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Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($)
9 Months Ended
Sep. 30, 2020
Sep. 30, 2019
Cash flows from operating activities:    
Net loss $ (327,237,000) $ (328,503,000)
Adjustments to reconcile net loss to net cash used in operating activities:    
Non-cash royalty revenue related to sale of future royalties (28,001,000) (27,585,000)
Non-cash interest expense on liability related to sale of future royalties 22,084,000 17,853,000
Stock-based compensation 72,274,000 74,787,000
Depreciation and amortization 10,937,000 9,582,000
Impairment of advance payments to contract manufacturers and equipment for terminated program 20,351,000 0
Accretion of premiums (discounts), net and other non-cash transactions 1,150,000 (9,147,000)
Changes in operating assets and liabilities:    
Accounts receivable (6,123,000) 2,008,000
Inventory (227,000) (2,339,000)
Operating leases, net 4,316,000 11,550,000
Other assets (5,588,000) 18,127,000
Accounts payable (3,337,000) 16,109,000
Accrued compensation 20,478,000 13,164,000
Other accrued expenses 9,340,000 10,401,000
Deferred revenue (5,070,000) (9,465,000)
Net cash used in operating activities (214,653,000) (203,458,000)
Cash flows from investing activities:    
Purchases of investments (791,445,000) (1,028,883,000)
Maturities of investments 1,158,722,000 1,122,902,000
Sales of investments 41,700,000 0
Purchases of property, plant and equipment (5,504,000) (22,614,000)
Net cash provided by investing activities 403,473,000 71,405,000
Cash flows from financing activities:    
Proceeds from shares issued under equity compensation plans 20,651,000 18,449,000
Repayment of senior notes (250,000,000) 0
Net cash provided by (used in) financing activities (229,349,000) 18,449,000
Effect of foreign exchange rates on cash and cash equivalents 9,000 (77,000)
Net decrease in cash and cash equivalents (40,520,000) (113,681,000)
Cash and cash equivalents at beginning of period 96,363,000 194,905,000
Cash and cash equivalents at end of period 55,843,000 81,224,000
Supplemental disclosures of cash flow information:    
Cash paid for interest 9,742,000 14,299,000
Operating lease right-of-use asset recognized in exchange for lease liabilities $ 2,133,000 $ 56,025,000