CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017		Mar. 31, 2016
CASH FLOWS FROM OPERATING ACTIVITIES:
Net loss	$ (16,290)		$ (83,051)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	19,412		18,726
Non-cash interest expense	7,755		7,337
Accretion of discount on investments	660		309
Stock-based compensation	30,674		30,177
Gain on the sale of equity investments	(3,252)		0
Deferred income taxes	(10,441)		(21,368)
Unrealized foreign exchange gain on forward contracts	(1,730)		(6,526)
Non-cash changes in the fair value of contingent acquisition consideration payable	1,353		2,936
Other	969		526
Changes in operating assets and liabilities:
Accounts receivable, net	(14,051)		(16,044)
Inventory	(22,660)		(10,285)
Other current assets	2,763		2,399
Other assets	(527)		(1,232)
Accounts payable and accrued liabilities	(77,822)		(90,744)
Other long-term liabilities	2,744		(4,614)
Net cash used in operating activities	(80,443)		(171,454)
CASH FLOWS FROM INVESTING ACTIVITIES:
Purchases of property, plant and equipment	(69,090)		(45,204)
Maturities and sales of investments	149,916		181,267
Purchase of available-for-sale securities	(54,388)		(58,914)
Other	(1,391)		(150)
Net cash provided by investing activities	25,047		76,999
CASH FLOWS FROM FINANCING ACTIVITIES:
Proceeds from exercises of stock options and the Employee Stock Purchase Plan	13,086		3,521
Taxes paid related to net share settlement of equity awards	(17,935)		(40,788)
Payment of contingent acquisition consideration payable	(1,894)		0
Other	0		3
Net cash used in financing activities	(6,743)		(37,264)
Effect of exchange rate changes on cash	2,043		5,132
NET DECREASE IN CASH AND CASH EQUIVALENTS	(60,096)		(126,587)
Cash and cash equivalents:
Beginning of period	408,330	[1]	397,040
End of period	348,234		270,453
SUPPLEMENTAL CASH FLOW DISCLOSURES:
Cash paid for income taxes	6,376		73,215
Stock-based compensation capitalized into inventory	3,226		2,469
Depreciation capitalized into inventory	5,508		4,135
SUPPLEMENTAL CASH FLOW DISCLOSURES FOR NON CASH INVESTING AND FINANCING ACTIVITIES:
Decrease in accounts payable and accrued liabilities related to fixed assets	(26,297)		(14,788)
Accrual for inventory purchases related to the acquisition of the Merck PKU Business	$ 0		$ 2,436

[1] December 31, 2016 balances were derived from the audited Consolidated Financial Statements included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016, filed with the Securities and Exchange Commission (the SEC) on February 27, 2017.