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Document And Entity Information - USD ($) $ in Millions	12 Months Ended
Document And Entity Information - USD ($) $ in Millions	Dec. 28, 2018	Feb. 12, 2019	Jun. 29, 2018
Document And Entity Information [Abstract]
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 28, 2018
Document Fiscal Year Focus	2018
Document Fiscal Period Focus	FY
Trading Symbol	exel
Entity Registrant Name	EXELIXIS, INC.
Entity Central Index Key	0000939767
Entity Filer Category	Large Accelerated Filer
Entity Emerging Growth Company	false
Entity Small Business	false
Entity Shell Company	false
Current Fiscal Year End Date	--12-28
Entity Common Stock, Shares Outstanding		300,129,630
Entity Well-known Seasoned Issuer	Yes
Entity Public Float			$ 5,531.1
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 29, 2017
Current assets:
Cash and cash equivalents	$ 314,775	$ 183,164
Short-term investments	378,559	204,607
Short-term restricted cash and investments	0	504
Trade receivables, net	162,771	77,300
Other receivables	16,056	3,892
Inventory, net	9,838	6,657
Prepaid expenses and other current assets	15,017	8,750
Total current assets	897,016	484,874
Long-term investments	157,187	64,255
Long-term restricted cash and investments	1,100	4,646
Property and equipment, net	50,897	25,743
Operating lease right-of-use assets	5,867	0
Deferred tax assets, net	244,111	0
Goodwill	63,684	63,684
Other long-term assets	2,424	12,092
Total assets	1,422,286	655,294
Current liabilities:
Accounts payable	10,901	9,575
Accrued compensation and benefits	32,142	21,073
Accrued clinical trial liabilities	18,231	19,849
Rebates and fees due to customers	14,954	7,565
Accrued collaboration liabilities	7,419	8,974
Current portion of deferred revenue	0	31,984
Other current liabilities	21,825	16,150
Total current liabilities	105,472	115,170
Long-term portion of deferred revenue	15,897	238,520
Long-term portion of lease liabilities	12,178	14,938
Other long-term liabilities	1,286	1,705
Total liabilities	134,833	370,333
Commitments
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	300	296
Additional paid-in capital	2,168,217	2,114,184
Accumulated other comprehensive loss	(701)	(347)
Accumulated deficit	(880,363)	(1,829,172)
Total stockholders’ equity	1,287,453	284,961
Total liabilities and stockholders’ equity	$ 1,422,286	$ 655,294

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 28, 2018	Dec. 29, 2017
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	299,876,080	296,209,426
Common stock, shares outstanding	299,876,080	296,209,426

Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Revenues:
Total revenues	$ 853,826	$ 452,477	$ 191,454
Operating expenses:
Cost of goods sold	26,348	15,066	6,552
Research and development	182,257	112,171	95,967
Selling, general and administrative	206,366	159,362	116,145
Restructuring (recovery) charge	0	(32)	914
Total operating expenses	414,971	286,567	219,578
Income (loss) from operations	438,855	165,910	(28,124)
Other income (expense), net:
Interest income	12,840	4,883	2,578
Interest expense	0	(8,679)	(33,060)
Other, net	397	(3,537)	(11,616)
Total other income (expense), net:	13,237	(7,333)	(42,098)
Income (loss) before income taxes	452,092	158,577	(70,222)
Income tax benefit (provision)	237,978	(4,350)	0
Net income (loss)	$ 690,070	$ 154,227	$ (70,222)
Net income (loss) per share, basic (in dollars per share)	$ 2.32	$ 0.52	$ (0.28)
Net income (loss) per share, diluted (in dollars per share)	$ 2.21	$ 0.49	$ (0.28)
Shares used in computing net income (loss) per share, basic (in shares)	297,892	293,588	250,531
Shares used in computing net income (loss) per share, diluted (in shares)	312,803	312,003	250,531
Net product revenues
Revenues:
Total revenues	$ 619,279	$ 349,008	$ 135,375
Collaboration revenue
Revenues:
Total revenues	$ 234,547	$ 103,469	$ 56,079

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

12 Months Ended

Dec. 28, 2018

Dec. 29, 2017

Dec. 30, 2016

Statement of Comprehensive Income [Abstract]

Net income (loss)

$ 690,070

$ 154,227

$ (70,222)

Other comprehensive income (loss)

^[1]

(354)

(184)

Comprehensive income (loss)

$ 689,716

$ 154,296

$ (70,406)

[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. During the year ended December 31, 2018, there was a tax benefit of $0.2 million related to other comprehensive income as a result of the release of our valuation allowance for our deferred tax assets; there was no income tax benefit or provision related to other comprehensive income (loss) during the remaining periods presented.

- Definition

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

+ References + Details

Consolidated Statements of Comprehensive Income (Loss) (Parenthetical) - USD ($)	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Statement of Comprehensive Income [Abstract]
Reclassification adjustments to net loss resulting from realized gains or losses on sale of securities	$ 0	$ 0	$ 0
Income tax expense (benefit) related to other comprehensive income	$ (200,000)	$ 0	$ 0

Consolidated Statements of Stockholders' Equity (Deficit) - USD ($)
$ in Thousands

Total

Common Stock

Additional Paid-in Capital

Accumulated Other Comprehensive Loss

Accumulated Deficit

Balance at beginning of period (in shares) at Jan. 01, 2016

227,960,943

Balance at beginning 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

(70,222)

Other comprehensive income (loss)

(184)

^[1]

(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

Balance at end of period (in shares) at Dec. 30, 2016

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]

Net income

154,227

Other comprehensive income (loss)

^[1]

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 exercise of warrants

$ 1

(1)

Stock-based compensation

$ 23,938

23,938

Balance at end of period (in shares) at Dec. 29, 2017

296,209,426

Balance at end of period at Dec. 29, 2017

$ 284,961

$ 296

2,114,184

(347)

(1,829,172)

Increase (Decrease) in Stockholders' Equity [Roll Forward]

Net income

690,070

Net income | ASU 2016-02

(500)

Other comprehensive income (loss)

(354)

^[1]

(354)

Issuance of common stock under equity incentive and stock purchase plans (in shares)

3,666,654

Issuance of common stock under equity incentive and stock purchase plans

13,411

$ 4

13,407

Stock-based compensation

$ 40,626

40,626

Balance at end of period (in shares) at Dec. 28, 2018

299,876,080

Balance at end of period at Dec. 28, 2018

$ 1,287,453

$ 300

$ 2,168,217

$ (701)

$ (880,363)

[1]

Consolidated Statements of Cash Flows - USD ($)
$ in Thousands

12 Months Ended

Dec. 28, 2018

Dec. 29, 2017

Dec. 30, 2016

Cash flows from operating activities:

Net income (loss)

$ 690,070

$ 154,227

$ (70,222)

Adjustments to reconcile net loss to net cash provided by (used in) operating activities:

Depreciation and amortization

4,915

1,187

1,002

Stock-based compensation

40,626

23,938

22,912

401(k) matching contributions made in common stock

3,696

1,640

1,036

Right-of-Use Asset, Amortization

2,854

Deferred taxes

(244,111)

Loss on extinguishment of debt

6,239

13,901

Amortization of debt discounts and debt issuance costs

182

8,432

Interest paid in kind

(11,825)

8,008

Gain on other equity investments

(209)

(2,980)

(2,494)

Other

(2,358)

(51)

562

Changes in operating assets and liabilities:

Trade and other receivables

(85,471)

(43,299)

(38,680)

Other receivables

(4,410)

2,460

3,362

Inventory, net

(3,181)

(3,319)

(722)

Prepaid expenses and other current assets

(3,029)

(3,268)

(1,610)

Other long-term assets

(1,086)

430

1,077

Accounts payable

856

3,010

164

Accrued compensation and benefits

11,069

739

16,705

Accrued clinical trial liabilities

(1,618)

5,718

(3,940)

Rebates and fees due customers

7,389

4,145

3,866

Accrued collaboration liabilities

(1,555)

6,928

(10,938)

Deferred revenue

271

13,745

256,759

Long-term portion of lease liabilities

(1,225)

14,938

Other current and long-term liabilities

2,227

(9,173)

1,224

Net cash used in operating activities

415,720

165,611

210,404

Cash flows from investing activities:

Purchases of property and equipment

(33,297)

(21,143)

(1,703)

Proceeds from sale of property and equipment

308

164

Purchases of investments

(557,832)

(319,090)

(369,187)

Proceeds from maturities of investments

280,826

336,590

151,485

Proceeds from sale of investments

11,936

37,294

2,266

Proceeds from other equity investments

209

2,980

2,494

Net cash (used in) provided by investing activities

(297,850)

36,795

(214,548)

Cash flows from financing activities:

Proceeds from exercise of stock options

12,076

17,555

25,327

Proceeds from employee stock purchase plan

5,202

4,868

2,187

(7,574)

(6,563)

(4,108)

Principal payments on financing lease obligation

(13)

Principal repayments of debt

(185,788)

(575)

Payments on conversion of convertible notes

(7,135)

Net cash provided by financing activities

9,691

(169,928)

15,696

Net increase in cash, cash equivalents and restricted cash

127,561

32,478

11,552

Cash, cash equivalents and restricted cash at beginning of period

188,314

155,836

144,284

Cash, cash equivalents and restricted cash at end of period

315,875

188,314

155,836

Supplemental cash flow disclosure:

Cash paid for interest

20,460

21,044

Cash paid for taxes

10,677

538

190

Non-cash investing and financing activity:

Property and equipment deemed to have been acquired in build-to-suit lease

14,530

Right-of-use assets obtained in exchange for lease obligations

^[1]

17,180

Unpaid liabilities incurred to acquire Property and equipment

802

524

Issuance of common stock in settlement of convertible notes

$ 0

$ 286,925

[1]	Amounts for the year ended December 31, 2018 include the transition adjustment for the adoption of Topic 842.

Organization and Summary of Significant Accounting Policies

12 Months Ended

Dec. 28, 2018

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 an oncology-focused biotechnology company that strives to accelerate the discovery, development and commercialization of new medicines for difficult-to-treat cancers. Since we were founded in 1994, four products resulting from our discovery efforts have progressed through clinical development and received regulatory approval; three have a growing commercial presence in markets worldwide, and we expect that the fourth will soon enter the marketplace in Japan. Two are derived from cabozantinib, an inhibitor of multiple tyrosine kinases including MET, AXL, VEGF receptors and RET. These are: CABOMETYX® (cabozantinib) tablets approved for advanced renal cell carcinoma (RCC) and previously treated hepatocellular carcinoma (HCC) and COMETRIQ® (cabozantinib) capsules approved for progressive, metastatic medullary thyroid cancer (MTC). Other commercially available products resulting from our discovery efforts include COTELLIC® (cobimetinib), an inhibitor of MEK approved as part of a combination regimen to treat advanced melanoma and marketed under a collaboration with Genentech, Inc. (a member of the Roche Group) (Genentech), and MINNEBRO™ (esaxerenone), an oral, non-steroidal, selective blocker of the mineralocorticoid receptor (MR) approved for the treatment of hypertension in Japan and licensed to Daiichi Sankyo Company, Limited (Daiichi Sankyo).

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 2016 ended on December 30, 2016; fiscal year 2017 ended on December 29, 2017; and fiscal year 2018 ended on December 28, 2018. For convenience, references in this report as of and for the fiscal years ended (or ending, as applicable) December 30, 2016, December 29, 2017, and December 28, 2018 are indicated as being as of and for the years ended (or ending, as applicable) December 31, 2016, 2017 and 2018, respectively. All annual periods presented are 52-week fiscal years and all interim periods presented are 13-week fiscal quarters.

Segment Information

We operate in one business segment that 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.

All of our long-lived assets are located in the U.S. See “Note 2. Revenues” for enterprise-wide disclosures about product sales, revenues from major customers and revenues by geographic region.

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 determining the nature and timing of satisfaction of performance obligations, and determining the standalone selling price of performance obligations, and variable consideration such as rebates, chargebacks, sales returns and sales allowances as well as milestones included in collaboration arrangements; the amounts of revenues and expenses under our profit and loss sharing agreement; recoverability of inventory; operating lease assets and liabilities; the amounts of deferred tax assets and liabilities including the related valuation allowance; the accrual for certain liabilities including accrued clinical trial liabilities; and valuations of equity awards used to determine stock-based compensation, including certain awards with vesting subject to market or performance conditions. 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.

Recently Adopted Accounting Pronouncements

Restricted Cash

In January 2018, we adopted 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. Therefore, amounts generally described as restricted cash are included with cash when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows. ASU 2016-18 was adopted using the retrospective transition method in the accompanying Consolidated Financial Statements.

As a result of the adoption of ASU 2016-18, we no longer include purchases of restricted cash and proceeds from maturities of restricted cash in our cash flows from investing activities. Accordingly, the adoption of ASU 2016-18 resulted in a $1.0 million and $1.5 million increase in Net cash provided by investing activities for the years ended December 31, 2017 and 2016, respectively.

See “Note 4. Cash and Investments—Cash, Cash Equivalents and Restricted Cash” for a reconciliation of cash and cash equivalents presented in our previously published Consolidated Statement of Cash Flows for the years ended December 31, 2017 and 2016 and Cash, cash equivalents and restricted cash reported in the accompanying Consolidated Statement of Cash Flows for the same periods.

Revenue

On January 1, 2018, we adopted Topic 606 using the modified retrospective method applied to those contracts that were not completed as of January 1, 2018. Results for the year ended December 31, 2018 are presented under Topic 606, while prior period amounts are not adjusted and continue to be reported in accordance with our historic accounting under previous revenue recognition guidance, Accounting Standards Codification (ASC) Topic 605: Revenue Recognition (Topic 605).

Leases

On July 1, 2018 we early adopted Topic 842. We adopted Topic 842 using the modified retrospective approach with a cumulative-effect adjustment as of January 1, 2018 in accordance with ASU No. 2018-11, Leases (Topic 842) - Targeted Improvements. Results for the year ended December 31, 2018 are presented under Topic 842. Prior period amounts have not been adjusted and continue to be reported in accordance with our historical accounting under previous lease guidance, ASC Topic 840: Leases (Topic 840). We elected the package of practical expedients permitted under the transition guidance within the new standard, which among other things, allowed us to carry forward the historical lease classification of those leases in place as of January 1, 2018.

Impact of Adoption of Topic 606 and Topic 842

We recorded a net reduction of $258.5 million to opening accumulated deficit as of January 1, 2018, due to the cumulative impact of adopting Topic 606, with the impact primarily relating to a change in the recognition of upfront and non-substantive milestone payments received related to our collaboration arrangements with Ipsen Pharma SAS (Ipsen) and Takeda Pharmaceutical Company Ltd. (Takeda). The adoption of Topic 606 did not have an impact on our recognition of revenue from product sales.

We also recorded a net reduction of $0.2 million to opening accumulated deficit as of January 1, 2018, due to the cumulative impact of adopting Topic 842, with the impact relating to a change in the classification of certain of our buildings in our Lease Agreement (the Lease) with Ascentris 105, LLC (Ascentris) from a build to suit lease to an operating lease. For a description of the Lease, see “Note 11. Commitments.”

The impact of the adoption of Topic 606 and Topic 842 on the accompanying Consolidated Balance Sheet as of January 1, 2018 was as follows (in thousands):



	December 31, 2017			Adjustments Due to the Adoption of Topic 606			Adjustments Due to the Adoption of Topic 842			January 1, 2018
Contract assets: unbilled collaboration revenue, gross:
Current portion	$	—		$	9,588		$	—		$	9,588
Long-term portion	$	—		$	12,247		$	—		$	12,247
Other receivables	$	3,892		$	—		$	7,743		$	11,635
Property and equipment, net	$	25,743		$	—		$	(14,530	)	$	11,213
Operating lease right-of-use assets	$	—		$	—		$	8,579		$	8,579
Contract liabilities: deferred revenue, gross:
Current portion	$	31,984		$	(23,591	)	$	—		$	8,393
Long-term portion	$	238,520		$	(213,079	)	$	—		$	25,441
Operating lease liabilities:
Other current liabilities⁽¹⁾	$	16,150		$	—		$	3,173		$	19,323
Long-term portion of lease liabilities ⁽²⁾	$	14,938		$	—		$	(1,615	)	$	13,323
Accumulated deficit	$	(1,829,172	)	$	258,505		$	234		$	(1,570,433	)

____________________

(1) Includes deferred rent and current portion of operating lease liabilities.

(2) Long-term portion of operating lease liabilities and Financing obligation for build-to-suit lease.

The adjustments due to the adoption of Topic 606 primarily related to a reduction in deferred revenue driven by the allocation of the transaction price to our license performance obligations in the Ipsen and Takeda collaborations, which were determined to be functional intellectual property that was transferred at a point in time and as a result, revenue was recorded at a point in time. Previously under Topic 605, revenue related to the upfront payments and one non-substantive milestone payment earned in 2016 had been deferred over the estimated period of performance pursuant to the terms of the contract. Contract assets as of January 1, 2018 primarily related to estimated revenue for reimbursements for our continuing research and development services and the $10.0 million milestone from Ipsen’s filing with the European Medicines Agency (EMA) for cabozantinib as a treatment for patients with previously treated HCC, that was deemed probable under Topic 606 prior to January 1, 2018. Deferred revenue as of January 1, 2018 was related to the up-front, nonrefundable, fees and milestones earned that were allocated to our research and development services performance obligation which had not been satisfied as of that date. Contract assets and liabilities are netted by collaboration agreement in our Consolidated Balance Sheets; however, for illustration purposes the above amounts are shown prior to netting.

The adjustments due to the adoption of Topic 842 primarily related to the recognition of an operating lease right-of-use asset and operating lease liability for the Lease. In addition, the adoption of Topic 842 resulted in a change in classification of the build-to-suit component of the Lease under Topic 840 to an operating lease under Topic 842 and as a result we derecognized the estimated fair value of the building shells that were included in Property and equipment, net as of December 31, 2017, as we had been deemed to own these buildings under Topic 840. For a description of the Lease, see “Note 11. Commitments” in these Consolidated Financial Statements.

The impact of the adoption of Topic 606 and Topic 842 on the accompanying Consolidated Statements of Operations for year ended December 31, 2018 was as follows (in thousands):



	Year Ended December 31, 2018
	As Reported		Effect of Adoption of Topic 606 Higher / (Lower)			Effect of Adoption of Topic 842 Higher / (Lower)			Balances Without the Adoption of Topic 606 or 842
Collaboration revenues	$	234,547	$	(35,882	)	$	—		$	270,429
Total revenues	$	853,826	$	(35,882	)	$	—		$	889,708
Selling, general and administrative expenses	$	206,366	$	—		$	1,204		$	205,162
Total operating expenses	$	414,971	$	—		$	1,204		$	413,767
Interest expense	$	—	$	—		$	(631	)	$	(631	)
Total other income (expense), net	$	13,237	$	—		$	631		$	12,606
Income before income taxes	$	452,092	$	(35,882	)	$	(573	)	$	488,547
Income tax benefit (provision)	$	237,978	$	(48,325	)	$	73		$	286,230
Net income	$	690,070	$	(84,207	)	$	(500	)	$	774,777
Net income per share, basic	$	2.32	$	(0.28	)	$	—		$	2.60
Net income per share, diluted	$	2.21	$	(0.27	)	$	—		$	2.48

If we had not adopted Topic 606, we would also have recognized a $10.0 million milestone in the first quarter of 2018 upon the validation of Ipsen’s filing with the EMA for cabozantinib as a treatment for patients with previously treated HCC that was recognized under Topic 606 as part of our adoption transition adjustment on January 1, 2018. The adoption of Topic 606 also resulted in a reduction of previously reported deferred revenue that was recorded as part of our adoption transition adjustment as of January 1, 2018.

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 in 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 in 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 nominal.

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 in 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 in the accompanying Consolidated Balance Sheets.

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
Lab equipment		5 years
Furniture and fixtures		7 years
Office equipment		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, 2018 and 2017. 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

Topic 606 supersedes all previous revenue recognition requirements in accordance with generally accepted accounting principles. This standard applies to all contracts with customers, except for contracts that are within the scope of other standards, such as leases, insurance, collaboration arrangements and financial instruments. Under Topic 606, an entity recognizes revenue when its customer obtains control of promised goods or services, in an amount that reflects the consideration to which the entity is entitled to in exchange for those goods or services. To determine revenue recognition for arrangements that we determine are within the scope of Topic 606, we perform the following five steps: (i) identify the contract(s) with a customer; (ii) identify the performance obligations in the contract; (iii) determine the transaction price; (iv) allocate the transaction price to the performance obligations in the contract; and (v) recognize revenue when (or as) we satisfy a performance obligation. We only apply the five-step model to contracts when it is probable that we will collect the consideration we are entitled to in exchange for the goods or services we transfer to the customer.

Net Product Revenues

We sell our products principally to specialty distributors and specialty pharmacy providers, or collectively, our Customers. These Customers subsequently resell our products to health care providers and patients. In addition to distribution agreements with Customers, we enter into arrangements with health care providers and payors that provide for government-mandated and/or privately-negotiated rebates, chargebacks and discounts with respect to the purchase of our products. Revenues from product sales are recognized when the Customer obtains control of our product, which occurs at a point in time, typically upon delivery to the Customer.

Product Sales Discounts and Allowances

Revenues from product sales are recorded at the net sales price (transaction price), which includes estimates of variable consideration for which reserves are established and that result from discounts, chargebacks, rebates, co-pay assistance, returns and other allowances that are offered within contracts between us and our Customers, health care providers, payors and other indirect customers relating to the sales of our products. These reserves are based on the amounts earned or to be claimed on the related sales and are classified as reductions of accounts receivable (if the amount is payable to the Customer) or a current liability (if the amount is payable to a party other than a Customer). Where appropriate, these estimates take into consideration a range of possible outcomes that are probability-weighted for relevant factors such as our historical experience, current contractual and statutory requirements, specific known market events and trends, industry data and forecasted Customer buying and payment patterns. Overall, these reserves reflect our best estimates of the amount of consideration to which we are entitled based on the terms of our contracts. The amount of variable consideration that is included in the transaction price may be constrained, and is included in the net sales price only to the extent that it is probable that a significant reversal in the amount of the cumulative revenue recognized will not occur in a future period. Actual amounts of consideration ultimately received may differ from our estimates. If actual results in the future vary from our estimates, we will adjust these estimates, which would affect net product revenues and earnings in the period such variances become known.

Chargebacks: Chargebacks are discounts that occur when contracted customers purchase directly from a specialty 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 distributor, in turn, charges back to us the difference between the price initially paid by the specialty distributor and the discounted price paid to the specialty distributor by the customer. The allowance for chargebacks is based on an estimate of sales to contracted customers.

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

Rebates: Allowances for rebates include mandated discounts under the Medicaid Drug Rebate Program, other government programs and commercial contracts. 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 or contractual 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. 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 quarters’ unpaid rebates. If actual future rebates vary from estimates, we may need to adjust our accruals, which would affect net product revenues in the period of adjustment.

Allowances for rebates also include amounts related to the Medicare Part D Coverage Gap Discount Program. In the U.S., the Medicare Part D prescription drug benefit mandates participating manufacturers to fund 50%, and increasing to 70% in 2019, of the Medicare Part D insurance coverage gap for prescription drugs sold to eligible patients. Our estimates for expected Medicare Part D coverage gap amounts are based on customer and payer data received from specialty pharmacies and distributors and historical utilization rates. 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 quarter’s shipments to customer, plus an accrual balance for known prior quarters’ unpaid claims. If actual future funding varies from estimates, we may need to adjust our accruals, which would affect net product revenues in the period of adjustment.

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 distributor that administers the copay program.

Other Customer Credits: We pay fees to our Customers for account management, data management and other administrative services. To the extent the services received are distinct from the sale of products to the Customer, these payments are classified in Selling, general and administrative expenses in our Consolidated Statements of Operations.

Collaboration Revenues

We enter into collaboration arrangements, under which we license certain rights to our intellectual property to third parties. The terms of these arrangements typically include payment to us for one or more of the following: non-refundable, up-front license fees; development, regulatory and commercial milestone payments; product supply services; development cost reimbursements; profit sharing arrangements; and royalties on net sales of licensed products. Except for profit sharing arrangements and payments for product supply services, each of these payment types were within the scope of Topic 606 during the year ended December 31, 2018. As part of the accounting for these arrangements, we must develop assumptions that require judgment to determine the standalone selling price for each performance obligation identified in the contract. These key assumptions may include forecasted revenues, clinical development timelines and costs, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success. Prior period amounts continue to be reported in accordance with our historic accounting under previous revenue recognition guidance, Topic 605. See “ — Recently Adopted Accounting Pronouncements — Impact of Adoption of Topic 606 and Topic 842” above, for more information about the impact of the adoption on Topic 606.

Up-front License Fees: If the license to our intellectual property is determined to be distinct from the other performance obligations identified in the arrangement, we recognize revenues from nonrefundable, up-front fees allocated to the license when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For licenses that are bundled with other promises, we utilize judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front fees. We evaluate the measure of progress each reporting period and, if necessary, adjust the measure of performance and related revenue recognition.

Regulatory and Development Milestone Payments: At the inception of each arrangement that includes development milestone payments, we evaluate whether the milestones are considered probable of being reached and estimate the amount to be included in the transaction price using the most likely amount method. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within our or the licensee’s control, such as regulatory approvals, are not considered probable of being achieved until uncertainty associated with the approvals has been resolved. The transaction price is then allocated to each performance obligation, on a relative standalone selling price basis, for which we recognize revenue as or when the performance obligations under the contract are satisfied. At the end of each subsequent reporting period, we re-evaluate the probability of achieving such development and regulatory milestones and any related constraint, and if necessary, adjust our estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect Collaboration revenues and earnings in the period of adjustment.

Product Supply Services: Arrangements that include a promise for future supply of drug product for either clinical development or commercial supply at the licensee’s discretion are generally considered as options. We assess if these options provide a material right to the licensee and if so, they are accounted for as separate performance obligations.

Development Cost Reimbursements: Our Ipsen and Takeda arrangements include promises of future clinical development and drug safety services, as well as participation on certain joint committees. We have determined that these services collectively are distinct from the licenses provided to Ipsen and Takeda and as such, these promises are accounted for as a separate performance obligation recorded over time. We record revenue for these services as the performance obligations are satisfied, which we estimate using internal development costs incurred and projections through the term of the arrangements.

Profit Sharing Arrangements: Under the terms of our collaboration agreement with Genentech for cobimetinib, we are entitled to a share of U.S. profits and losses received in connection with commercialization of cobimetinib. We are also entitled to low double-digit royalties on ex-U.S. net sales. We account for such arrangements in accordance with ASC Topic 808: Collaborative Arrangements (Topic 808). 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. We recognized an annual profit under the agreement for the year ending December 31, 2018 and accordingly, those profits are recognized as Collaboration revenues in the accompanying Consolidated Statements of Operations. Prior to 2018, the commercialization of cobimetinib in the U.S. had not been profitable for any annual period and accordingly, losses for periods prior to 2018 were recognized as Selling, general and administrative expenses in the accompanying Consolidated Statements of Operations.

Sales-based Milestone Payments and Royalties: For arrangements that include sales-based royalties, including milestone payments based on the volume of sales, the license is deemed to be the predominant item to which the royalties or sales-based milestones relate and we recognize revenue at the later of (i) when the related sales occur, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied (or partially satisfied).

Cost of Goods Sold

Cost of goods sold is related to our product revenues and consists primarily of a 3% royalty we are required to pay GlaxoSmithKline (GSK) on all net sales of any product incorporating cabozantinib, 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.

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 were not capitalized as inventory but are expensed as research and development costs. Portions of the manufacturing costs for inventory sold during the years ended December 31, 2018, 2017 and 2016 were incurred prior to the regulatory approval of CABOMETYX and COMETRIQ and, therefore, were expensed as research and development costs when incurred, rather than capitalized as inventory. There were no amounts remaining related to previously expensed materials in our inventory balances as of December 31, 2018.

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.

Leases

We determine if an arrangement includes a lease at inception. Operating leases are included in operating lease right-of-use assets, other current liabilities, and long-term lease liabilities in our Consolidated Balance Sheet at December 31, 2018. Right-of-use assets represent our right to use an underlying asset for the lease term and lease liabilities represent our obligation to make lease payments arising from the lease. Operating lease right-of-use assets and liabilities are recognized at the lease commencement date based on the present value of lease payments over the lease term. In determining the net present value of lease payments, we use our incremental borrowing rate based on the information available at the lease commencement date. The operating lease right-of-use assets also include any lease payments made and exclude lease incentives. Our leases may include options to extend or terminate the lease which are included in the lease term when it is reasonably certain that we will exercise any such options. Lease expense is recognized on a straight-line basis over the expected lease term. We have elected not to apply the recognition requirements of Topic 842 for short-term leases.

For lease agreements entered into after the adoption of Topic 842 that include lease and non-lease components, such components are generally accounted for separately. For our building leases, as a result of us having elected to adopt the package of practical expedients permitted under the Topic 842 transition guidance, we account for the lease and non-lease components, such as common area maintenance charges, as a single lease component.

Prior period amounts continue to be reported in accordance with our historic accounting under previous lease guidance, Topic 840. See “ — Recently Adopted Accounting Pronouncements — Impact of Adoption of Topic 606 and Topic 842” above, for more information about the impact of the adoption on Topic 842.

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. The grant date fair value of stock-options is estimated using a Monte Carlo simulation pricing model for stock options that include market vesting conditions and a Black-Scholes Merton option pricing model for other stock options. 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 an accelerated basis over the requisite service period for awards with a market or performance condition and on a straight-line basis over the requisite service period for all other awards. Compensation expense relating to awards subject to performance conditions is recognized when management determines that it is probable that the performance goals will be achieved; the probability of achievement is assessed on a quarterly basis. We have made an election to record forfeitures when they occur.

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, 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.

Income Taxes

Our income tax benefit (provision) is computed under the asset and liability method. Significant estimates are required in determining our income tax benefit (provision). Some of these estimates are based on interpretations of existing tax laws or regulations. We recognize deferred tax assets and liabilities for the expected future tax consequences of events that have been included in the financial statements or tax returns. Under this method, deferred tax assets and liabilities are determined on the basis of the difference between the tax basis of assets and liabilities and their respective financial reporting amounts (temporary differences) at enacted tax rates in effect for the years in which the differences are expected to reverse. A valuation allowance is established for deferred tax assets for which it is more likely than not that some portion or all of the deferred tax assets, including net operating losses and tax credits, will not be realized. We periodically re-assess the need for a valuation allowance against our deferred tax assets based on various factors including our historical earnings experience by taxing jurisdiction, and forecasts of future operating results and utilization of net operating losses and tax credits prior to their expiration. Significant judgment is required in making this assessment and, to the extent that a reversal of any portion of our valuation allowance against our deferred tax assets is deemed appropriate, a tax benefit will be recognized against our income tax provision in the period of such reversal. Prior to 2018, we recorded a valuation allowance that fully offset our deferred tax assets. In the fourth quarter of 2018, based on our evaluation of various factors, including our achievement of a cumulative three-year income position as of December 28, 2018 and forecasts of future operating results, we released substantially all of our valuation allowance against our deferred tax assets and recorded a corresponding income tax benefit as described in “Note 8. Income Taxes”, below. We continue to maintain a valuation allowance against our California state deferred tax assets.

We recognize tax benefits from uncertain tax positions only if it is more likely than not that the tax position will be sustained upon examination by the tax authorities based on the technical merits of the position. 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 Not Yet Adopted

In November 2018, the Financial Accounting Standards Board (the FASB) issued ASU No. 2018-18, Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606 (ASU 2018-18). ASU 2018-18 clarifies that certain transactions between collaborative arrangement participants should be accounted for as revenue under Topic 606 when the counterparty is a customer for a distinct good or service (i.e. a unit of account). For units of account that are in the scope of Topic 606, all of the guidance in Topic 606 should be applied, including the guidance on recognition, measurement, presentation and disclosure. ASU 2018-18 also adds a reference in Topic 808 to the unit of account guidance in ASC 606 and requires that it be applied only to assess whether transactions in a collaborative arrangement are in the scope of Topic 606. ASU 2018-18 will preclude entities from presenting amounts related to transactions with a counterparty in a collaborative arrangement that is not a customer as revenue from contracts with customers. ASU 2018-18 is effective for us for all interim and annual reporting periods beginning after December 15, 2019. Early adoption is permitted. We are in the process of assessing the impact of ASU 2018-18 on our Consolidated Financial Statements.

In August 2018, the FASB issued ASU No. 2018-15, Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer's Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract (ASU 2018-15). ASU 2018-15 aligns the requirements for capitalizing implementation costs incurred in a hosting arrangement that is a service contract with the requirements for capitalizing implementation costs incurred to develop or obtain internal-use software (and hosting arrangements that include an internal-use software license). Accordingly, ASU 2018-15 requires a customer in a hosting arrangement that is a service contract to follow the guidance in Subtopic 350-40 to determine which implementation costs to capitalize as an asset related to the service contract and which costs to expense. ASU 2018-15 also requires us to expense the capitalized implementation costs of a hosting arrangement that is a service contract over the term of the hosting arrangement, which includes reasonably certain renewals. ASU 2018-15 is effective for us for all interim and annual reporting periods beginning after December 15, 2019. Early adoption is permitted. We are in the process of assessing the impact of ASU 2018-15 on our Consolidated Financial Statements.

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.

Revenues

12 Months Ended

Dec. 28, 2018

Revenue from Contract with Customer [Abstract]

Revenues

REVENUES

Revenues by disaggregated category were as follows (in thousands):



	Year Ended December 31,
	2018			2017			2016
Product revenues:
Gross product revenues	$	738,529		$	402,569		$	151,499
Discounts and allowances	(119,250		)	(53,561		)	(16,124		)
Net product revenues	619,279			349,008			135,375
Collaboration revenues:
License revenues⁽¹⁾	192,188			96,637			56,286
Research and development service revenues⁽²⁾	39,501			8,737			—
Other collaboration revenues⁽³⁾	2,858			(1,905		)	(207		)
Total collaboration revenues	234,547			103,469			56,079
Total revenues	$	853,826		$	452,477		$	191,454

____________________

(1)

Upon the adoption of Topic 606 as of January 1, 2018, the allocation of proceeds from our collaboration partners, including upfront and milestone payments, between intellectual property licenses and research and development services as well as the resulting timing of recognition have changed. License revenues for the year ended December 31, 2018 included the immediate recognition of the portion of milestones that were allocated to the transfer of intellectual property licenses for those milestones for which it had become probable that a significant revenue reversal would not occur, as well as royalty revenues from Ipsen and Genentech. License revenues for the years ended December 31, 2017 and 2016 included the full recognition of substantive milestones achieved during the period, recognition of deferred revenues from upfront payments and a non-substantive milestone, which were being amortized over various periods, as well as royalty revenues from Ipsen and Genentech.

(2)

Research and development service revenues for the year ended December 31, 2018 included the recognition of deferred revenue for the portion of the upfront and milestone payments that have been allocated to the research and development service performance obligations which are being amortized through early 2030, as well as development cost reimbursements earned on our collaboration agreements. As described above, prior to the adoption of Topic 606, we did not allocate any of our upfront payments or milestones to research and development services; therefore, Research and development service revenues for the years ended December 31, 2017 included only development cost reimbursements earned on our collaboration agreements.

(3)

Other collaboration revenues for the year ended December 31, 2018 included royalties we paid to GSK on Ipsen’s sales of products containing cabozantinib, the profit on the U.S. commercialization of COTELLIC from Genentech and product supply revenues. Other collaboration revenues for the years ended years ended December 31, 2017 and 2016 included only royalties we paid to GSK on Ipsen’s sales of products containing cabozantinib and product supply revenues, as the profits and losses on the U.S. commercialization of COTELLIC for the period were included in Selling, general and administrative expenses.

During the year ended December 31, 2018, Net product revenues and License revenues related to goods and intellectual property licenses transferred at a point in time and Research and development services revenues related to services performed over time. License revenues and Research and development services revenues were recorded in accordance with Topic 606 during 2018 and Topic 605 in prior periods. Other collaboration revenues, which included royalties we paid to GSK on Ipsen’s sales of products containing cabozantinib, the profit on the U.S. commercialization of COTELLIC from Genentech and product supply revenue, were recorded in accordance with Topic 808 for all periods presented.

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



	Year Ended December 31,
	2018		2017		2016
CABOMETYX	$	599,946	$	324,000	$	93,481
COMETRIQ	19,333		25,008		41,894
Net product revenues	$	619,279	$	349,008	$	135,375

Total revenues disaggregated by significant customer were as follows (dollars in thousands):



	Year Ended December 31,
	2018				2017				2016
	Dollars		Percent of total		Dollars		Percent of total		Dollars		Percent of total
Ipsen	$	182,879	21	%	$	69,792	15	%	$	33,252	17	%
Caremark L.L.C.	110,698		13	%	73,921		16	%	17,746		9	%
Affiliates of McKesson Corporation	99,916		12	%	48,662		11	%	13,143		7	%
Accredo Health, Incorporated	81,028		9	%	50,716		11	%	16,631		9	%
Diplomat Specialty Pharmacy	74,244		9	%	83,059		18	%	63,826		33	%
Others, individually less than 10% of Total revenues for all periods presented	305,061		36	%	126,327		29	%	46,856		25	%
Total revenues	$	853,826	100	%	$	452,477	100	%	$	191,454	100	%

Total revenues disaggregated by geographic region were as follows (in thousands):



	Year Ended December 31,
	2018		2017		2016
U.S.	$	632,927	$	367,906	$	140,709
Europe	182,879		69,792		35,745
Rest of the world	38,020		14,779		15,000
Total revenues	$	853,826	$	452,477	$	191,454

Net product revenues are attributed to regions based on the ship-to location. Collaboration revenues are attributed to regions based on the location of our collaboration partners’ headquarters.

Product Sales Discounts and Allowances

The activities and ending reserve balances for each significant category of discounts and allowances (which constitute variable consideration) were as follows (in thousands):



	Chargebacks and Discounts for Prompt Payment			Other Customer Credits/Fees and Co-pay Assistance			Rebates			Returns			Total
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
Provision related to sales made in:
Current period	75,543			13,015			31,040			2			119,600
Prior periods	(403		)	206			(153		)	—			(350		)
Payments and customer credits issued	(74,746		)	(11,978		)	(24,741		)	(2		)	(111,467		)
Balance at December 31, 2018	$	2,322		$	3,038		$	11,916		$	—		$	17,276

Chargebacks and discounts for prompt payment are recorded as a reduction of Trade receivables, net and the remaining reserve balances are classified as Other current liabilities in the accompanying Consolidated Balance Sheets.

Contract Assets and Liabilities

We receive payments from our licensees based on billing schedules established in each contract. Amounts are recorded as accounts receivable when our right to consideration is unconditional. Upfront and milestone payments may require deferral of revenue recognition to a future period until we perform our obligations under these arrangements and are recorded as deferred revenue upon receipt or when due. We may also recognize revenue in advance of the contractual billing schedule and such amounts are recorded as unbilled collaboration revenue when recognized. Changes in our contract assets and liabilities under Topic 606 were as follows (in thousands):



	Contract Assets: Unbilled Collaboration Revenue						Contract Liabilities: Deferred Revenue
	Current Portion			Long-term Portion			Current Portion			Long-term Portion
Balance at December 31, 2017	$	—		$	—		$	31,984		$	238,520
Adoption of Topic 606	9,588			12,247			(23,591		)	(213,079		)
Balance at January 1, 2018	9,588			12,247			8,393			25,441
Increases as a result of a change in transaction price and recognition of revenues as services are performed	37,881			4,545			—			—
Transfer to receivables from contract assets recognized at the beginning of the period	(46,052		)	—			—			—
Increases as a result of the deferral of milestones achieved in period, excluding amounts recognized as revenue	—			—			1,718			7,237
Revenue recognized that was included in the contract liability balance at the beginning of the period	—			—			(8,683		)	—
Other adjustments ⁽¹⁾	(1,417		)	(16,792		)	(1,428		)	(16,781		)
Balance at December 31, 2018	$	—		$	—		$	—		$	15,897

____________________


(1)	Includes reclassification of deferred revenue from long-term to current and adjustments made due to netting of contract assets and liabilities by collaboration agreement.

During the year ended December 31, 2018, we recognized $198.1 million in revenues under Topic 606 for performance obligations satisfied in previous periods. Such revenues primarily related to milestone and royalty payments allocated to our license performance obligations of our collaborations with Ipsen and Daiichi Sankyo.

Collaboration Agreements

12 Months Ended

Dec. 28, 2018

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Collaboration Agreements

COLLABORATION AGREEMENTS

We have established multiple collaborations with leading pharmaceutical companies for the commercialization and further development of cabozantinib, as well as with smaller, discovery-focused biotechnology companies to expand our product pipeline. Additionally, in line with our business strategy prior to the commercialization of our first product, COMETRIQ, we entered into other collaborations with leading pharmaceutical companies including Genentech, Daiichi Sankyo, Merck & Co., Inc. (Merck) and Bristol-Myers Squibb Company (BMS) for other compounds and programs in our portfolio.

Under these collaborations, we are generally entitled to receive milestone and royalty payments, and for certain collaborations, payments for product supply services, development cost reimbursements, and/or profit sharing payments. See “Note 2. Revenues” for information on collaboration revenues recognized during the years ended December 31, 2018, 2017 and 2016.

Cabozantinib Commercial Collaborations

Ipsen Collaboration

Description of the 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.

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. A related 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. 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 were to terminate 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.

Consideration under the Collaboration

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. As of December 31, 2018, we have also achieved aggregate milestones of $275.0 million related to development, regulatory and commercial progress by Ipsen since the inception of the collaboration agreement, including $140.0 million in milestones recognized during 2018.

We are also eligible to receive future development and regulatory milestone payments from Ipsen, totaling an aggregate of $84.0 million upon additional approvals of cabozantinib in future indications and/or jurisdictions, as well as contingent payments of up to $519.5 million associated with sales-based milestones. We will further receive royalties on net sales of cabozantinib by Ipsen outside of the U.S. and Japan. We were initially entitled to receive a tiered royalty of 2% to 12% on the initial $150.0 million of net sales; this amount was reached in the second quarter of 2018. As of December 31, 2018 and going forward, we are entitled to receive a tiered royalty of 22% to 26% on annual net sales (with separate tiers for Canada); these 22% to 26% royalty tiers 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 to 26% on annual net sales; these 22% to 26% royalty tiers for Canada will also reset each calendar year.

Consistent with our historical agreement with GSK, we are required to pay a 3% royalty to GSK on all net sales of any product incorporating cabozantinib, including net sales by Ipsen.

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.

We are 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 to supply finished, labeled drug product to Ipsen for distribution in the territories outside of the U.S. and Japan for the term of the collaboration agreement. The product will be supplied at our cost, as defined in the agreement.

Revenues from the Collaboration

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



	Year Ended December 31,
	2018		2017		2016
Ipsen collaboration revenues	$	182,879	$	69,792	$	33,252

As of December 31, 2018, $48.0 million of the transaction price allocated to our research and development services performance obligation had not been satisfied. As of December 31, 2018, the net contract liability for the collaboration agreement with Ipsen was $13.3 million, which was included in Long-term portion of deferred revenue in the accompanying Consolidated Balance Sheets. See “—Performance Obligations and Transaction Prices for our Ipsen and Takeda Collaborations”, below, for additional information related to the revenue recognition for this collaboration.

Takeda Collaboration

Description of the Collaboration

In January 2017, we entered into a collaboration and license agreement with Takeda. Pursuant to this collaboration agreement, Takeda has exclusive commercialization rights for current and potential future cabozantinib indications in Japan, and the parties have agreed to collaborate on the clinical development of cabozantinib in Japan.

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.

Consideration under the Collaboration

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. During the year ended December 31, 2018, we also achieved a $10.0 million development related milestone.

As of December 31, 2018, we were eligible to receive development, regulatory and first-sale milestone payments of up to $90.0 million related to second-line RCC, first-line RCC and second-line HCC, as well as additional development, regulatory and first-sale milestone payments, without limit, for additional potential future indications. The collaboration agreement also provides that we are eligible to receive pre-specified payments of up to $83.0 million associated with sales volume milestones and 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 following this initial $300.0 million of net sales, we are then entitled to receive a tiered royalty of 20% to 30% on annual net sales thereafter; these 20% to 30% royalty tiers will reset each calendar year.

Consistent with our historical agreement with GSK, we are required to pay a 3% royalty to GSK on all net sales of any product incorporating cabozantinib, including net sales by Takeda.

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.

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 supply of cabozantinib to Takeda.

Revenues from the Collaboration

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



	Year Ended December 31,
	2018		2017
Takeda collaboration revenues	$	18,020	$	14,779

As of December 31, 2018, $25.6 million of the transaction price allocated to our research and development services performance obligation had not been satisfied. As of December 31, 2018, the net contract liability for the collaboration agreement with Takeda was $2.6 million, which was included in Long-term portion of deferred revenue in the accompanying Consolidated Balance Sheets.

Performance Obligations and Transaction Prices for our Ipsen and Takeda Collaborations

We identified two performance obligations for both the Ipsen and Takeda collaboration agreements: (1) the transfer of an exclusive license for the commercialization and further development of cabozantinib; and (2) research and development services, which includes certain committed studies for the development of cabozantinib, pharmacovigilance services and participation on various joint committees (as defined in the specific collaboration agreements).

We have allocated the transaction price for each of these collaborations, which are described below, to the identified performance obligations based on our best estimate of their relative standalone selling price. For the licenses, the estimate of the relative standalone selling price was determined using a discounted cash flow valuation utilizing forecasted revenues and costs, and a discount rate. For research and development services the estimate of the relative standalone selling price was determined using an adjusted market assessment approach that relies on internal and external costs and market factors.

The portion of the transaction price allocated to our license performance obligation are recorded immediately as our license represents functional intellectual property that was transferred at a point in time. The portion of the transaction price allocated to our research and development services performance obligation is being recognized as revenue using the inputs method based on our internal development projected cost estimates through the current estimated patent expiration of cabozantinib in the European Union (EU) for the Ipsen Collaboration and Japan for the Takeda Collaboration, both of which are early 2030.

Based on our evaluation of the collaboration agreements as of January 1, 2018, the date adoption of Topic 606, we determined that for both agreements, the up-front, nonrefundable payments, the milestones and royalties achieved as of December 31, 2017, and our estimate for the reimbursements of our research and development services performance obligation over the term of each agreement constituted the amount of the consideration to be included in the transaction price as of December 31, 2017. In addition, the transaction price for the Ipsen collaboration agreement included a $10.0 million milestone we expected to achieve during the three months ended March 31, 2018. Other than that $10.0 million milestone, variable consideration for both agreements related to regulatory and development milestones not previously recognized was constrained due to the fact that it was not probable that a significant reversal of cumulative revenue would not occur, given the inherent uncertainty of success with these milestones. Any variable consideration related to sales-based milestones and royalties will be recognized when the related sales occur as these amounts have been determined to relate to the relevant transferred license and therefore are recognized as the related sales occur.

We re-evaluate the transaction price for the collaboration agreements in each reporting period as uncertain events are resolved or other changes in circumstances occur and we allocate those changes in the transaction price between our performance obligations. During the year ended December 31, 2018, the transaction price increased as a result of the achievement of various milestones described above. We further updated the transaction price based upon the impact of research and development services performed during the period and changes in our estimated reimbursements for our future research and development services. The portion of the increase in transaction price that was allocated to the previously satisfied performance obligations for the transfer of an intellectual property license was recognized during the period and the portion allocated to research and development services will be recognized in future periods as those services are delivered through early 2030. As of December 31, 2018, variable consideration related to the remaining unearned regulatory and development milestones for both agreements remained constrained due to the fact that it was not probable that a significant reversal of cumulative revenue would not occur.

Cabozantinib Development Collaborations

BMS

In February 2017, we entered into a clinical trial collaboration agreement with BMS for the purpose of exploring the therapeutic potential of cabozantinib in combination with BMS’s immune checkpoint inhibitors (ICIs), nivolumab and/or ipilimumab, to treat a variety of types of cancer. As part of the collaboration, we are evaluating these combinations as treatment options for RCC and HCC in the CheckMate 9ER and CheckMate 040 trials, respectively.

Pursuant to the terms of the collaboration agreement with BMS, each party granted to the other a non-exclusive, worldwide (within the collaboration territory as defined in the collaboration agreement and its supplemental agreements), non-transferable, royalty-free license to use the other party’s compounds in the conduct of each clinical trial.

Each party will be responsible for supplying finished drug product for the applicable clinical trial and unless otherwise agreed between the parties, 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 for such study treatment arms and we will bear one-third of the costs. Unless earlier terminated, the 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. 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. Upon termination by either party, the licenses granted to each party to conduct a combined therapy trial will terminate.

The Roche Group (Roche) Collaboration

In February 2017, we entered into a master clinical supply agreement with Roche for the purpose of evaluating cabozantinib in combination with Roche’s ICI, atezolizumab, in locally advanced or metastatic solid tumors. As part of this agreement with Roche, in June 2017, we initiated COSMIC-021, a phase 1b trial evaluating the safety and tolerability of the combination in patients with locally advanced or metastatic tumors, and in December 2018, we initiated COSMIC-312, a phase 3 pivotal trial evaluating the combination versus sorafenib in previously untreated advanced HCC, with an exploratory arm also evaluating cabozantinib monotherapy in previously untreated advanced HCC. We are the trial sponsor, and Roche is providing atezolizumab free of charge.

GSK

In October 2002, we established a product development and commercialization collaboration agreement with GSK. Under the terms of the collaboration 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. Although the collaboration agreement was terminated during 2014, GSK continues to be entitled to a 3% royalty we are required to pay on all net sales of any product incorporating cabozantinib by us and our collaboration partners. Royalties accruing to GSK in connection with the sales of cabozantinib are included in Cost of goods sold for sales by us and as a reduction of Collaboration revenues for sales by Ipsen. Such royalties were as follows (in thousands):



	Year Ended December 31,
	2018		2017		2016
Royalties accruing to GSK	$	23,950	$	12,413	$	4,334

StemSynergy Therapeutics, Inc. (StemSynergy) Collaboration

In January 2018, we entered into an exclusive collaboration and license agreement with StemSynergy for the discovery and development of novel oncology compounds targeting Casein Kinase 1 alpha (CK1α), a component of the Wnt signaling pathway implicated in key oncogenic processes. Under the terms of the agreement, we will partner with StemSynergy to conduct preclinical and clinical studies with compounds targeting CK1α.

During the year ended December 31, 2018, we paid StemSynergy an upfront payment of $3.0 million in initial research and development funding and provided $1.2 million in additional research and development funding. StemSynergy is eligible for up to $2.3 million in additional such funding on an as needed basis. The research and development funding costs incurred to date were included in Research and development expenses in the accompanying Consolidated Statements of Operations.

StemSynergy will also be eligible for up to $56.5 million in milestones for the first product to emerge from the collaboration, including preclinical and clinical development and regulatory milestone payments, sales-based milestones, as well as single-digit royalties on worldwide sales. We will be solely responsible for the commercialization of products that arise from the collaboration.

Invenra, Inc. (Invenra) Collaboration

In May 2018, we entered into a collaboration and license agreement with Invenra, which is focused on developing next-generation biologics, to discover and develop multispecific antibodies for the treatment of cancer. Invenra is responsible for antibody lead discovery and generation while we will lead Investigational New Drug enabling studies, manufacturing, clinical development in single-agent and combination therapy regimens, and future regulatory and commercialization activities. The collaboration agreement also provides that we will receive an exclusive, worldwide license to one preclinical asset, and that we will pursue up to six additional discovery projects during the term of the collaboration, which in total are directed to three discovery programs.

In consideration for the exclusive worldwide license and other rights contained in the collaboration agreement, we paid Invenra an upfront payment of $2.0 million and a project initiation fee of $2.0 million during the year ended December 31, 2018. The payments were included in Research and development expenses in the accompanying Consolidated Statements of Operations. As of December 31, 2018, we also have the right to initiate five additional discovery projects for development subject to an upfront payment of $2.0 million for each project as well as additional global milestone payments and royalties for any products that arise from these discovery efforts. Invenra is eligible to receive payments based on the achievement of specific development and regulatory milestones of up to $131.5 million for a product containing the lead preclinical asset in the first indication and up to $127.5 million for a product developed from each addition project we initiate. Upon successful commercialization of a product, Invenra is eligible to receive global milestone payments up to $325.0 million per product if certain sales thresholds are achieved as well as single digit tiered royalties on net sales of the approved product.

Unless earlier terminated, the collaboration agreement has a term that continues, on a product-by-product and country-by-country basis, until the later of (i) ten years after the first commercial sale of such product in such country or (ii) expiration of patent claims covering the product in such country. We may terminate the collaboration agreement in its entirety or on a project-by-project, basis at any time prior to commercialization, for any or no reason, upon thirty days’ written notice to Invenra. The collaboration agreement also may be terminated by either party for a material breach by the other, subject to notice and cure provisions.

Other Collaborations

Genentech

Profits and losses on U.S. commercialization and Royalty revenues on ex-U.S. sales under the collaboration agreement with Genentech were as follows (in thousands):



	Year Ended December 31,
	2018		2017			2016
Profits and losses on U.S. commercialization	$	8,084	$	(2,140	)	$	8,771
Royalty revenues on ex-U.S. sales	$	5,564	$	6,398		$	2,827

Profits on the U.S. commercialization of COTELLIC for the year ended December 31, 2018 were included Collaboration revenues and profits and losses on for the years ended December 31, 2017 and 2016 were included in Selling, general and administrative expenses. The royalty revenues on ex-U.S. sales were included in Collaboration revenues for all periods presented. See “—Performance Obligations and Transaction Prices for our Other Collaborations”, below, for additional information related to revenue recognition for this collaboration.

In December 2006, we out-licensed the development and commercialization of cobimetinib to Genentech pursuant to a worldwide collaboration agreement. Cobimetinib is a reversible inhibitor of MEK, a kinase that is a component of the RAS/RAF/MEK/ERK pathway. Under the terms of the collaboration agreement, we developed cobimetinib through the determination of the maximum tolerated dose in a phase 1 clinical trial, and Genentech had the option to co-develop cobimetinib, an option that Genentech exercised, 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 the subsequent clinical development.

In November 2015, the U.S. Food and Drug Administration (FDA) approved cobimetinib, under the brand name COTELLIC, in combination with Genentech’s Zelboraf (vemurafenib) 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 allows for us to provide up to 25% of the total sales force for approved cobimetinib 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 review of the commercial landscape, commencing in January 2018, we and Genentech scaled back the personal promotion of COTELLIC in this indication in the U.S.

Cobimetinib Profit Sharing and Royalty Revenues

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 (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. We are not eligible for any additional milestone payments under the collaboration agreement with Genentech.

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.

Cobimetinib Clinical Development Program

Cobimetinib is being evaluated by Genentech in a development program consisting of more than 50 clinical trials. These trials are being sponsored by Genentech or through Genentech’s investigator sponsored trial program.

Daiichi Sankyo

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



	Year Ended December 31,
	2018		2017		2016
Daiichi Sankyo collaboration revenues	$	20,000	$	—	$	15,000

See “—Performance Obligations and Transaction Prices for our Other Collaborations”, below, for additional information related to revenue recognition for this collaboration.

In March 2006, we entered into a collaboration agreement with Daiichi Sankyo for the discovery, development and commercialization of novel therapies targeted against the 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 esaxerenone, an oral, non-steroidal, selective MR antagonist. Daiichi Sankyo is responsible for all further preclinical and clinical development, regulatory, manufacturing and commercialization activities for the compounds. In January 2019, subsequent to our year-end, Daiichi Sankyo received approval from the Japanese Ministry of Health, Labour and Welfare for MINNEBRO as a treatment for patients with hypertension.

We are eligible to receive additional development, regulatory and sales-based milestone payments of up to $110.0 million under this collaboration agreement, including a $20.0 million milestone payment upon the first arm’s-length sale of MINNEBRO in Japan. In addition, we are entitled to receive low double-digit royalties on sales of MINNEBRO. Daiichi Sankyo may terminate the agreement upon 90 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. In addition, pursuant to a license agreement we entered into with Ligand Pharmaceuticals, Inc. (Ligand), we are required to pay a royalty of 0.5% to Ligand on net sales of MINNEBRO.

Merck

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



	Year Ended December 31,
	2018		2017		2016
Merck collaboration revenues	$	—	$	—	$	5,000

See “—Performance Obligations and Transaction Price for our Other Collaborations”, below, for additional information related to revenue recognition for this collaboration.

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-δ) 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-δ program. Subsequent to December 31, 2018, we have been notified by Merck that they will be terminating their PI3K-δ program, including their development activities under this collaboration agreement. Upon the termination of the collaboration agreement by Merck, the license granted to Merck will terminate.

BMS - ROR Collaboration

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



	Year Ended December 31,
	2018		2017		2016
BMS collaboration revenues	$	—	$	12,500	$	—

See “—Performance Obligations and Transaction Prices for our Other Collaborations”, below, for additional information related to revenue recognition for this 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. Since July 2013, BMS has been solely responsible 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 sales-based 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.

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.

Performance Obligations and Transaction Prices for our Other Collaborations

We have evaluated our collaborations agreements with Genentech, Daiichi Sankyo, Merck and BMS and have determined that those collaboration agreements each have one performance obligation: the delivery of intellectual property licenses to the collaboration partner. We have further determined that the licenses we provided represent functional intellectual property that was transferred at a point in time, when the agreements were executed, prior to the adoption of Topic 606. Potential variable consideration for these collaborations related to regulatory and development milestones was constrained due to the fact that it was not probable that a significant reversal of cumulative revenue would not occur, given the inherent uncertainty of success with these milestones and therefore, any additional consideration earned and received from these collaborations will be fully recognized when the milestone is no longer constrained. Any variable consideration related to royalties and other sales-based milestones will be recognized when the related sales occur as these amounts have been determined to relate predominantly to the licenses transferred and therefore are recognized at the later of when the performance obligation is satisfied or the related sales occur.

Cash and Investments

12 Months Ended

Dec. 28, 2018

Investments, Debt and Equity Securities [Abstract]

Cash and Investments

CASH AND INVESTMENTS

Cash, Cash Equivalents and Restricted Cash

A reconciliation of Cash, cash equivalents, and restricted cash reported within our Consolidated Balance Sheets to the amount reported within the accompanying Consolidated Statements of Cash Flows was as follows (in thousands):



	December 31, 2018		December 31, 2017		December 31, 2016
Cash and cash equivalents	$	314,775	$	183,164	$	151,686
Restricted cash included in short-term restricted cash and investments	—		504		—
Restricted cash included in long-term restricted cash and investments	1,100		4,646		4,150
Cash, cash equivalents, and restricted cash as reported within the accompanying Consolidated Statements of Cash Flows	$	315,875	$	188,314	$	155,836

Restricted cash includes certificates of deposit used to collateralize letters of credit and, in prior periods, a purchasing card program.

Cash and Investments

Cash and investments by security type were as follows (in thousands):



	December 31, 2018
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Investments available-for-sale:
Money market funds	$	47,744	$	—	$	—		$	47,744
Commercial paper	381,134		—		(1		)	381,133
Corporate bonds	344,741		180		(857		)	344,064
U.S. Treasury and government sponsored enterprises	55,224		2		(25		)	55,201
Total investments available-for-sale	828,843		182		(883		)	828,142
Cash and restricted cash	6,883		—		—			6,883
Certificates of deposit	16,596		—		—			16,596
Total cash and investments	$	852,322	$	182	$	(883	)	$	851,621



	December 31, 2017
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Investments available-for-sale:
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 investments available-for-sale	440,756		18		(364		)	440,410
Cash and restricted cash	3,268		—		—			3,268
Certificates of deposit	13,498		—		—			13,498
Total cash and investments	$	457,522	$	18	$	(364	)	$	457,176

Gains and losses on the sales of investments available-for-sale were nominal or zero during the years ended December 31, 2018, 2017 and 2016.

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



	December 31, 2018
	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	$	236,162	$	(606	)	$	39,627	$	(251	)	$	275,789	$	(857	)
U.S. Treasury and government sponsored enterprises	28,105		(16		)	9,182		(9		)	37,287		(25		)
Commercial paper	7,091		(1		)	—		—			7,091		(1		)
Total	$	271,358	$	(623	)	$	48,809	$	(260	)	$	320,167	$	(883	)



	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	)

There were 199 and 134 investments in an unrealized loss position as of December 31, 2018 and 2017, respectively. During the years ended December 31, 2018, 2017 and 2016 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 investments available-for-sale by contractual maturity were as follows (in thousands):



	December 31,
	2018		2017
Maturing in one year or less	$	674,455	$	377,155
Maturing after one year through five years	153,687		63,255
Total investments available-for-sale	$	828,142	$	440,410

Other Cost Method Equity Investments

During the years ended December 31, 2018, 2017 and 2016, we recognized gains of $0.2 million, $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, net in the accompanying Consolidated Statements of Operations. We are eligible to earn additional such gains in the future as Allergan continues its development of XL335.

Related Party Transactions

During 2018, BlackRock, Inc. (BlackRock), a global provider of investment, advisory and risk management solutions, reported that their beneficial ownership increased to more than 10% of our outstanding common stock. BlackRock manages a portion of our cash and investments portfolio. As of December 31, 2018 and 2017, respectively, the fair value of cash and investments managed by BlackRock was $298.5 million and $141.0 million, which included $3.0 million and $1.0 million invested in the BlackRock Liquidity Money Market Fund. We incurred $0.2 million in fees for BlackRock advisory services performed during the year ended December 31, 2018.

Inventory

12 Months Ended

Dec. 28, 2018

Inventory Disclosure [Abstract]

Inventory

INVENTORY

Inventory consisted of the following (in thousands):



	December 31,
	2018		2017
Raw materials	$	1,922	$	498
Work in process	6,170		3,997
Finished goods	3,836		2,854
Total	$	11,928	$	7,349

Balance Sheet classification:
Inventory	$	9,838	$	6,657
Inventory included in Other long-term assets	2,090		692
Total	$	11,928	$	7,349

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 $1.1 million, $1.2 million and $0.5 million for the years ended December 31, 2018, 2017 and 2016, respectively.

Inventory expected to be used in production or sold in periods more than 12 months from the date presented is classified as Other long-term assets in the accompanying Consolidated Balance Sheets. As of both December 31, 2018 and 2017, the non-current portion of inventory consisted of a portion of our finished goods.

Property and Equipment

12 Months Ended

Dec. 28, 2018

Property, Plant and Equipment [Abstract]

Property and Equipment

PROPERTY AND EQUIPMENT

Property and equipment were as follows (in thousands):



	December 31, 2018			December 31, 2017
Leasehold improvements	$	33,941		$	4,715
Computer equipment and software	15,022			14,146
Furniture and fixtures	12,709			1,609
Laboratory equipment	5,668			5,959
Construction in progress	866			22,114
	68,206			48,543
Less: accumulated depreciation and amortization	(17,309		)	(22,800		)
Property and equipment, net	$	50,897		$	25,743

Depreciation expense was $4.9 million, $1.2 million and $1.0 million during the years ended December 31, 2018, 2017 and 2016, respectively.

In May 2017, we entered into the Lease for office and research facilities located at 1851, 1801, and 1751 Harbor Bay Parkway, Alameda, California (the Premises). The Lease was amended in October 2017 and June 2018 to increase the space leased to an aggregate of 134,765 square feet. For a description of the Lease, see “Note 11. Commitments.” In June 2018, we relocated our offices and research facilities to the Premises. Accordingly, we placed into service $46.3 million in related Leasehold improvements, Furniture and fixtures and Computer equipment and software, portions of which were included in Construction in progress at prior period ends.

Stock-based Compensation

12 Months Ended

Dec. 28, 2018

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

Stock-based Compensation

STOCK-BASED COMPENSATION

We allocated the stock-based compensation expense for our equity incentive plans and our 2000 Employee Stock Purchase Plan (ESPP) as follows (in thousands):



	Year Ended December 31,
	2018		2017		2016
Research and development	$	13,115	$	7,569	$	9,366
Selling, general and administrative	27,511		16,369		13,546
Total stock-based compensation	$	40,626	$	23,938	$	22,912

We have several equity incentive plans under which we granted stock options and RSUs to employees and directors. At December 31, 2018, 14,693,867 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 its outstanding 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 $2.2 million, $1.6 million, and $1.0 million for the years ended December 31, 2018, 2017 and 2016, respectively. As of December 31, 2018, we had 4,722,008 shares available for issuance under our ESPP. Pursuant to the ESPP, we issued 330,492 shares, 434,523 shares, and 559,936 shares of common stock at an average price per share of $15.74, $11.20 and $3.91 during the years ended December 31, 2018, 2017 and 2016, respectively. Cash received from purchases under the ESPP in the years ended December 31, 2018, 2017 and 2016 was $5.2 million, $4.9 million and $2.2 million, respectively.

We used a Monte Carlo simulation pricing model to value stock options that include market vesting conditions and a Black-Scholes Merton option pricing model to value other stock options and ESPP purchases. The weighted average grant-date fair value per share of stock options and ESPP purchases was as follows:



	Year Ended December 31,
	2018		2017		2016
Stock options	$	9.07	$	11.42	$	4.77
ESPP	$	6.40	$	6.00	$	2.17

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



	Year Ended December 31,
	2018		2017		2016
Stock options:
Risk-free interest rate	2.81	%	1.98	%	1.15	%
Dividend yield	—	%	—	%	—	%
Volatility	55	%	59	%	76	%
Expected life	4.4 years		4.5 years		4.4 years
ESPP:
Risk-free interest rate	1.93	%	1.09	%	0.55	%
Dividend yield	—	%	—	%	—	%
Volatility	53	%	58	%	65	%
Expected life	6 months		6 months		6 months

We considered our implied volatility and 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. The risk-free interest rate is based on U.S. Treasury rates with the same or similar term as the underlying award. Our dividend rate is based on historical experience and our investors’ current expectations.

The fair value of RSUs was based on the closing price of the underlying common stock on the date of grant.

Activity for stock options during the year ended December 31, 2018 was as follows (dollars in thousands, except per share amounts):



	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Stock options outstanding at December 31, 2017	22,208,446		$	6.83
Granted	3,238,473		$	19.40
Exercised	(2,466,579	)	$	4.90
Forfeited	(288,197	)	$	15.71
Expired	(18,081	)	$	20.64
Stock options outstanding at December 31, 2018	22,674,062		$	8.71	3.7 years	$	254,201
Exercisable at December 31, 2018	16,463,202		$	5.65	3.0 years	$	229,699

During the year ended December 31, 2018, in connection with our long-term incentive compensation program, we granted 308,365 stock options to our President and Chief Executive Officer that have a market vesting condition (PSOs). In addition to the standard service conditions included in our other stock options, these PSOs may not be exercised until, at any time after the grant date, the closing market price of a share of our Common Stock is equal to or greater than 125% of the per share exercise price of the PSO over a period of at least 30 consecutive calendar days. The stock-based compensation expense for the PSO is being recognized over the service period of the award, which commenced on the date of grant.

During the year ended December 31, 2016, 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 performance-based stock options vested during 2016 and we recognized $4.1 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 that year.

As of December 31, 2018, there was $48.0 million of unrecognized compensation expense related to our unvested stock options, including the PSOs described above. The compensation expense for the unvested stock options will be recognized over a weighted-average period of 2.5 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 2018 and the exercise prices, multiplied by the number of in-the-money options) that would have been received by the stock option holders had all stock option holders exercised their stock options on December 31, 2018. The total intrinsic value of stock options exercised on the dates of exercise was $39.1 million, $85.2 million and $50.0 million during the years ended December 31, 2018, 2017 and 2016, respectively. Cash received from option exercises during the years ended December 31, 2018, 2017 and 2016 was $12.1 million, $17.6 million and $25.3 million, respectively. The total estimated fair value of stock options vested and recorded as expense during the years ended December 31, 2018, 2017 and 2016 was $18.9 million, $13.1 million and $13.4 million, respectively.

Activity for RSUs during the year ended December 31, 2018 was as follows (dollars in thousands, except per share amounts):



	Shares		Weighted Average Grant Date Fair Value		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
RSUs outstanding at December 31, 2017	3,762,990		$	17.76
Awarded	2,519,425		$	18.46
Vested and released	(1,081,339	)	$	16.05
Forfeited	(343,742	)	$	18.99
RSUs outstanding at December 31, 2018	4,857,334		$	18.42	2.1 years	$	94,427

During the year ended December 31, 2018, in connection with our long-term incentive compensation program, we awarded 693,131 RSUs that will vest upon the achievement of certain product revenue, late-stage clinical development and pipeline expansion performance targets (PSUs). These PSUs are included in the RSU activity table presented above. The PSUs were designed to drive the performance of our management team toward the achievement of key corporate objectives and will be forfeited if the performance targets are not met by December 31, 2021. Expense recognition for PSUs commences when the attainment of the performance goal is determined by management to be probable. During the year ended December 31, 2018, we did not recognize any compensation expense related to these PSUs. As of December 31, 2018, the total unrecognized compensation expense related to the unvested PSUs was $12.7 million. There were no performance-based RSUs issued prior to 2018.

As of December 31, 2018, there was $81.8 million of unrecognized compensation expense related to our unvested RSUs, including the PSUs described above. The compensation expense for the unvested RSUs will be recognized over a weighted-average period of 3.1 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. During 2018, we made matching contributions in the form of our common stock of 100% of the first $8,500 of each participant’s contributions into the 401(k) Plan. We recorded compensation expense related to the stock match of $3.6 million, $1.7 million, and $1.1 million for the years ended December 31, 2018, 2017 and 2016, respectively. As of December 31, 2018, 571,674 shares were available for issuance under the 401(k) Plan.

Income Taxes

12 Months Ended

Dec. 28, 2018

Income Tax Disclosure [Abstract]

Income Taxes

INCOME TAXES

Our income (loss) before income taxes is derived solely from within the U.S. The Income tax benefit (provision) was as follows (in thousands):



	Year Ended December 31,
	2018			2017			2016
Current:
Federal	$	—		$	—		$	—
State	(6,133		)	(4,350		)	—
Total current tax expense	(6,133		)	(4,350		)	—
Deferred:
Federal	238,675			—			—
State	5,436			—			—
Total deferred tax expense	244,111			—			—
Income tax benefit (provision)	$	237,978		$	(4,350	)	$	—

The income tax benefit for the year ended December 31, 2018 primarily relates to the release of our valuation allowance against significantly all of our deferred tax assets offset by state taxes in jurisdictions outside of California, for which we do not have net operating loss carryforwards due to a limited operating history. Our historical net operating losses are sufficient to fully offset any federal taxable income. The Income tax provision for the year ended December 31, 2017, related to state taxes in jurisdictions outside of California, for which we do not have net operating loss carryforwards due to a limited operating history.

The reconciliation of the U.S. federal income tax (provision) benefit at the statutory federal income tax rates of 21%, 34% and 34% for the years ended December 31, 2018, 2017 and 2016, respectively, to our Income tax benefit (provision) was as follows (in thousands):



	Year Ended December 31,
	2018			2017			2016
U.S. federal income tax (provision) benefit at statutory rate	$	(94,939	)	$	(53,916	)	$	23,876
State tax expense	(4,690		)	(8,282		)	(6,520		)
Change in valuation allowance	315,394			34,266			(6,377		)
Research credits	18,308			—			—
Stock-based compensation	5,998			20,548			(3,155		)
Non-deductible interest	—			(1,367		)	(2,680		)
Debt extinguishment	—			—			(4,726		)
Other	(2,093		)	4,401			(418		)
Income tax benefit (provision)	$	237,978		$	(4,350	)	$	—

Deferred tax assets and liabilities reflect the net tax effects of net operating loss and tax credit carryforwards 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,
	2018			2017
Deferred tax assets:
Net operating loss carryforwards	$	146,701		$	244,205
Tax credit carryforwards	98,467			66,770
Book over tax depreciation and amortization	29,929			39,472
Amortization of deferred stock compensation – non-qualified	11,366			8,966
Accruals and reserves not currently deductible	10,425			4,914
Deferred revenue	5,474			53,543
Other assets	1,140			1,088
Total deferred tax assets	303,502			418,958
Valuation allowance	(58,112		)	(418,958		)
Net deferred tax assets	245,390			—
Deferred tax liabilities:
Operating lease right-of-use assets	(1,279		)	—
Total deferred tax liabilities	(1,279		)	—
Net deferred taxes	$	244,111		$	—

We applied the guidance in the Securities and Exchange Commission’s Staff Accounting Bulletin No. 118, Income Tax Accounting Implications of the Tax Cuts and Jobs Act, when accounting for the enactment-date effects of the Tax Cuts and Jobs Act in 2017 and throughout 2018. At December 31, 2017, we had not completed our accounting for all the enactment-date income tax effects of the Tax Cuts and Jobs Act for Section 162(m) related to the deduction limitation for the remuneration of certain employees. As of December 31, 2018, we have now completed our accounting for all of the enactment-date income tax effects of the Tax Cuts and Jobs Act and the impact was not material.

ASC Topic 740: Income Taxes (Topic 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. As of each reporting date, management considers new evidence, both positive and negative, that could affect its view of the future realization of deferred tax assets. As of December 31, 2018, based on the evaluation and weighting of both positive and negative evidence, including our achievement of a cumulative three-year income position as of December 31, 2018 and forecasts of future operating results, as well as considering the utilization of net operating losses and tax credits prior to their expiration, management determined that there is sufficient positive evidence to conclude that it is more likely than not the deferred tax assets of $244.1 million are realizable and the valuation allowance was reduced accordingly. As of December 31, 2018, we continue to carry a valuation allowance of $58.1 million against our California state deferred tax assets. Prior to December 31, 2018, because of our history of operating losses, management believed that recognition of the deferred tax assets was not more likely than not (as defined in Topic 740) to be realized and, accordingly, had provided a full valuation allowance. The valuation allowance decreased by $360.8 million and $210.1 million during 2018 and 2017, respectively.

At December 31, 2018, we had federal net operating loss carryforwards of approximately $614 million which expire in the years 2031 through 2036, and federal business tax credits of approximately $102 million which expire in the years 2021 through 2038. We also had state net operating loss carryforwards of approximately $453 million, which expire in the years 2028 through 2036, and California research and development tax credits of approximately $34 million, which do not expire.

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 carryforwards 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 carryforwards before utilization. We completed a Section 382 study through December 31, 2018, and concluded that an ownership change, as defined under Section 382, had not occurred.

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



	Year Ended December 31,
	2018			2017			2016
Beginning balance	$	79,342		$	61,809		$	88,638
Change relating to prior year provision	(4,254		)	247			(29,110		)
Change relating to current year provision	1,083			17,378			2,304
Reductions based on the lapse of the applicable statutes of limitations	(111		)	(92		)	(23		)
Ending balance	$	76,060		$	79,342		$	61,809

We do not anticipate that the amount of unrecognized tax benefits existing as of December 31, 2018 will significantly change over the next 12 months. As of December 31, 2018, we had $76.1 million in unrecognized tax benefits, of which $46.0 million would reduce our income tax provision and the effective tax rate, if recognized. Interest and penalties were nominal or zero for all periods presented. We have elected to record interest and penalties in the accompanying Consolidated Statements of Operations as a component of income taxes.

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 2018 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. 28, 2018

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,
	2018		2017			2016
Numerator:
Net income (loss)	$	690,070	$	154,227		$	(70,222	)
Net income allocated to participating securities	—		(367		)	—
Net income (loss) allocable to common stock for basic net income (loss) per share	690,070		153,860			(70,222		)
Adjustment to net income allocated to participating securities	—		22			—
Net income (loss) allocable to common stock for diluted net income (loss) per share	$	690,070	$	153,882		$	(70,222	)
Denominator:
Weighted-average shares of common stock outstanding used in computing basic net income (loss) per share	297,892		293,588			250,531
Dilutive securities	14,911		18,415			—
Weighted-average shares of common stock outstanding and dilutive securities used in computing diluted net income (loss) per share	312,803		312,003			250,531

Net income (loss) per share, basic	$	2.32	$	0.52		$	(0.28	)
Net income (loss) per share, diluted	$	2.21	$	0.49		$	(0.28	)

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



	Year Ended December 31,
	2018	2017	2016
Outstanding stock options, unvested RSUs and ESPP contributions	3,968	1,645	27,568
Secured Convertible Notes due 2018 held by entities associated with Deerfield Management Company, L.P. (Deerfield Notes)	—	—	33,890
2014 Warrants	—	—	1,000
Total	3,968	1,645	62,458

The Deerfield Notes were repaid in June 2017. Warrants to purchase an aggregate of 1,000,000 shares of our common stock issued in January 2014 (2014 Warrants) were participating securities. The warrant holders did not have a contractual obligation to share in our losses. The 2014 Warrants were fully exercised in September 2017.

Fair Value Measurements

12 Months Ended

Dec. 28, 2018

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 was as follows (in thousands):



	December 31, 2018
	Level 1		Level 2		Total
Money market funds	$	47,744	$	—	$	47,744
Commercial paper	—		381,133		381,133
Corporate bonds	—		344,064		344,064
U.S. Treasury and government sponsored enterprises	—		55,201		55,201
Total investments available-for-sale	47,744		780,398		828,142
Certificates of deposit	—		16,596		16,596
Total financial assets carried at fair value	$	47,744	$	796,994	$	844,738



	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 investments available-for-sale	45,478		394,932		440,410
Certificates of deposit	—		13,498		13,498
Total financial assets carried at fair value	$	45,478	$	408,430	$	453,908

We did not have any financial liabilities measured and recorded at fair value on a recurring basis as of December 31, 2018 or December 31, 2017. We did not have any financial assets or liabilities classified as Level 3 in the fair value hierarchy as of December 31, 2018 or December 31, 2017. There were no transfers of financial assets or liabilities between Levels 1, 2 and 3 during the years ended December 31, 2018 or 2017.

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.

See “Note 11. Commitments” regarding the determination of the amount of our operating lease liabilities as of December 31, 2018. Our remaining financial assets and liabilities include cash and restricted cash, Trade receivables, net, Other receivables, Accounts payable, Accrued compensation and benefits, Accrued clinical trial liabilities, Accrued collaboration liabilities, Rebates and fees due to customers and other current and long-term liabilities. Those financial assets and liabilities are carried at cost which approximates their fair values.

- 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. 28, 2018

Commitments and Contingencies Disclosure [Abstract]

Commitments

COMMITMENTS

Leases

As described further in “Note 1. Organization and Summary of Significant Accounting Policies”, we adopted Topic 842 as of January 1, 2018. Prior period amounts have not been adjusted and continue to be reported in accordance with our historic accounting under Topic 840.

In May 2017, we entered into the Lease with Ascentris for office and research facilities located at the Premises in Alameda, California. The Lease was amended in October 2017 and June 2018 to increase the space leased to an aggregate of 134,765 square feet. We have made certain tenant improvements to the space leased on the Premises, for which we received $8.2 million in reimbursements in January 2019. The Lease’s initial term is through January 31, 2028. Rent payments began February 1, 2018, following the conclusion of a partial twelve-month rent abatement period. 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; none of these optional periods have been considered in the determination of the right-of-use asset or the lease liability for the Lease as we did not consider it reasonably certain that we would exercise any such options. The Lease further provides that we are obligated to pay to Ascentris certain variable 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 at 1601, 1701 and 1751 Harbor Bay Parkway, Alameda, California over the remainder of the initial term of the Lease at a market rate determined pursuant to the Lease.

We had an additional operating lease which expired in July 2018 for two buildings in South San Francisco, California with a total area of 116,063 square feet.

We have performed an evaluation of our other contracts with customers and suppliers in accordance with Topic 842 and have determined that, except for the leases described above, a nominal operating lease for space at a data center to house our data servers and a nominal financing lease for office equipment, none of our contracts contain a lease.

The balance sheet classification of our lease liabilities was as follows (in thousands):



	December 31, 2018		December 31, 2017
Operating lease liabilities:
Current portion included in Other current liabilities	$	2,738	$	540
Long-term portion of lease liabilities	12,099		408
Total operating lease liabilities	14,837		948
Financing lease liabilities:
Financing obligation for build-to-suit lease	—		14,530
Current portion included in Other current liabilities	49		—
Long-term portion of lease liabilities	79		—
Total financing lease liabilities	128		14,530
Total lease liabilities	$	14,965	$	15,478

The components of lease costs, which were included in Operating expenses in our Consolidated Statements of Operations, were as follows (in thousands):



	Year Ended December 31,
	2018		2017			2016
Operating lease cost	$	4,189	$	3,944		$	8,620
Variable lease cost	1,661		2,216			1,056
Sublease income	—		(1,225		)	(3,553		)
Total lease costs	$	5,850	$	4,935		$	6,123

Cash paid for amounts included in the measurement of lease liabilities for the year ended December 31, 2018 was $3.9 million and was included in Net cash provided by operating activities in our Consolidated Statements of Cash Flows.

As of December 31, 2018, the maturities of our operating lease liabilities were as follows (in thousands):



	Operating leases
Years ending December 31,
2019	$	2,794
2020	2,823
2021	2,904
2022	3,000
2023	3,082
Thereafter	13,584
Total lease payments	28,187
Less:
Present value adjustment	(5,180		)
Tenant improvement reimbursements	(8,170		)
Operating lease liabilities	$	14,837

Operating lease liabilities are based on the net present value of the remaining lease payments over the remaining lease term. In determining the present value of lease payments, we use our incremental borrowing rate based on the information available at the lease commencement date. As of December 31, 2018, the weighted average remaining lease term is 9.0 years and the weighted average discount rate used to determine the operating lease liability was 4.50%.

Letters of Credit and Restricted Cash

We have obtained two standby letters of credit related to the Lease with Ascentris with a combined credit limit of $1.0 million as of both December 31, 2018 and 2017. We have also obtained standby letters of credit related to a workers compensation insurance policy with credit limits of $0.1 million and $0.6 million as of December 31, 2018 and 2017, respectively. We had also previously obtained a standby letter of credit related to our South San Francisco lease with a credit limit of $0.5 million as of December 31, 2017 which was released during 2018. As of December 31, 2018, none of our letters of credit have been drawn upon. All of the letters of credit are fully collateralized by certificates of deposit. The certificate of deposits used to collateralize the standby letters of credit were included in short-term and long-term restricted cash and investments.

We were previously required to provide collateral as part of an employee purchasing card program. The collateral requirement for the purchase card program at December 31, 2017 was $3.0 million. During 2018 we were notified that we had been released from this collateral requirement. The collateral was invested in certificates of deposit which were included in long-term restricted cash and investments.

Quarterly Financial Data (Unaudited)

12 Months Ended

Dec. 28, 2018

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,
2018:
Total revenues ⁽¹⁾	$	228,602	$	225,397	$	186,108	$	213,719
Gross profit ⁽²⁾	$	168,873	$	155,586	$	139,839	$	128,633
Income from operations	$	111,602	$	125,176	$	85,770	$	116,307
Net income	$	360,089	$	126,630	$	87,494	$	115,857
Net income per share, basic	$	1.20	$	0.42	$	0.29	$	0.39
Net income per share, diluted	$	1.15	$	0.41	$	0.28	$	0.37
2017:
Total revenues	$	120,072	$	152,510	$	99,008	$	80,887
Gross profit ⁽²⁾	$	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

____________________

(1)

Total revenues for the three months ended March 31, 2018 have been adjusted to reflect the reclassification of the $1.4 million profit related to the profit sharing arrangement with Genentech for the commercialization of COTELLIC. For three months ended March 31, 2018, the net profit had been classified as Selling, general and administrative expenses as we were expecting an overall loss for the year ended December 31, 2018. During the three months ended June 30, 2018, we determined that the U.S. commercialization of COTELLIC would result in a profit for the year ended December 31, 2018 and therefore, we reclassified the profit for the three months ended March 31, 2018 from Selling, general and administrative expenses to Collaboration revenues to be consistent with presentation for the three and six months ended June 30, 2018. See “Note 3. Collaboration Agreements” for more information on our collaboration agreement with Genentech.


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

Organization and Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 28, 2018

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Basis of Consolidation

Basis of Presentation

Segment Information

Use of Estimates

Recently Adopted Accounting Pronouncements and Recent Accounting Pronouncements Not Yet Adopted

Recently Adopted Accounting Pronouncements

Restricted Cash

Revenue

Leases

Impact of Adoption of Topic 606 and Topic 842

The impact of the adoption of Topic 606 and Topic 842 on the accompanying Consolidated Balance Sheet as of January 1, 2018 was as follows (in thousands):



	December 31, 2017			Adjustments Due to the Adoption of Topic 606			Adjustments Due to the Adoption of Topic 842			January 1, 2018
Contract assets: unbilled collaboration revenue, gross:
Current portion	$	—		$	9,588		$	—		$	9,588
Long-term portion	$	—		$	12,247		$	—		$	12,247
Other receivables	$	3,892		$	—		$	7,743		$	11,635
Property and equipment, net	$	25,743		$	—		$	(14,530	)	$	11,213
Operating lease right-of-use assets	$	—		$	—		$	8,579		$	8,579
Contract liabilities: deferred revenue, gross:
Current portion	$	31,984		$	(23,591	)	$	—		$	8,393
Long-term portion	$	238,520		$	(213,079	)	$	—		$	25,441
Operating lease liabilities:
Other current liabilities⁽¹⁾	$	16,150		$	—		$	3,173		$	19,323
Long-term portion of lease liabilities ⁽²⁾	$	14,938		$	—		$	(1,615	)	$	13,323
Accumulated deficit	$	(1,829,172	)	$	258,505		$	234		$	(1,570,433	)

____________________

(1) Includes deferred rent and current portion of operating lease liabilities.

(2) Long-term portion of operating lease liabilities and Financing obligation for build-to-suit lease.

The impact of the adoption of Topic 606 and Topic 842 on the accompanying Consolidated Statements of Operations for year ended December 31, 2018 was as follows (in thousands):



	Year Ended December 31, 2018
	As Reported		Effect of Adoption of Topic 606 Higher / (Lower)			Effect of Adoption of Topic 842 Higher / (Lower)			Balances Without the Adoption of Topic 606 or 842
Collaboration revenues	$	234,547	$	(35,882	)	$	—		$	270,429
Total revenues	$	853,826	$	(35,882	)	$	—		$	889,708
Selling, general and administrative expenses	$	206,366	$	—		$	1,204		$	205,162
Total operating expenses	$	414,971	$	—		$	1,204		$	413,767
Interest expense	$	—	$	—		$	(631	)	$	(631	)
Total other income (expense), net	$	13,237	$	—		$	631		$	12,606
Income before income taxes	$	452,092	$	(35,882	)	$	(573	)	$	488,547
Income tax benefit (provision)	$	237,978	$	(48,325	)	$	73		$	286,230
Net income	$	690,070	$	(84,207	)	$	(500	)	$	774,777
Net income per share, basic	$	2.32	$	(0.28	)	$	—		$	2.60
Net income per share, diluted	$	2.21	$	(0.27	)	$	—		$	2.48

Recent Accounting Pronouncements Not Yet Adopted

Cash

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 in 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.

Revenue

Net Product Revenues

Product Sales Discounts and Allowances

Collaboration Revenues

Cost of Goods Sold

Contract Assets and Liabilities

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
Lab equipment		5 years
Furniture and fixtures		7 years
Office equipment		5 years
Computer equipment and software		3 years
Leasehold improvements		7 to 15 years

Goodwill

Long-Lived Assets

Research and Development Expenses

Leases

Stock-Based Compensation

Foreign Currency Translation and Remeasurement

Income Taxes

Organization and Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 28, 2018

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Impact of Adoption of Topic 606 and Topic 842

The impact of the adoption of Topic 606 and Topic 842 on the accompanying Consolidated Balance Sheet as of January 1, 2018 was as follows (in thousands):



	December 31, 2017			Adjustments Due to the Adoption of Topic 606			Adjustments Due to the Adoption of Topic 842			January 1, 2018
Contract assets: unbilled collaboration revenue, gross:
Current portion	$	—		$	9,588		$	—		$	9,588
Long-term portion	$	—		$	12,247		$	—		$	12,247
Other receivables	$	3,892		$	—		$	7,743		$	11,635
Property and equipment, net	$	25,743		$	—		$	(14,530	)	$	11,213
Operating lease right-of-use assets	$	—		$	—		$	8,579		$	8,579
Contract liabilities: deferred revenue, gross:
Current portion	$	31,984		$	(23,591	)	$	—		$	8,393
Long-term portion	$	238,520		$	(213,079	)	$	—		$	25,441
Operating lease liabilities:
Other current liabilities⁽¹⁾	$	16,150		$	—		$	3,173		$	19,323
Long-term portion of lease liabilities ⁽²⁾	$	14,938		$	—		$	(1,615	)	$	13,323
Accumulated deficit	$	(1,829,172	)	$	258,505		$	234		$	(1,570,433	)

____________________

(1) Includes deferred rent and current portion of operating lease liabilities.

(2) Long-term portion of operating lease liabilities and Financing obligation for build-to-suit lease.

The impact of the adoption of Topic 606 and Topic 842 on the accompanying Consolidated Statements of Operations for year ended December 31, 2018 was as follows (in thousands):



	Year Ended December 31, 2018
	As Reported		Effect of Adoption of Topic 606 Higher / (Lower)			Effect of Adoption of Topic 842 Higher / (Lower)			Balances Without the Adoption of Topic 606 or 842
Collaboration revenues	$	234,547	$	(35,882	)	$	—		$	270,429
Total revenues	$	853,826	$	(35,882	)	$	—		$	889,708
Selling, general and administrative expenses	$	206,366	$	—		$	1,204		$	205,162
Total operating expenses	$	414,971	$	—		$	1,204		$	413,767
Interest expense	$	—	$	—		$	(631	)	$	(631	)
Total other income (expense), net	$	13,237	$	—		$	631		$	12,606
Income before income taxes	$	452,092	$	(35,882	)	$	(573	)	$	488,547
Income tax benefit (provision)	$	237,978	$	(48,325	)	$	73		$	286,230
Net income	$	690,070	$	(84,207	)	$	(500	)	$	774,777
Net income per share, basic	$	2.32	$	(0.28	)	$	—		$	2.60
Net income per share, diluted	$	2.21	$	(0.27	)	$	—		$	2.48

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
Lab equipment		5 years
Furniture and fixtures		7 years
Office equipment		5 years
Computer equipment and software		3 years
Leasehold improvements		7 to 15 years

Revenues (Tables)

12 Months Ended

Dec. 28, 2018

Revenue from Contract with Customer [Abstract]

Disaggregation of Revenue

Revenues by disaggregated category were as follows (in thousands):



	Year Ended December 31,
	2018			2017			2016
Product revenues:
Gross product revenues	$	738,529		$	402,569		$	151,499
Discounts and allowances	(119,250		)	(53,561		)	(16,124		)
Net product revenues	619,279			349,008			135,375
Collaboration revenues:
License revenues⁽¹⁾	192,188			96,637			56,286
Research and development service revenues⁽²⁾	39,501			8,737			—
Other collaboration revenues⁽³⁾	2,858			(1,905		)	(207		)
Total collaboration revenues	234,547			103,469			56,079
Total revenues	$	853,826		$	452,477		$	191,454

____________________

(1)

(2)

(3)

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



	Year Ended December 31,
	2018		2017		2016
CABOMETYX	$	599,946	$	324,000	$	93,481
COMETRIQ	19,333		25,008		41,894
Net product revenues	$	619,279	$	349,008	$	135,375

Total revenues disaggregated by significant customer were as follows (dollars in thousands):



	Year Ended December 31,
	2018				2017				2016
	Dollars		Percent of total		Dollars		Percent of total		Dollars		Percent of total
Ipsen	$	182,879	21	%	$	69,792	15	%	$	33,252	17	%
Caremark L.L.C.	110,698		13	%	73,921		16	%	17,746		9	%
Affiliates of McKesson Corporation	99,916		12	%	48,662		11	%	13,143		7	%
Accredo Health, Incorporated	81,028		9	%	50,716		11	%	16,631		9	%
Diplomat Specialty Pharmacy	74,244		9	%	83,059		18	%	63,826		33	%
Others, individually less than 10% of Total revenues for all periods presented	305,061		36	%	126,327		29	%	46,856		25	%
Total revenues	$	853,826	100	%	$	452,477	100	%	$	191,454	100	%

Total revenues disaggregated by geographic region were as follows (in thousands):



	Year Ended December 31,
	2018		2017		2016
U.S.	$	632,927	$	367,906	$	140,709
Europe	182,879		69,792		35,745
Rest of the world	38,020		14,779		15,000
Total revenues	$	853,826	$	452,477	$	191,454

Activities and Ending Reserve Balances for Significant Categories of Discounts and Allowances

The activities and ending reserve balances for each significant category of discounts and allowances (which constitute variable consideration) were as follows (in thousands):



	Chargebacks and Discounts for Prompt Payment			Other Customer Credits/Fees and Co-pay Assistance			Rebates			Returns			Total
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
Provision related to sales made in:
Current period	75,543			13,015			31,040			2			119,600
Prior periods	(403		)	206			(153		)	—			(350		)
Payments and customer credits issued	(74,746		)	(11,978		)	(24,741		)	(2		)	(111,467		)
Balance at December 31, 2018	$	2,322		$	3,038		$	11,916		$	—		$	17,276

Revenue

Net Product Revenues

Product Sales Discounts and Allowances

Collaboration Revenues

Cost of Goods Sold

Contract Assets and Liabilities

Contract Assets and Liabilities under Topic 606

Changes in our contract assets and liabilities under Topic 606 were as follows (in thousands):



	Contract Assets: Unbilled Collaboration Revenue						Contract Liabilities: Deferred Revenue
	Current Portion			Long-term Portion			Current Portion			Long-term Portion
Balance at December 31, 2017	$	—		$	—		$	31,984		$	238,520
Adoption of Topic 606	9,588			12,247			(23,591		)	(213,079		)
Balance at January 1, 2018	9,588			12,247			8,393			25,441
Increases as a result of a change in transaction price and recognition of revenues as services are performed	37,881			4,545			—			—
Transfer to receivables from contract assets recognized at the beginning of the period	(46,052		)	—			—			—
Increases as a result of the deferral of milestones achieved in period, excluding amounts recognized as revenue	—			—			1,718			7,237
Revenue recognized that was included in the contract liability balance at the beginning of the period	—			—			(8,683		)	—
Other adjustments ⁽¹⁾	(1,417		)	(16,792		)	(1,428		)	(16,781		)
Balance at December 31, 2018	$	—		$	—		$	—		$	15,897

____________________


(1)	Includes reclassification of deferred revenue from long-term to current and adjustments made due to netting of contract assets and liabilities by collaboration agreement.

Collaboration Agreements (Tables)

12 Months Ended

Dec. 28, 2018

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Schedule of Collaborative Revenues Under Collaboration Agreement

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



	Year Ended December 31,
	2018		2017		2016
Ipsen collaboration revenues	$	182,879	$	69,792	$	33,252

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



	Year Ended December 31,
	2018		2017		2016
Merck collaboration revenues	$	—	$	—	$	5,000

Profits and losses on U.S. commercialization and Royalty revenues on ex-U.S. sales under the collaboration agreement with Genentech were as follows (in thousands):



	Year Ended December 31,
	2018		2017			2016
Profits and losses on U.S. commercialization	$	8,084	$	(2,140	)	$	8,771
Royalty revenues on ex-U.S. sales	$	5,564	$	6,398		$	2,827

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



	Year Ended December 31,
	2018		2017		2016
BMS collaboration revenues	$	—	$	12,500	$	—

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



	Year Ended December 31,
	2018		2017		2016
Daiichi Sankyo collaboration revenues	$	20,000	$	—	$	15,000

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



	Year Ended December 31,
	2018		2017
Takeda collaboration revenues	$	18,020	$	14,779

Such royalties were as follows (in thousands):



	Year Ended December 31,
	2018		2017		2016
Royalties accruing to GSK	$	23,950	$	12,413	$	4,334

Cash and Investments (Tables)

12 Months Ended

Dec. 28, 2018

Investments, Debt and Equity Securities [Abstract]

Reconciliation of Cash, Cash Equivalents, and Restricted Cash



	December 31, 2018		December 31, 2017		December 31, 2016
Cash and cash equivalents	$	314,775	$	183,164	$	151,686
Restricted cash included in short-term restricted cash and investments	—		504		—
Restricted cash included in long-term restricted cash and investments	1,100		4,646		4,150
Cash, cash equivalents, and restricted cash as reported within the accompanying Consolidated Statements of Cash Flows	$	315,875	$	188,314	$	155,836

Reconciliation of Cash, Cash Equivalents, and Restricted Cash



	December 31, 2018		December 31, 2017		December 31, 2016
Cash and cash equivalents	$	314,775	$	183,164	$	151,686
Restricted cash included in short-term restricted cash and investments	—		504		—
Restricted cash included in long-term restricted cash and investments	1,100		4,646		4,150
Cash, cash equivalents, and restricted cash as reported within the accompanying Consolidated Statements of Cash Flows	$	315,875	$	188,314	$	155,836

Investments by Security Type

Cash and investments by security type were as follows (in thousands):



	December 31, 2018
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Investments available-for-sale:
Money market funds	$	47,744	$	—	$	—		$	47,744
Commercial paper	381,134		—		(1		)	381,133
Corporate bonds	344,741		180		(857		)	344,064
U.S. Treasury and government sponsored enterprises	55,224		2		(25		)	55,201
Total investments available-for-sale	828,843		182		(883		)	828,142
Cash and restricted cash	6,883		—		—			6,883
Certificates of deposit	16,596		—		—			16,596
Total cash and investments	$	852,322	$	182	$	(883	)	$	851,621



	December 31, 2017
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Investments available-for-sale:
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 investments available-for-sale	440,756		18		(364		)	440,410
Cash and restricted cash	3,268		—		—			3,268
Certificates of deposit	13,498		—		—			13,498
Total cash and investments	$	457,522	$	18	$	(364	)	$	457,176

Fair Value and Gross Unrealized Losses of Investments Available-for-Sale in an Unrealized Loss Position

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



	December 31, 2018
	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	$	236,162	$	(606	)	$	39,627	$	(251	)	$	275,789	$	(857	)
U.S. Treasury and government sponsored enterprises	28,105		(16		)	9,182		(9		)	37,287		(25		)
Commercial paper	7,091		(1		)	—		—			7,091		(1		)
Total	$	271,358	$	(623	)	$	48,809	$	(260	)	$	320,167	$	(883	)



	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	)

Fair Value of Cash Equivalents and Investments by Contractual Maturity

The fair value of investments available-for-sale by contractual maturity were as follows (in thousands):



	December 31,
	2018		2017
Maturing in one year or less	$	674,455	$	377,155
Maturing after one year through five years	153,687		63,255
Total investments available-for-sale	$	828,142	$	440,410

Inventory (Tables)

12 Months Ended

Dec. 28, 2018

Inventory Disclosure [Abstract]

Schedule of Inventory

Inventory consisted of the following (in thousands):



	December 31,
	2018		2017
Raw materials	$	1,922	$	498
Work in process	6,170		3,997
Finished goods	3,836		2,854
Total	$	11,928	$	7,349

Balance Sheet classification:
Inventory	$	9,838	$	6,657
Inventory included in Other long-term assets	2,090		692
Total	$	11,928	$	7,349

Property and Equipment (Tables)

12 Months Ended

Dec. 28, 2018

Property, Plant and Equipment [Abstract]

Schedule of Property and Equipment

Property and equipment were as follows (in thousands):



	December 31, 2018			December 31, 2017
Leasehold improvements	$	33,941		$	4,715
Computer equipment and software	15,022			14,146
Furniture and fixtures	12,709			1,609
Laboratory equipment	5,668			5,959
Construction in progress	866			22,114
	68,206			48,543
Less: accumulated depreciation and amortization	(17,309		)	(22,800		)
Property and equipment, net	$	50,897		$	25,743

Stock-based Compensation (Tables)

12 Months Ended

Dec. 28, 2018

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

Schedule of Allocated Employee Stock-Based Compensation Expense

We allocated the stock-based compensation expense for our equity incentive plans and our 2000 Employee Stock Purchase Plan (ESPP) as follows (in thousands):



	Year Ended December 31,
	2018		2017		2016
Research and development	$	13,115	$	7,569	$	9,366
Selling, general and administrative	27,511		16,369		13,546
Total stock-based compensation	$	40,626	$	23,938	$	22,912

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 per share of stock options and ESPP purchases was as follows:



	Year Ended December 31,
	2018		2017		2016
Stock options	$	9.07	$	11.42	$	4.77
ESPP	$	6.40	$	6.00	$	2.17

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

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



	Year Ended December 31,
	2018		2017		2016
Stock options:
Risk-free interest rate	2.81	%	1.98	%	1.15	%
Dividend yield	—	%	—	%	—	%
Volatility	55	%	59	%	76	%
Expected life	4.4 years		4.5 years		4.4 years
ESPP:
Risk-free interest rate	1.93	%	1.09	%	0.55	%
Dividend yield	—	%	—	%	—	%
Volatility	53	%	58	%	65	%
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 stock option grants and ESPP purchases was estimated using the following assumptions:



	Year Ended December 31,
	2018		2017		2016
Stock options:
Risk-free interest rate	2.81	%	1.98	%	1.15	%
Dividend yield	—	%	—	%	—	%
Volatility	55	%	59	%	76	%
Expected life	4.4 years		4.5 years		4.4 years
ESPP:
Risk-free interest rate	1.93	%	1.09	%	0.55	%
Dividend yield	—	%	—	%	—	%
Volatility	53	%	58	%	65	%
Expected life	6 months		6 months		6 months

Summary of All Stock Option Activity

Activity for stock options during the year ended December 31, 2018 was as follows (dollars in thousands, except per share amounts):



	Shares		Weighted Average Exercise Price		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
Stock options outstanding at December 31, 2017	22,208,446		$	6.83
Granted	3,238,473		$	19.40
Exercised	(2,466,579	)	$	4.90
Forfeited	(288,197	)	$	15.71
Expired	(18,081	)	$	20.64
Stock options outstanding at December 31, 2018	22,674,062		$	8.71	3.7 years	$	254,201
Exercisable at December 31, 2018	16,463,202		$	5.65	3.0 years	$	229,699

Summary of All RSU Activity

Activity for RSUs during the year ended December 31, 2018 was as follows (dollars in thousands, except per share amounts):



	Shares		Weighted Average Grant Date Fair Value		Weighted Average Remaining Contractual Term	Aggregate Intrinsic Value
RSUs outstanding at December 31, 2017	3,762,990		$	17.76
Awarded	2,519,425		$	18.46
Vested and released	(1,081,339	)	$	16.05
Forfeited	(343,742	)	$	18.99
RSUs outstanding at December 31, 2018	4,857,334		$	18.42	2.1 years	$	94,427

Income Taxes (Tables)

12 Months Ended

Dec. 28, 2018

Income Tax Disclosure [Abstract]

Schedule of Components of Income Tax Expense (Benefit)

The Income tax benefit (provision) was as follows (in thousands):



	Year Ended December 31,
	2018			2017			2016
Current:
Federal	$	—		$	—		$	—
State	(6,133		)	(4,350		)	—
Total current tax expense	(6,133		)	(4,350		)	—
Deferred:
Federal	238,675			—			—
State	5,436			—			—
Total deferred tax expense	244,111			—			—
Income tax benefit (provision)	$	237,978		$	(4,350	)	$	—

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



	Year Ended December 31,
	2018			2017			2016
U.S. federal income tax (provision) benefit at statutory rate	$	(94,939	)	$	(53,916	)	$	23,876
State tax expense	(4,690		)	(8,282		)	(6,520		)
Change in valuation allowance	315,394			34,266			(6,377		)
Research credits	18,308			—			—
Stock-based compensation	5,998			20,548			(3,155		)
Non-deductible interest	—			(1,367		)	(2,680		)
Debt extinguishment	—			—			(4,726		)
Other	(2,093		)	4,401			(418		)
Income tax benefit (provision)	$	237,978		$	(4,350	)	$	—

Schedule of Deferred Assets and Liabilities

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



	December 31,
	2018			2017
Deferred tax assets:
Net operating loss carryforwards	$	146,701		$	244,205
Tax credit carryforwards	98,467			66,770
Book over tax depreciation and amortization	29,929			39,472
Amortization of deferred stock compensation – non-qualified	11,366			8,966
Accruals and reserves not currently deductible	10,425			4,914
Deferred revenue	5,474			53,543
Other assets	1,140			1,088
Total deferred tax assets	303,502			418,958
Valuation allowance	(58,112		)	(418,958		)
Net deferred tax assets	245,390			—
Deferred tax liabilities:
Operating lease right-of-use assets	(1,279		)	—
Total deferred tax liabilities	(1,279		)	—
Net deferred taxes	$	244,111		$	—

Schedule of Unrecognized Tax Benefits

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



	Year Ended December 31,
	2018			2017			2016
Beginning balance	$	79,342		$	61,809		$	88,638
Change relating to prior year provision	(4,254		)	247			(29,110		)
Change relating to current year provision	1,083			17,378			2,304
Reductions based on the lapse of the applicable statutes of limitations	(111		)	(92		)	(23		)
Ending balance	$	76,060		$	79,342		$	61,809

Net Income (Loss) Per Share (Tables)

12 Months Ended

Dec. 28, 2018

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,
	2018		2017			2016
Numerator:
Net income (loss)	$	690,070	$	154,227		$	(70,222	)
Net income allocated to participating securities	—		(367		)	—
Net income (loss) allocable to common stock for basic net income (loss) per share	690,070		153,860			(70,222		)
Adjustment to net income allocated to participating securities	—		22			—
Net income (loss) allocable to common stock for diluted net income (loss) per share	$	690,070	$	153,882		$	(70,222	)
Denominator:
Weighted-average shares of common stock outstanding used in computing basic net income (loss) per share	297,892		293,588			250,531
Dilutive securities	14,911		18,415			—
Weighted-average shares of common stock outstanding and dilutive securities used in computing diluted net income (loss) per share	312,803		312,003			250,531

Net income (loss) per share, basic	$	2.32	$	0.52		$	(0.28	)
Net income (loss) per share, diluted	$	2.21	$	0.49		$	(0.28	)

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

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



	Year Ended December 31,
	2018	2017	2016
Outstanding stock options, unvested RSUs and ESPP contributions	3,968	1,645	27,568
Secured Convertible Notes due 2018 held by entities associated with Deerfield Management Company, L.P. (Deerfield Notes)	—	—	33,890
2014 Warrants	—	—	1,000
Total	3,968	1,645	62,458

Fair Value Measurements (Tables)

12 Months Ended

Dec. 28, 2018

Fair Value Disclosures [Abstract]

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

The classification of our financial assets within the fair value hierarchy that were measured and recorded at fair value on a recurring basis was as follows (in thousands):



	December 31, 2018
	Level 1		Level 2		Total
Money market funds	$	47,744	$	—	$	47,744
Commercial paper	—		381,133		381,133
Corporate bonds	—		344,064		344,064
U.S. Treasury and government sponsored enterprises	—		55,201		55,201
Total investments available-for-sale	47,744		780,398		828,142
Certificates of deposit	—		16,596		16,596
Total financial assets carried at fair value	$	47,744	$	796,994	$	844,738



	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 investments available-for-sale	45,478		394,932		440,410
Certificates of deposit	—		13,498		13,498
Total financial assets carried at fair value	$	45,478	$	408,430	$	453,908

Commitments (Tables)

12 Months Ended

Dec. 28, 2018

Commitments and Contingencies Disclosure [Abstract]

Balance Sheet Classification of Lease Liabilities

The balance sheet classification of our lease liabilities was as follows (in thousands):



	December 31, 2018		December 31, 2017
Operating lease liabilities:
Current portion included in Other current liabilities	$	2,738	$	540
Long-term portion of lease liabilities	12,099		408
Total operating lease liabilities	14,837		948
Financing lease liabilities:
Financing obligation for build-to-suit lease	—		14,530
Current portion included in Other current liabilities	49		—
Long-term portion of lease liabilities	79		—
Total financing lease liabilities	128		14,530
Total lease liabilities	$	14,965	$	15,478

Components of Lease Expense

The components of lease costs, which were included in Operating expenses in our Consolidated Statements of Operations, were as follows (in thousands):



	Year Ended December 31,
	2018		2017			2016
Operating lease cost	$	4,189	$	3,944		$	8,620
Variable lease cost	1,661		2,216			1,056
Sublease income	—		(1,225		)	(3,553		)
Total lease costs	$	5,850	$	4,935		$	6,123

Maturities of Operating Lease Liabilities

As of December 31, 2018, the maturities of our operating lease liabilities were as follows (in thousands):



	Operating leases
Years ending December 31,
2019	$	2,794
2020	2,823
2021	2,904
2022	3,000
2023	3,082
Thereafter	13,584
Total lease payments	28,187
Less:
Present value adjustment	(5,180		)
Tenant improvement reimbursements	(8,170		)
Operating lease liabilities	$	14,837

Quarterly Financial Data (Unaudited) (Tables)

12 Months Ended

Dec. 28, 2018

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,
2018:
Total revenues ⁽¹⁾	$	228,602	$	225,397	$	186,108	$	213,719
Gross profit ⁽²⁾	$	168,873	$	155,586	$	139,839	$	128,633
Income from operations	$	111,602	$	125,176	$	85,770	$	116,307
Net income	$	360,089	$	126,630	$	87,494	$	115,857
Net income per share, basic	$	1.20	$	0.42	$	0.29	$	0.39
Net income per share, diluted	$	1.15	$	0.41	$	0.28	$	0.37
2017:
Total revenues	$	120,072	$	152,510	$	99,008	$	80,887
Gross profit ⁽²⁾	$	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

____________________

(1)


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

Organization and Summary of Significant Accounting Policies (Narrative) (Details)		12 Months Ended			35 Months Ended
	Dec. 30, 2017 USD ($)	Dec. 28, 2018 USD ($) segment product	Dec. 29, 2017 USD ($)	Dec. 30, 2016 USD ($)	Dec. 28, 2018 USD ($)
Organization And Summary Of Significant Policies [Line Items]
Number of products that entered in the commercial marketplace \| product		4
Number of operating segments \| segment		1
Increase in net cash provided by investing activities		$ (297,850,000)	$ 36,795,000	$ (214,548,000)
Accumulated deficit	$ 1,570,433,000	$ 880,363,000	1,829,172,000		$ 880,363,000
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%
Inventory expensed as research and development, not capitalized as inventory		$ 0			0
Collaborative Arrangement with Ipsen
Organization And Summary Of Significant Policies [Line Items]
Milestone payments earned		$ 140,000,000			$ 275,000,000
Collaborative Arrangement with Ipsen \| Collaborative Arrangement with GlaxoSmithKline
Organization And Summary Of Significant Policies [Line Items]
Percent of royalty on net sale		3.00%
ASU 2016-18
Organization And Summary Of Significant Policies [Line Items]
Increase in net cash provided by investing activities			$ 1,000,000	$ 1,500,000
ASU 2014-09 \| Adjustments Due to the Adoption of Topic 606
Organization And Summary Of Significant Policies [Line Items]
Accumulated deficit	(258,505,000)
ASU 2014-09 \| Adjustments Due to the Adoption of Topic 606 \| Collaborative Arrangement with Ipsen \| EMA Filing Acceptance - HCC
Organization And Summary Of Significant Policies [Line Items]
Milestone payments earned	10,000,000
ASU 2016-02 \| Restatement
Organization And Summary Of Significant Policies [Line Items]
Accumulated deficit	$ (234,000)
Commercial Presence in Markets Worldwide
Organization And Summary Of Significant Policies [Line Items]
Number of products that entered in the commercial marketplace \| product		3
Products Derived from Cabozantinib
Organization And Summary Of Significant Policies [Line Items]
Number of products that entered in the commercial marketplace \| product		2

Organization and Summary of Significant Accounting Policies (Impact of Adoption of Topic 606 and Topic 842 on the Condensed Consolidated Balance Sheet) (Details) - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 30, 2017	Dec. 29, 2017
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Contract assets: unbilled collaboration revenue, gross: Current portion	$ 0	$ 9,588
Contract assets: unbilled collaboration revenue, gross: Long-term portion	0	12,247
Other receivables	162,771	11,635	$ 77,300
Property and equipment, net	50,897	11,213	25,743
Operating lease right-of-use assets	5,867	8,579	0
Current portion of deferred revenue	0	8,393	31,984
Long-term portion of deferred revenue	15,897	25,441	238,520
Other current liabilities	21,825	19,323	16,150
Long-term portion of lease liabilities	14,965	13,323
Accumulated deficit	$ (880,363)	(1,570,433)	(1,829,172)
Calculated under Revenue Guidance in Effect before Topic 606 [Member]
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Contract assets: unbilled collaboration revenue, gross: Current portion			0
Contract assets: unbilled collaboration revenue, gross: Long-term portion			0
Other receivables			3,892
Property and equipment, net			25,743
Operating lease right-of-use assets			0
Current portion of deferred revenue			31,984
Long-term portion of deferred revenue			238,520
Other current liabilities			16,150
Long-term portion of lease liabilities			14,938
Accumulated deficit			$ (1,829,172)
ASU 2014-09 \| Adjustments Due to the Adoption of Topic 606
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Contract assets: unbilled collaboration revenue, gross: Current portion		9,588
Contract assets: unbilled collaboration revenue, gross: Long-term portion		12,247
Current portion of deferred revenue		(23,591)
Long-term portion of deferred revenue		(213,079)
Accumulated deficit		258,505
Restatement \| ASU 2016-02
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Other receivables		7,743
Property and equipment, net		(14,530)
Operating lease right-of-use assets		8,579
Other current liabilities		3,173
Long-term portion of lease liabilities		(1,615)
Accumulated deficit		$ 234

Organization and Summary of Significant Accounting Policies (Impact of Adoption of Topic 606 and Topic 842 on the Consolidated Statements of Operations) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Selling, general and administrative									206,366	159,362	116,145
Total operating expenses									414,971	286,567	219,578
Interest expense									0	(8,679)	(33,060)
Total other income (expense), net									13,237	(7,333)	(42,098)
Income before income taxes									452,092	158,577	(70,222)
Income tax benefit (provision)									237,978	(4,350)	0
Net income (loss)	$ 360,089	$ 126,630	$ 87,494	$ 115,857	$ 38,489	$ 81,382	$ 17,656	$ 16,700	$ 690,070	$ 154,227	$ (70,222)
Net income per share, basic (in dollars per share)	$ 1.20	$ 0.42	$ 0.29	$ 0.39	$ 0.13	$ 0.28	$ 0.06	$ 0.06	$ 2.32	$ 0.52	$ (0.28)
Net income per share, diluted (in dollars per share)	$ 1.15	$ 0.41	$ 0.28	$ 0.37	$ 0.12	$ 0.26	$ 0.06	$ 0.05	$ 2.21	$ 0.49	$ (0.28)
Collaboration revenue
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									$ 234,547	$ 103,469	$ 56,079
Calculated under Revenue Guidance in Effect before Topic 606 [Member] \| Collaboration revenue
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									270,429
ASU 2014-09 \| Adjustments Due to the Adoption of Topic 606
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									(35,882)
Income before income taxes									(35,882)
Income tax benefit (provision)									(48,325)
Net income (loss)									$ (84,207)
Net income per share, basic (in dollars per share)									$ (0.28)
Net income per share, diluted (in dollars per share)									$ (0.27)
ASU 2014-09 \| Adjustments Due to the Adoption of Topic 606 \| Collaboration revenue
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									$ (35,882)
ASU 2016-02
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Selling, general and administrative									1,204
Total operating expenses									1,204
Interest expense									(631)
Total other income (expense), net									631
Income before income taxes									(573)
Income tax benefit (provision)									73
Net income (loss)									$ (500)
Net income per share, basic (in dollars per share)									$ 0.00
Net income per share, diluted (in dollars per share)									$ 0.00
Calculated Under Guidance In Effect Before Topic 606 And Topic 842 [Member]
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									$ 889,708
Selling, general and administrative									205,162
Total operating expenses									413,767
Interest expense									631
Total other income (expense), net									12,606
Income before income taxes									488,547
Income tax benefit (provision)									286,230
Net income (loss)									$ 774,777
Net income per share, basic (in dollars per share)									$ 2.60
Net income per share, diluted (in dollars per share)									$ 2.48

Organization and Summary of Significant Accounting Policies (Estimated Useful Lives of Property Plant And Equipment) (Details)	12 Months Ended
	Dec. 28, 2018
Laboratory equipment
Property, Plant and Equipment [Line Items]
Estimated useful lives	5 years
Furniture and fixtures
Property, Plant and Equipment [Line Items]
Estimated useful lives	7 years
Office equipment
Property, Plant and Equipment [Line Items]
Estimated useful lives	5 years
Computer equipment and software
Property, Plant and Equipment [Line Items]
Estimated useful lives	3 years
Leasehold improvements \| Minimum
Property, Plant and Equipment [Line Items]
Estimated useful lives	7 years
Leasehold improvements \| Maximum
Property, Plant and Equipment [Line Items]
Estimated useful lives	15 years

Revenues (Revenues by Disaggregated Category) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Disaggregation of Revenue [Line Items]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Net product revenues
Disaggregation of Revenue [Line Items]
Total revenues									619,279	349,008	135,375
Gross product revenues
Disaggregation of Revenue [Line Items]
Total revenues									738,529	402,569	151,499
Discounts and allowances
Disaggregation of Revenue [Line Items]
Total revenues									119,250	53,561	16,124
Total collaboration revenues
Disaggregation of Revenue [Line Items]
Total revenues									234,547	103,469	56,079
License revenues
Disaggregation of Revenue [Line Items]
Total revenues									192,188	96,637	56,286
Research and development services revenues
Disaggregation of Revenue [Line Items]
Total revenues									39,501	8,737	0
Other collaboration revenues
Disaggregation of Revenue [Line Items]
Total revenues									$ 2,858	$ (1,905)	$ (207)

Revenues (Net Product Revenues Disaggregated by Product) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Disaggregation of Revenue [Line Items]
Net product revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Net Product Revenues
Disaggregation of Revenue [Line Items]
Net product revenues									619,279	349,008	135,375
CABOMETYX
Disaggregation of Revenue [Line Items]
Net product revenues									599,946	324,000	93,481
COMETRIQ
Disaggregation of Revenue [Line Items]
Net product revenues									$ 19,333	$ 25,008	$ 41,894

Revenues (Revenues Disaggregated by Significant Customer) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Sales revenue, net \| Customer concentration risk
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Percent of total									100.00%	100.00%	100.00%
Ipsen
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									$ 182,879	$ 69,792	$ 33,252
Ipsen \| Sales revenue, net \| Customer concentration risk
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Percent of total									21.00%	15.00%	17.00%
Caremark L.L.C.
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									$ 110,698	$ 73,921	$ 17,746
Caremark L.L.C. \| Sales revenue, net \| Customer concentration risk
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Percent of total									13.00%	16.00%	9.00%
Affiliates of McKesson Corporation
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									$ 99,916	$ 48,662	$ 13,143
Affiliates of McKesson Corporation \| Sales revenue, net \| Customer concentration risk
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Percent of total									12.00%	11.00%	7.00%
Accredo Health, Incorporated
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									$ 81,028	$ 50,716	$ 16,631
Accredo Health, Incorporated \| Sales revenue, net \| Customer concentration risk
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Percent of total									9.00%	11.00%	9.00%
Diplomat Specialty Pharmacy
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									$ 74,244	$ 83,059	$ 63,826
Diplomat Specialty Pharmacy \| Sales revenue, net \| Customer concentration risk
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Percent of total									9.00%	18.00%	33.00%
Others, individually less than 10% of Total revenues for all periods presented
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Total revenues									$ 305,061	$ 126,327	$ 46,856
Others, individually less than 10% of Total revenues for all periods presented \| Sales revenue, net \| Customer concentration risk
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Percent of total									36.00%	29.00%	25.00%

Revenues (Revenues Disaggregated by Geographic Region) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Disaggregation of Revenue [Line Items]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
U.S.
Disaggregation of Revenue [Line Items]
Total revenues									632,927	367,906	140,709
Europe
Disaggregation of Revenue [Line Items]
Total revenues									182,879	69,792	35,745
Rest of the world
Disaggregation of Revenue [Line Items]
Total revenues									$ 38,020	$ 14,779	$ 15,000

Revenues (Activities and Ending Reserve Balances for Significant Categories of Discounts and Allowances) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017
SEC Schedule, 12-09, Movement in Valuation Allowances and Reserves [Roll Forward]
Balance at beginning of period	$ 9,493	$ 5,574
Provision related to sales made in:
Current period	119,600	55,001
Prior periods	(350)	(1,441)
Payments and customer credits issued	(111,467)	(49,641)
Balance at end of period	17,276	9,493
Chargebacks and Discounts for Prompt Payment
SEC Schedule, 12-09, Movement in Valuation Allowances and Reserves [Roll Forward]
Balance at beginning of period	1,928	1,802
Provision related to sales made in:
Current period	75,543	33,310
Prior periods	(403)	(817)
Payments and customer credits issued	(74,746)	(32,367)
Balance at end of period	2,322	1,928
Other Customer Credits/Fees and Co-pay Assistance
SEC Schedule, 12-09, Movement in Valuation Allowances and Reserves [Roll Forward]
Balance at beginning of period	1,795	794
Provision related to sales made in:
Current period	13,015	7,301
Prior periods	206	0
Payments and customer credits issued	(11,978)	(6,300)
Balance at end of period	3,038	1,795
Rebates
SEC Schedule, 12-09, Movement in Valuation Allowances and Reserves [Roll Forward]
Balance at beginning of period	5,770	2,627
Provision related to sales made in:
Current period	31,040	14,390
Prior periods	(153)	(624)
Payments and customer credits issued	(24,741)	(10,623)
Balance at end of period	11,916	5,770
Returns
SEC Schedule, 12-09, Movement in Valuation Allowances and Reserves [Roll Forward]
Balance at beginning of period	0	351
Provision related to sales made in:
Current period	2	0
Prior periods	0	0
Payments and customer credits issued	(2)	(351)
Balance at end of period	$ 0	$ 0

Revenues (Changes in Contract Assets and Liabilities under Topic 606) (Details) $ in Thousands	12 Months Ended
	Dec. 28, 2018 USD ($)
Contract Assets - Current Portion
Increases as a result of a change in transaction price and recognition of revenues as services are performed	$ 37,881
Transfer to receivables from contract assets recognized at the beginning of the period	(46,052)
Other	(1,417)
Balance	0
Contract Assets - Long-term Portion
Increases as a result of a change in transaction price and recognition of revenues as services are performed	4,545
Other	(16,792)
Balance	0
Contract Liabilities - Current Portion
Balance	31,984
Increases as a result of the deferral of milestones achieved in period, excluding amounts recognized as revenue	1,718
Revenue recognized that was included in the contract liability balance at the beginning of the period	(8,683)
Other	(1,428)
Balance	0
Contract Liabilities - Long-term Portion
Balance	238,520
Increases as a result of the deferral of milestones achieved in period, excluding amounts recognized as revenue	7,237
Revenue recognized that was included in the contract liability balance at the beginning of the period	0
Other	(16,781)
Balance	15,897
Revenues recognized for performance obligations satisfied in previous periods	198,100
Balances Without the Adoption of Topic 606
Contract Assets - Current Portion
Balance	0
Contract Assets - Long-term Portion
Balance	0
Contract Liabilities - Current Portion
Balance	31,984
Contract Liabilities - Long-term Portion
Balance	$ 238,520

Collaboration Agreements (Ipsen Collaboration, Narrative) (Details) - Collaborative arrangement with Ipsen		1 Months Ended	6 Months Ended	12 Months Ended		35 Months Ended
	Dec. 30, 2017 USD ($)	Feb. 29, 2016 USD ($)	Jun. 29, 2018 USD ($)	Dec. 28, 2018 USD ($)	Dec. 28, 2018 CAD ($)	Dec. 28, 2018 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration period to achieve specified levels of commercial performance				10 years	10 years
Upfront payment(s)		$ 210,000,000
Milestone payments earned				$ 140,000,000		$ 275,000,000
Eligible payment from collaboration for development and regulatory milestone achievement under collaborations agreement		84,000,000
Maximum amount eligible for commercial milestones under collaborations agreement		$ 519,500,000
Remaining performance obligation				$ 48,000,000		48,000,000
Research and development arrangement performed for others, reimbursement for costs incurred, percent				35.00%	35.00%
Net contract liability				$ 13,300,000		$ 13,300,000
Collaborative Arrangement with GlaxoSmithKline
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale				3.00%	3.00%
Final tier
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Royalty tier			$ 150,000,000		$ 30,000,000.0
Initial
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale			2.00%
Second
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale			12.00%
Minimum \| Final tier
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale				22.00%	22.00%
Maximum \| Final tier
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale				26.00%	26.00%
EMA Filing Acceptance - HCC \| Adjustments Due to the Adoption of Topic 606 \| ASU 2014-09
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone payments earned	$ 10,000,000

Collaboration Agreements (Collaboration Revenues - Ipsen) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Collaborative Arrangement with Ipsen
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues									$ 182,879	$ 69,792	$ 33,252

Collaboration Agreements (Takeda Collaboration, Narrative) (Details) - USD ($)	1 Months Ended	12 Months Ended
	Feb. 28, 2017	Dec. 28, 2018
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Sales volume period		6 years
Collaborative arrangement with Takeda
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront payment(s)	$ 50,000,000
Milestone payments earned		$ 10,000,000
Maximum amount eligible for development and regulatory milestones		90,000,000
Maximum amount eligible for commercial milestones under collaborations agreement		83,000,000
Remaining performance obligation		25,600,000
Net contract liability		$ 2,600,000
Collaborative arrangement with Takeda \| Global
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Research and development arrangement performed for others, reimbursement for costs incurred, percent		20.00%
Collaborative arrangement with Takeda \| Japan
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
Collaborative arrangement with Takeda \| Initial
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Royalty tier		$ 300,000,000.0
Collaborative arrangement with Takeda \| Minimum \| Initial
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale		15.00%
Collaborative arrangement with Takeda \| Minimum \| Final tier
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale		20.00%
Collaborative arrangement with Takeda \| Maximum \| Initial
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale		24.00%
Collaborative arrangement with Takeda \| Maximum \| Final tier
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale		30.00%

Collaboration Agreements (Collaboration Revenue - Takeda) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Collaborative arrangement with Takeda
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues									$ 18,020	$ 14,779

Collaboration Agreements (Royalty Revenues under the Collaboration Agreement with GSK) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Jan. 01, 2016
Collaborative Arrangements with Glaxo Smith Kline
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Royalty expense	$ 23,950	$ 12,413	$ 4,334
Collaborative Arrangement with GlaxoSmithKline \| Collaborative Arrangement with Ipsen
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale	3.00%

Collaboration Agreements (StemSynergy Collaboration, Narrative) (Details) - Collaborative Arrangement With StemSynergy - USD ($) $ in Millions	12 Months Ended
	Dec. 28, 2018	Jan. 31, 2018
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront and milestone payments	$ 3.0
Additional upfront and milestone payments	1.2
Eligible payment from collaboration for development and regulatory milestone achievement under collaborations agreement		$ 2.3
First Product To Reach Market
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Eligible payment from collaboration for development and regulatory milestone achievement under collaborations agreement	$ 56.5

Collaboration Agreements (Invenra Collaboration, Narrative) (Details) - Collaborative Arrangement With Invenra - USD ($) $ in Millions	12 Months Ended
	Dec. 28, 2018	May 31, 2018
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront and milestone payments	$ 2.0
Project initiation fee	2.0
Discovery Project
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront and milestone payments	2.0
Development and Regulatory Milestone
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Eligible payment from collaboration for development and regulatory milestone achievement under collaborations agreement	131.5
Additional Development and Regulatory Milestone
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Eligible payment from collaboration for development and regulatory milestone achievement under collaborations agreement	$ 127.5
Product Commercialization
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Eligible payment from collaboration for development and regulatory milestone achievement under collaborations agreement		$ 325.0

Collaboration Agreements (Collaboration Revenues - Genentech) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Collaborative Arrangement with Genentech \| Cotellic
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative Arrangement, Income (Loss) from Agreement									8,084	(2,140)	8,771
Total revenues									$ 5,564	$ 6,398	$ 2,827

Collaboration Agreements (Other Collaborations, Narrative) (Details)	1 Months Ended	12 Months Ended
	Nov. 30, 2015	Dec. 28, 2018 USD ($) clinical_trial
Collaborative Arrangement with Genentech
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percentage of share of the Company in promotions	25.00%
Number of clinical trials (more than) \| clinical_trial		50
Collaborative Arrangement with Daiichi Sankyo
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for development and regulatory milestones		$ 110,000,000
Collaborative Arrangement with Daiichi Sankyo \| Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sales		0.50%
Collaborative Arrangement with BMS
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for development and regulatory milestones		$ 240,000,000
Maximum amount eligible for royalties on sales under collaborations agreement		$ 150,000,000
Profit Sharing Tier One \| Collaborative Arrangement with Genentech
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of profits		50.00%
Profit Sharing Tier Two \| Collaborative Arrangement with Genentech \| Minimum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Profit threshold		$ 200,000,000
Profit Sharing Tier Three \| Collaborative Arrangement with Genentech
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of profits		30.00%
Profit Sharing Tier Three \| Collaborative Arrangement with Genentech \| Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Profit threshold		$ 400,000,000

Collaboration Agreements (Collaboration Revenues - Daiichi Sankyo) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Collaborative Arrangement with Daiichi Sankyo
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues									$ 20,000	$ 0	$ 15,000

Collaboration Agreements (Daiichi Sankyo, Narrative) (Details) - Collaborative Arrangement with Daiichi Sankyo	12 Months Ended
	Dec. 28, 2018 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum amount eligible for development and regulatory milestones	$ 110,000,000
Maximum amount eligible for development and regulatory milestones upon first arm's-length sale	$ 20,000,000
Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Percent of royalty on net sale	0.50%

Collaboration Agreements (Collaboration Revenues - Merck) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Collaborative Arrangement with Merck
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues									$ 0	$ 0	$ 5,000

Collaboration Agreements (Collaboration Revenues - BMS) (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Collaborative Arrangement with BMS
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total revenues									$ 0	$ 12,500	$ 0

Cash and Investments (Reconciliation of Cash, Cash Equivalents, and Restricted Cash) (Details) - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Investments, Debt and Equity Securities [Abstract]
Cash and cash equivalents	$ 314,775	$ 183,164	$ 151,686
Short-term restricted cash and investments	0	504	0
Long-term restricted cash and investments	1,100	4,646	4,150
Cash, cash equivalents, and restricted cash as reported within the accompanying Consolidated Statements of Cash Flows	$ 315,875	$ 188,314	$ 155,836	$ 144,284

Cash and Investments (Summary by Security Type) (Details) - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Investments available-for-sale:
Amortized Cost	$ 828,843	$ 440,756
Gross Unrealized Gains	182	18
Gross Unrealized Losses	(883)	(364)
Fair Value	828,142	440,410
Cash, Cash Equivalents, Restricted Cash and Restricted Cash Equivalents
Amortized Cost	315,875	188,314	$ 155,836	$ 144,284
Total, Amortized Cost	852,322	457,522
Total, Fair Value	851,621	457,176
Money market funds
Investments available-for-sale:
Amortized Cost	47,744	45,478
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	47,744	45,478
Commercial paper
Investments available-for-sale:
Amortized Cost	381,134	199,647
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(1)	0
Fair Value	381,133	199,647
Corporate bonds
Investments available-for-sale:
Amortized Cost	344,741	179,336
Gross Unrealized Gains	180	18
Gross Unrealized Losses	(857)	(332)
Fair Value	344,064	179,022
U.S. Treasury and government sponsored enterprises
Investments available-for-sale:
Amortized Cost	55,224	16,295
Gross Unrealized Gains	2	0
Gross Unrealized Losses	(25)	(32)
Fair Value	55,201	16,263
Cash and restricted cash
Cash, Cash Equivalents, Restricted Cash and Restricted Cash Equivalents
Amortized Cost	6,883	3,268
Fair Value	6,883	3,268
Certificates of deposit
Cash, Cash Equivalents, Restricted Cash and Restricted Cash Equivalents
Amortized Cost	16,596	13,498
Fair Value	$ 16,596	$ 13,498

Cash and Investments (Narrative) (Details)	3 Months Ended	12 Months Ended
Cash and Investments (Narrative) (Details)	Dec. 28, 2018 USD ($) investment	Dec. 28, 2018 USD ($) investment	Dec. 29, 2017 USD ($) investment	Dec. 30, 2016 USD ($)	Jan. 01, 2016 USD ($)	Aug. 31, 2016
Investment [Line Items]
Gain (loss) on sales of investments available-for-sale				$ 0	$ 0
Number of investments in an unrealized loss position \| investment	199	199	134
Other-than-temporary impairment charges on available-for-sale securities			$ 0	0	$ 0
Beneficial ownership interest by BlackRock (more than)	10.00%	10.00%
Fair value of cash and investments managed by BlackRock	$ 298,500,000	$ 298,500,000	141,000,000
Fair value of cash and investments managed by BlackRock in the BlackRock Liquidity Money Market Fund	3,000,000	3,000,000	1,000,000
Fees for advisory services paid to BlackRock	$ 200,000
Akarna Therapeutics, Ltd.
Investment [Line Items]
Realized gain on sale of cost method investment		$ 200,000
Realized gain on sale of cost method investment			$ 3,000,000	$ 2,500,000
Cost method investment ownership percentage						9.00%

Cash and Investments (Gross Unrealized Losses) (Details) - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 29, 2017
Fair Value
In an Unrealized Loss Position Less than 12 Months	$ 271,358	$ 154,357
In an Unrealized Loss Position 12 Months or Greater	48,809	22,698
Total	320,167	177,055
Gross Unrealized Losses
In an Unrealized Loss Position Less than 12 Months	(623)	(319)
In an Unrealized Loss Position 12 Months or Greater	(260)	(45)
Total	(883)	(364)
Corporate bonds
Fair Value
In an Unrealized Loss Position Less than 12 Months	236,162	140,746
In an Unrealized Loss Position 12 Months or Greater	39,627	20,047
Total	275,789	160,793
Gross Unrealized Losses
In an Unrealized Loss Position Less than 12 Months	(606)	(296)
In an Unrealized Loss Position 12 Months or Greater	(251)	(36)
Total	(857)	(332)
U.S. Treasury and government sponsored enterprises
Fair Value
In an Unrealized Loss Position Less than 12 Months	28,105	13,611
In an Unrealized Loss Position 12 Months or Greater	9,182	2,651
Total	37,287	16,262
Gross Unrealized Losses
In an Unrealized Loss Position Less than 12 Months	(16)	(23)
In an Unrealized Loss Position 12 Months or Greater	(9)	(9)
Total	(25)	$ (32)
Commercial paper
Fair Value
In an Unrealized Loss Position Less than 12 Months	7,091
In an Unrealized Loss Position 12 Months or Greater	0
Total	7,091
Gross Unrealized Losses
In an Unrealized Loss Position Less than 12 Months	(1)
In an Unrealized Loss Position 12 Months or Greater	0
Total	$ (1)

Cash and Investments (Summary by Contractual Maturity) (Details) - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 29, 2017
Investments, Debt and Equity Securities [Abstract]
Maturing in one year or less	$ 674,455	$ 377,155
Maturing after one year through five years	153,687	63,255
Total investments available-for-sale	$ 828,142	$ 440,410

Inventory (Schedule of Inventory) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Inventory [Line Items]
Raw materials	$ 1,922	$ 498
Work in process	6,170	3,997
Finished goods	3,836	2,854
Total	11,928	7,349
Inventory write-down	1,100	1,200	$ 500
Inventory
Inventory [Line Items]
Total	9,838	6,657
Inventory included in Other long-term assets
Inventory [Line Items]
Total	$ 2,090	$ 692

Property and Equipment (Schedule of Property and Equipment) (Details) - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 30, 2017	Dec. 29, 2017
Property, Plant and Equipment [Line Items]
Property and equipment, gross	$ 68,206		$ 48,543
Less: accumulated depreciation and amortization	(17,309)		(22,800)
Property and equipment, net	50,897	$ 11,213	25,743
Leasehold improvements
Property, Plant and Equipment [Line Items]
Property and equipment, gross	33,941		4,715
Computer equipment and software
Property, Plant and Equipment [Line Items]
Property and equipment, gross	15,022		14,146
Furniture and fixtures
Property, Plant and Equipment [Line Items]
Property and equipment, gross	12,709		1,609
Laboratory equipment
Property, Plant and Equipment [Line Items]
Property and equipment, gross	5,668		5,959
Construction in progress
Property, Plant and Equipment [Line Items]
Property and equipment, gross	$ 866		$ 22,114

Property and Equipment (Narrative) (Details) $ in Millions	12 Months Ended
Property and Equipment (Narrative) (Details) $ in Millions	Dec. 28, 2018 USD ($) ft²	Dec. 28, 2018 USD ($) ft²	Dec. 29, 2017 USD ($)	Dec. 30, 2016 USD ($)
Property, Plant and Equipment [Line Items]
Depreciation	$ 4.9		$ 1.2	$ 1.0
Leasehold Improvements, Buildings, Furniture and Fixtures, Computer Equipment and Software
Property, Plant and Equipment [Line Items]
Construction in progress capitalized		$ 46.3
Alameda, California
Property, Plant and Equipment [Line Items]
Area of leased property (in sqft) \| ft²	134,765	134,765

Stock-based Compensation (Narrative) (Details) - USD ($)	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016	Dec. 31, 2010
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares available for grant	14,693,867
Stock-based compensation expense	$ 40,626,000	$ 23,938,000	$ 22,912,000
Proceeds from employee stock purchase plan	$ 5,202,000	4,868,000	2,187,000
Stock options granted (in shares)	3,238,473
Cash received from option exercises and purchases under the ESPP	$ 12,076,000	$ 17,555,000	25,327,000
Options outstanding (in shares)	22,674,062	22,208,446
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)	850000.00%
Expenses relating to stock match	$ 3,600,000	$ 1,700,000	1,100,000
Number of shares available for issuance under 401(k) Retirement Plan (in shares)		571,674
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	$ 48,000,000
Unrecognized compensation expense weighted-average period for recognition	2 years 6 months 10 days
Intrinsic value of options exercised	$ 39,100,000	$ 85,200,000	50,000,000
Cash received from option exercises and purchases under the ESPP	12,100,000	17,600,000	25,300,000
Fair value of employee options vested and expensed	18,900,000	13,100,000	13,400,000
Performance Shares [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total unrecognized compensation expense	$ 12,700,000
Instruments awarded (in shares)	693,131
RSUs [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options, vesting period	4 years
Total unrecognized compensation expense	$ 81,800,000
Unrecognized compensation expense weighted-average period for recognition	3 years 25 days
Instruments awarded (in shares)	2,519,425
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares available for grant	4,722,008
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	$ 2,200,000	$ 1,600,000	$ 1,000,000
Common stock issued (in shares)	330,492	434,523	559,936
Average price per share (in dollars per share)	$ 15.74	$ 11.20	$ 3.91
Proceeds from employee stock purchase plan	$ 5,200,000	$ 4,900,000	$ 2,200,000
Performance Share Options (PSO) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options granted (in shares)	308,365
Exercise threshold, percentage of per share exercise price of the PSO	125.00%
Performance Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation expense		$ 0	$ 4,100,000.0
Number of options in vested (in shares)			5,870,303
Options outstanding (in shares)		0

Stock-based Compensation (Schedule of Allocated Employee Stock-Based Compensation Expense) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total stock-based compensation	$ 40,626	$ 23,938	$ 22,912
Research and development expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total stock-based compensation	13,115	7,569	9,366
Selling, general and administrative expense [Member]
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]
Total stock-based compensation	$ 27,511	$ 16,369	$ 13,546

Stock-based Compensation (Weighted Average Grant Date Fair Value) (Details) - $ / shares	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 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)	$ 9.07	$ 11.42	$ 4.77
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Weighted average grant-date fair value (in dollars per share)	$ 6.40	$ 6.00	$ 2.17

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. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	2.81%	1.98%	1.15%
Dividend yield	0.00%	0.00%	0.00%
Volatility	55.00%	59.00%	76.00%
Expected life	4 years 4 months 20 days	4 years 5 months 23 days	4 years 4 months 9 days
ESPP [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	1.93%	1.09%	0.55%
Dividend yield	0.00%	0.00%	0.00%
Volatility	53.00%	58.00%	65.00%
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. 28, 2018 USD ($) $ / shares shares
Shares
Options outstanding at beginning of the year (in shares) \| shares	22,208,446
Granted (in shares) \| shares	3,238,473
Exercised (in shares) \| shares	(2,466,579)
Forfeited (in shares) \| shares	(288,197)
Expired (in shares) \| shares	(18,081)
Options outstanding at ending of the year (in shares) \| shares	22,674,062
Exercisable at December 31, 2018 (in shares) \| shares	16,463,202
Weighted Average Exercise Price
Options outstanding at beginning of the year (in dollars per share) \| $ / shares	$ 6.83
Granted (in dollars per share) \| $ / shares	19.40
Exercised (in dollars per share) \| $ / shares	4.90
Forfeited (in dollars per share) \| $ / shares	15.71
Expired (in dollars per share) \| $ / shares	20.64
Options outstanding at ending of the year (in dollars per share) \| $ / shares	8.71
Exercisable at December 31, 2018 (in dollars per share) \| $ / shares	$ 5.65
Weighted Average Remaining Contractual Term, Options outstanding at December 31, 2018	3 years 8 months 15 days
Weighted Average Remaining Contractual Term, Exercisable at December 31, 2018	2 years 11 months 15 days
Aggregate Intrinsic Value, Options outstanding at December 31, 2018 \| $	$ 254,201
Aggregate Intrinsic Value, Exercisable at December 31, 2018 \| $	$ 229,699

Stock-based Compensation (Summary of All RSU Activity) (Details) - RSUs [Member] $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 28, 2018 USD ($) $ / shares shares
Shares
Awards outstanding at beginning of period (in shares) \| shares	3,762,990
Awarded (in shares) \| shares	2,519,425
Vested and released (in shares) \| shares	(1,081,339)
Forfeited (in shares) \| shares	(343,742)
Awards outstanding at end of period (in shares) \| shares	4,857,334
Weighted Average Grant Date Fair Value
Awards outstanding at beginning of period (in dollars per share) \| $ / shares	$ 17.76
Awarded (in dollars per share) \| $ / shares	18.46
Vested and released (in dollars per share) \| $ / shares	16.05
Forfeited (in dollars per share) \| $ / shares	18.99
Awards outstanding at end of period (in dollars per share) \| $ / shares	$ 18.42
Weighted Average Remaining Contractual Term, Awards outstanding at December 31, 2018	2 years 1 month 24 days
Aggregate Intrinsic Value, Awards outstanding at December 31, 2018 \| $	$ 94,427

Income Taxes (Components of Income Tax Expense (Benefit)) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Current:
Federal	$ 0	$ 0	$ 0
State	(6,133)	(4,350)	0
Total current tax expense	(6,133)	(4,350)	0
Deferred:
Federal	238,675	0	0
State	5,436	0	0
Total deferred tax expense	244,111	0	0
Income tax benefit (provision)	$ 237,978	$ (4,350)	$ 0

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. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Income Tax Disclosure [Abstract]
Federal income tax rate	21.00%	34.00%	34.00%
U.S. federal income tax (provision) benefit at statutory rate	$ (94,939)	$ (53,916)	$ 23,876
State tax expense	(4,690)	(8,282)	(6,520)
Change in valuation allowance	315,394	34,266	(6,377)
Research credits	18,308	0	0
Stock-based compensation	5,998	20,548	(3,155)
Non-deductible interest	0	(1,367)	(2,680)
Debt extinguishment	0	0	(4,726)
Other	(2,093)	4,401	(418)
Income tax benefit (provision)	$ 237,978	$ (4,350)	$ 0

Income Taxes (Schedule of Deferred Assets and Liabilities) (Details) - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 29, 2017
Deferred tax assets:
Net operating loss carryforwards	$ 146,701	$ 244,205
Tax credit carryforwards	98,467	66,770
Book over tax depreciation and amortization	29,929	39,472
Amortization of deferred stock compensation – non-qualified	11,366	8,966
Accruals and reserves not currently deductible	10,425	4,914
Deferred revenue	5,474	53,543
Other assets	1,140	1,088
Total deferred tax assets	303,502	418,958
Valuation allowance	(58,112)	(418,958)
Net deferred tax assets	245,390	0
Deferred tax liabilities:
Operating lease right-of-use assets	(1,279)	0
Total deferred tax liabilities	(1,279)	0
Net deferred taxes	$ 244,111	$ 0

Income Taxes (Narrative) (Details) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Narrative) (Details) - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016	Jan. 01, 2016
Income Tax Disclosure [Abstract]
Deferred tax assets	$ 244,111	$ 0
Valuation allowance	58,112	418,958
Valuation allowance increase (decrease)	(360,800)	(210,100)
Income Tax Examination [Line Items]
Unrecognized tax benefits	76,060	79,342	$ 61,809	$ 88,638
Unrecognized tax benefits that would reduce income tax provision and effective tax rate	$ 46,000
Federal [Member]
Income Tax Examination [Line Items]
Net operating loss carryforwards		614,000
Research and development tax credits		102,000
State and Local Jurisdiction [Member]
Income Tax Examination [Line Items]
Net operating loss carryforwards		453,000
State and Local Jurisdiction [Member] \| Research Tax Credit Carryforward [Member]
Income Tax Examination [Line Items]
Research and development tax credits		$ 34,000

Income Taxes (Schedule of Unrecognized Tax Benefits) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Reconciliation of Unrecognized Tax Benefits, Excluding Amounts Pertaining to Examined Tax Returns [Roll Forward]
Beginning balance	$ 79,342	$ 61,809	$ 88,638
Change relating to prior year provision	(4,254)	247	(29,110)
Change relating to current year provision	1,083	17,378	2,304
Reductions based on the lapse of the applicable statutes of limitations	(111)	(92)	(23)
Ending balance	$ 76,060	$ 79,342	$ 61,809

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. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Numerator:
Net income (loss)	$ 360,089	$ 126,630	$ 87,494	$ 115,857	$ 38,489	$ 81,382	$ 17,656	$ 16,700	$ 690,070	$ 154,227	$ (70,222)
Net income allocated to participating securities									0	(367)	0
Net income (loss) allocable to common stock for basic net income (loss) per share									690,070	153,860	(70,222)
Adjustment to net income allocated to participating securities									0	22	0
Net income (loss) allocable to common stock for diluted net income (loss) per share									$ 690,070	$ 153,882	$ (70,222)
Denominator:
Weighted-average shares of common stock outstanding used in computing basic net income (loss) per share (in shares)									297,892	293,588	250,531
Outstanding stock options, unvested RSUs and ESPP contributions (in shares)									14,911	18,415	0
Weighted-average shares of common stock outstanding and dilutive securities used in computing diluted net income (loss) per share (in shares)									312,803	312,003	250,531
Net income (loss) per share, basic (in dollars per share)	$ 1.20	$ 0.42	$ 0.29	$ 0.39	$ 0.13	$ 0.28	$ 0.06	$ 0.06	$ 2.32	$ 0.52	$ (0.28)
Net income (loss) per share, diluted (in dollars per share)	$ 1.15	$ 0.41	$ 0.28	$ 0.37	$ 0.12	$ 0.26	$ 0.06	$ 0.05	$ 2.21	$ 0.49	$ (0.28)

Net Income (Loss) Per Share (Potentially Dilutive Shares of Common Stock) (Details) - shares shares in Thousands	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	3,968	1,645	62,458
Outstanding stock options, unvested RSUs and ESPP contributions [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	3,968	1,645	27,568
2014 Warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	0	0	1,000
Deerfield Notes [Member] \| Convertible debt [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total potentially dilutive shares	0	0	33,890

Net Income (Loss) Per Share - Narrative (Details)	Dec. 31, 2016 shares
2014 Warrants [Member]
Class of Warrant or Right [Line Items]
Warrants outstanding (in shares)	1,000,000

Fair Value Measurements (Schedule of Fair Value of Financial Assets Measured on A Recurring Basis) (Details) - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 29, 2017
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	$ 828,142	$ 440,410
Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	828,142	440,410
Financial assets	844,738	453,908
Recurring \| Level 1
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	47,744	45,478
Financial assets	47,744	45,478
Recurring \| Level 2
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	780,398	394,932
Financial assets	796,994	408,430
Money market funds
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	47,744	45,478
Money market funds \| Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	47,744	45,478
Money market funds \| Recurring \| Level 1
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	47,744	45,478
Money market funds \| Recurring \| Level 2
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	0	0
Commercial paper
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	381,133	199,647
Commercial paper \| Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	381,133	199,647
Commercial paper \| Recurring \| Level 1
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	0	0
Commercial paper \| Recurring \| Level 2
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	381,133	199,647
Corporate bonds
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	344,064	179,022
Corporate bonds \| Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	344,064	179,022
Corporate bonds \| Recurring \| Level 1
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	0	0
Corporate bonds \| Recurring \| Level 2
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	344,064	179,022
U.S. Treasury and government sponsored enterprises
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	55,201	16,263
U.S. Treasury and government sponsored enterprises \| Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	55,201	16,263
U.S. Treasury and government sponsored enterprises \| Recurring \| Level 1
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	0	0
U.S. Treasury and government sponsored enterprises \| Recurring \| Level 2
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments available-for-sale	55,201	16,263
Certificates of deposit
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Certificates of deposit	16,596	13,498
Certificates of deposit \| Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Certificates of deposit	16,596	13,498
Certificates of deposit \| Recurring \| Level 1
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Certificates of deposit	0	0
Certificates of deposit \| Recurring \| Level 2
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Certificates of deposit	$ 16,596	$ 13,498

Commitments (Leases Narrative (Details) $ in Thousands	12 Months Ended
Commitments (Leases Narrative (Details) $ in Thousands	Dec. 28, 2018 USD ($) ft² option
Lessee, Lease, Description [Line Items]
Tenant improvement reimbursements \| $	$ 8,170
Cash paid for amounts included in the measurement of lease liabilities \| $	$ 3,900
Weighted average remaining lease term for operating lease	9 years
Weighted average operating discount rate used to determine the operating lease liability	4.50%
Alameda, California
Lessee, Lease, Description [Line Items]
Area of leased property (in sqft)	134,765
Area of property available for lease (in squire feet)	170,000
South San Francisco, California
Lessee, Lease, Description [Line Items]
Area of leased property (in sqft)	116,063
Number of renewal options \| option	2

Commitments (Balance Sheet Classification of Lease Liabilities) (Details) - USD ($) $ in Thousands	Dec. 28, 2018	Dec. 30, 2017	Dec. 29, 2017
Operating lease liabilities:
Current portion included in Other current liabilities	$ 2,738
Current portion included in Other current liabilities			$ 540
Long-term portion of lease liabilities	12,099
Long-term portion of lease liabilities			408
Total operating lease liabilities	14,837
Total operating lease liabilities			948
Financing lease liabilities:
Financing obligation for build-to-suit lease	0		14,530
Current portion included in Other current liabilities	49		0
Long-term portion of lease liabilities	79		0
Total financing lease liabilities	128
Total lease liabilities	$ 14,965	$ 13,323
Total lease liabilities			$ 15,478

Commitments (Components of Lease Expense) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Operating lease cost	$ 4,189	$ 3,944	$ 8,620
Variable lease cost	1,661	2,216	1,056
Sublease income	0	(1,225)	(3,553)
Total lease costs	$ 5,850	$ 4,935	$ 6,123

Commitments (Maturities of Operating Lease Liabilities) (Details) $ in Thousands	Dec. 28, 2018 USD ($)
Years ending December 31,
2019	$ 2,794
2020	2,823
2021	2,904
2022	3,000
2023	3,082
Thereafter	13,584
Thereafter	28,187
Less:
Present value adjustment	(5,180)
Tenant improvement reimbursements	(8,170)
Operating lease liabilities	$ 14,837

Commitments (Letters of Credit and Restricted Cash Narrative) (Details)	12 Months Ended
	Dec. 28, 2018 USD ($) debt_instrument	Dec. 29, 2017 USD ($)
Operating Leased Assets [Line Items]
Collateral provided for purchasing card program	$ 3,000,000
Workers Compensation Insurance Policy
Operating Leased Assets [Line Items]
Line of credit borrowing capacity	100,000	$ 600,000
Building lease
Operating Leased Assets [Line Items]
Line of credit borrowing capacity	$ 500,000
Standby letters of credit
Operating Leased Assets [Line Items]
Number of letters of credit entered into (in debt instruments) \| debt_instrument	2
Line of credit borrowing capacity	$ 1,000,000	$ 1,000,000.0
Letters of credit outstanding	$ 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. 28, 2018	Sep. 28, 2018	Jun. 29, 2018	Mar. 30, 2018	Dec. 29, 2017	Sep. 30, 2017	Jun. 30, 2017	Mar. 31, 2017	Dec. 28, 2018	Dec. 29, 2017	Dec. 30, 2016
Quarterly Financial Information Disclosure [Abstract]
Total revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	$ 853,826	$ 452,477	$ 191,454
Gross profit	168,873	155,586	139,839	128,633	91,520	91,758	84,990	65,674
Income from operations	111,602	125,176	85,770	116,307	37,431	81,180	27,113	20,186	438,855	165,910	(28,124)
Net income	$ 360,089	$ 126,630	$ 87,494	$ 115,857	$ 38,489	$ 81,382	$ 17,656	$ 16,700	$ 690,070	$ 154,227	$ (70,222)
Net income per share, basic (in dollars per share)	$ 1.20	$ 0.42	$ 0.29	$ 0.39	$ 0.13	$ 0.28	$ 0.06	$ 0.06	$ 2.32	$ 0.52	$ (0.28)
Net income per share, diluted (in dollars per share)	$ 1.15	$ 0.41	$ 0.28	$ 0.37	$ 0.12	$ 0.26	$ 0.06	$ 0.05	$ 2.21	$ 0.49	$ (0.28)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Selling, general and administrative									$ 206,366	$ 159,362	$ 116,145
Revenues	$ 228,602	$ 225,397	$ 186,108	$ 213,719	$ 120,072	$ 152,510	$ 99,008	$ 80,887	853,826	452,477	191,454
Restatement
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Selling, general and administrative				$ (1,400)
Collaboration revenue
Quarterly Financial Information Disclosure [Abstract]
Total revenues									234,547	103,469	56,079
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Revenues									$ 234,547	$ 103,469	$ 56,079
Collaboration revenue \| Restatement
Quarterly Financial Information Disclosure [Abstract]
Total revenues								1,400
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Revenues								$ 1,400

Label	Element	Value
Accounting Standards Update 2014-09 [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 258,505,000
Accounting Standards Update 2014-09 [Member] \| Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	258,505,000
Accounting Standards Update 2016-09 [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	0
Accounting Standards Update 2016-09 [Member] \| Additional Paid-in Capital [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	252,000
Accounting Standards Update 2016-09 [Member] \| Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	(252,000)
Accounting Standards Update 2016-02 [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	234,000
Accounting Standards Update 2016-02 [Member] \| Retained Earnings [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 234,000