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Document And Entity Information - USD ($)	12 Months Ended
Document And Entity Information - USD ($)	Dec. 29, 2017	Feb. 12, 2018	Jun. 30, 2017
Document And Entity Information [Abstract]
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 29, 2017
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	FY
Trading Symbol	exel
Entity Registrant Name	EXELIXIS, INC.
Entity Central Index Key	0000939767
Entity Filer Category	Large Accelerated Filer
Current Fiscal Year End Date	--12-29
Entity Common Stock, Shares Outstanding		296,307,278
Entity Well-known Seasoned Issuer	Yes
Entity Public Float			$ 7,116,352,282
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 29, 2017	Dec. 30, 2016
Current assets:
Cash and cash equivalents	$ 183,164	$ 151,686
Short-term investments	204,607	268,117
Short-term restricted cash and investments	504	0
Trade and other receivables, net	81,192	40,444
Inventory, net	6,657	3,338
Prepaid expenses and other current assets	8,750	5,416
Total current assets	484,874	469,001
Long-term investments	64,255	55,601
Long-term restricted cash and investments	4,646	4,150
Property and equipment, net	25,743	2,071
Goodwill	63,684	63,684
Other long-term assets	12,092	1,232
Total assets	655,294	595,739
Current liabilities:
Accounts payable	9,575	6,565
Accrued compensation and benefits	21,073	20,334
Accrued clinical trial liabilities	19,849	14,131
Accrued collaboration liabilities	8,974	2,046
Rebates and fees due to customers	7,565	3,420
Current portion of deferred revenue	31,984	19,665
Convertible notes	0	109,122
Term loan payable	0	80,000
Other current liabilities	16,150	13,503
Total current liabilities	115,170	268,786
Long-term portion of deferred revenue	238,520	237,094
Other long-term liabilities	16,643	541
Total liabilities	370,333	506,421
Commitments (Note 12)
Stockholders’ equity:
Preferred stock, $0.001 par value, 10,000,000 shares authorized and no shares issued	0	0
Common stock, $0.001 par value; 400,000,000 shares authorized; issued and outstanding: 296,209,426 and 289,923,798 at December 31, 2017 and 2016, respectively	296	290
Additional paid-in capital	2,114,184	2,072,591
Accumulated other comprehensive loss	(347)	(416)
Accumulated deficit	(1,829,172)	(1,983,147)
Total stockholders’ equity	284,961	89,318
Total liabilities and stockholders’ equity	$ 655,294	$ 595,739

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 29, 2017	Dec. 30, 2016
Statement of Financial Position [Abstract]
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized	10,000,000	10,000,000
Preferred stock, shares issued	0	0
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, shares authorized	400,000,000	400,000,000
Common stock, shares issued	296,209,426	289,923,798
Common stock, shares outstanding	296,209,426	289,923,798

Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Revenues:
Net product revenues	$ 349,008	$ 135,375	$ 34,158
Collaboration revenues	103,469	56,079	3,014
Total revenues	452,477	191,454	37,172
Operating expenses:
Cost of goods sold	15,066	6,552	3,895
Research and development	112,171	95,967	96,351
Selling, general and administrative	159,362	116,145	57,305
Restructuring (recovery) charge	(32)	914	1,042
Total operating expenses	286,567	219,578	158,593
Income (loss) from operations	165,910	(28,124)	(121,421)
Other income (expense), net:
Interest income	4,883	2,578	793
Interest expense	(8,679)	(33,060)	(40,680)
Other, net	(3,537)	(11,616)	(381)
Total other expense, net	(7,333)	(42,098)	(40,268)
Income (loss) before income taxes	158,577	(70,222)	(161,689)
Provision for income taxes	4,350	0	55
Net income (loss)	$ 154,227	$ (70,222)	$ (161,744)
Net income (loss) per share, basic (in dollars per share)	$ 0.52	$ (0.28)	$ (0.77)
Net income (loss) per share, diluted (in dollars per share)	$ 0.49	$ (0.28)	$ (0.77)
Shares used in computing net income (loss) per share, basic (in shares)	293,588	250,531	209,227
Shares used in computing net income (loss) per share, diluted (in shares)	312,003	250,531	209,227

Consolidated Statements of Comprehensive Income (Loss) - USD ($)
$ in Thousands

12 Months Ended

Dec. 29, 2017

Dec. 30, 2016

Jan. 01, 2016

Statement of Comprehensive Income [Abstract]

Net income (loss)

$ 154,227

$ (70,222)

$ (161,744)

Other comprehensive income (loss)

^[1]

(184)

(111)

Comprehensive income (loss)

$ 154,296

$ (70,406)

$ (161,855)

[1]

Other comprehensive income (loss) consisted solely of unrealized gains or losses, net, on available-for-sale securities arising during the periods presented. There were nominal or no reclassification adjustments to net income (loss) resulting from realized gains or losses on the sale of securities and there was no income tax expense related to other comprehensive income (loss) during the periods presented.

Consolidated Statements of Comprehensive Income (Loss) (Parenthetical) - USD ($)	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Statement of Comprehensive Income [Abstract]
Reclassification adjustments to net loss resulting from realized gains or losses on sale of securities	$ 0	$ 0	$ 0
Other comprehensive income, tax	$ 0	$ 0	$ 0

Consolidated Statements of Stockholders' Equity (Deficit) - USD ($) $ in Thousands	Total	Common Stock [Member]	Additional Paid-In Capital [Member]	Accumulated Other Comprehensive (Loss) Income [Member]	Accumulated Deficit [Member]
Balance at beginning of period (in shares) at Jan. 02, 2015		195,895,769
Balance at beginning of period at Jan. 02, 2015	$ (159,324)	$ 196	$ 1,591,782	$ (121)	$ (1,751,181)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss)	(161,744)				(161,744)
Other comprehensive (loss) income	(111)			(111)
Sale of shares of common stock, net (in shares)		28,750,000
Sale of shares of common stock, net	145,649	$ 29	145,620
Issuance of common stock under equity incentive and stock purchase plans (in shares)		3,315,174
Issuance of common stock under equity incentive and stock purchase plans	11,277	$ 3	11,274
Stock-based compensation	21,977		21,977
Warrants transferred from other long-term liabilities	1,470		1,470
Balance at end of period (in shares) at Jan. 01, 2016		227,960,943
Balance at end of period at Jan. 01, 2016	(140,806)	$ 228	1,772,123	(232)	(1,912,925)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Net income (loss)	(70,222)				(70,222)
Other comprehensive (loss) income	(184)			(184)
Issuance of common stock in settlement of convertible notes (in shares)		54,009,279
Issuance of common stock in settlement of convertible notes	253,080	$ 54	253,026
Issuance of common stock under equity incentive and stock purchase plans (in shares)		7,953,576
Issuance of common stock under equity incentive and stock purchase plans	24,538	$ 8	24,530
Stock-based compensation	$ 22,912		22,912
Balance at end of period (in shares) at Dec. 30, 2016	289,923,798	289,923,798
Balance at end of period at Dec. 30, 2016	$ 89,318	$ 290	2,072,591	(416)	(1,983,147)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Adoption of Accounting Standards Update No. 2016-09	0		252		(252)
Net income (loss)	154,227				154,227
Other comprehensive (loss) income	69			69
Issuance of common stock under equity incentive and stock purchase plans (in shares)		5,408,177
Issuance of common stock under equity incentive and stock purchase plans	17,409	$ 5	17,404
Issuance of common stock on warrant exercise (in shares)		877,451
Issuance of common stock on warrant exercise	0	$ 1	(1)
Stock-based compensation	$ 23,938		23,938
Balance at end of period (in shares) at Dec. 29, 2017	296,209,426	296,209,426
Balance at end of period at Dec. 29, 2017	$ 284,961	$ 296	$ 2,114,184	$ (347)	$ (1,829,172)

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Cash flows from operating activities:
Net income (loss)	$ 154,227	$ (70,222)	$ (161,744)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Depreciation and amortization	1,187	1,002	1,406
Stock-based compensation	23,938	22,912	21,977
Loss on extinguishment of debt	6,239	13,901	0
Amortization of debt discounts and debt issuance costs	182	8,432	17,041
Interest paid in kind	(11,825)	8,008	3,817
Gain on other equity investments	(2,980)	(2,494)	(112)
Changes in warrant fair value	0	0	548
Other	1,589	1,598	1,861
Changes in assets and liabilities:
Trade and other receivables	(40,839)	(35,318)	(540)
Inventory, net	(3,319)	(722)	(235)
Prepaid expenses and other current assets	(3,268)	(1,610)	(325)
Other long-term assets	430	1,077	1,340
Accounts payable	3,010	164	(12)
Accrued compensation and benefits	739	16,705	279
Accrued clinical trial liabilities	5,718	(3,940)	(23,474)
Accrued collaboration liabilities	6,928	(10,938)	10,206
Deferred revenue	13,745	256,759	(2,582)
Other current and long-term liabilities	9,910	5,090	(10,502)
Net cash used in operating activities	165,611	210,404	(141,051)
Cash flows from investing activities:
Purchases of property and equipment	(21,143)	(1,703)	(447)
Proceeds from sale of property and equipment	164	97	1,346
Purchases of investments	(319,090)	(369,187)	(143,992)
Proceeds from maturities of investments	336,590	151,485	178,936
Proceeds from sale of investments	37,294	2,266	0
Purchase of restricted cash and investments	(15,650)	(8,650)	(5,650)
Proceeds from maturities of restricted cash and investments	14,650	7,150	19,789
Proceeds from other equity investments	2,980	2,494	95
Net cash (used in) provided by investing activities	35,795	(216,048)	50,077
Cash flows from financing activities:
Principal repayments of debt	(185,788)	(575)	(4,381)
Payments on conversion of convertible notes	0	(7,135)	0
Proceeds from issuance of common stock, net	0	0	145,649
Proceeds from exercise of stock options	17,555	25,327	10,911
Proceeds from employee stock purchase plan	4,868	2,187	568
Taxes paid related to net share settlement of equity awards	(6,563)	(4,108)	(534)
Net cash provided by financing activities	(169,928)	15,696	152,213
Net increase (decrease) in cash and cash equivalents	31,478	10,052	61,239
Cash and cash equivalents at beginning of year	151,686	141,634	80,395
Cash and cash equivalents at end of year	183,164	151,686	141,634
Supplemental cash flow disclosure:
Cash paid for interest	20,460	21,044	19,822
Cash paid for taxes	538	190	192
Non-cash investing and financing activity:
Construction in progress deemed to have been acquired under build-to-suit lease	14,530	0	0
Issuance of common stock in settlement of convertible notes	$ 0	$ 286,925	$ 0

Organization and Summary of Significant Accounting Policies

12 Months Ended

Dec. 29, 2017

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Organization and Summary of Significant Accounting Policies

ORGANIZATION AND SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Organization

Exelixis, Inc. (“Exelixis,” “we,” “our” or “us”) is a biotechnology company committed to the discovery, development and commercialization of new medicines to improve care and outcomes for people with cancer. Since our founding in 1994, three products discovered at Exelixis have progressed through clinical development, received regulatory approval, and entered the marketplace. Two are derived from cabozantinib, an inhibitor of multiple tyrosine kinases including MET, AXL, VEGF receptors and RET: CABOMETYX® (cabozantinib) tablets approved for advanced renal cell carcinoma (“RCC”) and COMETRIQ® (cabozantinib) capsules approved for progressive, metastatic medullary thyroid cancer. The third product, COTELLIC® (cobimetinib) tablets, is a formulation of cobimetinib and is an inhibitor of MEK, marketed under a collaboration with Genentech, Inc. (a member of the Roche Group), and is approved as part of a combination regimen to treat advanced melanoma.

Basis of Consolidation

The accompanying Consolidated Financial Statements include the accounts of Exelixis and those of our wholly-owned subsidiaries. These entities’ functional currency is the U.S. dollar. All intercompany balances and transactions have been eliminated.

Basis of Presentation

We have adopted a 52- or 53-week fiscal year policy that generally ends on the Friday closest to December 31st. Fiscal year 2015 ended on January 1, 2016; fiscal year 2016 ended on December 30, 2016; fiscal year 2017 ended on December 29, 2017; and fiscal year 2018 will end on December 28, 2018. For convenience, references in this report as of and for the fiscal years ended January 1, 2016, December 30, 2016 and December 29, 2017 are indicated as being as of and for the years ended December 31, 2015, 2016 and 2017, respectively. All annual periods presented are 52-week fiscal years and all interim periods presented are 13-week fiscal quarters.

Use of Estimates

The preparation of the accompanying Consolidated Financial Statements conforms to accounting principles generally accepted in the U.S. which requires management to make judgments, estimates and assumptions that affect the reported amounts of assets, liabilities, equity, revenues and expenses, and related disclosures. On an ongoing basis, management evaluates its estimates including, but not limited to: those related to revenue recognition, including deductions from revenues (such as rebates, chargebacks, sales returns and sales allowances), the period of performance, identification of deliverables and evaluation of milestones with respect to our collaborations; the amounts of revenues and expenses under our profit and loss sharing agreement; recoverability of inventory; the accrual for certain liabilities including accrued clinical trial liability; and valuations of awards used to determine stock-based compensation. We base our estimates on historical experience and on various other market-specific and other relevant assumptions that we believe to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. Actual results could differ materially from those estimates.

Reclassifications

Certain prior period amounts on the accompanying Consolidated Financial Statements have been reclassified to conform to current period presentation.

Cash and Investments

We consider all highly liquid investments purchased with an original maturity of three months or less to be cash equivalents. Cash equivalents include high-grade, short-term investments in money market funds and marketable debt securities which are subject to minimal credit and market risk.

We have designated all investments in marketable debt securities as available-for-sale and therefore, such investments are reported at fair value, with unrealized gains and losses recorded in accumulated other comprehensive loss. For securities sold prior to maturity, the cost of securities sold is based on the specific identification method. Realized gains and losses on the sale of investments are included in Interest and other income, net on the accompanying Consolidated Statements of Operations.

We classify those investments that we do not require for use in current operations and that mature in more than 12 months as Long-term investments on the accompanying Consolidated Balance Sheets.

All of our investments are subject to a quarterly impairment review. We recognize an impairment charge when a decline in the fair value of an investment below its cost basis is judged to be other-than-temporary. Factors considered in determining whether a loss is temporary include the length of time and extent to which the investments fair value has been less than their cost basis, the financial condition and near-term prospects of the issuer, extent of the loss related to credit of the issuer, the expected cash flows from the security, our intent to sell the security and whether or not we will be required to sell the security before we are able to recover our carrying value.

Accounts Receivable

Trade accounts receivable are recorded net of allowances for chargebacks and cash discounts for prompt payment, as described further below. Estimates of our allowance for doubtful accounts are determined based on existing contractual payment terms, historical payment patterns of our customers and individual customer circumstances, an analysis of days sales outstanding by geographic region and a review of the local economic environment and its potential impact on government funding and reimbursement practices. Historically, the amounts of uncollectible accounts receivable that have been written off were insignificant.

Fair Value Measurements

Fair value reflects the amounts that would be received upon sale of an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date (exit price). We disclose the fair value of financial instruments for assets and liabilities for which the value is practicable to estimate. For those financial instruments measured and recorded at fair value on a recurring basis, we also provide fair value hierarchy information in these Notes to Consolidated Financial Statements. The fair value hierarchy has the following three levels:

Level 1 – Fair values are determined utilizing quoted prices (unadjusted) in active markets for identical assets and liabilities that the reporting entity can access at the measurement date.

Level 2 – Fair values are determined utilizing observable inputs that are observable either directly or indirectly, other than quoted prices in active markets for identical assets and liabilities. These inputs include using prices from independent pricing services based on quoted prices in active markets for similar instruments or on industry models using data inputs, such as interest rates and prices that can be directly observed or corroborated in active markets.

Level 3 – Fair values are determined utilizing inputs that are both significant to the fair value measurement and unobservable.

A review of the fair value hierarchy classification is conducted on a quarterly basis. Changes in the observability of valuation inputs may result in a reclassification of levels for certain investments within the fair value hierarchy.

Inventory

We value inventory at the lower of cost or net realizable value. We determine the cost of inventory using the standard-cost method, which approximates actual cost based on a first-in, first-out method. We analyze our inventory levels quarterly and write down inventory subject to expiry in excess of expected requirements, or that has a cost basis in excess of its expected net realizable value. These inventory related costs are recognized as Cost of goods sold on the accompanying Consolidated Statements of Operations.

On a quarterly basis, we analyze our estimated production levels for the following twelve month period, which is our normal operating cycle, and reclassify inventory we expect to use or sell in periods beyond the next twelve months into Other long-term assets on the accompanying Consolidated Balance Sheets.

We consider regulatory approval of product candidates to be uncertain and product manufactured prior to regulatory approval may not be sold unless regulatory approval is obtained. As such, the manufacturing costs for product candidates incurred prior to regulatory approval are not capitalized as inventory but are expensed as research and development costs. Only once regulatory approval is obtained, would we begin capitalization of these inventory related costs.

Property and Equipment

Property and equipment are recorded at cost and depreciated using the straight-line method over the following estimated useful lives once it is placed into service:



Asset Category		Estimated Useful Life
Buildings		40 years
Lab equipment		5 years
Furniture and fixtures		5 years
Computer equipment and software		3 years
Leasehold improvements		7 to 15 years

Leasehold improvements are depreciated over the lesser of their estimated useful lives or the remainder of the lease term. Capitalized software includes certain internal use computer software costs. Repairs and maintenance costs are charged to expense as incurred.

Goodwill

Goodwill amounts have been recorded as the excess purchase price over tangible assets, liabilities and intangible assets acquired based on their estimated fair value. Goodwill is not subject to amortization. We assess the recoverability of our goodwill annually, or more frequently whenever events or changes in circumstances indicate that the carrying amount of a reporting unit may exceed its fair value. The assessment of recoverability may first consider qualitative factors to determine whether the existence of events or circumstances leads to a determination that it is more likely than not that the fair value of a reporting unit is less than its carrying amount. A quantitative assessment is performed if the qualitative assessment results in a more-likely-than-not determination or if a qualitative assessment is not performed. The quantitative assessment considers whether the carrying amount of a reporting unit exceeds its fair value, in which case an impairment charge is recorded to the extent the carrying amount of the reporting unit’s goodwill exceeds its implied fair value. We continue to operate in one segment, which is also considered to be our sole reporting unit and therefore, goodwill was tested for impairment at the enterprise level as of December 31, 2017 and 2016. We did not recognize any impairment charges in any of the periods presented.

Long-Lived Assets

The carrying value of our long-lived assets, which includes property and equipment, is reviewed for impairment whenever events or changes in circumstances indicate that the asset may not be recoverable. An impairment loss would be recognized when estimated future cash flows expected to result from the use of the asset and its eventual disposition is less than its carrying amount.

Revenue Recognition

We will adopt ASU 2014-09 using the modified retrospective method in the first quarter of fiscal year 2018. For information on our adoption of ASU 2014-09, see “- Recent Accounting Pronouncements,” below.

Revenue is recognized when the following criteria have been met: persuasive evidence of an arrangement exists; delivery has occurred and title has transferred or services have been performed; the price is fixed or determinable; and collectability of the resulting receivable is reasonably assured.

Net Product Revenues

We recognize net product revenues upon delivery of the product and when there are no remaining customer acceptance requirements which is frequently referred to as the “sell-in” revenue recognition model.

Discounts and Allowances

We calculate gross product revenues based on the price that we charge to the specialty pharmacies and distributors in the U.S. We estimate our domestic net product revenues by deducting from our gross product revenues: (a) trade allowances, such as discounts for prompt payment; (b) estimated government rebates and chargebacks; (c) certain other fees paid to specialty pharmacies and distributors; and (d) returns.

We initially record estimates for these deductions at the time we recognize the gross revenue. We update our estimates on a recurring basis as new information becomes available.

Chargebacks: Chargebacks are discounts that occur when contracted customers purchase directly from a specialty pharmacy or distributor. Contracted customers, which currently consist primarily of Public Health Service institutions, non-profit clinics, Federal government entities purchasing via the Federal Supply Schedule and Group Purchasing Organizations, and health maintenance organizations generally purchase the product at a discounted price. The specialty pharmacy or distributor, in turn, charges back to us the difference between the price initially paid by the specialty pharmacy or distributor and the discounted price paid to the specialty pharmacy or distributor by the customer. The allowance for chargebacks is based on an estimate of sales to contracted customers.

Discounts for Prompt Payment: The specialty pharmacies and distributors in the U.S. receive a discount of 2% for prompt payment. We expect the specialty pharmacies and distributors will earn 100% of its prompt payment discounts and, therefore, we deduct the full amount of these discounts from total product sales when revenues are recognized.

Other Customer Credits: We pay fees to our customers for account management, data management and other administrative services.

Co-payment Assistance: Patients who have commercial insurance and meet certain eligibility requirements may receive co-payment assistance. We accrue a liability for co-payment assistance based on actual program participation and estimates of program redemption using customer data provided by the specialty pharmacies and distributors.

Rebates: Allowances for rebates include mandated discounts under the Medicaid Drug Rebate Program and other government programs. Rebate amounts owed after the final dispensing of the product to a benefit plan participant are based upon contractual agreements or legal requirements with public sector benefit providers, such as Medicaid. The allowance for rebates is based on statutory discount rates and expected utilization. Our estimates for the expected utilization of rebates are based on customer and payer data received from the specialty pharmacies and distributors and historical utilization rates as well as third-party market research data. Rebates are generally invoiced by the payer and paid in arrears, such that the accrual balance consists of an estimate of the amount expected to be incurred for the current quarter’s shipments to our customers, plus an accrual balance for known prior quarter’s unpaid rebates. If actual future rebates vary from estimates, we may need to adjust our accruals, which would affect net revenue in the period of adjustment.

Allowances for rebates also includes the Medicare Part D Coverage Gap. In the U.S., the Medicare Part D prescription drug benefit mandates manufacturers to fund 50% of the Medicare Part D insurance coverage gap for prescription drugs sold to eligible patients. Our estimates for expected Medicare Part D coverage gap are based in part on historical utilization rates, specialty pharmacy and distributor customer and payer data and third-party market research data. We also estimate when eligible patients who are prescribed our product enter and exit the insurance coverage gap. Funding of the coverage gap is invoiced and paid in arrears so that the accrual balance consists of an estimate of the amount expected to be incurred for the current quarters’ shipments to patients, plus an accrual balance for prior sales. If actual future funding varies from estimates, we may need to adjust our accruals, which would affect net revenue in the period of adjustment.

The activities and ending reserve balances for each significant category of discount and allowance were as follows (dollars in thousands):



	Chargebacks and discounts for prompt payment			Other customer credits/fees and co-pay assistance			Rebates			Returns			Total
Balance at December 31, 2015	$	119		$	251		$	891		$	38		$	1,299
Provision related to sales made in:													—
Current period	8,271			2,747			5,105			359			16,482
Prior periods	(39		)	2			(313		)	(8		)	(358		)
Payments and customer credits issued	(6,549		)	(2,206		)	(3,056		)	(38		)	(11,849		)
Balance at December 31, 2016	1,802			794			2,627			351			5,574
Provision related to sales made in:
Current period	33,310			7,301			14,390			—			55,001
Prior periods	(817		)	—			(624		)	—			(1,441		)
Payments and customer credits issued	(32,367		)	(6,300		)	(10,623		)	(351		)	(49,641		)
Balance at December 31, 2017	$	1,928		$	1,795		$	5,770		$	—		$	9,493

Chargebacks and discounts for prompt payment are recorded as a reduction of trade receivables and the remaining reserve balances are classified as Rebates and fees due to customers on the accompanying Consolidated Balance Sheets. Balances as of December 31, 2016 have been reclassified to reflect that presentation.

Collaboration Revenues

We enter into collaboration agreements under which we may obtain upfront license fees, milestone, royalty, development cost reimbursements, and/or product supply payments. These arrangements have multiple elements, and our deliverables may include intellectual property rights, distribution rights, delivery of manufactured product, commercial and development activities and participation on joint steering, commercial and development committees. In order to account for these arrangements, we identify the deliverables and evaluate whether the delivered elements have value to our collaboration partner on a stand-alone basis and represent separate units of accounting. Analyzing the arrangement to identify deliverables requires the use of judgment, and each deliverable may be an obligation to deliver future goods or services, a right or license to use an asset, or another performance obligation. If we determine that multiple deliverables exist, the consideration is allocated to one or more units of accounting based upon the best estimate of the selling price of each deliverable. The selling price used for each deliverable will be based on vendor-specific objective evidence, if available, third-party evidence if vendor-specific objective evidence is not available, or estimated selling price if neither vendor-specific or third-party evidence is available. A delivered item or items that do not qualify as a separate unit of accounting within the arrangement will be combined with the other applicable undelivered items within the arrangement. The allocation of arrangement consideration and the recognition of revenue then will be determined for those combined deliverables as a single unit of accounting. For a combined unit of accounting, non-refundable upfront fees are recognized in a manner consistent with the final deliverable, which has generally been ratably over the period of our continued involvement. Amounts received in advance of performance are recorded as deferred revenue.

We record royalty revenues based on estimates of the sales that occurred during the period. The relevant period estimates of sales are based on interim data provided by licensees and analysis of historical royalties that have been paid to us, adjusted for any changes in facts and circumstances, as appropriate. Historically, adjustments have not been material when compared to actual amounts paid by licensees. However, additional information may subsequently become available to us, which may allow us to make a more accurate estimate in future periods. In this event, we are required to record adjustments in future periods when the actual level of activity becomes more certain. Such increases or decreases in revenue are generally considered to be changes in estimates and will be reflected in the period they become known. If we are unable to reasonably estimate royalty revenue, we record royalty revenues when they are received. We consider sales-based contingent payments to be royalty revenue which is generally recognized at the date the contingency is achieved.

Our product supply revenues are recognized upon delivery of the product. See “Note 2. Collaboration Agreements” for a description of our product supply agreements with our collaboration partners.

For certain milestone payments under collaboration agreements, we have made a policy election to recognize revenue using the milestone method. A milestone is an event: (i) that can be achieved based in whole or in part on either our performance or on the occurrence of a specific outcome resulting from our performance, (ii) for which there is substantive uncertainty at the date the arrangement is entered into that the event will be achieved and (iii) that would result in additional payments being due to us. The determination that a milestone is substantive requires estimation and judgment and is made at the inception of the arrangement. Milestones are considered substantive when the consideration earned from the achievement of the milestone is: (i) commensurate with either our performance to achieve the milestone or the enhancement of value of the item delivered as a result of a specific outcome resulting from our performance to achieve the milestone, (ii) relates solely to past performance and (iii) reasonable relative to all deliverables and payment terms in the arrangement. In making the determination as to whether a milestone is substantive or not, we consider all facts and circumstances relevant to the arrangement, including factors such as the scientific, regulatory, commercial and other risks that must be overcome to achieve the respective milestone, the level of effort and investment required to achieve the respective milestone and whether any portion of the milestone consideration is related to future performance or deliverables. A substantive milestone is recognized as revenue in its entirety in the period in which the milestone is achieved. A non-substantive milestone is recognized as revenues over the estimated period of our continued involvement.

Under the terms of our collaboration agreement with Genentech for cobimetinib, we are also entitled to a share of U.S. profits and losses received in connection with commercialization of cobimetinib. We are entitled to low double-digit royalties on ex-U.S. net sales. See “Note 2. Collaboration Agreements” for additional information about our collaboration agreement with Genentech. We have determined that we are an agent under the agreement and therefore revenues are recorded net of costs incurred. We record U.S. profits and losses under the collaboration agreement in the period earned based on our estimate of those amounts. As of December 31, 2017, we have not recognized a profit for any year to date period from the commercialization of cobimetinib in the U.S. Until we have recognized a profit under the agreement, losses are recognized as Selling, general and administrative expenses on the accompanying Consolidated Statements of Operations. In connection with our agreement to co-promote with Genentech, we were responsible for providing up to 25% of the sales force necessary to assist with the promotion of cobimetinib. Genentech reimburses us for these costs which we include as a reduction of our Selling, general and administrative costs when the obligations are incurred or we become entitled to the cost recovery.

Patient Assistance Programs

We provide CABOMETYX and COMETRIQ at no cost to eligible patients who have no insurance and meet certain financial and clinical criteria through our patient assistance programs. We record the cost of the product as a selling, general and administrative expense at the time the product is shipped to the specialty pharmacy for patient assistance use.

Cost of Goods Sold

Cost of goods sold is related to our product revenues and consists primarily of a 3% royalty on sales of any product incorporating cabozantinib payable to GlaxoSmithKline (“GSK”), indirect labor costs, the cost of manufacturing, write-downs related to expiring and excess inventory, shipping and other third-party logistics and distribution costs for our product. A portion of the manufacturing costs for product sales were incurred prior to regulatory approval of COMETRIQ and CABOMETYX and therefore, were expensed as research and development costs when those costs were incurred, rather than capitalized as inventory. See “Note 2. Collaboration Agreements” for additional information on the royalty payable to GSK on sales of any product incorporating cabozantinib.

Research and Development Expenses

Research and development costs are expensed as incurred and include costs associated with research performed pursuant to collaborative agreements. Research and development costs consist of direct and indirect internal costs related to specific projects as well as fees paid to other entities that conduct certain research activities on our behalf.

Substantial portions of our preclinical studies and all of our clinical trials have been executed with support from third-party contract research organizations and other vendors. We accrue expenses for preclinical studies performed by our vendors based on certain estimates over the term of the service period and adjust our estimates as required. We accrue expenses for clinical trial activities performed by contract research organizations based upon the estimated amount of work completed on each trial. For clinical trial expenses, the significant factors used in estimating accruals include the number of patients enrolled, the number of active clinical sites, and the duration for which the patients will be enrolled in the trial. We monitor patient enrollment levels and related activities to the extent possible through internal reviews, correspondence with contract research organizations and review of contractual terms. We base our estimates on the best information available at the time. However, additional information may become available to us which may allow us to make a more accurate estimate in future periods. In this event, we may be required to record adjustments to research and development expenses in future periods when the actual level of activity becomes more certain.

Foreign Currency Translation and Remeasurement

Monetary assets and liabilities denominated in currencies other than the functional currency are remeasured using exchange rates in effect at the end of the period and related gains or losses are recorded in Other expenses, net. Gains and losses on the remeasurement of monetary assets and liabilities were not material for any of the years presented. We do not have any nonmonetary assets or liabilities denominated in currencies other than the U.S. dollar.

Stock-Based Compensation

The expense for stock-based compensation is based on the grant date fair value of the award; the grant date fair value of Restricted Stock Units (“RSUs”) is estimated as the value of the underlying shares of our common stock and the grant date fair value of stock-options is estimated using the Black-Scholes Merton option pricing model. Because there is a market for options on our common stock, we have considered implied volatilities as well as our historical realized volatilities when developing an estimate of expected volatility. We estimate the term using historical data. We recognize compensation expense on a straight-line basis over the requisite service period. Compensation expense relating to awards subject to performance conditions is recognized if it is probable that the performance goals will be achieved; the probability of achievement is assessed on a quarterly basis.

In January 2017, we adopted Accounting Standards Update (“ASU”) No. 2016-09, Compensation—Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting, (“ASU 2016-09”). ASU 2016-09 is aimed at the simplification of several aspects of the accounting for employee share-based payment transactions, including accounting for forfeitures, income tax consequences and classification on the statement of cash flows.

Pursuant to the adoption of ASU 2016-09, we have made an election to record forfeitures when they occur. Previously, stock-based compensation was based on the number of awards expected to vest after considering estimated forfeitures. The change in accounting principle with regards to forfeitures was adopted using a modified retrospective approach, with a cumulative adjustment of $0.3 million to accumulated deficit and additional paid-in capital as of January 1, 2017. No prior periods were restated as a result of this change in accounting principle.

ASU 2016-09 also requires that cash paid to taxing authorities when directly withholding shares for tax withholding purposes be classified as a financing activity on the accompanying Consolidated Statement of Cash Flows. Previously, we classified such payments as operating cash flows. The change in accounting principle with regards to such cash flows was adopted using a retrospective approach. Accordingly, we recorded a reclassification that resulted in an increase in operating cash flows of $4.1 million and $0.5 million along with a corresponding decrease in financing cash flows on the accompanying Consolidated Statement of Cash Flows for the years ended December 31, 2016 and 2015, respectively.

Income Taxes

Our income tax provision is computed under the asset and liability method. Deferred tax assets and liabilities are determined based on the difference between the financial statement and tax basis of assets and liabilities together with assessing carry-forwards using enacted tax rates in effect for the year in which the differences are expected to reverse. Significant estimates are required in determining our provision for income taxes. Some of these estimates are based on interpretations of existing tax laws or regulations. We record a valuation allowance to reduce our deferred tax assets to the amount of future tax benefit that is more likely than not to be realized.

We record an unrecognized tax benefit from an uncertain tax position only if it is more likely than not that the tax position will be sustained upon examination by the tax authorities. An adverse resolution of one or more of these uncertain tax positions in any period could have a material impact on the results of operations for that period.

Recent Accounting Pronouncements

In May 2014, the Financial Accounting Standards Board (“FASB”) issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606) (“ASU 2014-09”). In August 2015, the FASB issued ASU No. 2015-14, Revenue from Contracts with Customers (Topic 606): Deferral of the Effective Date, which delayed the effective date of ASU 2014-09 by one year. ASU 2014-09, as amended, becomes effective for us in the first quarter of fiscal year 2018, which is when we will adopt the standard. ASU 2014-09 also permits two methods of adoption: retrospectively to each prior reporting period presented (full retrospective method), or retrospectively with the cumulative effect of initially applying the guidance recognized at the date of initial application (the modified retrospective method). We will adopt ASU 2014-09 using the modified retrospective method. The core principle of ASU 2014-09 is that an entity should recognize revenue when it transfers promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. ASU 2014-09 defines a five step process to achieve this core principle and, in doing so, has created the possibility that more judgment and estimates may be required within the revenue recognition process than required under existing U.S. generally accepted accounting pronouncements. We have completed our analysis on the adoption of ASU 2014-09 and have determined the adoption will not have a material impact on the recognition of net product revenues. ASU 2014-09 will materially impact the timing of recognition of revenue for our collaboration agreements with Ipsen Pharma SAS (“Ipsen”) and Takeda Pharmaceutical Company Ltd. (“Takeda”). We will record a net adjustment of approximately $260 million to accumulated deficit (a concept known as “lost revenue”) for amounts associated with these collaboration agreements upon recording our transition adjustment in the first quarter of 2018, primarily due to the timing of recognition of revenue related to intellectual property licenses that we have transferred for development and commercialization of our products. Additionally, for all of our collaboration agreements, the timing of recognition of certain of our development and regulatory milestones could change as a result of the variable consideration guidance included in ASU 2014-09. ASU 2014-09 will also require additional disclosures regarding our revenue transactions.

In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842), (“ASU 2016-02”). Under ASU 2016-02, a lessee will be required to recognize assets and liabilities for leases with lease terms of more than 12 months. Recognition, measurement, and presentation of expenses and cash flows arising from a lease by a lessee primarily will depend on its classification as a finance or operating lease. ASU 2016-02 will require both types of leases to be recognized on the balance sheet. The ASU also will require disclosures to help investors and other financial statement users better understand the amount, timing, and uncertainty of cash flows arising from leases. These disclosures include qualitative and quantitative requirements, providing additional information about the amounts recorded in the financial statements. ASU 2016-02 is effective for us for all interim and annual reporting periods beginning after December 15, 2018. Early adoption is permitted. We are in the process of assessing the impact of ASU No. 2016-02 on our Consolidated Financial Statements and are considering early adoption of this standard in the first half of 2018.

In August 2016, the FASB issued ASU No. 2016-15, Statement of Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments (a consensus of the FASB Emerging Issues Task Force), (“ASU 2016-15”). ASU 2016-15 addresses eight specific cash flow issues including debt prepayment or debt extinguishment costs, settlement of zero-coupon debt instruments or other debt instruments with coupon interest rates that are insignificant in relation to the effective interest rate of the borrowing and contingent consideration payments made after a business combination. ASU 2016-15 is effective for all interim and annual reporting periods beginning after December 15, 2017. Early adoption is permitted. We do not expect the adoption of ASU 2016-15 to have a material impact on our Consolidated Statements of Cash Flows.

In November 2016, the FASB issued ASU No. 2016-18, Statement of Cash Flows (Topic 230): Restricted Cash (a consensus of the FASB Emerging Issues Task Force), (“ASU 2016-18”). ASU 2016-18 requires that a statement of cash flows explain the change during the period in the total of cash, cash equivalents, and amounts generally described as restricted cash or restricted cash equivalents. Therefore, amounts generally described as restricted cash and restricted cash equivalents should be included with cash and cash equivalents when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows. ASU 2016-18 is effective for all interim and annual reporting periods beginning after December 15, 2017. Early adoption is permitted. We do not expect the adoption of ASU 2016-18 to have a material impact on our Consolidated Statements of Cash Flows.

In January 2017, the FASB issued ASU No. 2017-04, Intangibles—Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment, (“ASU 2017-04”). ASU 2017-04 eliminated Step 2 from the goodwill impairment test. Instead, under the amendments in ASU 2017-04, an entity should perform its annual, or interim, goodwill impairment test by comparing the fair value of a reporting unit with its carrying amount. An entity should recognize an impairment charge for the amount by which the carrying amount exceeds the reporting unit’s fair value; however, the loss recognized should not exceed the total amount of goodwill allocated to that reporting unit. Additionally, an entity should consider income tax effects from any tax deductible goodwill on the carrying amount of the reporting unit when measuring the goodwill impairment loss, if applicable. ASU 2017-04 is effective for all interim and annual reporting periods beginning after December 15, 2019. Early adoption is permitted. We do not expect the adoption of ASU 2017-04 to have a material impact on our Consolidated Financial Statements.

In May 2017, the FASB issued ASU No. 2017-09, Compensation - Stock Compensation (Topic 718): Scope of Modification Accounting, (“ASU 2017-09”). ASU 2017-09 streamlines the application of modification accounting by stating that when making a change to the terms or conditions of a share-based payment award, a company should apply modification accounting to the award, unless each of the following conditions is met: 1. The fair value (or calculated value or intrinsic value, if such an alternative measurement method is used) of the modified award is the same as the fair value (or calculated value or intrinsic value, if such an alternative measurement method is used) of the original award immediately before the original award is modified. If the modification does not affect any of the inputs to the valuation technique that the entity uses to value the award, the entity is not required to estimate the value immediately before and after the modification, and 2. The vesting conditions of the modified award are the same as the vesting conditions of the original award immediately before the original award is modified, and 3. The classification of the modified award as an equity instrument or a liability instrument is the same as the classification of the original award immediately before the original award is modified. ASU 2017-09 is effective for all interim and annual reporting periods beginning after December 15, 2017. Early adoption is permitted. We do not expect the adoption of ASU 2017-09 to have a material impact on our Consolidated Financial Statements.

Collaboration Agreements

12 Months Ended

Dec. 29, 2017

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Collaboration Agreements

COLLABORATION AGREEMENTS

Cabozantinib Collaborations

Ipsen Collaboration

In February 2016, we entered into a collaboration and license agreement with Ipsen for the commercialization and further development of cabozantinib. Pursuant to the terms of the collaboration agreement, Ipsen received exclusive commercialization rights for current and potential future cabozantinib indications outside of the U.S., Canada and Japan. The collaboration agreement was subsequently amended in December 2016 to include commercialization rights in Canada. We have also agreed to collaborate with Ipsen on the development of cabozantinib for current and potential future indications. The parties’ efforts are governed through a joint steering committee and appropriate subcommittees established to guide and oversee the collaboration’s operation and strategic direction; provided, however, that we retain final decision-making authority with respect to cabozantinib’s ongoing development.

In consideration for the exclusive license and other rights contained in the collaboration agreement, including commercialization rights in Canada, Ipsen paid us aggregate upfront payments of $210.0 million. The collaboration agreement contains multiple deliverables consisting of intellectual property licenses, delivery of products and/or materials containing cabozantinib to Ipsen for all development and commercial activities, research and development services, and participation on the joint steering, development and commercialization committees (as defined in the collaboration agreement). We determined that these deliverables do not have stand-alone value and accordingly, combined these deliverables into a single unit of accounting and allocated the entire arrangement consideration to that combined unit of accounting. As a result, the aggregate upfront payment of $210.0 million has been recognized ratably over the term of the collaboration agreement, through early 2030, which is the current estimated patent expiration of cabozantinib in the European Union (“EU”). At the time we entered into the collaboration agreement, we determined that the $60.0 million milestone we achieved in September 2016 upon the approval of cabozantinib by the European Commission in previously treated advanced RCC was not substantive due to the relatively low degree of uncertainty and relatively low amount of effort required on our part to achieve the milestone as of the date of the collaboration agreement; the $60.0 million was deferred and has been recognized ratably over the remainder of the term of the Ipsen collaboration agreement. We will adopt ASU 2014-09 using the modified retrospective method in the first quarter of fiscal year 2018, which will materially impact the timing of recognition of revenue for our collaboration agreement with Ipsen. For information on our adoption of ASU 2014-09, see “Note 1. Organization and Summary of Significant Accounting Policies” in the “Notes to Consolidated Financial Statements” contained in Part II, Item 8 of this Annual Report on Form 10-K.

At the time we entered into the collaboration agreement we determined that the remaining development and regulatory milestones are substantive and will be recognized as revenue in the periods in which they are achieved. We have achieved additional milestones of $45.0 million and $20.0 million during the years ended December 31, 2017 and 2016, respectively. We are also eligible to receive future development and regulatory milestone payments, totaling up to an additional $209.0 million, including milestone payments of $10.0 million and $40.0 million upon European Medicines Agency (“EMA”) filing and the approval of cabozantinib as a treatment for patients with previously treated advanced hepatocellular carcinoma (“HCC”) and additional milestone payments for other future indications and/or jurisdictions. The collaboration agreement also provides that we will be eligible to receive contingent payments of up to $546.0 million associated with the achievement of specified levels of Ipsen sales to end users. We consider the contingent payments due to us upon the achievement of specified sales volumes to be similar to royalty payments. We will also receive royalties on net sales of cabozantinib by Ipsen outside of the U.S. and Japan. Excluding Ipsen sales in Canada, we received a 2% royalty on the initial $50.0 million of net sales, which was achieved in the fourth quarter of 2017, and are entitled to receive a 12% royalty on the next $100.0 million of net sales, and following this initial $150.0 million of net sales, we are then entitled to receive a tiered royalty of 22% to 26% on annual net sales. These tiers will reset each calendar year. In Canada, we are entitled to receive a tiered royalty of 22% on the first CAD$30.0 million of annual net sales and a tiered royalty thereafter, up to 26% on annual net sales; these tiers will also reset each calendar year.

We are primarily responsible for funding cabozantinib-related development costs for those trials in existence at the time we entered into the collaboration agreement with Ipsen; global development costs for additional trials are shared between the parties, with Ipsen reimbursing us for 35% of such costs, provided Ipsen chooses to opt into such trials. In accordance with the collaboration agreement, Ipsen has opted into and is co-funding: CheckMate 9ER, the phase 3 pivotal trial evaluating the combination of cabozantinib with nivolumab versus sunitinib in patients with previously untreated, advanced or metastatic RCC being conducted in collaboration with Bristol-Myers Squibb Company (“BMS”); CheckMate 040, the phase 1/2 study evaluating the combination of cabozantinib with nivolumab in patients with both previously treated and previously untreated advanced HCC being conducted in collaboration with BMS (though Ipsen will not be co-funding the triplet arm of the study evaluating cabozantinib with nivolumab and ipilimumab); and the phase 1b trial evaluating cabozantinib in combination with atezolizumab in locally advanced or metastatic solid tumors being conducted in collaboration with Roche. We will record reimbursements for development costs as revenue as the development services represent a part of our ongoing major or central operations. As a result of a change in operational responsibilities for certain clinical programs, in March 2017, we reclassified $9.0 million of deferred revenue to Accrued collaboration liabilities and accordingly adjusted our amortization of the aggregate upfront payment of $210.0 million. As of December 31, 2017, we had paid $3.9 million toward the $9.0 million of reimbursements due to Ipsen for these clinical programs.

We remain responsible for the manufacture and supply of cabozantinib for all development and commercialization activities under the collaboration agreement. In connection with the collaboration agreement, we entered into a supply agreement with Ipsen in February 2016, which, pursuant to its amended terms, effective October 2017, we will supply finished, labeled drug product to Ipsen for distribution in the territories outside of the U.S. and Japan, indefinitely. The product will be supplied at our cost, as defined in the agreement, which excludes the 3% royalty we are required to pay GSK on Ipsen’s net sales of any product incorporating cabozantinib.

Unless terminated earlier, the collaboration agreement has a term that continues, on a product-by-product and country-by-country basis, until the latter of (i) the expiration of patent claims related to cabozantinib, (ii) the expiration of regulatory exclusivity covering cabozantinib or (iii) ten years after the first commercial sale of cabozantinib, other than COMETRIQ. The supply agreement will continue in effect until expiration or termination of the collaboration agreement. The collaboration agreement may be terminated for cause by either party based on uncured material breach of either the collaboration agreement or the supply agreement by the other party, bankruptcy of the other party or for safety reasons. We may terminate the collaboration agreement if Ipsen challenges or opposes any patent covered by the collaboration agreement. Ipsen may terminate the collaboration agreement if the U.S. Food and Drug Administration (“FDA”) or EMA orders or requires substantially all cabozantinib clinical trials to be terminated. Ipsen also has the right to terminate the collaboration agreement on a region-by-region basis after the first commercial sale of cabozantinib in advanced RCC in the given region. Upon termination by either party, all licenses granted by us to Ipsen will automatically terminate, and, except in the event of a termination by Ipsen for our material breach, the licenses granted by Ipsen to us shall survive such termination and shall automatically become worldwide, or, if Ipsen terminated only for a particular region, then for the terminated region. Following termination by us for Ipsen’s material breach, or termination by Ipsen without cause or because we undergo a change of control by a party engaged in a competing program, Ipsen is prohibited from competing with us for a period of time.

Collaboration revenues under the collaboration agreement with Ipsen were as follows (in thousands):



	Year Ended December 31,
	2017			2016
Milestones achieved	$	45,000		$	20,000
Amortization of upfront payments and deferred milestone	18,531			13,284
Royalty revenue	3,831			175
Development cost reimbursements	4,417			—
Product supply agreement revenue	6,390			1,612
Cost of supplied product	(6,390		)	(1,555		)
Royalty payable to GSK on net sales by Ipsen	(1,987		)	(264		)
Collaboration revenues under the collaboration agreement with Ipsen	$	69,792		$	33,252

There were no such revenues for the year ended December 31, 2015. As of December 31, 2017, short-term and long-term deferred revenue relating to the collaboration agreement was $19.0 million and $210.2 million, respectively.

Takeda Collaboration

In January 2017, we entered into a collaboration and license agreement with Takeda for the commercialization and further clinical development of cabozantinib in Japan. Pursuant to the terms of the collaboration agreement, Takeda has exclusive commercialization rights for current and potential future cabozantinib indications in Japan. The parties have also agreed to collaborate on the future clinical development of cabozantinib in Japan. The operation and strategic direction of the parties’ collaboration is governed through a joint executive committee and appropriate subcommittees.

In consideration for the exclusive license and other rights contained in the collaboration agreement, we received a $50.0 million upfront nonrefundable payment from Takeda. The collaboration agreement contains multiple deliverables consisting of intellectual property licenses, delivery of products and/or materials containing cabozantinib to Takeda for all development and commercial activities, research and development services, and participation on the joint executive, development and commercialization committees (as defined in the collaboration agreement). We determined that these deliverables, other than the commercial supply and joint commercialization committee participation, are non-contingent in nature. The commercial supply deliverable was deemed contingent, primarily due to the fact that there is uncertainty around approval in Japan, which is dependent on successful clinical trial results from a study in Japanese patients. We also determined that the non-contingent deliverables do not have stand-alone value, because each one of them has value only if we meet our obligation as a whole to provide Takeda with research and development services, including clinical supply of cabozantinib under the collaboration agreement. Accordingly, we combined the non-contingent deliverables into a single unit of accounting and allocated the $50.0 million upfront fee to that combined unit of accounting. We also determined that the level of effort required of us to meet our obligations under the collaboration agreement is not expected to vary significantly over the development period of the collaboration agreement. As a result, the upfront payment of $50.0 million, received in the first quarter of 2017, has been recognized ratably over the development period of the collaboration agreement of approximately four years. We will adopt ASU 2014-09 using the modified retrospective method in the first quarter of fiscal year 2018, which will materially impact the timing of recognition of revenue for our collaboration agreement with Takeda. For information on our adoption of ASU 2014-09, see “Note 1. Organization and Summary of Significant Accounting Policies” in the “Notes to Consolidated Financial Statements” contained in Part II, Item 8 of this Annual Report on Form 10-K.

We are eligible to receive development, regulatory and first-sale milestone payments of up to $95.0 million related to second-line RCC, first-line RCC and second-line HCC, as well as additional development, regulatory and first-sale milestones payments for potential future indications. We determined that the development and regulatory milestones are substantive and will be recognized as revenue in the periods in which they are achieved. The collaboration agreement also provides that we are eligible to receive pre-specified payments of up to $83.0 million associated with potential sales milestones. We consider the contingent payments due to us upon the achievement of specified sales volumes to be similar to royalty payments. We will also receive royalties on net sales of cabozantinib in Japan. We are entitled to receive a tiered royalty of 15% to 24% on the initial $300.0 million of net sales, and after the initial $300.0 million of net sales, we are then entitled to receive a tiered royalty of 20% to 30% on annual net sales. These tiers will reset each calendar year.

Takeda is responsible for 20% of the costs associated with the global cabozantinib development plan’s current and future trials, provided Takeda opts into such trials, and 100% of costs associated with the cabozantinib development activities that are exclusively for the benefit of Japan. Pursuant to the terms of the collaboration agreement, we are responsible for the manufacture and supply of cabozantinib for all development and commercialization activities under the collaboration, and consequently, we entered into a clinical supply agreement covering the manufacture and supply of cabozantinib to Takeda, as well as a quality agreement setting forth, in detail, the quality assurance arrangements and procedures for our manufacture of cabozantinib. We will record reimbursements for development costs as revenue as the development services represent a part of our ongoing major or central operations.

Unless earlier terminated, the collaboration agreement has a term that continues, on a product-by-product basis, until the earlier of (i) two years after first generic entry with respect to such product in Japan or (ii) the later of (A) the expiration of patent claims related to cabozantinib and (B) the expiration of regulatory exclusivity covering cabozantinib in Japan. The collaboration agreement may be terminated for cause by either party based on uncured material breach by the other party, bankruptcy of the other party or for safety reasons. For clarity, Takeda’s failure to achieve specified levels of commercial performance, based upon sales volume and/or promotional effort, during the first six years of the collaboration shall constitute a material breach of the collaboration agreement. We may terminate the agreement if Takeda challenges or opposes any patent covered by the collaboration agreement. At any time prior to August 1, 2023, the parties may mutually agree to terminate the collaboration agreement if Japan’s Pharmaceuticals and Medical Devices Agency is unlikely to grant any approval of the marketing authorization application in any cancer indication in Japan. After the commercial launch of cabozantinib in Japan, Takeda may terminate the collaboration agreement upon twelve months’ prior written notice following the third anniversary of the first commercial sale of cabozantinib in Japan. Upon termination by either party, all licenses granted by us to Takeda will automatically terminate, and the licenses granted by Takeda to us shall survive such termination and shall automatically become worldwide.

Collaboration revenues under the collaboration agreement with Takeda were as follows (in thousands):



	Year Ended December 31, 2017
Amortization of upfront payment	$	10,377
Development cost reimbursements	4,320
Product supply agreement revenue	82
Collaboration revenues under the collaboration agreement with Takeda	$	14,779

There were no such revenues for the year ended December 31, 2016 or 2015. As of December 31, 2017, short-term and long-term deferred revenue relating to the collaboration agreement was $11.3 million and $28.3 million, respectively.

Cobimetinib Collaboration

Genentech Collaboration

In December 2006, we out-licensed the further development and commercialization of cobimetinib to Genentech pursuant to a worldwide collaboration agreement. Under the terms of the collaboration agreement, we were responsible for developing cobimetinib through the determination of the maximum-tolerated dose in a phase 1 clinical trial, and Genentech had the option to co-develop cobimetinib, which Genentech could exercise after receipt of certain phase 1 data from us. In March 2008, Genentech exercised its option to co-develop cobimetinib, and in March 2009, we granted to Genentech an exclusive worldwide revenue-bearing license to cobimetinib, at which point Genentech became responsible for completing the phase 1 clinical trial and subsequent clinical development.

On November 10, 2015, the FDA approved cobimetinib, under the brand name COTELLIC, in combination with Zelboraf as a treatment for patients with BRAF V600E or V600K mutation-positive advanced melanoma. COTELLIC in combination with Zelboraf has also been approved in Switzerland, the EU, Canada, Australia, Brazil and multiple additional countries for use in the same indication. Prior to the FDA’s approval of COTELLIC, in November 2013, we exercised an option under the collaboration agreement to co-promote COTELLIC in the U.S., which allowed us to provide up to 25% of the total sales force for approved cobimentinib indications in the U.S. Between November 2015 and December 2017, we fielded 25% of the sales force promoting COTELLIC in combination with Zelboraf as a treatment for patients with BRAF mutation-positive advanced melanoma in the U.S. However, following a recent commercial review, commencing in January 2018, we and Genentech scaled back the personal promotion of COTELLIC in this indication in the U.S. This decision is not indicative of any change in our intention to promote COTELLIC for other therapeutic indications for which it may be approved in the future.

Under the terms of our collaboration agreement, as amended in July 2017, we share in the profits and losses received or incurred in connection with COTELLIC’s commercialization in the U.S. This profit and loss share has multiple tiers: we receive 50% of profits and losses from the first $200.0 million of U.S. actual sales, decreasing to 30% of profits and losses from U.S. actual sales in excess of $400.0 million. These tiers will reset each calendar year. The revenue for each sale of COTELLIC applied to the profit and loss statement for the collaboration agreement (the “Genentech Collaboration P&L”) is calculated using the average of the quarterly net selling prices of COTELLIC and any additional branded Genentech product(s) prescribed with COTELLIC in such sale. U.S. commercialization costs for COTELLIC are then applied to the Genentech Collaboration P&L, subject to reduction based on the number of Genentech products in any given combination including COTELLIC. In addition to our profit share in the U.S., under the terms of the collaboration agreement, we are entitled to low double-digit royalties on net sales of COTELLIC outside the U.S.

Unless earlier terminated, the collaboration agreement has a term that continues until the expiration of the last payment obligation with respect to the licensed products under the collaboration. Genentech has the right to terminate the collaboration agreement without cause at any time. If Genentech terminates the collaboration agreement without cause, all licenses that were granted to Genentech under the agreement terminate and revert to us. Additionally, if Genentech terminates the collaboration agreement without cause, or we terminate the collaboration agreement for cause, we would receive, subject to certain conditions, licenses from Genentech to research, develop and commercialize reverted product candidates. The collaboration agreement may be terminated for cause by either party based on uncured material breach by the other party.

Collaboration revenues and U.S. (loss) net cost recovery under the collaboration agreement were as follows (in thousands):



	Year Ended December 31,
	2017			2016		2015
Collaboration revenues:
Royalty revenues on ex-U.S. sales of COTELLIC	$	6,398		$	2,827	$	14
U.S. (loss) net cost recovery under the collaboration agreement included in Selling, general and administrative expenses	$	(2,140	)	$	8,771	$	(16,600	)

In December 2016 Genentech stated that it changed, both retroactively and prospectively, the manner in which it allocates promotional expenses of the COTELLIC plus Zelboraf combination therapy. As a result of Genentech’s decision to change its cost allocation approach, we were relieved of our obligation to pay certain disputed costs that had been accrued by us; we were also able to invoice Genentech for certain expenses, with interest, that we had previously paid. Accordingly, during the year ended December 31, 2016, we offset Selling, general and administrative expenses with a $13.3 million recovery of disputed losses that we had recognized and recorded prior to 2016 and also recognized a loss under the collaboration agreement of $4.5 million for 2016 activities, resulting in a net cost recovery of $8.8 million.

Other Collaborations

We have established collaborations with other leading pharmaceutical and biotechnology companies, including BMS, Daiichi Sankyo Company Limited (“Daiichi Sankyo”), Roche, Merck (known as MSD outside of the U.S. and Canada) and Sanofi, for various compounds and programs in our portfolio. Pursuant to these collaborations, we have fully out-licensed compounds or programs to a partner for further development and commercialization. Under each of our collaborations, we are entitled to receive milestones and royalties.

With respect to our partnered compounds, other than cabozantinib and cobimetinib, we are eligible to receive potential contingent payments totaling approximately $1.9 billion in the aggregate on a non-risk adjusted basis, of which 9% are related to clinical development milestones, 49% are related to regulatory milestones and 42% are related to commercial milestones, all to be achieved by the various licensees, which may not be paid, if at all, until certain conditions are met.

Daiichi Sankyo

In March 2006, we entered into a collaboration agreement with Daiichi Sankyo for the discovery, development and commercialization of novel therapies targeted against the mineralocorticoid receptor (“MR”), a nuclear hormone receptor implicated in a variety of cardiovascular and metabolic diseases. Under the terms of the agreement, we granted to Daiichi Sankyo an exclusive, worldwide license to certain intellectual property primarily relating to compounds that modulate MR, including CS-3150/esaxerenone (a specific rotational isomer of XL550). Daiichi Sankyo is responsible for all further preclinical and clinical development, regulatory, manufacturing and commercialization activities for the compounds and we do not have rights to reacquire such compounds, except as described below. In September 2017, Daiichi Sankyo reported positive top-line results from the phase 3 pivotal trial of CS-3150/esaxerenone and communicated its intention to submit a Japanese regulatory application for CS-3150/esaxerenone for an essential hypertension indication in the first quarter of 2018.

We are eligible to receive additional development, regulatory and commercialization milestone payments of up to $130.0 million. In addition, we are entitled to receive royalties on any sales of certain products commercialized under the collaboration. Daiichi Sankyo may terminate the agreement upon ninety days’ written notice in which case Daiichi Sankyo’s payment obligations would cease, its license relating to compounds that modulate MR would terminate and revert to us and we would receive, subject to certain terms and conditions, licenses from Daiichi Sankyo to research, develop and commercialize compounds that were discovered under the collaboration.

We recognized contract revenues of $15.0 million for milestone payments during the year ended December 31, 2016 under our collaboration agreement with Daiichi Sankyo. We did not recognize any such revenue during the years ended December 31, 2017 or 2015.

The Roche Group Collaboration

In February 2017, we established a clinical trial collaboration with The Roche Group (“Roche”) for the purpose of evaluating the safety and tolerability of cabozantinib in combination with Roche’s atezolizumab in patients with locally advanced or metastatic solid tumors. Each party is responsible for supplying drug product for the applicable clinical trial in accordance with the terms of the clinical supply agreement entered into by the parties in February 2017. Based on the dose-escalation results, the trial has the potential to enroll up to four expansion cohorts, including a cohort of patients with previously untreated advanced clear cell RCC and three cohorts of urothelial carcinoma, namely platinum eligible first-line patients, first or second-line platinum ineligible patients and patients previously treated with platinum-containing chemotherapy. The trial was initiated in June 2017 and is open for enrollment. We are the sponsor of the trial, and Roche is responsible for supplying atezolizumab to us. Ipsen has opted to participate in the study and will have access to the results to support potential future development in its territories.

Merck

In December 2011, we entered into an agreement with Merck pursuant to which we granted Merck an exclusive worldwide license to our phosphoinositide-3 kinase-delta (“PI3K-d”) program, including XL499 and other related compounds. Pursuant to the terms of the agreement, Merck has sole responsibility to research, develop, and commercialize compounds from our PI3K-d program.

We are eligible to receive additional payments associated with the successful achievement of potential development and regulatory milestones for multiple indications of up to $231.0 million. We will also be eligible to receive payments for combined sales performance milestones of up to $375.0 million and royalties on net-sales of products emerging from the agreement.

Merck may at any time, upon specified prior notice to us, terminate the license. In addition, either party may terminate the agreement for the other party’s uncured material breach. In the event of termination by Merck at will or by us for Merck’s uncured material breach, the license granted to Merck would terminate. In the event of a termination by us for Merck’s uncured material breach, we would receive a royalty-free license from Merck to develop and commercialize certain joint products. In the event of termination by Merck for our uncured material breach, Merck would retain the licenses from us, and we would receive reduced royalties from Merck on commercial sales of products.

We recognized contract revenues of $5.0 million and $3.0 million for milestone payments during the years ended December 31, 2016 and 2015, respectively, under our collaboration agreement with Merck. We did not recognize any such revenue during the year ended December 31, 2017.

Bristol-Myers Squibb

Previously Untreated Advanced RCC, Bladder Cancer and Previously Treated HCC Combination Studies

In February 2017, we entered into a clinical trial collaboration agreement with BMS for the purpose of evaluating the combination of cabozantinib and nivolumab with or without ipilimumab in various tumor types, including, in RCC, HCC and bladder cancer. To date, CheckMate 9ER, a phase 3 pivotal trial in previously untreated, advanced or metastatic RCC, and CheckMate 040, a phase 1/2 trial in both previously treated and previously untreated advanced HCC evaluating these combinations has been initiated. Pursuant to the terms of the collaboration agreement, each party will grant to the other a non-exclusive, worldwide (within the collaboration territory as defined in the collaboration agreement), non-transferable, royalty-free license to use the other party’s compounds in the conduct of each clinical trial. The parties’ efforts are governed through a joint development committee established to guide and oversee the collaboration’s operation. Each trial will be conducted under a combination Investigational New Drug Application, unless otherwise required by a regulatory authority. Each party will be responsible for supplying drug product for the applicable clinical trial in accordance with the terms of the supply agreement entered into between the parties in April 2017, and costs for each such trial will be shared equally between the parties, unless two BMS compounds will be utilized in such trial, in which case BMS will bear two-thirds of the costs and we will bear one-third of the costs for such study treatment arms. Unless earlier terminated, the BMS collaboration agreement will remain in effect until the completion of all clinical trials under the collaboration, all related trial data has been delivered to both parties and the completion of any then agreed upon analysis. Ipsen has opted in to participate in both trials (though Ipsen will not be co-funding the triplet arm of the study evaluating cabozantinib with nivolumab and ipilimumab) and will have access to the results to support potential future regulatory submissions. Ipsen may also participate in future studies at its choosing.

ROR Collaboration

In October 2010, we entered into a worldwide collaboration with BMS pursuant to which each party granted to the other certain intellectual property licenses to enable the parties to discover, optimize and characterize ROR antagonists that may subsequently be developed and commercialized by BMS. Under the terms of the collaboration agreement, we were responsible for activities related to the discovery, optimization and characterization of the ROR antagonists during the collaborative research period which began on October 8, 2010 and ended on July 8, 2013. Since the end of the collaborative research period, BMS has and will continue to have sole responsibility for any further research, development, manufacture and commercialization of products developed under the collaboration and will bear all costs and expenses associated with those activities.

We are eligible for additional development and regulatory milestone payments of up to $240.0 million in the aggregate and commercialization milestones of up to $150.0 million in the aggregate, as well as royalties on commercial net sales, depending on the advancement of the product candidate and eventual product.

The collaboration agreement was amended and restated in April 2011 in connection with an assignment of patents to a wholly-owned subsidiary. BMS may, at any time, terminate the collaboration agreement upon certain prior notice to us on a product-by-product and country-by-country basis. In addition, either party may terminate the agreement for the other party’s uncured material breach. In the event of termination by BMS at will or by us for BMS’s uncured material breach, the license granted to BMS would terminate, the right to such product would revert to us and we would receive a royalty-bearing license for late-stage reverted compounds and a royalty-free license for early-stage reverted compounds from BMS to develop and commercialize such product in the related country. In the event of termination by BMS for our uncured material breach, BMS would retain the right to such product, subject to continued payment of milestones and royalties.

We recognized contract revenues of $12.5 million for milestone payments during the year ended December 31, 2017 under our collaboration agreement with BMS. We did not recognize any such revenue during the years ended December 31, 2016 or 2015.

Sanofi

In May 2009, we entered into a global license agreement with Sanofi for SAR245408 (XL147) and SAR245409 (XL765), leading inhibitors of phosphoinositide-3 kinase (“PI3K”), and a broad collaboration for the discovery of inhibitors of PI3K for the treatment of cancer. The license agreement and collaboration agreement became effective on July 7, 2009.

Under the license agreement, Sanofi received a worldwide exclusive license to SAR245408 (XL147) and SAR245409 (XL765), which entered into a series of phase 1, phase 1b/2 or phase 2 clinical trials, and has sole responsibility, including funding, for all subsequent clinical, regulatory, commercial and manufacturing activities. We were notified by Sanofi that the initial clinical trials involving XL147 or XL765 have been terminated or are in the process of concluding, and that Sanofi is still considering whether to initiate any further trials. We are eligible to receive contingent payments associated with development, regulatory and commercial milestones under the license agreement of $745.0 million in the aggregate, as well as royalties on sales of any products commercialized under the license. Sanofi may, upon certain prior notice to us, terminate the license as to products containing SAR245408 (XL147) and SAR245409 (XL765). In the event of such termination election, Sanofi’s license relating to such product would terminate and revert to us, and we would receive, subject to certain terms, conditions and potential payment obligations, licenses from Sanofi to research, develop and commercialize such products.

We did not recognize any revenue under our collaboration agreement with Sanofi during the three years ended December 31, 2017, 2016 and 2015.

GlaxoSmithKline

In October 2002, we established a collaboration with GSK to discover and develop novel therapeutics in the areas of vascular biology, inflammatory disease and oncology. Under the terms of the product development and commercialization agreement, GSK had the right to choose cabozantinib for further development and commercialization, but notified us in October 2008 that it had waived its right to select the compound for such activities. As a result, we retained the rights to develop, commercialize, and license cabozantinib, subject to payment to GSK of a 3% royalty on net sales of any product incorporating cabozantinib. The product development and commercialization agreement was terminated during 2014, although GSK will continue to be entitled to a 3% royalty on net sales by us or our collaboration partners of any product incorporating cabozantinib, including COMETRIQ and CABOMETYX.

Royalties accruing to GSK in connection with the sales of COMETRIQ and CABOMETYX were as follows (in thousands):



	Year Ended December 31,
	2017		2016		2015
Royalties accruing to GSK	$	12,413	$	4,334	$	1,029

Royalties accruing to GSK are included in Cost of goods sold for net sales by us and as a reduction of Collaboration revenues for net sales by Ipsen on the accompanying Consolidated Statements of Operations.

Investments

12 Months Ended

Dec. 29, 2017

Investments, Debt and Equity Securities [Abstract]

Investments

INVESTMENTS

Investments Available-for-Sale

Cash equivalents and investments by security type were as follows. The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	December 31, 2017
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	45,478	$	—	$	—		$	45,478
Commercial paper	199,647		—		—			199,647
Corporate bonds	179,336		18		(332		)	179,022
U.S. Treasury and government sponsored enterprises	16,295		—		(32		)	16,263
Total	$	440,756	$	18	$	(364	)	$	440,410



	December 31, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	71,457	$	—	$	—		$	71,457
Commercial paper	165,375		—		—			165,375
Corporate bonds	152,712		3		(308		)	152,407
U.S. Treasury and government sponsored enterprises	70,730		11		(14		)	70,727
Total	$	460,274	$	14	$	(322	)	$	459,966

Gains and losses on the sales of investments available-for-sale were nominal or zero during the years ended December 31, 2017, 2016 and 2015.

The fair value and gross unrealized losses of investments available-for-sale in an unrealized loss position were as follows (in thousands):



	December 31, 2017
	In an Unrealized Loss Position Less than 12 Months					In an Unrealized Loss Position 12 Months or Greater					Total
	Fair Value		Gross Unrealized Losses			Fair Value		Gross Unrealized Losses			Fair Value		Gross Unrealized Losses
Corporate bonds	$	140,746	$	(296	)	$	20,047	$	(36	)	$	160,793	$	(332	)
U.S. Treasury and government sponsored enterprises	13,611		(23		)	2,651		(9		)	16,262		(32		)
Total	$	154,357	$	(319	)	$	22,698	$	(45	)	$	177,055	$	(364	)



	December 31, 2016
	In an Unrealized Loss Position Less than 12 Months					In an Unrealized Loss Position 12 Months or Greater					Total
	Fair Value		Gross Unrealized Losses			Fair Value		Gross Unrealized Losses			Fair Value		Gross Unrealized Losses
Corporate bonds	$	140,559	$	(305	)	$	3,001	$	(3	)	$	143,560	$	(308	)
U.S. Treasury and government sponsored enterprises	27,657		(14		)	—		—			27,657		(14		)
Commercial paper⁽¹⁾	998		—			—		—			998		—
Total	$	169,214	$	(319	)	$	3,001	$	(3	)	$	172,215	$	(322	)

____________________


(1)	Gross unrealized losses on commercial paper were less than $1 thousand.

There were 134 and 86 investments in an unrealized loss position as of December 31, 2017 and 2016, respectively. During the years ended December 31, 2017, 2016 and 2015 we did not record any other-than-temporary impairment charges on our available-for-sale securities. Based upon our quarterly impairment review, we determined that the unrealized losses were not attributed to credit risk, but were primarily associated with changes in interest rates. Based on the scheduled maturities of our investments and our determination that it was more likely than not that we will hold these investments for a period of time sufficient for a recovery of our cost basis, we concluded that the unrealized losses in our investment securities were not other-than-temporary.

The fair value of cash equivalents and investments by contractual maturity were as follows (in thousands):



	December 31,
	2017		2016
Maturing in one year or less	$	377,155	$	404,365
Maturing after one year through five years	63,255		55,601
Total	$	440,410	$	459,966

Cash is excluded from the table above. The classification of certain restricted investments was dependent upon the term of the underlying restriction on the asset and not the maturity date of the investment. As a result, certain investments with contractual maturities within one year were classified as long-term restricted cash and investments.

As of December 31, 2016, we were required to maintain compensating balances of $81.6 million in connection with our term loan payable to Silicon Valley Bank, which was included in short-term investments on the accompanying Consolidated Balance Sheet; as a result of our repayment of the term loan, the compensating balance requirement was terminated in March 2017.

Other Cost Method Equity Investments

During the years ended December 31, 2017 and 2016 we recognized gains of $3.0 million and $2.5 million, respectively, related to the August 2016 sale of our 9% interest in Akarna Therapeutics, Ltd. (“Akarna”) to Allergan Holdco UK Limited (“Allergan”). We acquired our interest in Akarna in 2015 in exchange for intellectual property rights related to the Exelixis discovered compound XL335. The gain on sale was included in Other expenses, net on the accompanying Consolidated Statements of Operations. We are eligible to earn additional such gains in the future as Allergan continues its development of XL335. The gain on sale of other cost method equity investments was nominal during the year ended December 31, 2015.

Inventory

12 Months Ended

Dec. 29, 2017

Inventory Disclosure [Abstract]

Inventory

INVENTORY

Inventory consisted of the following (in thousands):



	December 31,
	2017		2016
Raw materials	$	498	$	863
Work in process	3,997		2,343
Finished goods	2,854		738
Total	$	7,349	$	3,944

Balance Sheet classification:
Inventory	$	6,657	$	3,338
Other long-term assets	692		606
Total	$	7,349	$	3,944

A portion of the manufacturing costs for inventory was incurred prior to regulatory approval of CABOMETYX and COMETRIQ and therefore was expensed as research and development costs when those costs were incurred, rather than capitalized as inventory. Write-downs related to excess and expiring inventory are charged to either Cost of goods sold or the cost of supplied product included in Collaboration revenues. Such write-downs were $1.2 million, $0.5 million and $1.2 million for the years ended December 31, 2017, 2016 and 2015, respectively.

Inventory expected to be used or sold in periods more than 12 months from the date presented is classified as Other long-term assets on the accompanying Consolidated Balance Sheets. As of December 31, 2017, the non-current portion of inventory consisted of finished goods. As of December 31, 2016, the non-current portion of inventory consisted of raw materials and a portion of the active pharmaceutical ingredient that was included in work in process inventories.

Property and Equipment

12 Months Ended

Dec. 29, 2017

Property, Plant and Equipment [Abstract]

Property and Equipment

PROPERTY AND EQUIPMENT

Property and equipment were as follows (in thousands):



	December 31, 2017			December 31, 2016
Computer equipment and software	$	14,146		$	13,738
Laboratory equipment	5,959			4,310
Leasehold improvements	4,715			6,646
Furniture and fixtures	1,609			2,240
Construction in progress	22,114			19
	48,543			26,953
Less: accumulated depreciation and amortization	(22,800		)	(24,882		)
Property and equipment, net	$	25,743		$	2,071

Depreciation expense was $1.2 million, $1.0 million and $1.4 million during the years ended December 31, 2017, 2016 and 2015, respectively.

Build-to-Suit Lease

On May 2, 2017, we entered into a Lease Agreement (the “Lease”) with Ascentris 105, LLC (“Ascentris”), to lease 110,783 square feet of space in office and research facilities located at 1751, 1801, and 1851 Harbor Bay Parkway, Alameda, California (the “Premises”). On October 16, 2017, we executed an amendment to the Lease for 19,778 square feet of additional space located at the Premises with terms consistent with the original Lease. See “Note 12. Commitments” for a description of the Lease.

In connection with the Lease, we received a tenant improvement allowance of $7.7 million from Ascentris, for the costs associated with the design, development and construction of tenant improvements for the Premises. We are obligated to fund all costs incurred in excess of the tenant improvement allowance and to certain indemnification obligations related to the construction activities. We evaluated our involvement during the construction period and determined the scope of the tenant improvements on portions of the Premises including the building shells did not qualify as “normal tenant improvements” under Accounting Standards Codification (“ASC”) Topic 840, Leases. Accordingly, for accounting purposes, we are the deemed owner of such portions of the Premises during the construction period. As such, we will capitalize the construction costs as a build-to-suit property within property and equipment, net, including the estimated fair value of the building shells that we are deemed to own at the lease inception date, as determined using a third-party appraisal. The capitalized construction costs will also include the estimated tenant improvements incurred by Ascentris. Accordingly, we capitalized $14.5 million of costs related to the Lease in construction in progress as of May 2, 2017, with a corresponding build-to-suit lease obligation in Other long-term liabilities. As of December 31, 2017, we have capitalized an additional $6.6 million of construction in progress for tenant improvements related to the Premises. As of December 31, 2017, we have also prepaid an additional $11.1 million for future constructions costs which is included in Other long-term assets on the accompanying Consolidated Balance Sheets.

Once the construction is complete, we will consider the requirements for sale-leaseback accounting treatment, including evaluating whether all risks of ownership have been transferred back to Ascentris, as evidenced by a lack of continuing involvement in the leased property. If the arrangement does not qualify for sale-leaseback accounting treatment, the building assets will remain on the accompanying Consolidated Balance Sheets at their historical cost.

Debt

12 Months Ended

Dec. 29, 2017

Debt Disclosure [Abstract]

Debt

DEBT

The amortized carrying amount of our debt was as follows (in thousands):



	December 31,
	2017		2016
Convertible notes	$	—	$	109,122
Term loan payable	—		80,000
Total debt	$	—	$	189,122

The balance of unamortized fees and costs was $0.4 million as of December 31, 2016, which was recorded as a reduction of the carrying amount of the Convertible notes on the accompanying Consolidated Balance Sheet.

Convertible notes

Secured Convertible Notes due 2018 (“Deerfield Notes”)

On June 28, 2017, we repaid all amounts outstanding under the Deerfield Notes. The repayment amount totaled $123.8 million which comprised $113.9 million in principal, including $13.9 million of interest paid in kind paid through the repayment date, a $5.8 million prepayment penalty associated with the early repayment of the notes and $4.2 million in accrued and unpaid interest. As a result of the early repayment, there was a $6.2 million loss on the extinguishment of the debt which comprised the prepayment penalty and the unamortized fees and costs on the date of the repayment.

Prior to our early repayment of the Deerfield Notes, the outstanding principal amount of the notes bore interest at the rate of 7.5% per annum to be paid in cash, quarterly in arrears, and 7.5% per annum to be paid in kind, quarterly in arrears, for a total interest rate of 15% per annum.

4.25% Convertible Senior Subordinated Notes due 2019 (“2019 Notes”)

Between August and November 2016, all $287.5 million aggregate principal amount outstanding under the 2019 Notes was either converted into 54,009,279 shares of common stock or redeemed for $0.6 million in cash. In addition, certain holders received inducements of $6.0 million which included an aggregate cash payment of $2.4 million and $3.6 million in accrued interest payments which would have been payable if the notes had not been exchanged. Under the terms of the indenture for the 2019 Notes, certain holders who exchanged their notes on August 9, 2016 would have been required to repay the interest payment they received as holders of record on August 1. The exchange transactions were structured such that the holders were not required to repay this interest. We have included those payments as an additional inducement and as financing activities on the accompanying Consolidated Statement of Cash Flows. A summary of loss on extinguishment of debt for the conversion and redemption of the 2019 Notes was as follows (in thousands):



	Year Ended December 31, 2016
Cash inducements	$	2,394
Waiver of requirement to repay interest, described above	3,572
Difference between the total settlement consideration attributed to the liability component of the 2019 Notes and the net carrying value of the liability	7,338
Unamortized discount on redeemed notes	83
Third-party costs	514
Loss on extinguishment of debt	$	13,901

The stock issuance on the conversion of the notes resulted in an increase to common stock and additional paid-in capital of $592.7 million. A portion of the settlement consideration transferred to the holders of the notes was allocated to the reacquisition of the conversion option embedded in the notes, which resulted in a $342.7 million reduction of additional paid-in capital.

Prior to the extinguishment of the 2019 Notes, the outstanding principal amount of the notes bore interest at a rate of 4.25% per annum, payable semi-annually in arrears on February 15 and August 15 of each year.

Term loan payable

On March 29, 2017, we repaid all amounts outstanding under our term loan payable to Silicon Valley Bank. The repayment included $80.0 million in principal plus $0.1 million in accrued and unpaid interest. There was no gain or loss on the extinguishment of debt as a result of the repayment of the term loan.

Prior to our early repayment of the term loan payable, the outstanding principal amount of the loan bore interest at the rate of 1.0% per annum, which was due and payable monthly.

Common Stock and Warrants	12 Months Ended
Common Stock and Warrants	Dec. 29, 2017
Warrants and Rights Note Disclosure [Abstract]
Common Stock and Warrants	COMMON STOCK AND WARRANTS Conversion of Debt into Common Stock Between August and November 2016, we issued 54,009,279 shares of our common stock pursuant to the conversion of $286.9 million of aggregate principal amount of the 2019 Notes. The conversions resulted in a $253.1 million increase to shareholder’s equity and a $13.9 million loss on extinguishment of debt. See “Note 6. Debt” for more information on the conversion of the 2019 Notes. Sale of Shares of Common Stock In July 2015, we completed a registered underwritten public offering of 28,750,000 shares of our common stock, including 3,750,000 shares issued under the underwriters’ 30-day option to buy shares, at a price of $5.40 per share pursuant to a shelf registration statement previously filed with the Securities and Exchange Commission, which was filed and automatically became effective on July 1, 2015. We received $145.6 million in net proceeds from the offering after deducting the underwriting discount and other expenses. 2014 Warrants In connection with an amendment to the note purchase agreement for the Secured Convertible Notes due 2015, (the “Original Deerfield Notes”), in January 2014 we issued two-year warrants to purchase an aggregate of 1,000,000 shares of our common stock at an exercise price of $9.70 per share (the “2014 Warrants”). Subsequent to our March 2015 notification of our election to extend the maturity date of the Deerfield Notes, the exercise price of the 2014 Warrants was reset to $3.445 per share, the term was extended by two years to January 22, 2018, and the 2014 Warrants were transferred to Additional paid-in capital as of that date at their then estimated fair value of $1.5 million as their terms had become fixed. On September 11, 2017, we issued an aggregate of 877,451 shares of common stock pursuant to the cashless exercises of the 2014 Warrants issued to an accredited investor transferee. The number of shares issued upon exercise was net of 122,549 shares withheld to effect the cashless exercise of the 2014 Warrants in accordance with their terms. As of December 31, 2017, there are no remaining warrants outstanding.

Stock-based Compensation

12 Months Ended

Dec. 29, 2017

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

Stock-based Compensation

STOCK-BASED COMPENSATION

The allocation of stock-based compensation for our equity incentive plans and our Employee Stock Purchase Plan (the “ESPP”) was as follows (in thousands):



	Year Ended December 31,
	2017		2016		2015
Research and development	$	7,569	$	9,366	$	11,691
Selling, general and administrative	16,369		13,546		10,286
Total stock-based compensation	$	23,938	$	22,912	$	21,977

We have several equity incentive plans under which we have granted stock options and RSUs to employees, directors and consultants. At December 31, 2017, 20,328,545 shares were available for grant under our equity incentive plans. The Board of Directors or a designated Committee of the Board is responsible for administration of our equity incentive plans and determines the term, exercise price and vesting terms of each grant. Stock options have a four-year vesting term, an exercise price equal to the fair market value on the date of grant, and a seven year life from the date of grant. Stock options issued prior to May 2011 have a ten year life from the date of grant. RSUs granted to our employees generally vest annually over a four year term.

We have adopted a Change in Control and Severance Benefit Plan for executives and certain non-executives. Eligible Change in Control and Severance Benefit Plan participants include employees with the title of vice president and above. If a participant’s employment is terminated without cause during a period commencing one month before and ending thirteen months following a change in control, as defined in the plan document, then the Change in Control and Severance Benefit Plan participant is entitled to have the vesting of all of such participant’s stock options accelerated with the exercise period being extended to no more than one year.

We have an ESPP that allows for qualified employees (as defined in the ESPP) to purchase shares of our common stock at a price equal to the lower of 85% of the closing price at the beginning of the offering period or 85% of the closing price at the end of each six month purchase period. Compensation expense related to our ESPP was $1.6 million, $1.0 million, and $0.4 million for the years ended December 31, 2017, 2016 and 2015, respectively. As of December 31, 2017, we had 5,052,500 shares available for issuance under our ESPP. Pursuant to the ESPP, we issued 434,523 shares, 559,936 shares, and 324,315 shares of common stock at an average price per share of $11.20, $3.91 and $1.75 during the years ended December 31, 2017, 2016 and 2015, respectively. Cash received from purchases under the ESPP in the years ended December 31, 2017, 2016 and 2015 was $4.9 million, $2.2 million and $0.6 million, respectively.

We use the Black-Scholes Merton option pricing model to value our stock options. The weighted average grant-date fair value of our stock option grants and ESPP purchases were as follows:



	Year Ended December 31,
	2017		2016		2015
Stock options	$	11.42	$	4.77	$	2.55
ESPP	$	6.00	$	2.17	$	1.20

The grant-date fair value of employee stock option grants and ESPP purchases was estimated using the following assumptions:



	Year Ended December 31,
	2017		2016		2015
Stock options:
Risk-free interest rate	1.98	%	1.15	%	1.22	%
Dividend yield	—	%	—	%	—	%
Volatility	59	%	76	%	93	%
Expected life	4.5 years		4.4 years		4.5 years
ESPP:
Risk-free interest rate	1.09	%	0.55	%	0.15	%
Dividend yield	—	%	—	%	—	%
Volatility	58	%	65	%	98	%
Expected life	6 months		6 months		6 months

We considered implied volatility as well as our historical volatility in developing our estimates of expected volatility. The assumptions for the expected life of stock options were based on historical exercise patterns and post-vesting termination behavior.

Stock option activity for the year ended December 31, 2017 was as follows (dollars in thousands, except per share amounts):



	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Options outstanding at December 31, 2016	24,999,665		$	4.91
Granted	2,166,110		$	23.43
Exercised	(4,469,203	)	$	3.91
Forfeited	(229,793	)	$	8.09
Expired	(258,333	)	$	9.91
Options outstanding at December 31, 2017	22,208,446		$	6.83	4.05 years	$	523,448
Exercisable at December 31, 2017	16,158,740		$	4.51	3.46 years	$	418,304

As of December 31, 2017, $39.7 million of unrecognized compensation expense related to stock options will be recognized over a weighted-average period of 2.57 years.

The aggregate intrinsic value in the table above represents the total intrinsic value (the difference between our closing stock price on the last trading day of fiscal 2017 and the exercise prices, multiplied by the number of in-the-money options) that would have been received by the option holders had all option holders exercised their options on December 31, 2017. The total intrinsic value of options exercised was $85.2 million, $50.0 million and $2.9 million during the years ended December 31, 2017, 2016 and 2015, respectively. Cash received from option exercises during the years ended December 31, 2017, 2016 and 2015 was $17.6 million, $25.3 million and $10.9 million, respectively. The total estimated fair value of employee options vested and recorded as expense during the years ended December 31, 2017, 2016 and 2015 was $13.1 million, $13.4 million and $18.9 million, respectively.

In April 2016, March 2016 and July 2015, the Compensation Committee of the Board of Directors of Exelixis convened to determine we had met certain performance objectives for performance-based stock options granted to employees in 2013, 2014 and 2015. As a result of these determinations, 5,870,303 and 6,982,613 performance-based stock options vested during the years ended December 31, 2016 and 2015, respectively. During the years ended December 31, 2016 and 2015 we recognized $4.1 million and $13.2 million in stock-based compensation for those performance-based stock option grants. We did not have any performance-based stock options outstanding during the year ended December 31, 2017 and therefore, did not record any stock-based compensation for performance-based stock options during the year.

The fair value of RSUs was determined based on the value of the underlying common stock on the date of grant. The expenses relating to RSUs are recognized over their vesting period. A summary of all RSU activity were as follows (dollars in thousands, except per share amounts):



	Shares		Weighted Average Grant Date Fair Value		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Awards outstanding at December 31, 2016	2,469,791		$	8.69
Awarded	2,137,817		$	24.60
Vested and released	(708,541	)	$	7.97
Forfeited	(136,077	)	$	11.48
Awards outstanding at December 31, 2017	3,762,990		$	17.76	1.95 years	$	114,395

As of December 31, 2017, $61.2 million of unrecognized compensation expense related to employee RSUs will be recognized over a weighted-average period of 3.20 years.

401(k) Retirement Plan

We sponsor the Exelixis, Inc. 401(k) Plan (the “401(k) Plan”) whereby eligible employees may elect to contribute up to the lesser of 50% of their annual compensation or the statutorily prescribed annual limit allowable under Internal Revenue Service regulations. We make matching contributions in the form of our common stock of 100% of the first 3% of each participant’s contributions into the 401(k) Plan. We recorded compensation expense related to the stock match of $1.7 million, $1.1 million, and $0.4 million for the years ended December 31, 2017, 2016 and 2015, respectively. As of December 31, 2017, 231,090 shares were available for issuance under the 401(k) Plan.

Income Taxes

12 Months Ended

Dec. 29, 2017

Income Tax Disclosure [Abstract]

Income Taxes

INCOME TAXES

The Provision for income taxes was based on the following income (loss) before income taxes (in thousands):



	Year Ended December 31,
	2017		2016			2015
Domestic	$	158,577	$	(70,222	)	$	(150,846	)
Foreign	—		—			(10,843		)
Income (loss) before income taxes	$	158,577	$	(70,222	)	$	(161,689	)

The Provision for income taxes was as follows (in thousands):



	Year Ended December 31,
	2017		2016		2015
Current:
Federal	$	—	$	—	$	—
State	4,350		—		55
Total current tax expense	4,350		—		55
Deferred:
Federal	—		—		—
State	—		—		—
Total deferred tax expense	—		—		—
Provision for income taxes	$	4,350	$	—	$	55

The Provision for income taxes for the year ended December 31, 2017 primarily relates to state taxes in jurisdictions outside of California, for which we do not have net operating loss carry-forwards due to a limited operating history. Our historical losses are sufficient to fully offset any federal taxable income. The Provision for income taxes for the year ended December 31, 2016 related to state minimum and franchise taxes and were nominal. The Provision for income taxes for the year ended December 31, 2015 relates to state minimum and franchise tax expenses as well as true ups related to prior year tax returns.

The reconciliation of income taxes at the statutory federal income tax rate to our Provision for income taxes included on the accompanying Consolidated Statements of Operations was as follows (in thousands):



	Year Ended December 31,
	2017			2016			2015
U.S. federal income tax provision (benefit) at statutory rate	$	53,916		$	(23,876	)	$	(54,974	)
Change in valuation allowance	(34,266		)	6,377			51,421
State tax expense	8,282			6,520			55
Debt extinguishment	—			4,726			—
Non-deductible interest	1,367			2,680			3,308
Stock-based compensation	(20,548		)	3,155			195
Other	(4,401		)	418			50
Provision for income taxes	$	4,350		$	—		$	55

Deferred tax assets and liabilities reflect the net tax effects of net operating loss and tax credit carry-forwards and temporary differences between the carrying amounts of assets and liabilities for financial reporting and the amounts used for income tax purposes.

Our deferred tax assets and liabilities were as follows (in thousands):



	December 31,
	2017			2016
Deferred tax assets:
Net operating loss carry-forwards	$	244,205		$	471,327
Book over tax depreciation and amortization	39,472			70,617
Tax credit and charitable contribution carry-forwards	66,770			64,367
Deferred revenue	53,543			—
Amortization of deferred stock compensation – non-qualified	8,966			14,780
Accruals and reserves not currently deductible	4,914			8,117
Other assets	1,088			106
Total deferred tax assets	418,958			629,314
Valuation allowance	(418,958		)	(629,062		)
Net deferred tax assets	—			252
Deferred tax liabilities:
Unrealized gains on derivatives and other liabilities	—			(252		)
Total deferred tax liabilities	—			(252		)
Net deferred taxes	$	—		$	—

On December 22, 2017, the Tax Cuts and Jobs Act of 2017 was signed into law. The Tax Cuts and Jobs Act contains significant changes to corporate taxation, including among other items, a reduction of the corporate tax rate from a top marginal rate of 35% to a flat rate of 21%. As a result of the signing of the Tax Cuts and Jobs Act, we recorded a $184.8 million reduction of our deferred tax assets along with a corresponding reduction of our valuation allowance. The Tax Cuts and Jobs Act could be amended or subject to technical correction, which could change the financial impacts that were recorded at December 31, 2017, or are expected to be recorded in future periods. Additionally, further guidance may be forthcoming from the FASB and the Securities and Exchange Commission, as well as regulations, interpretations and rulings from federal and state tax agencies, which could result in additional impacts.

ASC Topic 740 (“ASC 740”) requires that the tax benefit of net operating losses, temporary differences and credit carry forwards be recorded as an asset to the extent that management assesses that realization is "more likely than not." Realization of the future tax benefits is dependent on our ability to generate sufficient taxable income within the carry forward period. Because of our recent history of operating losses, management believes that recognition of the deferred tax assets arising from the above-mentioned future tax benefits is currently not likely (as defined in ASC 740) to be realized and, accordingly, has provided a valuation allowance. The valuation allowance decreased by $210.1 million during 2017 and increased by $92.7 million and $7.9 million during 2016 and 2015, respectively.

At December 31, 2017, we had federal net operating loss carry-forwards of approximately $1,105 million which expire in the years 2024 through 2036, and federal business tax credits of approximately $83 million which expire in the years 2020 through 2037. We also had state net operating loss carry-forwards of approximately $424 million, which expire in the years 2028 through 2036, and California research and development tax credits of approximately $28 million, which have no expiration.

Under the Internal Revenue Code and similar state provisions, certain substantial changes in our ownership could result in an annual limitation on the amount of net operating loss and credit carry-forwards that can be utilized in future years to offset future taxable income. The annual limitation may result in the expiration of net operating losses and credit carry-forwards before utilization. We completed a Section 382 study through December 31, 2017, and concluded that an ownership change, as defined under Section 382, had not occurred.

ASC 740 clarifies the accounting for uncertainty in income taxes by prescribing the recognition threshold a tax position is required to meet before being recognized in the financial statements. It also provides guidance on derecognition, classification, interest and penalties, accounting in interim periods, disclosure and transition. The following table summarizes the activity related to our unrecognized tax benefits (in thousands):



	Year Ended December 31,
	2017			2016			2015
Beginning balance	$	61,809		$	88,638		$	58,215
Change relating to prior year provision	247			(29,110		)	21,696
Change relating to current year provision	17,378			2,304			8,727
Reductions based on the lapse of the applicable statutes of limitations	(92		)	(23		)	—
Ending balance	$	79,342		$	61,809		$	88,638

We do not anticipate that the amount of unrecognized tax benefits existing as of December 31, 2017 will significantly decrease over the next 12 months.

We file U.S. and state income tax returns in jurisdictions with varying statues of limitations during which such tax returns may be audited and adjusted by the relevant tax authorities. The 1999 through 2016 tax years generally remain subject to examination by federal and most state tax authorities to the extent net operating losses and credits generated during these periods are being utilized in the open tax periods.

Net Income (Loss) Per Share

12 Months Ended

Dec. 29, 2017

Earnings Per Share [Abstract]

Net Income (Loss) Per Share

NET INCOME (LOSS) PER SHARE

The computation of basic and diluted net income (loss) per share was as follows (in thousands, except per share amounts):



	Year Ended December 31,
	2017			2016			2015
Numerator:
Net income (loss)	$	154,227		$	(70,222	)	$	(161,744	)
Net income allocated to participating securities	(367		)	—			—
Net income allocable to common stock for basic net income (loss) per share	153,860			(70,222		)	(161,744		)
Adjustment to net income allocated to participating securities	22			—			—
Net income allocable to common stock for diluted net income (loss) per share	$	153,882		$	(70,222	)	$	(161,744	)
Denominator:
Weighted-average shares of common stock outstanding used in computing basic net income (loss) per share	293,588			250,531			209,227
Dilutive securities:
Outstanding stock options, unvested RSUs and ESPP contributions	18,415			—			—
Weighted-average shares of common stock outstanding and dilutive securities used in computing diluted net income (loss) per share	312,003			250,531			209,227

Net income (loss) per share, basic	$	0.52		$	(0.28	)	$	(0.77	)
Net income (loss) per share, diluted	$	0.49		$	(0.28	)	$	(0.77	)

The 2014 Warrants were participating securities and the warrant holders did not have a contractual obligation to share in our losses. See “Note 7. Common Stock and Warrants” for a description of the 2014 Warrants.

Potentially dilutive shares of common stock not included in the computation of diluted net income (loss) per share because to do so would be anti-dilutive were as follows (in thousands):



	Year Ended December 31,
	2017	2016	2015
Outstanding stock options, unvested RSUs and ESPP contributions	1,645	27,568	28,470
Deerfield Notes	—	33,890	33,890
2014 Warrants	—	1,000	1,000
2019 Notes	—	—	54,118
Total potentially dilutive shares	1,645	62,458	117,478

The Deerfield Notes were repaid in June 2017. The 2014 Warrants were exercised in September 2017. The 2019 Notes were converted or redeemed between August and November 2016.

Fair Value Measurements

12 Months Ended

Dec. 29, 2017

Fair Value Disclosures [Abstract]

Fair Value Measurements

FAIR VALUE MEASUREMENTS

The classification of our financial assets within the fair value hierarchy that were measured and recorded at fair value on a recurring basis were as follows. The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	December 31, 2017
	Level 1		Level 2		Total
Money market funds	$	45,478	$	—	$	45,478
Commercial paper	—		199,647		199,647
Corporate bonds	—		179,022		179,022
U.S. Treasury and government sponsored enterprises	—		16,263		16,263
Total financial assets	$	45,478	$	394,932	$	440,410



	December 31, 2016
	Level 1		Level 2		Total
Money market funds	$	71,457	$	—	$	71,457
Commercial paper	—		165,375		165,375
Corporate bonds	—		152,407		152,407
U.S. Treasury and government sponsored enterprises	—		70,727		70,727
Total financial assets	$	71,457	$	388,509	$	459,966

We did not have any financial liabilities measured and recorded at fair value on a recurring basis as of those dates. We did not have any financial assets or liabilities classified as Level 3 in the fair value hierarchy as of December 31, 2017 or December 31, 2016 and there were no transfers of financial assets or liabilities classified as Level 3 during the years ended December 31, 2017 or 2016.

The estimated fair value of our financial instruments that are carried at amortized cost was as follows (in thousands):



	December 31, 2016
	Carrying Amount		Fair Value
Convertible notes	$	109,122	$	121,220
Term loan payable	$	80,000	$	79,784

The carrying amounts of cash, trade and other receivables, accounts payable, accrued collaboration liability, accrued compensation and benefits, accrued clinical trial liabilities, rebates fees due customers, and other liabilities approximate their fair values and are excluded from the tables above. We had no additional financial instruments carried at amortized cost as of December 31, 2017.

The following methods and assumptions were used to estimate the fair value of each class of financial instrument:


•	When available, we value investments based on quoted prices for those financial instruments, which is a Level 1 input. Our remaining investments are valued using third-party pricing sources, which use observable market prices, interest rates and yield curves observable at commonly quoted intervals for similar assets as observable inputs for pricing, which is a Level 2 input.

•

We estimated the fair value of our debt instruments using the net present value of estimated future cash flows through maturity. For the Deerfield Notes, we used a discount rate of 9.5%, which we estimated as our current borrowing rate for similar debt as of December 31, 2016, which is a Level 3 input. For the term loan payable, we used an interest rate that is consistent with money-market rates that would have been earned on our non-interest-bearing compensating balances as our discount rate, which is a Level 2 input.

Financial Assets, Liabilities and Equity Measured on a Nonrecurring Basis

In connection with the conversions of our 2019 Notes during 2016, we were required to determine the fair value of the settlement consideration received by the holders and the fair value of the liability component of the 2019 Notes, as of the various settlement dates of the conversions. The following methods and assumptions were used to estimate the fair value of those financial instruments:


•	The settlement consideration comprises, in part, shares of our Common Stock. The fair value of our Common Stock was determined based on the closing market price of our Common Stock on the various settlement dates of the conversions, which are level 1 inputs;


•	The carrying value of the remaining settlement consideration, which includes cash and the forgiveness of the repayment of certain prior interest payments, approximates fair value;


•	We estimated the fair value of the liability component of the 2019 Notes using the net present value of estimated future cash flows through maturity. We used a discount rate of 9.5%, which we estimated as our current borrowing rate for straight debt as of September 30, 2016, which is a Level 3 input.

- Definition

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

+ References + Details

Commitments

12 Months Ended

Dec. 29, 2017

Commitments and Contingencies Disclosure [Abstract]

Commitments

COMMITMENTS

Leases

On May 2, 2017, we entered into a Lease with Ascentris for an aggregate of 110,783 square feet of space in office and research facilities located at the Premises in Alameda, California. We also have the right to make certain tenant improvements to the space leased on the Premises. The Lease has an initial term of 10 years with a target commencement date of February 1, 2018, and, subject to a partial twelve-month rent abatement period, rent payments will begin upon the target commencement date. We have two five-year options to extend the Lease and a one-time option to terminate the Lease without cause on the last day of the 8^th year of the initial term. The Lease further provides that we are obligated to pay to Ascentris certain costs, including taxes and operating expenses. We also have a right of first offer to lease certain additional space, in the aggregate of approximately 170,000 square feet of space, as that additional space becomes available over the remainder of the initial term at 1601, 1701, 1751, and 1801 Harbor Bay Parkway, Alameda, California at a market rate determined according to the Lease.

We are deemed, for accounting purposes only, to be the owner of portions of the Premises, including two building shells, even though we are not the legal owner. See “Note 5. Property and Equipment - Build-to-Suit Lease” for a further description of the accounting for that portion of the Premises.

On May 2, 2017, we also entered into an Agreement for Conditional Option to Amend Lease (the “Optional Amendment Agreement”) with Ascentris. Under the terms of the Optional Amendment Agreement, a current tenant (the “Tenant”) occupying approximately 16,343 square feet of the facility located at 1801 Harbor Bay Parkway was given the option to relocate to another building on the premises or terminate their current lease early, requiring them to relocate within six months from the termination date. Under the terms of the Optional Amendment Agreement, we would reimburse Ascentris for the first $1.5 million of costs incurred to induce the Tenant to relocate. In August 2017, the Tenant communicated to Ascentris that they were terminating their lease early. During 2017, we recorded a $1.4 million expense for our anticipated reimbursement of costs to Ascentris for the Tenant’s relocation of which $1.2 million remains payable as of December 31, 2017. On October 16, 2017, we executed an amendment to the Lease for an additional 19,778 square feet of space located on the Premises, which includes the space vacated by the Tenant, with terms consistent with the original Lease. Including the amendment, we are obligated to make lease payments totaling $28.5 million over the Lease term.

We also lease two buildings in South San Francisco, California with a total area of 116,063 square feet, the lease for which expires in July 2018.

As of December 31, 2017, the aggregate future minimum lease payments under our leases were as follows (in thousands):



	Operating leases		Other financing obligations⁽¹⁾
Year ending December 31,
2018	$	2,864	$	800
2019	664		1,905
2020	684		2,129
2021	694		2,213
2022	704		2,282
Thereafter	3,730		12,164
	$	9,340	$	21,493

____________________


(1)	Other financing obligations includes payments related to our build-to-suit lease.

Rent expense and sublease income were as follows (in thousands):



	Year Ended December 31,
	2017			2016			2015
Gross rental expense	$	6,160		$	9,676		$	13,942
less: Sublease income	(1,225		)	(3,553		)	(5,205		)
Net rental expense	$	4,935		$	6,123		$	8,737

Letters of Credit and Restricted Cash

We obtained a standby letter of credit related to our South San Francisco lease with a credit limit of $0.5 million at both December 31, 2017 and 2016. We obtained two standby letters of credit related to a workers compensation insurance policy with a combined credit limit of $0.6 million at both December 31, 2017 and 2016. We obtained two standby letters of credit related to the Lease with Ascentris for a combined credit limit of $1.0 million at December 31, 2017. All of the letters of credit are fully collateralized by certificates of deposit. As of December 31, 2017, none of our letters of credit have been drawn upon.

As part of a purchasing card program we initiated during 2007, we were required to provide collateral in the form of certificates of deposit. The collateral requirement at both December 31, 2017 and 2016 was $3.0 million.

The certificate of deposit used to collateralize the standby letter of credit related to our South San Francisco lease was included in short-term restricted cash and investments. The certificates of deposit used to collateralize all other letters of credit and the purchase card program were included in long-term restricted cash and investments.

Segment Information

12 Months Ended

Dec. 29, 2017

Segment Reporting [Abstract]

Segment Information

SEGMENT INFORMATION

We operate in one business segment which focuses on discovery, development and commercialization of new medicines to improve care and outcomes for people with cancer. Our Chief Executive Officer, as the chief operating decision-maker, manages and allocates resources to our operations on a total consolidated basis. Consistent with this decision-making process, our Chief Executive Officer uses consolidated, single-segment financial information for purposes of evaluating performance, forecasting future period financial results, allocating resources and setting incentive targets. Enterprise-wide disclosures about product sales, revenues from major customers, revenues and long-lived assets by geographic area are presented below.

Net product revenues by product were as follows (dollars in thousands):



	Year Ended December 31,
	2017		2016		2015
CABOMETYX	$	324,000	$	93,481	$	—
COMETRIQ	25,008		41,894		34,158
Net product revenues	$	349,008	$	135,375	$	34,158

The percentage of total revenues recognized by customer that represent 10% or more of total revenues was as follows:



	Year Ended December 31,
	2017		2016		2015
Diplomat Specialty Pharmacy	18	%	33	%	83	%
Caremark L.L.C.	16	%	9	%	—	%
Ipsen	15	%	17	%	—	%
Accredo Health, Incorporated	11	%	9	%	—	%
Affiliates of McKesson Corporation	11	%	7	%	—	%

Revenues earned by geographic region were as follows (dollars in thousands):



	Year Ended December 31,
	2017		2016		2015
U.S.	$	367,906	$	140,709	$	33,869
Europe	69,792		35,745		3,303
Rest of the world	14,779		15,000		—

Net product revenues are attributed to regions based on ship-to location and Collaboration revenues are attributed to regions based on the location of the collaboration partner.

We recorded a $0.2 million loss, a $0.2 million loss and a $0.1 million gain relating to foreign exchange fluctuations for the years ended December 31, 2017, 2016 and 2015, respectively.

All of our long-lived assets are located in the U.S.

Quarterly Financial Data (Unaudited)

12 Months Ended

Dec. 29, 2017

Quarterly Financial Information Disclosure [Abstract]

Quarterly Financial Data (Unaudited)

QUARTERLY FINANCIAL DATA (UNAUDITED)

The unaudited quarterly financial data for the last two fiscal years was as follows (in thousands, except per share data):



	Quarter Ended
	December 31,		September 30,			June 30,			March 31,
2017:
Total revenues	$	120,072	$	152,510		$	99,008		$	80,887
Gross profit ⁽¹⁾	$	91,520	$	91,758		$	84,990		$	65,674
Income from operations	$	37,431	$	81,180		$	27,113		$	20,186
Net income	$	38,489	$	81,382		$	17,656		$	16,700
Net income per share, basic	$	0.13	$	0.28		$	0.06		$	0.06
Net income per share, diluted	$	0.12	$	0.26		$	0.06		$	0.05
2016:
Total revenues	$	77,581	$	62,194		$	36,252		$	15,427
Gross profit ⁽¹⁾	$	50,064	$	40,287		$	30,058		$	8,414
Income (loss) from operations	$	38,883	$	7,264		$	(25,136	)	$	(49,135	)
Net income (loss)	$	35,123	$	(11,284	)	$	(34,838	)	$	(59,223	)
Net income (loss) per share, basic	$	0.12	$	(0.04	)	$	(0.15	)	$	(0.26	)
Net income (loss) per share, diluted	$	0.12	$	(0.04	)	$	(0.15	)	$	(0.26	)

____________________


(1)	Gross profit is computed as Net product revenues less Cost of goods sold.

In December 2016 Genentech stated that it changed, both retroactively and prospectively, the manner in which it allocates promotional expenses of the COTELLIC plus Zelboraf combination therapy. As a result of Genentech’s decision to change its cost allocation approach, we were relieved of our obligation to pay $18.7 million of disputed costs that had been accrued by us as of September 30, 2016; we were also able to invoice Genentech for certain expenses, with interest, that we had previously paid. Accordingly, during the quarter ended December 31, 2016, we offset Selling, general and administrative expenses for a $23.1 million recovery of net losses which had been recorded from 2013 through September 30, 2016, which included $9.8 million of losses that we had recognized and recorded during the three quarters ended September 30, 2016.

Organization and Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 29, 2017

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of Consolidation

Basis of Presentation

Use of Estimates

Reclassifications

Certain prior period amounts on the accompanying Consolidated Financial Statements have been reclassified to conform to current period presentation.

Cash and Investments

Investments

We classify those investments that we do not require for use in current operations and that mature in more than 12 months as Long-term investments on the accompanying Consolidated Balance Sheets.

Accounts Receivable

Fair Value Measurements

Level 1 – Fair values are determined utilizing quoted prices (unadjusted) in active markets for identical assets and liabilities that the reporting entity can access at the measurement date.

Level 3 – Fair values are determined utilizing inputs that are both significant to the fair value measurement and unobservable.

Inventory

Property and Equipment

Property and equipment are recorded at cost and depreciated using the straight-line method over the following estimated useful lives once it is placed into service:



Asset Category		Estimated Useful Life
Buildings		40 years
Lab equipment		5 years
Furniture and fixtures		5 years
Computer equipment and software		3 years
Leasehold improvements		7 to 15 years

Goodwill

Long-Lived Assets

Revenue Recognition

Net Product Revenues

Discounts and Allowances

We initially record estimates for these deductions at the time we recognize the gross revenue. We update our estimates on a recurring basis as new information becomes available.

Other Customer Credits: We pay fees to our customers for account management, data management and other administrative services.

The activities and ending reserve balances for each significant category of discount and allowance were as follows (dollars in thousands):



	Chargebacks and discounts for prompt payment			Other customer credits/fees and co-pay assistance			Rebates			Returns			Total
Balance at December 31, 2015	$	119		$	251		$	891		$	38		$	1,299
Provision related to sales made in:													—
Current period	8,271			2,747			5,105			359			16,482
Prior periods	(39		)	2			(313		)	(8		)	(358		)
Payments and customer credits issued	(6,549		)	(2,206		)	(3,056		)	(38		)	(11,849		)
Balance at December 31, 2016	1,802			794			2,627			351			5,574
Provision related to sales made in:
Current period	33,310			7,301			14,390			—			55,001
Prior periods	(817		)	—			(624		)	—			(1,441		)
Payments and customer credits issued	(32,367		)	(6,300		)	(10,623		)	(351		)	(49,641		)
Balance at December 31, 2017	$	1,928		$	1,795		$	5,770		$	—		$	9,493

Collaboration Revenues

Our product supply revenues are recognized upon delivery of the product. See “Note 2. Collaboration Agreements” for a description of our product supply agreements with our collaboration partners.

Patient Assistance Programs

Cost of Goods Sold

Research and Development Expenses

Foreign Currency Translation and Remeasurement

Stock-Based Compensation

Income Taxes

Recent Accounting Pronouncements

Organization and Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 29, 2017

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Estimated Useful Lives of Property and Equipment

Property and equipment are recorded at cost and depreciated using the straight-line method over the following estimated useful lives once it is placed into service:



Asset Category		Estimated Useful Life
Buildings		40 years
Lab equipment		5 years
Furniture and fixtures		5 years
Computer equipment and software		3 years
Leasehold improvements		7 to 15 years

Reserve Balances for Discounts and Allowances

The activities and ending reserve balances for each significant category of discount and allowance were as follows (dollars in thousands):



	Chargebacks and discounts for prompt payment			Other customer credits/fees and co-pay assistance			Rebates			Returns			Total
Balance at December 31, 2015	$	119		$	251		$	891		$	38		$	1,299
Provision related to sales made in:													—
Current period	8,271			2,747			5,105			359			16,482
Prior periods	(39		)	2			(313		)	(8		)	(358		)
Payments and customer credits issued	(6,549		)	(2,206		)	(3,056		)	(38		)	(11,849		)
Balance at December 31, 2016	1,802			794			2,627			351			5,574
Provision related to sales made in:
Current period	33,310			7,301			14,390			—			55,001
Prior periods	(817		)	—			(624		)	—			(1,441		)
Payments and customer credits issued	(32,367		)	(6,300		)	(10,623		)	(351		)	(49,641		)
Balance at December 31, 2017	$	1,928		$	1,795		$	5,770		$	—		$	9,493

Collaboration Agreements (Tables)

12 Months Ended

Dec. 29, 2017

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Schedule of Collaborative Revenues Under Collaboration Agreement

Royalties accruing to GSK in connection with the sales of COMETRIQ and CABOMETYX were as follows (in thousands):



	Year Ended December 31,
	2017		2016		2015
Royalties accruing to GSK	$	12,413	$	4,334	$	1,029

Collaboration revenues under the collaboration agreement with Ipsen were as follows (in thousands):



	Year Ended December 31,
	2017			2016
Milestones achieved	$	45,000		$	20,000
Amortization of upfront payments and deferred milestone	18,531			13,284
Royalty revenue	3,831			175
Development cost reimbursements	4,417			—
Product supply agreement revenue	6,390			1,612
Cost of supplied product	(6,390		)	(1,555		)
Royalty payable to GSK on net sales by Ipsen	(1,987		)	(264		)
Collaboration revenues under the collaboration agreement with Ipsen	$	69,792		$	33,252

Collaboration revenues and U.S. (loss) net cost recovery under the collaboration agreement were as follows (in thousands):



	Year Ended December 31,
	2017			2016		2015
Collaboration revenues:
Royalty revenues on ex-U.S. sales of COTELLIC	$	6,398		$	2,827	$	14
U.S. (loss) net cost recovery under the collaboration agreement included in Selling, general and administrative expenses	$	(2,140	)	$	8,771	$	(16,600	)

Collaboration revenues under the collaboration agreement with Takeda were as follows (in thousands):



	Year Ended December 31, 2017
Amortization of upfront payment	$	10,377
Development cost reimbursements	4,320
Product supply agreement revenue	82
Collaboration revenues under the collaboration agreement with Takeda	$	14,779

Investments (Tables)

12 Months Ended

Dec. 29, 2017

Investments, Debt and Equity Securities [Abstract]

Summary of Cash Equivalents and Investments by Security Type

The amounts presented exclude cash, but include investments classified as cash equivalents (in thousands):



	December 31, 2017
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	45,478	$	—	$	—		$	45,478
Commercial paper	199,647		—		—			199,647
Corporate bonds	179,336		18		(332		)	179,022
U.S. Treasury and government sponsored enterprises	16,295		—		(32		)	16,263
Total	$	440,756	$	18	$	(364	)	$	440,410



	December 31, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Money market funds	$	71,457	$	—	$	—		$	71,457
Commercial paper	165,375		—		—			165,375
Corporate bonds	152,712		3		(308		)	152,407
U.S. Treasury and government sponsored enterprises	70,730		11		(14		)	70,727
Total	$	460,274	$	14	$	(322	)	$	459,966

Fair Value and Gross Unrealized Losses on Investments

The fair value and gross unrealized losses of investments available-for-sale in an unrealized loss position were as follows (in thousands):



	December 31, 2017
	In an Unrealized Loss Position Less than 12 Months					In an Unrealized Loss Position 12 Months or Greater					Total
	Fair Value		Gross Unrealized Losses			Fair Value		Gross Unrealized Losses			Fair Value		Gross Unrealized Losses
Corporate bonds	$	140,746	$	(296	)	$	20,047	$	(36	)	$	160,793	$	(332	)
U.S. Treasury and government sponsored enterprises	13,611		(23		)	2,651		(9		)	16,262		(32		)
Total	$	154,357	$	(319	)	$	22,698	$	(45	)	$	177,055	$	(364	)



	December 31, 2016
	In an Unrealized Loss Position Less than 12 Months					In an Unrealized Loss Position 12 Months or Greater					Total
	Fair Value		Gross Unrealized Losses			Fair Value		Gross Unrealized Losses			Fair Value		Gross Unrealized Losses
Corporate bonds	$	140,559	$	(305	)	$	3,001	$	(3	)	$	143,560	$	(308	)
U.S. Treasury and government sponsored enterprises	27,657		(14		)	—		—			27,657		(14		)
Commercial paper⁽¹⁾	998		—			—		—			998		—
Total	$	169,214	$	(319	)	$	3,001	$	(3	)	$	172,215	$	(322	)

____________________


(1)	Gross unrealized losses on commercial paper were less than $1 thousand.

Summary of Cash Equivalents and Investments by Contractual Maturity

fair value of cash equivalents and investments by contractual maturity were as follows (in thousands):



	December 31,
	2017		2016
Maturing in one year or less	$	377,155	$	404,365
Maturing after one year through five years	63,255		55,601
Total	$	440,410	$	459,966

Inventory (Tables)

12 Months Ended

Dec. 29, 2017

Inventory Disclosure [Abstract]

Schedule of Inventory

Inventory consisted of the following (in thousands):



	December 31,
	2017		2016
Raw materials	$	498	$	863
Work in process	3,997		2,343
Finished goods	2,854		738
Total	$	7,349	$	3,944

Balance Sheet classification:
Inventory	$	6,657	$	3,338
Other long-term assets	692		606
Total	$	7,349	$	3,944

Property and Equipment (Tables)

12 Months Ended

Dec. 29, 2017

Property, Plant and Equipment [Abstract]

Schedule of Property and Equipment

Property and equipment were as follows (in thousands):



	December 31, 2017			December 31, 2016
Computer equipment and software	$	14,146		$	13,738
Laboratory equipment	5,959			4,310
Leasehold improvements	4,715			6,646
Furniture and fixtures	1,609			2,240
Construction in progress	22,114			19
	48,543			26,953
Less: accumulated depreciation and amortization	(22,800		)	(24,882		)
Property and equipment, net	$	25,743		$	2,071

Debt (Tables)

12 Months Ended

Dec. 29, 2017

Debt Disclosure [Abstract]

Schedule of Debt

The amortized carrying amount of our debt was as follows (in thousands):



	December 31,
	2017		2016
Convertible notes	$	—	$	109,122
Term loan payable	—		80,000
Total debt	$	—	$	189,122

Summary of Loss on Extinguishment of Debt

A summary of loss on extinguishment of debt for the conversion and redemption of the 2019 Notes was as follows (in thousands):



	Year Ended December 31, 2016
Cash inducements	$	2,394
Waiver of requirement to repay interest, described above	3,572
Difference between the total settlement consideration attributed to the liability component of the 2019 Notes and the net carrying value of the liability	7,338
Unamortized discount on redeemed notes	83
Third-party costs	514
Loss on extinguishment of debt	$	13,901

Stock-based Compensation (Tables)

12 Months Ended

Dec. 29, 2017

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

Schedule of Allocated Employee Stock-Based Compensation Expense

The allocation of stock-based compensation for our equity incentive plans and our Employee Stock Purchase Plan (the “ESPP”) was as follows (in thousands):



	Year Ended December 31,
	2017		2016		2015
Research and development	$	7,569	$	9,366	$	11,691
Selling, general and administrative	16,369		13,546		10,286
Total stock-based compensation	$	23,938	$	22,912	$	21,977

Share-based Compensation Arrangement by Share-based Payment Award, Options, Grants in Period, Weighted Average Grant Date Fair Value

The weighted average grant-date fair value of our stock option grants and ESPP purchases were as follows:



	Year Ended December 31,
	2017		2016		2015
Stock options	$	11.42	$	4.77	$	2.55
ESPP	$	6.00	$	2.17	$	1.20

Schedule of Fair Value of Employee Share-Based Payments Awards Stock Option Assumptions and Weighted Average Fair Values

The grant-date fair value of employee stock option grants and ESPP purchases was estimated using the following assumptions:



	Year Ended December 31,
	2017		2016		2015
Stock options:
Risk-free interest rate	1.98	%	1.15	%	1.22	%
Dividend yield	—	%	—	%	—	%
Volatility	59	%	76	%	93	%
Expected life	4.5 years		4.4 years		4.5 years
ESPP:
Risk-free interest rate	1.09	%	0.55	%	0.15	%
Dividend yield	—	%	—	%	—	%
Volatility	58	%	65	%	98	%
Expected life	6 months		6 months		6 months

Schedule of Fair Value of Employee Share-Based Payments Awards ESPP Assumptions and Weighted Average Fair Values

The grant-date fair value of employee stock option grants and ESPP purchases was estimated using the following assumptions:



	Year Ended December 31,
	2017		2016		2015
Stock options:
Risk-free interest rate	1.98	%	1.15	%	1.22	%
Dividend yield	—	%	—	%	—	%
Volatility	59	%	76	%	93	%
Expected life	4.5 years		4.4 years		4.5 years
ESPP:
Risk-free interest rate	1.09	%	0.55	%	0.15	%
Dividend yield	—	%	—	%	—	%
Volatility	58	%	65	%	98	%
Expected life	6 months		6 months		6 months

Summary of All Stock Option Activity

Stock option activity for the year ended December 31, 2017 was as follows (dollars in thousands, except per share amounts):



	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Options outstanding at December 31, 2016	24,999,665		$	4.91
Granted	2,166,110		$	23.43
Exercised	(4,469,203	)	$	3.91
Forfeited	(229,793	)	$	8.09
Expired	(258,333	)	$	9.91
Options outstanding at December 31, 2017	22,208,446		$	6.83	4.05 years	$	523,448
Exercisable at December 31, 2017	16,158,740		$	4.51	3.46 years	$	418,304

Summary of All RSU Activity

A summary of all RSU activity were as follows (dollars in thousands, except per share amounts):



	Shares		Weighted Average Grant Date Fair Value		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Awards outstanding at December 31, 2016	2,469,791		$	8.69
Awarded	2,137,817		$	24.60
Vested and released	(708,541	)	$	7.97
Forfeited	(136,077	)	$	11.48
Awards outstanding at December 31, 2017	3,762,990		$	17.76	1.95 years	$	114,395

Income Taxes (Tables)

12 Months Ended

Dec. 29, 2017

Income Tax Disclosure [Abstract]

Schedule of Consolidated Net Income (Loss)

The Provision for income taxes was based on the following income (loss) before income taxes (in thousands):



	Year Ended December 31,
	2017		2016			2015
Domestic	$	158,577	$	(70,222	)	$	(150,846	)
Foreign	—		—			(10,843		)
Income (loss) before income taxes	$	158,577	$	(70,222	)	$	(161,689	)

Schedule of Components of Income Tax Expense (Benefit)

The Provision for income taxes was as follows (in thousands):



	Year Ended December 31,
	2017		2016		2015
Current:
Federal	$	—	$	—	$	—
State	4,350		—		55
Total current tax expense	4,350		—		55
Deferred:
Federal	—		—		—
State	—		—		—
Total deferred tax expense	—		—		—
Provision for income taxes	$	4,350	$	—	$	55

Schedule of Reconciliation of Income Taxes At The Statutory Federal Income Tax Rate to Net Income Taxes



	Year Ended December 31,
	2017			2016			2015
U.S. federal income tax provision (benefit) at statutory rate	$	53,916		$	(23,876	)	$	(54,974	)
Change in valuation allowance	(34,266		)	6,377			51,421
State tax expense	8,282			6,520			55
Debt extinguishment	—			4,726			—
Non-deductible interest	1,367			2,680			3,308
Stock-based compensation	(20,548		)	3,155			195
Other	(4,401		)	418			50
Provision for income taxes	$	4,350		$	—		$	55

Schedule of Deferred Assets and Liabilities

Our deferred tax assets and liabilities were as follows (in thousands):



	December 31,
	2017			2016
Deferred tax assets:
Net operating loss carry-forwards	$	244,205		$	471,327
Book over tax depreciation and amortization	39,472			70,617
Tax credit and charitable contribution carry-forwards	66,770			64,367
Deferred revenue	53,543			—
Amortization of deferred stock compensation – non-qualified	8,966			14,780
Accruals and reserves not currently deductible	4,914			8,117
Other assets	1,088			106
Total deferred tax assets	418,958			629,314
Valuation allowance	(418,958		)	(629,062		)
Net deferred tax assets	—			252
Deferred tax liabilities:
Unrealized gains on derivatives and other liabilities	—			(252		)
Total deferred tax liabilities	—			(252		)
Net deferred taxes	$	—		$	—

Schedule of Unrecognized Tax Benefits

The following table summarizes the activity related to our unrecognized tax benefits (in thousands):



	Year Ended December 31,
	2017			2016			2015
Beginning balance	$	61,809		$	88,638		$	58,215
Change relating to prior year provision	247			(29,110		)	21,696
Change relating to current year provision	17,378			2,304			8,727
Reductions based on the lapse of the applicable statutes of limitations	(92		)	(23		)	—
Ending balance	$	79,342		$	61,809		$	88,638

Net Income (Loss) Per Share (Tables)

12 Months Ended

Dec. 29, 2017

Earnings Per Share [Abstract]

Schedule of Reconciliation of Basic and Diluted Net Loss Per Share

The computation of basic and diluted net income (loss) per share was as follows (in thousands, except per share amounts):



	Year Ended December 31,
	2017			2016			2015
Numerator:
Net income (loss)	$	154,227		$	(70,222	)	$	(161,744	)
Net income allocated to participating securities	(367		)	—			—
Net income allocable to common stock for basic net income (loss) per share	153,860			(70,222		)	(161,744		)
Adjustment to net income allocated to participating securities	22			—			—
Net income allocable to common stock for diluted net income (loss) per share	$	153,882		$	(70,222	)	$	(161,744	)
Denominator:
Weighted-average shares of common stock outstanding used in computing basic net income (loss) per share	293,588			250,531			209,227
Dilutive securities:
Outstanding stock options, unvested RSUs and ESPP contributions	18,415			—			—
Weighted-average shares of common stock outstanding and dilutive securities used in computing diluted net income (loss) per share	312,003			250,531			209,227

Net income (loss) per share, basic	$	0.52		$	(0.28	)	$	(0.77	)
Net income (loss) per share, diluted	$	0.49		$	(0.28	)	$	(0.77	)

Schedule of Potential Shares of Common Stock Not Included In Computation of Diluted Net Loss Per Share

Potentially dilutive shares of common stock not included in the computation of diluted net income (loss) per share because to do so would be anti-dilutive were as follows (in thousands):



	Year Ended December 31,
	2017	2016	2015
Outstanding stock options, unvested RSUs and ESPP contributions	1,645	27,568	28,470
Deerfield Notes	—	33,890	33,890
2014 Warrants	—	1,000	1,000
2019 Notes	—	—	54,118
Total potentially dilutive shares	1,645	62,458	117,478

Fair Value Measurements (Tables)

12 Months Ended

Dec. 29, 2017

Fair Value Disclosures [Abstract]

Schedule of Fair Value of Financial Assets Measured on a Recurring Basis



	December 31, 2017
	Level 1		Level 2		Total
Money market funds	$	45,478	$	—	$	45,478
Commercial paper	—		199,647		199,647
Corporate bonds	—		179,022		179,022
U.S. Treasury and government sponsored enterprises	—		16,263		16,263
Total financial assets	$	45,478	$	394,932	$	440,410



	December 31, 2016
	Level 1		Level 2		Total
Money market funds	$	71,457	$	—	$	71,457
Commercial paper	—		165,375		165,375
Corporate bonds	—		152,407		152,407
U.S. Treasury and government sponsored enterprises	—		70,727		70,727
Total financial assets	$	71,457	$	388,509	$	459,966

Schedule of Estimated Fair Value of Financial Instruments

The estimated fair value of our financial instruments that are carried at amortized cost was as follows (in thousands):



	December 31, 2016
	Carrying Amount		Fair Value
Convertible notes	$	109,122	$	121,220
Term loan payable	$	80,000	$	79,784

Commitments (Tables)

12 Months Ended

Dec. 29, 2017

Commitments and Contingencies Disclosure [Abstract]

Schedule of Aggregate Future Minimum Lease Payments Under Operating Leases

As of December 31, 2017, the aggregate future minimum lease payments under our leases were as follows (in thousands):



	Operating leases		Other financing obligations⁽¹⁾
Year ending December 31,
2018	$	2,864	$	800
2019	664		1,905
2020	684		2,129
2021	694		2,213
2022	704		2,282
Thereafter	3,730		12,164
	$	9,340	$	21,493

____________________


(1)	Other financing obligations includes payments related to our build-to-suit lease.

Schedule of Rent Expense

Rent expense and sublease income were as follows (in thousands):



	Year Ended December 31,
	2017			2016			2015
Gross rental expense	$	6,160		$	9,676		$	13,942
less: Sublease income	(1,225		)	(3,553		)	(5,205		)
Net rental expense	$	4,935		$	6,123		$	8,737

Segment Information (Tables)

12 Months Ended

Dec. 29, 2017

Segment Reporting [Abstract]

Schedule of Net Product Revenue by Product

Net product revenues by product were as follows (dollars in thousands):



	Year Ended December 31,
	2017		2016		2015
CABOMETYX	$	324,000	$	93,481	$	—
COMETRIQ	25,008		41,894		34,158
Net product revenues	$	349,008	$	135,375	$	34,158

Schedules of Revenue Concentration Risk

The percentage of total revenues recognized by customer that represent 10% or more of total revenues was as follows:



	Year Ended December 31,
	2017		2016		2015
Diplomat Specialty Pharmacy	18	%	33	%	83	%
Caremark L.L.C.	16	%	9	%	—	%
Ipsen	15	%	17	%	—	%
Accredo Health, Incorporated	11	%	9	%	—	%
Affiliates of McKesson Corporation	11	%	7	%	—	%

Revenue Earned from Geographic Region

Revenues earned by geographic region were as follows (dollars in thousands):



	Year Ended December 31,
	2017		2016		2015
U.S.	$	367,906	$	140,709	$	33,869
Europe	69,792		35,745		3,303
Rest of the world	14,779		15,000		—

Quarterly Financial Data (Unaudited) (Tables)

12 Months Ended

Dec. 29, 2017

Quarterly Financial Information Disclosure [Abstract]

Schedule of Quarterly Financial Data

The unaudited quarterly financial data for the last two fiscal years was as follows (in thousands, except per share data):



	Quarter Ended
	December 31,		September 30,			June 30,			March 31,
2017:
Total revenues	$	120,072	$	152,510		$	99,008		$	80,887
Gross profit ⁽¹⁾	$	91,520	$	91,758		$	84,990		$	65,674
Income from operations	$	37,431	$	81,180		$	27,113		$	20,186
Net income	$	38,489	$	81,382		$	17,656		$	16,700
Net income per share, basic	$	0.13	$	0.28		$	0.06		$	0.06
Net income per share, diluted	$	0.12	$	0.26		$	0.06		$	0.05
2016:
Total revenues	$	77,581	$	62,194		$	36,252		$	15,427
Gross profit ⁽¹⁾	$	50,064	$	40,287		$	30,058		$	8,414
Income (loss) from operations	$	38,883	$	7,264		$	(25,136	)	$	(49,135	)
Net income (loss)	$	35,123	$	(11,284	)	$	(34,838	)	$	(59,223	)
Net income (loss) per share, basic	$	0.12	$	(0.04	)	$	(0.15	)	$	(0.26	)
Net income (loss) per share, diluted	$	0.12	$	(0.04	)	$	(0.15	)	$	(0.26	)

____________________


(1)	Gross profit is computed as Net product revenues less Cost of goods sold.

Organization and Summary of Significant Accounting Policies (Narrative) (Details)	1 Months Ended		12 Months Ended
	Nov. 30, 2015	Oct. 31, 2008	Dec. 29, 2017 USD ($) segment product	Dec. 30, 2016 USD ($)	Jan. 01, 2016 USD ($)
Organization And Summary Of Significant Policies [Line Items]
Number of products that entered in the commercial marketplace \| product			3
Number of reportable segments \| segment			1
Impairment charge on goodwill			$ 0	$ 0	$ 0
Percent discount for prompt payment			2.00%
Discount expected to be earned			100.00%
Adoption of Accounting Standards Update No. 2016-09				0
Net cash provided by operating activities			$ 165,611,000	210,404,000	(141,051,000)
Net cash used in financing activities			169,928,000	(15,696,000)	(152,213,000)
Accumulated deficit			$ 1,829,172,000	1,983,147,000
GlaxoSmithKline [Member]
Organization And Summary Of Significant Policies [Line Items]
Percent of royalty on net sale		3.00%
Collaborative Arrangement with Genentech [Member]
Organization And Summary Of Significant Policies [Line Items]
Percentage of share of the Company in promotions	25.00%
Collaborative Arrangement with Genentech [Member] \| Maximum [Member]
Organization And Summary Of Significant Policies [Line Items]
Percentage of share of the Company in promotions			25.00%
Products Derived from Cabozantinib [Member]
Organization And Summary Of Significant Policies [Line Items]
Number of products that entered in the commercial marketplace \| product			2
Accounting Standards Update 2016-09 [Member]
Organization And Summary Of Significant Policies [Line Items]
Net cash provided by operating activities				4,100,000	500,000
Net cash used in financing activities				4,100,000	$ 500,000
Accumulated Deficit [Member]
Organization And Summary Of Significant Policies [Line Items]
Adoption of Accounting Standards Update No. 2016-09				252,000
Accumulated Deficit [Member] \| Accounting Standards Update 2016-09 [Member]
Organization And Summary Of Significant Policies [Line Items]
Adoption of Accounting Standards Update No. 2016-09				300,000
Additional Paid-In Capital [Member]
Organization And Summary Of Significant Policies [Line Items]
Adoption of Accounting Standards Update No. 2016-09				$ (252,000)
Additional Paid-In Capital [Member] \| Accounting Standards Update 2016-09 [Member]
Organization And Summary Of Significant Policies [Line Items]
Adoption of Accounting Standards Update No. 2016-09			$ (300,000)
Difference between Revenue Guidance in Effect before and after Topic 606 [Member] \| Accounting Standards Update 2014-09 [Member] \| Pro Forma [Member]
Organization And Summary Of Significant Policies [Line Items]
Accumulated deficit			$ 260,000,000

Organization and Summary of Significant Accounting Policies (Estimated Useful Lives of Property Plant And Equipment) (Details)	12 Months Ended
	Dec. 29, 2017
Building [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives	40 years
Lab equipment [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives	5 years
Furniture and fixtures [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives	5 years
Computer equipment and software [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives	3 years
Leasehold improvements [Member] \| Minimum [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives	7 years
Leasehold improvements [Member] \| Maximum [Member]
Property, Plant and Equipment [Line Items]
Estimated useful lives	15 years

Organization and Summary of Significant Accounting Policies (Allowance Reserve) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016
Reserve Rollforward [Roll Forward]
Discounts and Allowances	$ 5,574	$ 1,299
Current period	55,001	16,482
Prior periods	(1,441)	(358)
Payment and Credits Issued	(49,641)	(11,849)
Discounts and Allowances	9,493	5,574
Chargebacks and Prompt Payment [Member]
Reserve Rollforward [Roll Forward]
Discounts and Allowances	1,802	119
Current period	33,310	8,271
Prior periods	(817)	(39)
Payment and Credits Issued	(32,367)	(6,549)
Discounts and Allowances	1,928	1,802
Other Discounts [Member]
Reserve Rollforward [Roll Forward]
Discounts and Allowances	794	251
Current period	7,301	2,747
Prior periods	0	2
Payment and Credits Issued	(6,300)	(2,206)
Discounts and Allowances	1,795	794
Rebates [Member]
Reserve Rollforward [Roll Forward]
Discounts and Allowances	2,627	891
Current period	14,390	5,105
Prior periods	(624)	(313)
Payment and Credits Issued	(10,623)	(3,056)
Discounts and Allowances	5,770	2,627
Returns [Member]
Reserve Rollforward [Roll Forward]
Discounts and Allowances	351	38
Current period	0	359
Prior periods	0	(8)
Payment and Credits Issued	(351)	(38)
Discounts and Allowances	$ 0	$ 351

Collaboration Agreements (Ipsen Collaboration, Narrative) (Details)	1 Months Ended		3 Months Ended		12 Months Ended
	Sep. 30, 2016 USD ($)	Oct. 31, 2008	Dec. 29, 2017 USD ($)	Dec. 29, 2017 CAD ($)	Dec. 29, 2017 USD ($)	Dec. 30, 2016 USD ($)	Mar. 31, 2017 USD ($)	Feb. 29, 2016 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Accrued collaboration liabilities			$ 16,643,000		$ 16,643,000	$ 541,000
Current portion of deferred revenue			31,984,000		31,984,000	19,665,000
Long-term portion of deferred revenue			238,520,000		238,520,000	237,094,000
GlaxoSmithKline [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale		3.00%
Collaborative arrangement with Ipsen [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront and milestone payments					210,000,000
Revenue recognized, milestones					$ 45,000,000	$ 20,000,000
Eligible payment from collaboration for development and regulatory milestone achievement under collaborations agreement								$ 209,000,000
Maximum amount eligible for commercial milestones under collaborations agreement								546,000,000
Research and development arrangement performed for others, reimbursement for costs incurred, percent					35.00%
Payment of reimbursements from collaboration arrangement			3,900,000
Collaboration period to achieve specified levels of commercial performance					10 years
Current portion of deferred revenue			19,000,000		$ 19,000,000
Long-term portion of deferred revenue			$ 210,200,000		$ 210,200,000
Collaborative arrangement with Ipsen [Member] \| Initial [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale			2.00%	2.00%
Royalty tier			$ 50,000,000	$ 30,000,000.0
Collaborative arrangement with Ipsen [Member] \| Second [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale					12.00%
Royalty tier					$ 100,000,000
Collaborative arrangement with Ipsen [Member] \| Final tier [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Royalty tier					$ 150,000,000
Collaborative arrangement with Ipsen [Member] \| Final tier [Member] \| Minimum [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale					22.00%
Collaborative arrangement with Ipsen [Member] \| Final tier [Member] \| Maximum [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale					26.00%
Collaborative arrangement with Ipsen [Member] \| HCC Filing [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Eligible payment from collaboration for development and regulatory milestone achievement under collaborations agreement								10,000,000
Collaborative arrangement with Ipsen [Member] \| HCC Acceptance [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Eligible payment from collaboration for development and regulatory milestone achievement under collaborations agreement								$ 40,000,000
Collaborative arrangement with Ipsen, approval of product by EC in Second-Line RCC [Member] \| Cabometyx [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Revenue recognized, milestones	$ 60,000,000
Restatement adjustment [Member] \| Collaborative arrangement with Ipsen [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront payment reclassified							$ 9,000,000
Accrued collaboration liabilities							$ 9,000,000

Collaboration Agreements (Collaboration Revenues - Ipsen) (Details) - USD ($)	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Product supply agreement revenue	$ 349,008,000	$ 135,375,000	$ 34,158,000
Cost of supplied product	(15,066,000)	(6,552,000)	(3,895,000)
Collaboration revenues under the Ipsen Collaboration Agreement	103,469,000	56,079,000	3,014,000
Collaborative arrangement with Ipsen [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestones achieved	45,000,000	20,000,000
Amortization of upfront payments and deferred milestone	18,531,000	13,284,000
Royalty revenue	3,831,000	175,000
Development cost reimbursements	4,417,000	0
Product supply agreement revenue	6,390,000	1,612,000
Cost of supplied product	(6,390,000)	(1,555,000)
Royalty payable to GSK on net sales by Ipsen	(1,987,000)	(264,000)
Collaboration revenues under the Ipsen Collaboration Agreement	$ 69,792,000	$ 33,252,000	$ 0

Collaboration Agreements (Takeda Collaboration, Narrative) (Details) - USD ($)	1 Months Ended	12 Months Ended
	Feb. 28, 2017	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration revenues		$ 103,469,000	$ 56,079,000	$ 3,014,000
Current portion of deferred revenue		31,984,000	19,665,000
Long-term portion of deferred revenue		$ 238,520,000	237,094,000
Collaborative arrangement with Takeda [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront and milestone payments	$ 50,000,000
Deferred revenue, recognition period		4 years
Maximum amount eligible for development and regulatory milestones		$ 95,000,000
Maximum amount eligible for commercial milestones under collaborations agreement		83,000,000
Collaboration revenues		14,779,000	$ 0	$ 0
Current portion of deferred revenue		11,300,000
Long-term portion of deferred revenue		$ 28,300,000
Period for specific commercial performance		6 years
Initial [Member] \| Collaborative arrangement with Takeda [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Royalty tier		$ 300,000,000.0
Initial [Member] \| Minimum [Member] \| Collaborative arrangement with Takeda [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale		15.00%
Initial [Member] \| Maximum [Member] \| Collaborative arrangement with Takeda [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale		24.00%
Final tier [Member] \| Minimum [Member] \| Collaborative arrangement with Takeda [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale		20.00%
Final tier [Member] \| Maximum [Member] \| Collaborative arrangement with Takeda [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale		30.00%
Global [Member] \| Collaborative arrangement with Takeda [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Research and development arrangement performed for others, reimbursement for costs incurred, percent		20.00%
Japan [Member] \| Collaborative arrangement with Takeda [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Research and development arrangement performed for others, reimbursement for costs incurred, percent		100.00%
Collaboration period to achieve specified levels of commercial performance		2 years

Collaboration Agreements (Collaboration Revenue - Takeda) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Product supply agreement revenue	$ 349,008	$ 135,375	$ 34,158
Collaboration revenues	103,469	56,079	3,014
Collaborative arrangement with Takeda [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Amortization of upfront payments and deferred milestone	10,377
Development cost reimbursements	4,320
Product supply agreement revenue	82
Collaboration revenues	$ 14,779	$ 0	$ 0

Collaboration Agreements (Genentech Collaboration, Narrative) (Details) - Genentech [Member] - USD ($) $ in Millions	1 Months Ended	12 Months Ended
	Nov. 30, 2015	Dec. 29, 2017	Dec. 30, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percentage of share of the Company in promotions	25.00%
Recovery (loss) of expenses, expenses prior to current fiscal year			$ 8.8
Selling, general and administrative expense [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Recovery (loss) of expenses, expenses prior to current fiscal year			13.3
Contract revenue [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Recovery (loss) of expenses, expenses prior to current fiscal year			$ (4.5)
Profit Sharing Tier One [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of profits		50.00%
Profit Sharing Tier Three [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of profits		30.00%
Minimum [Member] \| Profit Sharing Tier Two [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Profit threshold		$ 200.0
Maximum [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percentage of share of the Company in promotions		25.00%
Maximum [Member] \| Profit Sharing Tier Three [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Profit threshold		$ 400.0

Collaboration Agreements (Collaboration Revenues - Genentech) (Details) - Genentech [Member] - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Selling, general and administrative expense [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
U.S. (loss) net cost recovery under the collaboration agreement included in Selling, general and administrative expenses	$ (2,140)	$ 8,771	$ (16,600)
COTELLIC [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Royalty revenues on ex-U.S. sales of COTELLIC	$ 6,398	$ 2,827	$ 14

Collaboration Agreements (Other Collaborations) (Details) - USD ($)	1 Months Ended	12 Months Ended			36 Months Ended
	Oct. 31, 2008	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016	Dec. 29, 2017
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum potential milestone payments		$ 1,900,000,000			$ 1,900,000,000
Percentage of maximum potential milestone payments - clinical development		9.00%			9.00%
Percentage of maximum potential milestone payments - regulatory		49.00%			49.00%
Percentage of maximum potential milestone payments - commercial		42.00%			42.00%
GlaxoSmithKline [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sales	3.00%
Collaborative Arrangement with Two Bristol-Myers Squibb Compound Utilized [Member] [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percentage of costs		33.33%
Daiichi Sankyo [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for development and regulatory milestones		$ 130,000,000			$ 130,000,000
Revenue recognized, milestones		0	$ 15,000,000	$ 0
Merck [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for development and regulatory milestones		231,000,000			231,000,000
Revenue recognized, milestones		0	5,000,000	3,000,000
Maximum amount eligible for royalties on sales under collaborations agreement		375,000,000			375,000,000
Collaborative Arrangement with BMS [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for development and regulatory milestones		240,000,000			240,000,000
Revenue recognized, milestones		12,500,000	0	0
Maximum amount eligible for royalties on sales under collaborations agreement		150,000,000			150,000,000
Sanofi [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for development and regulatory milestones		$ 745,000,000.0			745,000,000.0
Revenue recognized, milestones			$ 0	$ 0	$ 0
Bristol Myers Squibb [Member] \| Collaborative Arrangement with Two Bristol-Myers Squibb Compound Utilized [Member] [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percentage of costs		66.67%

Collaboration Agreements (Collaboration Revenues - GSK) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Collaborative Arrangements with Glaxo Smith Kline [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Royalty expense	$ 12,413	$ 4,334	$ 1,029

Investments (Narrative) (Details)	12 Months Ended
Investments (Narrative) (Details)	Dec. 29, 2017 USD ($) investment	Dec. 30, 2016 USD ($) investment	Jan. 01, 2016 USD ($)	Aug. 31, 2016
Investment [Line Items]
Gain (loss) on sale of available-for-sale securities	$ 0	$ 0	$ 0
Available-for-sale, Securities in Unrealized Loss Positions, Qualitative Disclosure, Number of Positions \| investment	134	86
Other-than-temporary impairment charges on available-for-sale securities	$ 0	$ 0	0
Akarna Therapeutics, Ltd. [Member]
Investment [Line Items]
Realized gain on sale of cost method investment	$ 3,000,000	2,500,000	$ 0
Cost method investment ownership percentage				9.00%
Silicon Valley Bank Term Loan and Line of Credit [Member]
Investment [Line Items]
Collateral balance		$ 81,600,000

Investments (Summary by Security Type) (Details) - USD ($) $ in Thousands	Dec. 29, 2017	Dec. 30, 2016
Investment [Line Items]
Amortized Cost	$ 440,756	$ 460,274
Gross Unrealized Gains	18	14
Gross Unrealized Losses	(364)	(322)
Fair Value	440,410	459,966
Money market funds [Member]
Investment [Line Items]
Amortized Cost	45,478	71,457
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	45,478	71,457
Commercial paper [Member]
Investment [Line Items]
Amortized Cost	199,647	165,375
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	199,647	165,375
Corporate bonds [Member]
Investment [Line Items]
Amortized Cost	179,336	152,712
Gross Unrealized Gains	18	3
Gross Unrealized Losses	(332)	(308)
Fair Value	179,022	152,407
US Treasury and Government [Member]
Investment [Line Items]
Amortized Cost	16,295	70,730
Gross Unrealized Gains	0	11
Gross Unrealized Losses	(32)	(14)
Fair Value	$ 16,263	$ 70,727

Investments (Gross Unrealized Losses) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016
Schedule of Available-for-sale Securities [Line Items]
Unrealized loss position, fair value, less than 12 months	$ 154,357	$ 169,214
Gross unrealized losses, less than 12 months	(319)	(319)
Unrealized loss position, fair value,12 months or greater	22,698	3,001
Gross unrealized losses, 12 months or greater	(45)	(3)
Unrealized loss position, fair value	177,055	172,215
Gross unrealized losses	(364)	(322)
Corporate bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Unrealized loss position, fair value, less than 12 months	140,746	140,559
Gross unrealized losses, less than 12 months	(296)	(305)
Unrealized loss position, fair value,12 months or greater	20,047	3,001
Gross unrealized losses, 12 months or greater	(36)	(3)
Unrealized loss position, fair value	160,793	143,560
Gross unrealized losses	(332)	(308)
US Treasury and Government [Member]
Schedule of Available-for-sale Securities [Line Items]
Unrealized loss position, fair value, less than 12 months	13,611	27,657
Gross unrealized losses, less than 12 months	(23)	(14)
Unrealized loss position, fair value,12 months or greater	2,651	0
Gross unrealized losses, 12 months or greater	(9)	0
Unrealized loss position, fair value	16,262	27,657
Gross unrealized losses	$ (32)	(14)
Commercial paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Unrealized loss position, fair value, less than 12 months		998
Gross unrealized losses, less than 12 months		0
Unrealized loss position, fair value,12 months or greater		0
Gross unrealized losses, 12 months or greater		0
Unrealized loss position, fair value		998
Gross unrealized losses		$ 0

Investments (Summary by Contractual Maturity) (Details) - USD ($) $ in Thousands	Dec. 29, 2017	Dec. 30, 2016
Investments, Debt and Equity Securities [Abstract]
Maturing in one year or less	$ 377,155	$ 404,365
Maturing after one year through five years	63,255	55,601
Total	$ 440,410	$ 459,966

Inventory (Schedule of Inventory) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Inventory [Line Items]
Raw materials	$ 498	$ 863
Work in process	3,997	2,343
Finished goods	2,854	738
Total	7,349	3,944
Inventory write-down	1,200	500	$ 1,200
Inventory [Member]
Inventory [Line Items]
Total	6,657	3,338
Other long-term assets [Member]
Inventory [Line Items]
Total	$ 692	$ 606

Property and Equipment (Schedule of Property and Equipment) (Details) - USD ($) $ in Thousands	Dec. 29, 2017	Dec. 30, 2016
Property, Plant and Equipment [Line Items]
Property and equipment, gross	$ 48,543	$ 26,953
Less: accumulated depreciation and amortization	(22,800)	(24,882)
Property and equipment, net	25,743	2,071
Computer equipment and software [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, gross	14,146	13,738
Lab equipment [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, gross	5,959	4,310
Leasehold improvements [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, gross	4,715	6,646
Furniture and fixtures [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, gross	1,609	2,240
Construction-in-progress [Member]
Property, Plant and Equipment [Line Items]
Property and equipment, gross	$ 22,114	$ 19

Property and Equipment (Narrative) (Details) $ in Millions		12 Months Ended
Property and Equipment (Narrative) (Details) $ in Millions	May 02, 2017 USD ($) ft²	Dec. 29, 2017 USD ($)	Dec. 30, 2016 USD ($)	Jan. 01, 2016 USD ($)	Oct. 16, 2017 ft²
Property, Plant and Equipment [Line Items]
Depreciation		$ 1.2	$ 1.0	$ 1.4
Construction-in-progress [Member]
Property, Plant and Equipment [Line Items]
Construction in process costs capitalized	$ 14.5	6.6
Prepaid construction costs		$ 11.1
Capital lease and other financing lease [Member]
Property, Plant and Equipment [Line Items]
Tenant improvements allowance	$ 7.7
Alameda, California [Member] \| Operating lease and other financing lease [Member]
Property, Plant and Equipment [Line Items]
Area of leased property (in sqft) \| ft²	110,783
Alameda, California [Member] \| Optional amendment agreement [Member]
Property, Plant and Equipment [Line Items]
Area of leased property (in sqft) \| ft²	16,343				19,778

Debt (Schedule of Debt) (Details) - USD ($) $ in Thousands	Dec. 29, 2017	Dec. 30, 2016
Debt Instrument [Line Items]
Total debt	$ 0	$ 189,122
Convertible notes [Member]
Debt Instrument [Line Items]
Total debt	0	109,122
Balance of unamortized closing fees and expenses		400
Term loans payable [Member]
Debt Instrument [Line Items]
Total debt	$ 0	$ 80,000

Debt (Secured Convertible Notes) (Details) - USD ($) $ in Thousands		12 Months Ended
	Jun. 28, 2017	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016	Jun. 27, 2017
Debt Instrument [Line Items]
Interest paid in kind		$ (11,825)	$ 8,008	$ 3,817
Accrued and unpaid interest		20,460	21,044	19,822
Loss on extinguishment of debt		$ 6,239	$ 13,901	$ 0
Convertible notes [Member] \| Secured Convertible Notes due June 2018 [Member]
Debt Instrument [Line Items]
Repayment of principal	$ 123,800
Extinguishment of debt amount	113,900
Interest paid in kind	13,900
Prepayment penalty	5,800
Accrued and unpaid interest	4,200
Loss on extinguishment of debt	$ 6,200
Stated interest after extension option election					15.00%
Coupon interest [Member] \| Convertible notes [Member] \| Secured Convertible Notes due June 2018 [Member]
Debt Instrument [Line Items]
Stated interest after extension option election					7.50%
Payment-in-kind interest [Member] \| Convertible notes [Member] \| Secured Convertible Notes due June 2018 [Member]
Debt Instrument [Line Items]
Stated interest after extension option election					7.50%

Debt (2019 Notes) (Details) - USD ($) $ in Thousands	4 Months Ended	12 Months Ended
Debt (2019 Notes) (Details) - USD ($) $ in Thousands	Nov. 30, 2016	Dec. 30, 2016	Dec. 29, 2017	Jul. 31, 2016	Jan. 01, 2016
Debt Instrument [Line Items]
Aggregate principal amount of debt converted		$ 189,122	$ 0
Issuance of common stock in settlement of convertible notes		253,080
Senior subordinated notes [Member] \| 2019 Notes [Member]
Debt Instrument [Line Items]
Aggregate principal amount of debt converted				$ 287,500
Number of shares issued pursuant to conversion (in shares)	54,009,279
Redemption of convertible debt	$ 600
Inducements in conversion	6,000
Cash inducements	2,400	2,394
Repayments of interest required upon a conversion under the terms of the indenture that were not repaid under the terms of the exchange agreements	3,600	$ 3,572
Issuance of common stock in settlement of convertible notes	592,700
Reduction of additional paid-in capital resulting from conversion	$ 342,700
Stated interest rate					4.25%

Debt (Summary of Loss on Extinguishment of Debt) (Details) - USD ($) $ in Thousands	4 Months Ended	12 Months Ended
	Nov. 30, 2016	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Debt Instrument [Line Items]
Loss on extinguishment of debt		$ 6,239	$ 13,901	$ 0
Senior subordinated notes [Member] \| 2019 Notes [Member]
Debt Instrument [Line Items]
Cash inducements	$ 2,400		2,394
Waiver of requirement to repay interest, described above	3,600		3,572
Difference between the total settlement consideration attributed to the liability component of the 2019 Notes and the net carrying value of the liability			7,338
Unamortized discount on redeemed notes			83
Third-party costs			514
Loss on extinguishment of debt	$ 13,900		$ 13,901

Debt (Term Loan Payable) (Details) - USD ($) $ in Thousands		12 Months Ended
Debt (Term Loan Payable) (Details) - USD ($) $ in Thousands	Mar. 29, 2017	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Term loan payable
Accrued and unpaid interest		$ 20,460	$ 21,044	$ 19,822
Silicon Valley Bank Loan And Security Agreement [Member]
Term loan payable
Compensating balance			$ 81,600
Term loans payable [Member] \| Silicon Valley Bank Loan And Security Agreement [Member]
Term loan payable
Extinguishment of debt amount	$ 80,000
Accrued and unpaid interest	$ 100
Stated interest rate			1.00%

Common Stock and Warrants (Narrative) (Details) - USD ($) $ / shares in Units, $ in Thousands			1 Months Ended		4 Months Ended	12 Months Ended
	Sep. 11, 2017	Mar. 18, 2015	Jul. 31, 2015	Jan. 31, 2014	Nov. 30, 2016	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Class of Warrant or Right [Line Items]
Increase to shareholder's equity							$ 253,080
Loss on extinguishment of debt						$ 6,239	13,901	$ 0
Public offering of common stock (in shares)			28,750,000
Share price (in dollars per share)			$ 5.40
Net proceeds from public offering			$ 145,600			$ 0	0	$ 145,649
2014 Warrants [Member]
Class of Warrant or Right [Line Items]
Warrant period		2 years		2 years
Warrants outstanding (in shares)	0			1,000,000
Exercise price per share (in dollars per share)		$ 3.445		$ 9.70
Fair Value of warrants		$ 1,500
Issuance of common stock on warrant exercise (in shares)	877,451
Shares withheld for exercise of warrants (in shares)	122,549
Over-allotment option [Member]
Class of Warrant or Right [Line Items]
Public offering of common stock (in shares)			3,750,000
Senior subordinated notes [Member] \| 2019 Notes [Member]
Class of Warrant or Right [Line Items]
Number of shares issued pursuant to conversion (in shares)					54,009,279
Aggregate principal amount of debt converted					$ 286,900
Increase to shareholder's equity					592,700
Loss on extinguishment of debt					$ 13,900		$ 13,901

Stock-based Compensation (Narrative) (Details) - USD ($)	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016	Dec. 31, 2010
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares available for grant	20,328,545
Stock-based compensation expense	$ 23,938,000	$ 22,912,000	$ 21,977,000
Proceeds from employee stock purchase plan	4,868,000	2,187,000	568,000
Cash received from option exercises and purchases under the ESPP	$ 17,555,000	$ 25,327,000	10,911,000
Options outstanding (in shares)	22,208,446	24,999,665
Retirement Plan, employee contribution (as a percent)	50.00%
Employer matching contributions for first 3% of participant contributions (as a percent)	100.00%
Percentage of participant contributions into the 401(k) Retirement Plan (as a percent)	3.00%
Expenses relating to stock match	$ 1,700,000	$ 1,100,000	400,000
Number of shares available for issuance under 401(k) Retirement Plan (in shares)	231,090
Change in Control and Severance Benefit Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Termination period prior to change in control	1 month
Termination period subsequent to change in control	13 months
Change in Control and Severance Benefit Plan [Member] \| Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Extension of exercise period	1 year
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options, vesting period	4 years			10 years
Life of stock options granted	7 years
Total unrecognized compensation expense	$ 39,700,000
Unrecognized compensation expense weighted-average period for recognition	2 years 6 months 25 days
Intrinsic value of options exercised	$ 85,200,000	50,000,000	2,900,000
Cash received from option exercises and purchases under the ESPP	17,600,000	25,300,000	10,900,000
Fair value of employee options vested and expensed	$ 13,100,000	13,400,000	18,900,000
RSUs [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options, vesting period	4 years
Total unrecognized compensation expense	$ 61,200,000
Unrecognized compensation expense weighted-average period for recognition	3 years 2 months 12 days
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares available for grant	5,052,500
Discount rate from market value on purchase date (as a percent)	85.00%
Discount rate from market value on offering date (as a percent)	85.00%
Purchase period	6 months
Stock-based compensation expense	$ 1,600,000	$ 1,000,000	$ 400,000
Common stock issued (in shares)	434,523	559,936	324,315
Average price per share (in dollars per share)	$ 11.20	$ 3.91	$ 1.75
Proceeds from employee stock purchase plan	$ 4,900,000	$ 2,200,000	$ 600,000
Performance Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation expense	$ 0	$ 4,100,000	$ 13,200,000
Number of options in vested (in shares)		5,870,303	6,982,613
Options outstanding (in shares)	0

Stock-based Compensation (Schedule of Allocated Employee Stock-Based Compensation Expense) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total stock-based compensation	$ 23,938	$ 22,912	$ 21,977
Research and development expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total stock-based compensation	7,569	9,366	11,691
Selling, general and administrative expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total stock-based compensation	$ 16,369	$ 13,546	$ 10,286

Stock-based Compensation (Weighted Average Grant Date Fair Value) (Details) - $ / shares	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant-date fair value (in dollars per share)	$ 11.42	$ 4.77	$ 2.55
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant-date fair value (in dollars per share)	$ 6.00	$ 2.17	$ 1.20

Stock-based Compensation (Schedule of Fair Value of Employee Share-Based Payments Awards ESPP Assumptions and Weighted Average Fair Values) (Details)	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	1.98%	1.15%	1.22%
Dividend yield	0.00%	0.00%	0.00%
Volatility	59.00%	76.00%	93.00%
Expected life	4 years 5 months 23 days	4 years 4 months 9 days	4 years 6 months
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	1.09%	0.55%	0.15%
Dividend yield	0.00%	0.00%	0.00%
Volatility	58.00%	65.00%	98.00%
Expected life	6 months	6 months	6 months

Stock-based Compensation (Summary of All Stock Option Activity) (Details) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 29, 2017 USD ($) $ / shares shares
Shares
Options outstanding at beginning of the year (in shares) \| shares	24,999,665
Granted (in shares) \| shares	2,166,110
Exercised (in shares) \| shares	(4,469,203)
Forfeited (in shares) \| shares	(229,793)
Expired (in shares) \| shares	(258,333)
Options outstanding at ending of the year (in shares) \| shares	22,208,446
Exercisable at December 31, 2017 (in shares) \| shares	16,158,740
Weighted Average Exercise Price
Options outstanding at beginning of the year (in dollars per share) \| $ / shares	$ 4.91
Granted (in dollars per share) \| $ / shares	23.43
Exercised (in dollars per share) \| $ / shares	3.91
Forfeited (in dollars per share) \| $ / shares	8.09
Expired (in dollars per share) \| $ / shares	9.91
Options outstanding at ending of the year (in dollars per share) \| $ / shares	6.83
Exercisable at December 31, 2017 (in dollars per share) \| $ / shares	$ 4.51
Weighted Average Remaining Contractual Term, Options outstanding at December 31, 2017	4 years 18 days
Weighted Average Remaining Contractual Term, Exercisable at December 31, 2017	3 years 5 months 15 days
Aggregate Intrinsic Value, Options outstanding at December 31, 2017 \| $	$ 523,448
Aggregate Intrinsic Value, Exercisable at December 31, 2017 \| $	$ 418,304

Stock-based Compensation (Summary of All RSU Activity) (Details) - RSUs [Member] $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 29, 2017 USD ($) $ / shares shares
Shares
Awards outstanding at beginning of period (in shares) \| shares	2,469,791
Awarded (in shares) \| shares	2,137,817
Vested and released (in shares) \| shares	(708,541)
Forfeited (in shares) \| shares	(136,077)
Awards outstanding at end of period (in shares) \| shares	3,762,990
Weighted Average Grant Date Fair Value
Awards outstanding at beginning of period (in dollars per share) \| $ / shares	$ 8.69
Awarded (in dollars per share) \| $ / shares	24.60
Vested and released (in dollars per share) \| $ / shares	7.97
Forfeited (in dollars per share) \| $ / shares	11.48
Awards outstanding at end of period (in dollars per share) \| $ / shares	$ 17.76
Weighted Average Remaining Contractual Term, Awards outstanding at December 31, 2017	1 year 11 months 12 days
Aggregate Intrinsic Value, Awards outstanding at December 31, 2017 \| $	$ 114,395

Income Taxes (Schedule of Consolidated Net Income (Loss)) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Income Tax Disclosure [Abstract]
Domestic	$ 158,577	$ (70,222)	$ (150,846)
Foreign	0	0	(10,843)
Income (loss) before income taxes	$ 158,577	$ (70,222)	$ (161,689)

Income Taxes (Components of Income Tax Expense (Benefit)) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Current:
Federal	$ 0	$ 0	$ 0
State	4,350	0	55
Total current tax expense	4,350	0	55
Deferred:
Federal	0	0	0
State	0	0	0
Total deferred tax expense	0	0	0
Provision for income taxes	$ 4,350	$ 0	$ 55

Income Taxes (Schedule of Reconciliation of Income Taxes at the Statutory Federal Income Tax Rate to Net Income Taxes) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Income Tax Disclosure [Abstract]
U.S. federal income tax provision (benefit) at statutory rate	$ 53,916	$ (23,876)	$ (54,974)
Change in valuation allowance	(34,266)	6,377	51,421
State tax expense	8,282	6,520	55
Debt extinguishment	0	4,726	0
Non-deductible interest	1,367	2,680	3,308
Stock-based compensation	(20,548)	3,155	195
Other	(4,401)	418	50
Provision for income taxes	$ 4,350	$ 0	$ 55

Income Taxes (Schedule of Deferred Assets and Liabilities) (Details) - USD ($) $ in Thousands	Dec. 29, 2017	Dec. 30, 2016
Deferred tax assets:
Net operating loss carry-forwards	$ 244,205	$ 471,327
Book over tax depreciation and amortization	39,472	70,617
Tax credit and charitable contribution carry-forwards	66,770	64,367
Deferred revenue	53,543	0
Amortization of deferred stock compensation – non-qualified	8,966	14,780
Accruals and reserves not currently deductible	4,914	8,117
Other assets	1,088	106
Total deferred tax assets	418,958	629,314
Valuation allowance	(418,958)	(629,062)
Net deferred tax assets		252
Deferred tax liabilities:
Unrealized gains on derivatives and other liabilities	0	(252)
Total deferred tax liabilities	0	(252)
Net deferred taxes	$ 0	$ 0

Income Taxes (Narrative) (Details) - USD ($) $ in Millions	12 Months Ended
Income Taxes (Narrative) (Details) - USD ($) $ in Millions	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Income Tax Examination [Line Items]
Tax Cuts and Jobs Act of 2017, reduction in deferred tax asset	$ 184.8
Tax Cuts and Jobs Act of 2017, change in valuation allowance	184.8
Valuation allowance increase (decrease)	(210.1)	$ 92.7	$ 7.9
Federal [Member]
Income Tax Examination [Line Items]
Net operating loss carryforwards	1,105.0
Research and development tax credits	83.0
State and Local Jurisdiction [Member]
Income Tax Examination [Line Items]
Net operating loss carryforwards	424.0
State and Local Jurisdiction [Member] \| Research Tax Credit Carryforward [Member]
Income Tax Examination [Line Items]
Research and development tax credits	$ 28.0

Income Taxes (Schedule of Unrecognized Tax Benefits) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Reconciliation of Unrecognized Tax Benefits, Excluding Amounts Pertaining to Examined Tax Returns [Roll Forward]
Beginning balance	$ 61,809	$ 88,638	$ 58,215
Change relating to prior year provision	247	(29,110)	21,696
Change relating to current year provision	17,378	2,304	8,727
Reductions based on the lapse of the applicable statutes of limitations	(92)	(23)	0
Ending balance	$ 79,342	$ 61,809	$ 88,638

Net Income (Loss) Per Share (Computation of Basic and Diluted Net Income (Loss) Per Share) (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 29, 2017	Sep. 29, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 30, 2016	Sep. 30, 2016	Jul. 01, 2016	Apr. 01, 2016	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Numerator:
Net loss	$ 38,489	$ 81,382	$ 17,656	$ 16,700	$ 35,123	$ (11,284)	$ (34,838)	$ (59,223)	$ 154,227	$ (70,222)	$ (161,744)
Net income allocated to participating securities									(367)	0	0
Net income allocable to common stock for basic net income (loss) per share									153,860	(70,222)	(161,744)
Adjustment to net income allocated to participating securities									22	0	0
Net income allocable to common stock for diluted net income (loss) per share									$ 153,882	$ (70,222)	$ (161,744)
Denominator:
Weighted-average shares of common stock outstanding used in computing basic net income (loss) per share (in shares)									293,588	250,531	209,227
Outstanding stock options, unvested RSUs and ESPP contributions (in shares)									18,415	0	0
Weighted-average shares of common stock outstanding and dilutive securities used in computing diluted net income (loss) per share (in shares)									312,003	250,531	209,227
Net income (loss) per share, basic (in dollars per share)	$ 0.13	$ 0.28	$ 0.06	$ 0.06	$ 0.12	$ (0.04)	$ (0.15)	$ (0.26)	$ 0.52	$ (0.28)	$ (0.77)
Net income (loss) per share, diluted (in dollars per share)	$ 0.12	$ 0.26	$ 0.06	$ 0.05	$ 0.12	$ (0.04)	$ (0.15)	$ (0.26)	$ 0.49	$ (0.28)	$ (0.77)

Net Income (Loss) Per Share (Potentially Dilutive Shares of Common Stock) (Details) - shares shares in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	1,645	62,458	117,478
Outstanding stock options, unvested RSUs and ESPP contributions [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	1,645	27,568	28,470
2014 Warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	0	1,000	1,000
Deerfield Notes [Member] \| Convertible debt [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	0	33,890	33,890
2019 Notes [Member] \| Convertible debt [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	0	0	54,118

Fair Value Measurements (Schedule of Estimated Fair Value of Outstanding Debt) (Details) $ in Thousands	Dec. 30, 2016 USD ($)
Carrying Amount [Member] \| Convertible notes [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of financial instruments	$ 109,122
Carrying Amount [Member] \| Term loans payable [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of financial instruments	80,000
Fair Value [Member] \| Convertible notes [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of financial instruments	121,220
Fair Value [Member] \| Term loans payable [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of financial instruments	$ 79,784

Fair Value Measurements (Narrative) (Details) - Level 3 [Member] - Senior subordinated notes [Member]	12 Months Ended
	Dec. 30, 2016
Deerfield Notes [Member]
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Fair value inputs, discount rate	9.50%
2019 Notes [Member]
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Fair value inputs, discount rate	9.50%

Commitments (Schedule of Aggregate Future Minimum Lease Payments) (Details) $ in Thousands	Dec. 29, 2017 USD ($)
Operating leases
2018	$ 2,864
2019	664
2020	684
2021	694
2022	704
Thereafter	3,730
Future minimum lease payments, operating leases	9,340
Other financing obligations
2018	800
2019	1,905
2020	2,129
2021	2,213
2022	2,282
Thereafter	12,164
Future minimum lease payments, capital leases	$ 21,493

Commitments (Schedule of Rent Expense and Sublease Income) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Commitments and Contingencies Disclosure [Abstract]
Gross rental expense	$ 6,160	$ 9,676	$ 13,942
less: Sublease income	(1,225)	(3,553)	(5,205)
Net rental expense	$ 4,935	$ 6,123	$ 8,737

Commitments (Narrative) (Details)		12 Months Ended
Commitments (Narrative) (Details)	May 02, 2017 USD ($) ft² property option	Dec. 29, 2017 USD ($) ft² debt_instrument option	Oct. 16, 2017 ft²	Dec. 30, 2016 USD ($)
Operating Leased Assets [Line Items]
Number of letters of credit entered into (in debt instruments) \| debt_instrument		2
Letters of credit outstanding		$ 0
Collateral provided for purchasing card program		3,000,000		$ 3,000,000
Building lease [Member]
Operating Leased Assets [Line Items]
Line of credit borrowing capacity		500,000.0		500,000.0
Workers Compensation Insurance Policy [Member]
Operating Leased Assets [Line Items]
Line of credit borrowing capacity		600,000.0		$ 600,000.0
Building shells [Member] \| Operating lease and other financing lease [Member]
Operating Leased Assets [Line Items]
Number of properties \| property	2
Standby letters of credit [Member]
Operating Leased Assets [Line Items]
Line of credit borrowing capacity		1,000,000
Alameda, California [Member] \| Operating lease and other financing lease [Member]
Operating Leased Assets [Line Items]
Area of leased property (in sqft) \| ft²	110,783
Term of lease contract	10 years
Number of renewal options \| option	2
Renewal option term	5 years
Number of options to terminate \| option	1
Option for additional area of lease (sq ft) \| ft²	170,000
Alameda, California [Member] \| Optional amendment agreement [Member]
Operating Leased Assets [Line Items]
Area of leased property (in sqft) \| ft²	16,343		19,778
Term of lease contract	6 months
Reimbursement cost for contract termination	$ 1,500,000
Accrual for contract termination		1,400,000
Rent payable		1,200,000
Capital and operating leases, Minimum lease payments due		$ 28,500,000
South San Francisco, California [Member] \| Leasing Arrangement [Member]
Operating Leased Assets [Line Items]
Area of leased property (in sqft) \| ft²		116,063
Number of renewal options \| option		2

Segment Information Segment Information (Narrative) (Details) $ in Millions	12 Months Ended
	Dec. 29, 2017 USD ($) segment	Dec. 30, 2016 USD ($)	Jan. 01, 2016 USD ($)
Segment Reporting [Abstract]
Number of operating segments \| segment	1
Gain (loss) on foreign exchange \| $	$ (0.2)	$ (0.2)	$ 0.1

Segment Information (Schedule of Revenues by Customer) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Revenue, Major Customer [Line Items]
Net product revenues	$ 349,008	$ 135,375	$ 34,158
Cabometyx [Member]
Revenue, Major Customer [Line Items]
Net product revenues	324,000	93,481	0
Cometriq [Member]
Revenue, Major Customer [Line Items]
Net product revenues	$ 25,008	$ 41,894	$ 34,158

Segment Information (Concentration Risk by Customer) (Details) - Sales revenue, net [Member] - Customer concentration risk [Member]	12 Months Ended
	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Diplomat Specialty Pharmacy [Member]
Concentration Risk [Line Items]
Concentration risk	18.00%	33.00%	83.00%
Caremark L.L.C. [Member]
Concentration Risk [Line Items]
Concentration risk	16.00%	9.00%	0.00%
Ipsen [Member]
Concentration Risk [Line Items]
Concentration risk	15.00%	17.00%	0.00%
Accredo Health, Incorporated [Member]
Concentration Risk [Line Items]
Concentration risk	11.00%	9.00%	0.00%
Affiliates of McKesson Corporation [Member]
Concentration Risk [Line Items]
Concentration risk	11.00%	7.00%	0.00%

Segment Information (Revenues from Geographic Regions) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 29, 2017	Sep. 29, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 30, 2016	Sep. 30, 2016	Jul. 01, 2016	Apr. 01, 2016	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 77,581	$ 62,194	$ 36,252	$ 15,427	$ 452,477	$ 191,454	$ 37,172
Geographic concentration risk [Member] \| Sales revenue, net [Member] \| U.S. [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues									367,906	140,709	33,869
Geographic concentration risk [Member] \| Sales revenue, net [Member] \| Europe [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues									69,792	35,745	3,303
Geographic concentration risk [Member] \| Sales revenue, net [Member] \| Rest of the world [Member]
Revenues from External Customers and Long-Lived Assets [Line Items]
Revenues									$ 14,779	$ 15,000	$ 0

Quarterly Financial Data (Unaudited) (Summary of Unaudited Quarterly Financial Data) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 29, 2017	Sep. 29, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 30, 2016	Sep. 30, 2016	Jul. 01, 2016	Apr. 01, 2016	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Quarterly Financial Information Disclosure [Abstract]
Total revenues	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 77,581	$ 62,194	$ 36,252	$ 15,427	$ 452,477	$ 191,454	$ 37,172
Gross profit	91,520	91,758	84,990	65,674	50,064	40,287	30,058	8,414
Income (loss) from operations	37,431	81,180	27,113	20,186	38,883	7,264	(25,136)	(49,135)	165,910	(28,124)	(121,421)
Net income (loss)	$ 38,489	$ 81,382	$ 17,656	$ 16,700	$ 35,123	$ (11,284)	$ (34,838)	$ (59,223)	$ 154,227	$ (70,222)	$ (161,744)
Net income (loss) per share, basic (in dollars per share)	$ 0.13	$ 0.28	$ 0.06	$ 0.06	$ 0.12	$ (0.04)	$ (0.15)	$ (0.26)	$ 0.52	$ (0.28)	$ (0.77)
Net income (loss) per share, diluted (in dollars per share)	$ 0.12	$ 0.26	$ 0.06	$ 0.05	$ 0.12	$ (0.04)	$ (0.15)	$ (0.26)	$ 0.49	$ (0.28)	$ (0.77)

Quarterly Financial Data (Unaudited) (Narrative) (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Dec. 30, 2016	Sep. 30, 2016	Dec. 29, 2017
Deferred Revenue Arrangement [Line Items]
Accrued clinical trial liabilities	$ 14,131	$ 18,700	$ 19,849
Collaborative Arrangement with Genentech [Member]
Deferred Revenue Arrangement [Line Items]
Recovery of net losses	$ 23,100
Recovery of net losses, recognized in current fiscal year		$ 9,800