Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Cash flows from operating activities
Net loss	$ (18,542)	$ (115,344)	$ (83,862)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	7,326	7,583	6,336
(Gain) loss on sales of available-for-sale securities	(9)	2	(3)
Stock-based compensation	23,783	24,916	19,009
Loss on disposal of equipment	196		33
Forgiveness of notes receivable		16	8
Changes in operating assets and liabilities:
Receivables from collaboration partners	(841)	(29)	81
Prepaid and other current assets	(441)	2,288	652
Inventories	(4,822)
Other assets, non-current	(441)
Accounts payable	(1,480)	3,310	(236)
Accrued personnel-related expenses and other accrued liabilities	(1,829)	5,124	3,321
Deferred rent	(747)	2,429	1,446
Deferred revenue	(130,107)	(18,633)	(21,801)
Other long-term liabilities			(128)
Net cash used in operating activities	(127,954)	(88,338)	(75,144)
Cash flows from investing activities
Purchases of property and equipment	(2,590)	(3,628)	(861)
Purchases of short-term investments and marketable securities	(330,484)	(301,563)	(183,899)
Maturities of short-term investments and marketable securities	224,902	231,476	131,855
Sales of short-term investments and marketable securities	49,729	17,321	12,024
Sale of equipment			12
Release of restricted cash	60		417
Issuance of notes receivable	(140)	(140)
Payments received on notes receivable	240	715	140
Net cash used in investing activities	(58,283)	(55,819)	(40,312)
Cash flows from financing activities
Payments on note payable and capital leases	(69)	(206)	(184)
Proceeds from issuances of common stock, net	236,377	25,808	231,429
Net cash provided by financing activities	236,308	25,602	231,245
Net increase (decrease) in cash and cash equivalents	50,071	(118,555)	115,789
Cash and cash equivalents at beginning of period	44,778	163,333	47,544
Cash and cash equivalents at end of period	94,849	44,778	163,333
Supplemental Disclosure of Cash Flow Information
Cash paid for interest	$ 5,177	$ 5,195	$ 5,217