If followed by healthcare providers and payers or insurers, such recommendations, guidelines or studies could impact the use of our products and, if such recommendations, guidelines or studies are negative about our products, our business could be harmed.

We rely on licenses of key technology from third parties and may require additional licenses for many of our new product candidates.

We rely on third-party licenses to be able to sell many of our products, and we could lose these third-party licenses for a number of reasons, including, for example, early terminations of such agreements due to breaches or alleged breaches by either party to the agreement. If we are unable to enter into a new agreement for licensed technologies, either on terms that are acceptable to us or at all, we may be unable to sell some of our products or access some geographic or industry markets. We also need to introduce new products and product features in order to market our products to a broader customer base and grow our revenue, and many new products and product features could require us to obtain additional licenses and pay additional license fees and royalties. Furthermore, for some markets, we intend to manufacture reagents and tests for use on our systems. We believe that manufacturing reagents and developing tests for our systems is important to our business and growth prospects but may require additional licenses, which may not be available on commercially reasonable terms or at all. Our ability to develop, manufacture and sell products, and our strategic plans and growth, could be impaired if we are unable to obtain these licenses or if these licenses are terminated or expire and cannot be renewed. We may not be able to obtain or renew licenses for a given product or product feature or for some reagents on commercially reasonable terms, if at all. Furthermore, some of our competitors have rights to technologies and reagents that we do not have, which may put us at a competitive disadvantage in certain circumstances and could adversely affect our performance.

We may be subject to third-party claims that require additional licenses for our products and we could face costly litigation, which could cause us to pay substantial damages and limit our ability to sell some or all of our products.

Our industry is characterized by a large number of patents, claims of which appear to overlap in many cases. As a result, there is a significant amount of uncertainty regarding the extent of patent protection and infringement. Companies may have pending patent applications, which are typically confidential for the first eighteen months following filing, that cover technologies we incorporate in our products. Accordingly, we may be subjected to substantial damages for past infringement or be required to modify our products or stop selling them if it is ultimately determined that our products infringe a third party’s proprietary rights. Moreover, from time to time, we are subject to patent litigation and receive correspondence and other communications from companies that ask us to evaluate the need for a license of patents they hold, and indicating or suggesting that we need a license to their patents in order to offer our products and services or to conduct our business operations. For example, we are currently engaged in litigation as further described in Part II, Item 1 “Legal Proceedings.” At this point in time we believe that it is probable that the Roche arbitration proceeding disclosed in Part II, Item 1 “Legal Proceedings” could result in a material loss. Accordingly, we recorded an estimated charge of $20 million as our best estimate of the potential loss as of December 31, 2014, which was included in our consolidated balance sheet. This continues to be our best estimate for this potential loss as of September 30, 2016. Further, if we were to incur a loss in the arbitration proceeding, depending on the final ruling of the arbitrators, it is possible that we could also be responsible for certain fees, costs and/or interest, if any; however, we are unable at this time to determine the likelihood of whether these potential outcomes will occur or estimate their respective potential amounts. Even if we are successful in defending against any current or future patent claims, we would likely incur substantial costs in doing so. Any litigation related to existing claims and others that may arise in the future would likely consume our resources and could lead to significant damages, royalty payments or an injunction on the sale of certain products. Any additional licenses to patented technology could obligate us to pay substantial additional royalties, which could adversely impact our product costs and harm our business.

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If we fail to maintain and protect our intellectual property rights, our competitors could use our technology to develop competing products and our business will suffer.

Our competitive success will be affected in part by our continued ability to obtain and maintain patent protection for our inventions, technologies and discoveries, including our intellectual property that includes technologies that we license. Our ability to do so will depend on, among other things, complex legal and factual questions. We have patents related to some of our technology and have licensed some of our technology under patents of others. Our patents and licenses may not successfully preclude others from using our technology. Our pending patent applications may lack priority over applications submitted by third parties or may not result in the issuance of patents. Even if issued, our patents may not be sufficiently broad to provide protection against competitors with similar technologies and may be challenged, invalidated or circumvented.

In addition, there are numerous recent changes to the patent laws and proposed changes to the rules of the USPTO, which may have a significant impact on our ability to protect our technology and enforce our intellectual property rights. For example, in September 2011, the United States enacted sweeping changes to the United States patent system under the Leahy-Smith America Invents Act, including changes that would transition the United States from a “first-to-invent” system to a “first-to-file” system and alter the processes for challenging issued patents. These changes could increase the uncertainties and costs surrounding the prosecution of our patent applications and the enforcement or defense of our issued patents. In addition to patents, we rely on a combination of trade secrets, copyright and trademark laws, nondisclosure agreements, licenses and other contractual provisions and technical measures to maintain and develop our competitive position with respect to intellectual property. Nevertheless, these measures may not be adequate to safeguard the technology underlying our products. For example, employees, consultants and others who participate in the development of our products may breach their agreements with us regarding our intellectual property or otherwise act improperly in relation to our proprietary information, and we may not have adequate remedies for the breach or improper actions. We also may not be able to effectively protect our intellectual property rights in some foreign countries, as many countries do not offer the same level of legal protection for intellectual property as the United States. Furthermore, for a variety of reasons, we may decide not to file for patent, copyright or trademark protection outside of the United States. Our trade secrets could become known through other unforeseen means. Notwithstanding our efforts to protect our intellectual property, our competitors may independently develop similar or alternative technologies or products that are equal or superior to our technology. Our competitors may also develop similar products without infringing on any of our intellectual property rights or design around our proprietary technologies.

Furthermore, any efforts to enforce our proprietary rights could result in disputes and legal proceedings that could be costly and divert attention from our business. For example, the America Invents Act enacted proceedings involving various forms of post-issuance patent review proceedings, such as IPR and covered business method review. These proceedings are conducted before the Patent Trial and Appeal Board (“PTAB”) of the United States Patent and Trademark Office. Each has different eligibility criteria and different types of challenges that can be raised. The IPR process permits any person (except a party who has been litigating the patent for more than a year) to challenge the validity of a patent on the grounds that it was known from the prior art. Recently, entities associated with hedge funds have begun challenging valuable pharmaceutical patents through IPR proceedings. The filing of such proceedings or the issuance of an adverse decision in such proceedings could result in the loss of valuable patent rights that could have a material adverse effect on our business, financial condition, results of operations and growth prospects.

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Data breaches and cyber-attacks could compromise our intellectual property or other sensitive information and cause significant damage to our business and reputation.

In the ordinary course of our business, we maintain sensitive data on our networks, including our intellectual property and proprietary or confidential information relating to our business and that of our customers and business partners. The secure maintenance of this information is critical to our business and reputation. Companies have been increasingly subject to a wide variety of security incidents, cyber-attacks and other attempts to gain unauthorized access. These threats can come from a variety of sources, ranging in sophistication from an individual hacker to malfeasance by employees, consultants or other service providers to state-sponsored attacks. Cyber threats may be generic, or they may be custom-crafted against our information systems. Over the past several years, cyber-attacks have become more prevalent and much harder to detect and defend against. Our network and storage applications may be vulnerable to cyber-attack, malicious intrusion, malfeasance, loss of data privacy or other significant disruption and may be subject to unauthorized access by hackers, employees, consultants or other service providers. For example, in the second quarter of 2015, an individual, whose association with us has since been terminated, accessed our system and downloaded material in an unauthorized manner. Such data breaches and any unauthorized access or disclosure of our information or intellectual property could compromise our intellectual property and expose other confidential information and sensitive business information. Cyber-attacks could also cause us to incur significant remediation costs, result in product development delays, disrupt key business operations and divert attention of management and key information technology resources. These incidents could also subject us to liability, expose us to significant expense and cause significant harm to our reputation and business. It is often difficult to anticipate or immediately detect such incidents and the damage caused by such incidents. There can be no assurance that our systems and data protection efforts will prevent future business interruptions or loss or corruption of data.

The United States Government has certain rights to use and disclose some of the intellectual property that we license and could exclusively license it to a third party if we fail to achieve practical application of the intellectual property.

Aspects of the technology licensed by us under agreements with third party licensors may be subject to certain government rights. Government rights in inventions conceived or reduced to practice under a government-funded program may include a non-exclusive, royalty-free worldwide license to practice or have practiced such inventions for any governmental purpose. In addition, the United States federal government has the right to require us or our licensors (as applicable) to grant licenses which would be exclusive under any of such inventions to a third party if they determine that: (1) adequate steps have not been taken to commercialize such inventions in a particular field of use; (2) such action is necessary to meet public health or safety needs; or (3) such action is necessary to meet requirements for public use under federal regulations. Further, the government rights include the right to use and disclose, without limitation, technical data relating to licensed technology that was developed in whole or in part at government expense. At least one of our technology license agreements contains a provision recognizing these government rights.

We may need to initiate lawsuits to protect or enforce our patents, which would be expensive and, if we lose, may cause us to lose some, if not all, of our intellectual property rights and thereby impair our ability to compete.

We rely on patents to protect a large part of our intellectual property. To protect or enforce our patent rights, we may initiate patent litigation against third parties, such as infringement suits or interference proceedings. These lawsuits could be expensive, take significant time and divert management’s attention from other business concerns. They would also put our patents at risk of being invalidated or interpreted narrowly, and our patent applications at risk of not issuing. We may also provoke these third parties to assert claims against us. Patent law relating to the scope of claims in the technology fields in which we operate is still evolving and, consequently, patent positions in our industry are generally uncertain. We cannot be assured that we would prevail in any of these suits or that the damages or other remedies awarded, if any, would be commercially valuable. During the course of these suits, there may be public announcements of the results of hearings, motions and other interim proceedings or developments in the litigation. Any public announcements related to such patent suits could cause our stock price to decline.

Our international operations subject us to additional risks and costs.

We conduct operations on a global basis. These operations are subject to a number of difficulties and special costs, including:

• compliance with multiple, conflicting and changing governmental laws and regulations, including United States laws such as the Foreign Corrupt Practices Act and local laws that prohibit bribes and certain payments to governmental officials such as the UK Bribery Act 2010, data privacy requirements, labor relations laws, tax laws, anti-competition regulations, import and trade restrictions, governmental rebate requirements and export requirements;

• increased regulatory risk, including additional regulatory requirements different or more stringent than those in the United States;

• laws and business practices favoring local competitors;

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• foreign exchange and currency risks;

• exposure to risks associated with sovereign debt uncertainties in Europe and other foreign countries, including the potential implication of the recent "Brexit" vote;

• difficulties in collecting accounts receivable or longer payment cycles;

• bank guarantee requirements;

• import and export restrictions and tariffs;

• difficulties staffing and managing foreign operations;

• reliance on partners with local expertise and resources (for example, our relationship with a partner in India related to delivery, installation and acceptance of certain of our systems in India);

• difficulties and expense in enforcing intellectual property rights;

• business risks, including fluctuations in demand for our products and the cost and effort to conduct international operations and travel abroad to promote international distribution and overall global economic conditions;

• multiple conflicting tax laws and regulations;

• timing and uncertainty of system orders; and

• political and economic instability and outbreak of military hostilities.

In addition, foreign court judgments or regulatory actions could impact our ability to transfer, process and receive transnational data, including data relating to customers or partners outside the United States. Such judgments or actions could affect the manner in which we operate or adversely affect our financial results.

We intend to expand our international sales and marketing activities, including through our direct sales operations and through relationships with additional international distribution partners. We may not be able to attract international distribution partners that will be able to market our products effectively or may have trouble entering geographic markets that are less receptive to sales from foreign entities. Our reliance on international distribution partners may subject us to increased financial and operational risk, as our revenue and costs will be impacted by how successfully such distribution partners sell our products in international markets and by the terms on which such distribution partners are engaged. Further, should we need to transition between international distribution partners, we could be exposed to various costs and risks as further described above under the heading “If our distributor relationships are not successful, our ability to market and sell our products would be harmed and our financial performance will be adversely affected.”

Additionally, our continued expansion into less developed countries in connection with our HBDC program, which may have less political, social or economic stability and less developed infrastructure and legal systems, heightens the exposure of the risks set forth above. An adverse development relating to one or more of these risks, or any other risks associated with our operations in less developed countries, could adversely affect our ability to conduct and expand our business, which could negatively impact our business, results of operations and financial condition.

Our international operations could also increase our exposure to international laws and regulations. If we cannot comply with foreign laws and regulations, which are often complex and subject to variation and unexpected changes, we could incur unexpected costs and potential litigation. For example, the governments of foreign countries might attempt to regulate our products and services, require mandatory rebates to the government, or levy sales or other taxes relating to our activities. In addition, foreign countries may impose tariffs, duties, price controls or other restrictions on foreign currencies or trade barriers, any of which could make it more difficult for us to conduct our business.

Further, as we continue to expand our operations worldwide and potentially sell our products and services to governmental institutions, compliance with Foreign Corrupt Practices Act and local laws that also prohibit corrupt payments to governmental officials such as the UK Bribery Act 2010 will become increasingly more important and we will need to continue to enhance our internal controls to ensure compliance with applicable laws and regulations.

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We intend to expand our business into new geographic markets, and this expansion may be costly and may not be successful.

We plan to make substantial investments of both time and money as part of our continued and existing expansion into new geographic markets. For example, we expect to expand operations in China, India and Japan. When we expand into new geographic markets, we incur set up costs for new personnel, facilities, travel, inventory and related expenses in advance of securing new customer contracts. We may face challenges operating in new business climates with which we are unfamiliar, including facing difficulties in staffing and managing our new operations, fluctuations in currency exchange rates, exposure to additional regulatory requirements such as additional regulatory filing and approval requirements for our products, changes in political and economic conditions and exposure to additional and potentially adverse tax regimes. Our success in any new markets will depend, in part, on our ability to anticipate and effectively manage these and other risks. It is also possible that we will face increased competition in any new markets as other companies attempt to take advantage of the new market opportunities, and any such competitors could have substantially more resources than we do and may have better relationships and a greater understanding of the region. If we fail to manage the risks inherent in our geographic expansion, we could incur substantial capital and operating costs without any related increase in revenue, which would harm our operating results. Further, even if our geographic expansion is successful, failure to effectively manage our growth in a cost-effective manner could result in declines in customer satisfaction, increased costs or disruption of our operations.

A significant portion of our sales are denominated in foreign currencies and currency fluctuations and hedging expenses may cause our revenue and earnings to fluctuate and our foreign currency hedging program may not adequately offset foreign currency exposure.

A significant percentage of our product sales are denominated in foreign currencies, primarily the Euro. When the United States dollar strengthens against these foreign currencies, as it has recently, the relative value of sales made in the respective foreign currency decreases. Overall, we are a net receiver of foreign currencies and, therefore, benefit from a weaker United States dollar and are adversely affected by a stronger United States dollar relative to those foreign currencies in which we transact significant amounts of business.

We use foreign currency exchange forward contracts to hedge a portion of our forecasted revenue. We also hedge certain monetary assets and liabilities denominated in foreign currencies, which reduces but does not eliminate our exposure to currency fluctuations between the date a transaction is recorded and the date that cash is collected or paid. We cannot predict future fluctuations in the foreign currency exchange rate. If the United States dollar appreciates significantly against certain currencies and our hedging program does not sufficiently offset the effects of such appreciation, our results of operations will be adversely affected and our stock price may decline. For example, the impact of foreign currency exchange contributed to lower than expected revenue and gross margin for fiscal 2015. We expect that foreign currency rates will continue to negatively impact our international revenue. In 2015, we realized a $7.4 million benefit from foreign currency exchange forward contracts. The majority of our foreign currency exchange forward contracts that we expect to mature in 2016 were placed after the strengthening of the United States dollar. Therefore, we do not expect to recognize similar hedging gains in revenue in 2016 and we may even recognize hedging losses in revenue, which may adversely impact periodic revenue comparisons.

Additionally, the expenses that we recognize in relation to our hedging activities can cause our earnings to fluctuate. The changes in forward points paid or received driven by the interest rate spreads between the foreign currencies that we hedge and the United States dollar impact the level and timing of hedging expenses that we recognize in a particular period.

The nature of some of our products may also subject us to export control regulation by the United States Department of State and the Department of Commerce. Violations of these regulations can result in monetary penalties and denial of export privileges.

Our sales to customers outside the United States are subject to government export regulations that require us to obtain licenses to export such products. If the United States government was to amend its export control regulations, such amendments could create uncertainty in our industry, result in increased costs of compliance, and further restrict our ability to sell our products abroad. In particular, we are required to obtain a new license for each purchase order of our biothreat products that are exported outside the United States. Delays or denial of the grant of any required license, or changes to the regulations that make such delays or denials more likely or frequent, could make it difficult to make sales to foreign customers and could adversely affect our revenue. In addition, we could be subject to fines and penalties for violation of these export regulations if we were found in violation. Such violation could result in penalties, including prohibiting us from exporting our products to one or more countries, and could materially and adversely affect our business.

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If we fail to retain key members of our staff or successfully manage our succession planning, our ability to conduct and expand our business would be impaired.

We are highly dependent on the principal members of our management, scientific and engineering staff and on the development of adequate succession plans for such employees. If we lose the services of any of these persons and we are unable to find a suitable replacement in a timely manner or we fail to successfully manage our succession planning and organizational development, we may be challenged to effectively manage our business and execute our strategy, which could seriously harm our product development and commercialization efforts. In addition, we require skilled personnel in areas such as microbiology, clinical, sales, marketing and finance. We generally do not enter into employment agreements requiring these employees to continue in our employment for any period of time. Attracting, retaining, developing and training personnel, including management, with the requisite skills remains challenging, particularly in the Silicon Valley, where our main office is located. Additionally, if at any point we are unable to hire, train, develop and retain a sufficient number of qualified employees to support our growth, our ability to conduct and expand our business could be seriously reduced.

We may face issues in connection with our recent implementation of an ERP system.

In order to support our growth, we recently implemented a new ERP system that became operational in the first quarter of 2015. This process has been and continues to be complex and time-consuming and we expect to incur additional expenses as we continue to make enhancements to our integrated financial and supply chain management systems. For example, following implementation we experienced delays in our customer billing and collection processes. Our ERP system implementation and additional enhancements to our financial and supply chain management systems may further disrupt our operations and may not result in improvements that outweigh its costs. Many companies have experienced delays and difficulties with the implementation of new or changed ERP systems that have had a negative effect on their business. Additionally, our ability to forecast sales demand, ship products, manage our product inventory and record and report financial and management information on a timely and accurate basis could be impaired while we are making further enhancements to our financial and supply chain management systems. Significant disruptions or operational impacts could have a material adverse impact on our results of operation.

If we become subject to claims relating to improper handling, storage or disposal of hazardous materials, we could incur significant cost and time to comply.

Our research and development processes involve the controlled storage, use and disposal of hazardous materials, including biological hazardous materials. We are subject to foreign, federal, state and local regulations governing the use, manufacture, storage, handling and disposal of materials and waste products. We may incur significant costs complying with both existing and future environmental laws and regulations. In particular, we are subject to regulation by the Occupational Safety and Health Administration (“OSHA”) and the Environmental Protection Agency (“EPA”), and to regulation under the Toxic Substances Control Act and the Resource Conservation and Recovery Act in the United States OSHA or the EPA may adopt regulations that may affect our research and development programs. We are unable to predict whether any agency will adopt any regulations that would have a material adverse effect on our operations.

The risk of accidental contamination or injury from hazardous materials cannot be eliminated completely. In the event of an accident, we could be held liable for any damages that result, and any liability could exceed the limits or fall outside the coverage of our workers’ compensation insurance. We may not be able to maintain insurance on acceptable terms, if at all.

If a catastrophe strikes our manufacturing or warehousing facilities, we may be unable to manufacture or distribute our products for a substantial amount of time and we may experience inventory shortfalls, which would cause us to experience lost revenue.

Our manufacturing facilities are located in Sunnyvale and Lodi, California, Seattle, Washington and Stockholm, Sweden. Although we have business interruption insurance, our facilities and some pieces of manufacturing equipment are difficult to replace and could require substantial replacement lead-time. Various types of disasters, including earthquakes, fires, floods and acts of terrorism, may affect our manufacturing facilities or the manufacturing facilities of our contract manufacturer. Earthquakes are of particular significance since our primary manufacturing facilities in California are located in an earthquake-prone area. In the event our existing manufacturing facilities or equipment, or the manufacturing facilities or equipment of our contract manufacturer, are affected by man-made or natural disasters, we may be unable to manufacture products for sale or meet customer demands or sales projections. If our manufacturing operations were curtailed or ceased, it would seriously harm our business.

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We might require additional capital to respond to business challenges or acquisitions, and such capital might not be available.

We may in the future need to obtain additional equity or debt financing to respond to business challenges or acquire complementary businesses and technologies. Any additional equity or debt financing, however, might not be available when needed or, if available, might not be available on terms satisfactory to us. In addition, to the extent that additional capital is raised through the sale of equity or convertible debt securities, the issuance of these securities could result in dilution to our shareholders. In addition, these securities may be sold at a discount from the market price of our common stock and may include rights, preferences or privileges senior to those of our common stock. If additional equity or debt financing is needed and we are unable to obtain adequate financing or financing on terms satisfactory to us, our ability to continue to support our business growth and to respond to business challenges could be significantly limited.

We rely on relationships with collaborative partners and other third parties for development, supply and marketing of certain products and potential products, and such collaborative partners or other third parties could fail to perform sufficiently.

We believe that our success in penetrating our target markets depends in part on our ability to develop and maintain collaborative relationships with other companies. Relying on collaborative relationships is risky to our future success for our products because, among other things:

• our collaborative partners may not devote sufficient resources to the success of our collaborations;

• our collaborative partners may not obtain regulatory approvals necessary to continue the collaborations in a timely manner;

• our collaborative partners may be acquired by other companies and decide to terminate our collaborative partnership or become insolvent;

• our collaborative partners may develop technologies or components competitive with our products;

• components developed by collaborators could fail to meet specifications, possibly causing us to lose potential projects and subjecting us to liability;

• disagreements with collaborators could result in the termination of the relationship or litigation;

• collaborators may not have sufficient capital resources;

• collaborators may pursue tests or other products that will not generate significant volume for us, but may consume significant research and development and manufacturing resources;

• we may not be able to negotiate future collaborative arrangements, or renewals of existing collaborative agreements, on acceptable terms; and

• our collaborations may not result in the development of products that achieve commercial success or these collaborations could be terminated prior to developing any products.

Because these and other factors may be beyond our control, the development or commercialization of our products involved in collaborative partnerships may be delayed or otherwise adversely affected.

If we or any of our collaborative partners terminate a collaborative arrangement, we may be required to devote additional resources to product development and commercialization or we may need to cancel some development programs, which could adversely affect our product pipeline and business.

We maintain cash balances in our bank accounts that exceed the FDIC insurance limitation.

We maintain our cash assets at commercial banks in amounts in excess of the Federal Deposit Insurance Corporation insurance limit of $250,000. In the event of the commercial banks failing, we may lose the amount of our deposits over any federally-insured amount, which could have a material adverse effect on our financial conditions and our results of operations. Accordingly, we monitor the credit rating of our commercial banks.

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Our participation in the USPS BDS program may not result in predictable revenue in the future.

Our participation in the USPS BDS program involves significant uncertainties related to governmental decision-making and timing of purchases and is highly sensitive to changes in national priorities and budgets. The USPS continued to report significant losses for the 2015, 2014 and 2013 fiscal years. Budgetary pressures may result in reduced allocations to projects such as the BDS program, sometimes without advance notice. We cannot be certain that actual funding and operating parameters, or product purchases, will occur at currently expected levels or in the currently expected timeframe.

Compliance with laws and regulations governing public company corporate governance and reporting is complex and expensive.

We are subject to laws and regulations affecting our domestic and international operations in a number of areas. Many laws and regulations, notably those adopted in connection with the Sarbanes-Oxley Act of 2002 by the SEC, the Dodd-Frank Wall Street Reform and Consumer Protection Act and The NASDAQ Stock Market, impose obligations on public companies, such as ours, which have increased the scope, complexity and cost of corporate governance, reporting and disclosure practices. Compliance with these laws, regulations and similar requirements can be onerous and inconsistent from jurisdiction to jurisdiction, which has required and will continue to require substantial management time and oversight and requires us to incur significant additional accounting, legal and compliance costs. Any such costs that may arise in the future as a result of changes in these laws and regulations or in their interpretation could individually or in the aggregate make our products and services more expensive to our customers, delay the introduction of new products in one or more regions or cause us to change or limit our business practices. We have implemented policies and procedures designed to ensure compliance with applicable laws and regulations, but there can be no assurance that our employees, contractors or agents will not violate such laws and regulations or our policies and procedures.

Additionally, changes to existing accounting rules and standards and the implementation of new accounting rules or standards, such as the new lease accounting or revenue recognition rules, may adversely impact our reported financial results and business, and may further require us to incur greater accounting fees as further described below under the heading “Changes in accounting standards and subjective assumptions, estimates, and judgments by management related to complex accounting matters could significantly affect our financial results or financial condition.”

Our operating results could be materially affected by unanticipated changes in our tax provisions or exposure to additional income tax liabilities.

Our determination of our tax liability (like any company’s determination of its tax liability) is subject to review by applicable tax authorities. Any adverse outcome of such a review could have an adverse effect on our operating results and financial condition. In addition, the determination of our provision for income taxes and other tax liabilities requires significant judgment, including our determination of whether a valuation allowance against deferred tax assets is appropriate. We expect to maintain such valuation allowance as long as there is insufficient evidence that we will be able to realize the benefit of our deferred tax assets. We reassess the realizability of the deferred tax assets as facts and circumstances dictate. If after future assessments of the realizability of the deferred tax assets, we determine that a lesser or greater allowance is required, or that no such allowance is appropriate, we will record a corresponding change to the income tax expense and the valuation allowance in the period of such determination. The uncertainty surrounding the future realization of our net deferred tax assets could adversely impact our results of operations. Although we believe our estimates and judgments are reasonable, including those related to our valuation allowance, the ultimate tax outcome may differ from the amounts recorded in our financial statements and may materially affect our financial results in the period or periods for which such determination is made.

Changes in accounting standards and subjective assumptions, estimates, and judgments by management related to complex accounting matters could significantly affect our financial results or financial condition.

Generally accepted accounting principles and related accounting pronouncements, implementation guidelines, and interpretations with regard to a wide range of matters that are relevant to our business, such as revenue recognition, asset impairment and fair value determinations, stock-based compensation, inventories, convertible debt, business combinations and intangible asset valuations, lease accounting, and litigation, are highly complex and involve many subjective assumptions, estimates, and judgments. Changes in these rules or their interpretation or changes in underlying assumptions, estimates, or judgments could significantly change our reported or expected financial performance or financial condition or the way we conduct business and could require us to incur greater accounting fees. For example, significant changes to revenue recognition rules have been enacted and will be effective for us in the first quarter of fiscal year 2018. We could incur significant costs to implement these new rules, including costs to modify our IT systems. In addition, accounting policies affecting many other aspects of our business are under review or being revised by the International Accounting Standards Board.

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The “conflict minerals” rule of the Securities and Exchange Commission, or SEC, has caused us to incur additional expenses, could limit the supply and increase the cost of certain minerals used in manufacturing our products, and could make us less competitive in our target markets.

The SEC's "conflict minerals" rule requires disclosure by public companies of the origin, source and chain of custody of specified minerals, known as conflict minerals, that are necessary to the functionality or production of products manufactured or contracted to be manufactured. The rule requires companies to obtain sourcing data from suppliers, engage in supply chain due diligence, and file annually with the SEC an audited specialized disclosure report on Form SD covering the prior calendar year. The rule could limit our ability to source at competitive prices and to secure sufficient quantities of certain minerals (or derivatives thereof) used in the manufacture of our products, specifically tantalum, tin, gold and tungsten, as the number of suppliers that provide conflict-free minerals may be limited. We may incur material costs associated with complying with the rule, such as costs related to the determination of the origin, source and chain of custody of the minerals used in our products, the adoption of conflict minerals-related governance policies, processes and controls, and possible changes to products or sources of supply as a result of such activities. Within our supply chain, we may not be able to sufficiently verify the origins of the relevant minerals used in our products through the data collection and due diligence procedures that we implement, which may harm our reputation. Furthermore, we may encounter challenges in satisfying those customers that require that all of the components of our products be certified as conflict free, and if we cannot satisfy these customers, they may choose a competitor’s products. We continue to investigate the presence of conflict materials within our supply chain.

We have indebtedness in the form of convertible senior notes.

In February 2014, we completed an offering of $345 million of convertible senior notes due in 2021 (the “Notes”).

As a result of the issuance of the Notes, we incurred $345 million principal amount of indebtedness, the principal amount of which we may be required to pay at maturity in 2021, or upon the occurrence of a make-whole fundamental change (as defined in the applicable indenture). There can be no assurance that we will be able to repay this indebtedness when due, or that we will be able to refinance this indebtedness on acceptable terms or at all. In addition, this indebtedness could, among other things:

• make it difficult for us to pay other obligations;

• make it difficult to obtain favorable terms for any necessary future financing for working capital, capital expenditures, debt service requirements or other purposes;

• require us to dedicate a substantial portion of our cash flow from operations to service the indebtedness, reducing the amount of cash flow available for other purposes; and

• limit our flexibility in planning for and reacting to changes in our business.

Conversion of the Notes may affect the price of our common stock.

The conversion of some or all of our Notes may dilute the ownership interest of existing shareholders to the extent we deliver shares of common stock upon conversion. Holders of the outstanding Notes will be able to convert them only upon the satisfaction of certain conditions prior to August 1, 2020. Upon conversion, holders of the Notes will receive cash, shares of common stock or a combination of cash and shares of common stock, at our election. Any sales in the public market of shares of common stock issued upon conversion of such notes could adversely affect the trading price of our common stock.

We have broad discretion in the use of the net proceeds from the issuance of our Notes and may not use them effectively.

We have broad discretion in the application of the net proceeds that we received from the issuance of the Notes, including working capital, possible acquisitions and other general corporate purposes, and we may spend or invest these proceeds in a way with which our investors disagree. The failure by our management to apply these funds effectively could adversely affect our business and financial condition. We may invest the net proceeds from our Notes in a manner that does not produce income or that loses value. These investments may not yield a favorable return to our investors, and may negatively impact the price of our securities.

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Servicing our debt requires a significant amount of cash, and we may not have sufficient cash flow from our business to pay our substantial debt.

Our ability to make scheduled payments of the principal, to pay interest on or to refinance our indebtedness, including the Notes, depends on our future performance, which is subject to economic, financial, competitive and other factors beyond our control. Our business may not generate cash flow from operations in the future sufficient to service our debt obligations and make necessary capital expenditures. If we are unable to generate the necessary cash flow, we may be required to adopt one or more alternatives, such as selling assets, restructuring debt or obtaining additional capital on terms that may be onerous or highly dilutive. Our ability to refinance our indebtedness will depend on the capital markets and our financial condition at such time. We may not be able to engage in any of these activities or engage in these activities on desirable terms, which could result in a default on our debt obligations.

We may not have the ability to raise the funds necessary to settle conversions of the Notes or to repurchase the Notes upon a fundamental change, and our future debt may contain limitations on our ability to pay cash upon conversion or repurchase of the Notes.

Holders of the Notes will have the right to require us to repurchase their Notes upon the occurrence of a fundamental change at a fundamental change repurchase price equal to 100% of the principal amount of the Notes to be repurchased, plus accrued and unpaid interest, if any. In addition, upon conversion of the Notes, unless we elect to deliver solely shares of our common stock to settle such conversion (other than paying cash in lieu of delivering any fractional share), we will be required to make cash payments in respect of the Notes being converted. However, we may not have enough available cash or be able to obtain financing at the time we are required to make repurchases of Notes surrendered therefor or Notes being converted. In addition, our ability to repurchase the Notes or to pay cash upon conversions of the Notes may be limited by law, by regulatory authority or by agreements governing our future indebtedness. Our failure to repurchase Notes at a time when the repurchase is required by the indenture governing the Notes or to pay any cash payable on future conversions of the Notes as required by the indenture governing the Notes would constitute a default under the indenture governing the Notes. A default under the indenture governing the Notes or the fundamental change itself could also lead to a default under agreements governing our future indebtedness. If the repayment of the future indebtedness were to be accelerated after any applicable notice or grace periods, we might not have sufficient funds to repay the indebtedness and repurchase the Notes or make cash payments upon conversions thereof.

The Notes contain a conditional conversion feature, which, if triggered, may adversely affect our financial condition and operating results.

The Notes contain a conditional conversion feature. If such feature is triggered, holders of Notes will be entitled to convert the Notes at any time during specified periods at their option. If one or more holders elect to convert their Notes, unless we elect to satisfy our conversion obligation by delivering solely shares of our common stock (other than paying cash in lieu of delivering any fractional share), we would be required to settle a portion or all of our conversion obligation through the payment of cash, which could adversely affect our liquidity. In addition, even if holders do not elect to convert their Notes, we could be required under applicable accounting rules to reclassify all or a portion of the outstanding principal of the Notes as a current rather than non-current liability, which would result in a material reduction of our net working capital.

Our stock price is highly volatile and investing in our stock involves a high degree of risk, which could result in substantial losses for investors.

The market price of our common stock, like the securities of many other medical product companies, fluctuates over a wide range, and is likely to continue to be highly volatile in the future. During the period commencing on January 1, 2015 and through September 30, 2016, the closing sale price of our common stock on The NASDAQ Global Select Market ranged from $25.64 to $63.52 per share. Because our stock price has been volatile, investing in our common stock is risky. Furthermore, volatility in the stock price of other companies has often led to securities class action litigation against those companies. Any future securities litigation against us could result in substantial costs and divert management’s attention and resources, which could seriously harm our business, financial condition and results of operations.

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

Not applicable.

ITEM 3. DEFAULTS UPON SENIOR SECURITIES

Not Applicable.

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ITEM 4. MINE SAFETY DISCLOSURES

Not Applicable.

ITEM 5. OTHER INFORMATION

Not Applicable.

ITEM 6. EXHIBITS

(a) Exhibits

Exhibit Number		Incorporated by Reference			Filing	Filed
	Exhibit Description	Form	File No.	Exhibit	Date	Herewith
2.1	Agreement and Plan of Merger, dated September 2, 2016, by and among Cepheid, Danaher Corporation and Copper Merger Sub, Inc.	8-K	000-30755	2.1	9/6/2016
10.1 †	Form of Performance-Based Restricted Stock Unit Award Agreement, including Notice of Performance Based Restricted Stock Unit Award.					X
31.1	Certification of Chief Executive Officer pursuant to Rule 13a-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.					X
31.2	Certification of Chief Financial Officer pursuant to Rule 13a-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.					X
32.1*	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.					X
32.2*	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.					X
101	The following materials from Cepheid’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2016, formatted in XBRL (Extensible Business Reporting Language): (i) the unaudited Condensed Consolidated Balance Sheets, (ii) the unaudited Condensed Consolidated Statements of Operations, (iii) the unaudited Condensed Consolidated Statements of Comprehensive Income (Loss), (iv) the unaudited Condensed Consolidated Statements of Cash Flows, and (v) Notes to Condensed Consolidated Financial Statements, tagged as blocks of text.					X

* As contemplated by SEC Release No. 33-8212, these exhibits are furnished with this Quarterly Report on Form 10-Q and are not deemed filed with the Securities and Exchange Commission and are not incorporated by reference in any filing of Cepheid under the Securities Act of 1933, as amended, or the Exchange Act of 1934, as amended, whether made before or after the date hereof and irrespective of any general incorporation language in such filings.

† Confidential treatment has been requested for certain portions of this document pursuant to an application for confidential treatment sent to the Securities and Exchange Commission. Such portions are omitted from this filing, and have been filed separately with the Securities and Exchange Commission.

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized, in the City of Sunnyvale, State of California on November 3, 2016.

CEPHEID

(Registrant)

/S/    JOHN L. BISHOP

John L. Bishop

Chairman and Chief Executive Officer

(Principal Executive Officer)

/S/    Daniel E. Madden

Daniel E. Madden

Executive Vice President, Chief Financial Officer

(Principal Financial and Accounting Officer)

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Exhibit Index

Exhibit Number	Exhibit Description
2.1	Agreement and Plan of Merger, dated September 2, 2016, by and among Cepheid, Danaher Corporation and Copper Merger Sub, Inc.
10.1 †	Form of Performance-Based Restricted Stock Unit Award Agreement, including Notice of Performance Based Restricted Stock Unit Award.
31.1	Certification of Chief Executive Officer pursuant to Rule 13a-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
31.2	Certification of Chief Financial Officer pursuant to Rule 13a-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
32.1*	Certification of Chief Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
32.2*	Certification of Chief Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.
101	The following materials from Cepheid’s Quarterly Report on Form 10-Q for the quarter ended September 30, 2016, formatted in XBRL (Extensible Business Reporting Language): (i) the unaudited Condensed Consolidated Balance Sheets, (ii) the unaudited Condensed Consolidated Statements of Operations, (iii) the unaudited Condensed Consolidated Statements of Comprehensive Income (Loss), (iv) the unaudited Condensed Consolidated Statements of Cash Flows, and (v) Notes to Condensed Consolidated Financial Statements, tagged as blocks of text.

 * As contemplated by SEC Release No. 33-8212, these exhibits are furnished with this Quarterly Report on Form 10-Q and are not deemed filed with the Securities and Exchange Commission and are not incorporated by reference in any filing of Cepheid under the Securities Act of 1933, as amended, or the Exchange Act of 1934, as amended, whether made before or after the date hereof and irrespective of any general incorporation language in such filings.

† Confidential treatment has been requested for certain portions of this document pursuant to an application for confidential treatment sent to the Securities and Exchange Commission. Such portions are omitted from this filing, and have been filed separately with the Securities and Exchange Commission.