Collaborative Arrangements (Tables)

9 Months Ended

Sep. 30, 2012

Collaborative Arrangements

Revenues related to collaborative arrangements

	Three Months Ended September 30,						Nine Months Ended September 30,
	2012			2011			2012			2011
	(in thousands)
Royalty revenues	$	19,957		$	1,276		$	80,811		$	3,825
Collaborative revenues:
Amortized portion of up-front payment	$	3,107		$	3,107		$	9,321		$	9,321
Milestone revenues		—			200,000			—			250,000
Net payment for telaprevir development costs		(503	)		(2,557	)		(2,569	)		(6,810	)
Reimbursement for manufacturing services		—			7,170			4,449			20,383
Total collaborative revenues attributable to the Janssen collaboration	$	2,604		$	207,720		$	11,201		$	272,894
Total revenues attributable to the Janssen collaboration	$	22,561		$	208,996		$	92,012		$	276,719

	Three Months Ended September 30,				Nine Months Ended September 30,
	2012		2011		2012		2011
	(in thousands)
Amortized portion of up-front payments	$	—	$	9,558	$	12,744	$	28,674
Milestone revenues		—		1,758		485		3,152
Payments for manufacturing services		—		8,184		5,650		14,032
Total collaborative revenues attributable to the Mitsubishi Tanabe collaboration	$	—	$	19,500	$	18,879	$	45,858

Summary of activity related to net loss (income) attributable to noncontrolling interest (Alios)

	Three Months Ended September 30,						Nine Months Ended September 30,
	2012			2011			2012			2011
	(in thousands)
Loss (income) before provision for income taxes	$	5,090		$	5,258		$	14,581		$	6,059
Decrease (increase) in fair value of contingent milestone and royalty payments		(57,560	)		(17,450	)		(112,760	)		(17,450	)
Provision for income taxes		21,394			4,850			40,354			29,298
Net loss (income) attributable to noncontrolling interest (Alios)	$	(31,076	)	$	(7,342	)	$	(57,825	)	$	17,907

Summary of Alios' items included in the Company's consolidated balance sheets

	As of September 30, 2012		As of December 31, 2011
	(in thousands)
Restricted cash and cash equivalents (Alios)	$	74,954	$	51,878
Prepaid expenses and other current assets		1,642		2,299
Property and equipment, net		1,754		1,925
Intangible assets		250,600		250,600
Goodwill		4,890		4,890
Other assets		153		133
Accounts payable		1,616		4,132
Accrued expenses		4,983		4,304
Income taxes payable (Alios)		3,871		12,075
Deferred tax liability		151,880		116,121
Other liabilities, excluding current portion		1,174		1,030
Redeemable noncontrolling interest (Alios)		38,299		37,036
Noncontrolling interest (Alios)		198,714		141,633