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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($)
$ in Thousands
 6 Months Ended
Jun. 30, 2018
Jun. 30, 2017
Cash flows from operating activities:    
Net loss $ (304,774) $ (225,710)
Adjustments to reconcile net loss to net cash used in operating activities:    
Depreciation, amortization and accretion, net 5,417 6,066
Stock-based compensation 41,825 39,747
Non-cash gain on litigation settlement (10,000)  
Charge for 401(k) company stock match 2,326 1,074
Unrealized gain on marketable equity securities (2,044)  
Realized loss on sale of marketable equity securities   1,894
Other   608
Changes in operating assets and liabilities:    
Proceeds from landlord lease incentive for tenant improvements 4,480  
Billed and unbilled collaboration receivables 31,041 7,929
Prepaid expenses and other assets (21,261) (198)
Accounts payable (9,735) (8,326)
Accrued expenses and other 7,261 (3,404)
Deferred revenue (2,887) (1,059)
Net cash used in operating activities (258,351) (181,379)
Cash flows from investing activities:    
Purchases of property, plant and equipment (43,965) (57,803)
Purchases of restricted investments (14,825)  
Purchases of marketable debt securities (642,787) (237,184)
Sales and maturities of marketable securities 629,384 302,392
Net cash (used in) provided by investing activities (72,193) 7,405
Cash flows from financing activities:    
Proceeds from exercise of stock options and other types of equity 47,735 12,644
Proceeds from issuance of common stock, net of offering costs   355,150
Proceeds from issuance of common stock to Sanofi Genzyme   21,381
Payments for repurchase of common stock for employee tax withholding (632) (147)
Net cash provided by financing activities 47,103 389,028
Net (decrease) increase in cash, cash equivalents and restricted cash (283,441) 215,054
Cash, cash equivalents and restricted cash, beginning of period 646,832 195,088
Cash, cash equivalents and restricted cash, end of period $ 363,391 $ 410,142