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