Collaborative Arrangements and Licensing Agreements (Details)	3 Months Ended		9 Months Ended																	9 Months Ended										1 Months Ended		9 Months Ended		12 Months Ended	9 Months Ended		9 Months Ended					9 Months Ended	1 Months Ended	9 Months Ended	1 Months Ended		3 Months Ended		9 Months Ended			1 Months Ended			3 Months Ended	9 Months Ended		12 Months Ended	24 Months Ended	36 Months Ended	1 Months Ended		3 Months Ended	9 Months Ended			1 Months Ended						3 Months Ended		9 Months Ended			1 Months Ended			3 Months Ended			9 Months Ended		19 Months Ended		9 Months Ended	3 Months Ended	9 Months Ended	12 Months Ended			9 Months Ended		12 Months Ended	1 Months Ended	9 Months Ended	12 Months Ended			1 Months Ended	9 Months Ended	12 Months Ended	1 Months Ended	9 Months Ended		12 Months Ended		1 Months Ended		9 Months Ended	12 Months Ended		9 Months Ended		1 Months Ended				3 Months Ended	9 Months Ended		1 Months Ended				3 Months Ended		9 Months Ended		12 Months Ended			3 Months Ended		9 Months Ended			3 Months Ended		9 Months Ended						1 Months Ended	3 Months Ended
	Sep. 30, 2011 USD ($)	Sep. 30, 2010 USD ($)	Sep. 30, 2011 USD ($)	Sep. 30, 2010 USD ($)	Sep. 30, 2011 Regulatory milestones Collaborations Genzyme Corporation USD ($)	Sep. 30, 2011 Regulatory milestones Collaborations Alnylam USD ($)	Apr. 30, 2005 Regulatory milestones Collaborations OncoGenex USD ($)	Aug. 31, 2003 Regulatory milestones Collaborations OncoGenex USD ($)	Sep. 30, 2011 Regulatory milestones Collaborations Bristol-Myers Squibb USD ($)	Sep. 30, 2011 Regulatory milestones Collaborations GlaxoSmithKline USD ($)	Sep. 30, 2011 Regulatory milestones Collaborations Eli Lilly and Company USD ($)	Sep. 30, 2011 Regulatory milestones Collaborations Atlantic Pharmaceuticals Limited, formerly Atlantic Healthcare (UK) Limited USD ($)	Sep. 30, 2011 Regulatory milestones Collaborations Excaliard Pharmaceuticals, Inc USD ($)	Sep. 30, 2011 Regulatory milestones Collaborations iCo Therapeutics Inc. USD ($)	Sep. 30, 2011 Regulatory milestones Collaborations Xenon Pharmaceuticals Inc. USD ($)	Sep. 30, 2011 Commercialized milestones Collaborations Genzyme Corporation USD ($)	Sep. 30, 2011 Commercialized milestones Collaborations GlaxoSmithKline USD ($)	Sep. 30, 2011 Commercialized milestones Collaborations Eli Lilly and Company USD ($)	Sep. 30, 2011 Commercialized milestones Collaborations Xenon Pharmaceuticals Inc. USD ($)	Sep. 30, 2011 Development milestones Collaborations Genzyme Corporation USD ($)	Sep. 30, 2011 Development milestones Collaborations Alnylam USD ($)	Apr. 30, 2005 Development milestones Collaborations OncoGenex USD ($)	Aug. 31, 2003 Development milestones Collaborations OncoGenex USD ($)	Sep. 30, 2011 Development milestones Collaborations Bristol-Myers Squibb USD ($)	Sep. 30, 2011 Development milestones Collaborations GlaxoSmithKline USD ($)	Sep. 30, 2011 Development milestones Collaborations Eli Lilly and Company USD ($)	Sep. 30, 2011 Development milestones Collaborations Excaliard Pharmaceuticals, Inc USD ($)	Sep. 30, 2011 Development milestones Collaborations iCo Therapeutics Inc. USD ($)	Sep. 30, 2011 Development milestones Collaborations Xenon Pharmaceuticals Inc. USD ($)	Feb. 28, 2009 Collaborations Phase 1 iCo Therapeutics Inc. CAD	Sep. 30, 2007 Collaborations Phase 1 iCo Therapeutics Inc. USD ($)	Sep. 30, 2011 Collaborations Phase 2 OncoGenex USD ($)	Sep. 30, 2011 Collaborations Phase 2 GlaxoSmithKline USD ($)	Dec. 31, 2010 Collaborations Phase 2 Achaogen, Inc. USD ($)	Sep. 30, 2011 Collaborations Phase 3 Alnylam USD ($)	Sep. 30, 2011 Collaborations Phase 3 OncoGenex USD ($)	Sep. 30, 2011 Collaborations Phase 3 Eli Lilly and Company USD ($)	Sep. 30, 2011 Collaborations Phase 3 Excaliard Pharmaceuticals, Inc USD ($)	Sep. 30, 2011 Collaborations Phase 3 iCo Therapeutics Inc. USD ($)	Apr. 30, 2005 Collaborations Clinical and regulatory milestones OncoGenex USD ($)	Aug. 31, 2003 Collaborations Clinical and regulatory milestones OncoGenex USD ($)	Sep. 30, 2011 Collaborations Minimum Genzyme Corporation	Dec. 31, 2009 Collaborations Minimum OncoGenex	Sep. 30, 2011 Collaborations Maximum Genzyme Corporation	Dec. 31, 2009 Collaborations Maximum OncoGenex	Jun. 30, 2008 Collaborations Genzyme Corporation USD ($)	Sep. 30, 2011 Collaborations Genzyme Corporation USD ($)	Sep. 30, 2010 Collaborations Genzyme Corporation USD ($)	Sep. 30, 2011 Collaborations Genzyme Corporation USD ($) D Y	Sep. 30, 2010 Collaborations Genzyme Corporation USD ($)	Dec. 31, 2010 Collaborations Genzyme Corporation USD ($)	Dec. 31, 2010 Collaborations Alnylam USD ($)	Nov. 30, 2010 Collaborations Alnylam USD ($)	Mar. 31, 2004 Collaborations Alnylam USD ($)	Sep. 30, 2010 Collaborations Alnylam USD ($)	Sep. 30, 2011 Collaborations Alnylam USD ($)	Sep. 30, 2010 Collaborations Alnylam USD ($)	Dec. 31, 2009 Collaborations Alnylam USD ($)	Dec. 31, 2010 Collaborations Alnylam USD ($)	Dec. 31, 2007 Collaborations Alnylam USD ($)	Dec. 31, 2009 Collaborations OncoGenex USD ($) D	Aug. 31, 2003 Collaborations OncoGenex USD ($)	Mar. 31, 2011 Collaborations OncoGenex USD ($)	Sep. 30, 2011 Collaborations OncoGenex USD ($)	Dec. 31, 2010 Collaborations OncoGenex USD ($)	Dec. 30, 2009 Collaborations OncoGenex USD ($)	Sep. 30, 2007 Collaborations Ortho-McNeil-Janssen Pharmaceuticals, Inc., formerly Ortho-McNeil, Inc. Programs	Jul. 31, 2010 Collaborations Bristol-Myers Squibb Y	Apr. 30, 2010 Collaborations Bristol-Myers Squibb USD ($)	Mar. 31, 2010 Collaborations Bristol-Myers Squibb USD ($)	Apr. 30, 2008 Collaborations Bristol-Myers Squibb USD ($)	May 31, 2007 Collaborations Bristol-Myers Squibb USD ($) Y	Sep. 30, 2011 Collaborations Bristol-Myers Squibb USD ($)	Sep. 30, 2010 Collaborations Bristol-Myers Squibb USD ($)	Sep. 30, 2011 Collaborations Bristol-Myers Squibb USD ($)	Sep. 30, 2010 Collaborations Bristol-Myers Squibb USD ($)	Sep. 30, 2011 Collaborations Bristol-Myers Squibb Development and regulatory milestones USD ($)	Oct. 31, 2011 Collaborations GlaxoSmithKline USD ($)	May 31, 2011 Collaborations GlaxoSmithKline USD ($) Y	Mar. 31, 2010 Collaborations GlaxoSmithKline Programs	Sep. 30, 2011 Collaborations GlaxoSmithKline USD ($)	Jun. 30, 2011 Collaborations GlaxoSmithKline USD ($)	Sep. 30, 2010 Collaborations GlaxoSmithKline USD ($)	Sep. 30, 2011 Collaborations GlaxoSmithKline USD ($)	Sep. 30, 2010 Collaborations GlaxoSmithKline USD ($)	Sep. 30, 2011 Collaborations GlaxoSmithKline USD ($)	Dec. 31, 2010 Collaborations GlaxoSmithKline USD ($)	Sep. 30, 2011 Collaborations Eli Lilly and Company USD ($)	Sep. 30, 2011 Collaborations Achaogen, Inc. USD ($)	Sep. 30, 2011 Collaborations Achaogen, Inc. USD ($)	Dec. 31, 2010 Collaborations Achaogen, Inc.	Dec. 31, 2006 Collaborations Achaogen, Inc. USD ($)	Dec. 31, 2009 Collaborations Achaogen, Inc. Pre-specified events USD ($)	Sep. 30, 2011 Collaborations Altair Therapeutics Inc.	Sep. 30, 2010 Collaborations Altair Therapeutics Inc. USD ($)	Dec. 31, 2010 Collaborations Altair Therapeutics Inc. USD ($)	Oct. 31, 2009 Collaborations Antisense Therapeutics Limited	Sep. 30, 2011 Collaborations Antisense Therapeutics Limited USD ($)	Dec. 31, 2010 Collaborations Antisense Therapeutics Limited USD ($)	Dec. 31, 2009 Collaborations Antisense Therapeutics Limited USD ($)	Dec. 31, 2008 Collaborations Antisense Therapeutics Limited USD ($)	Mar. 31, 2007 Collaborations Atlantic Pharmaceuticals Limited, formerly Atlantic Healthcare (UK) Limited USD ($)	Sep. 30, 2011 Collaborations Atlantic Pharmaceuticals Limited, formerly Atlantic Healthcare (UK) Limited USD ($)	Dec. 31, 2010 Collaborations Atlantic Pharmaceuticals Limited, formerly Atlantic Healthcare (UK) Limited	Nov. 30, 2007 Collaborations Excaliard Pharmaceuticals, Inc USD ($)	Sep. 30, 2011 Collaborations Excaliard Pharmaceuticals, Inc	Sep. 30, 2010 Collaborations Excaliard Pharmaceuticals, Inc USD ($)	Dec. 31, 2010 Collaborations Excaliard Pharmaceuticals, Inc	Sep. 30, 2011 Collaborations Excaliard Pharmaceuticals, Inc Clinical and regulatory milestones USD ($)	Jan. 31, 2010 Collaborations iCo Therapeutics Inc.	Aug. 31, 2005 Collaborations iCo Therapeutics Inc. USD ($)	Sep. 30, 2011 Collaborations iCo Therapeutics Inc. USD ($)	Dec. 31, 2010 Collaborations iCo Therapeutics Inc.	Sep. 30, 2011 Collaborations iCo Therapeutics Inc. Clinical and regulatory milestones USD ($)	Sep. 30, 2011 Collaborations Xenon Pharmaceuticals Inc. USD ($)	Sep. 30, 2011 Collaborations Archemix Corp. Pre-specified events USD ($)	Nov. 30, 2007 Collaborations Archemix Corp. Phase 2a USD ($)	Mar. 31, 2008 Collaborations AVI BioPharma, Inc., formerly Ercole Biotech, Inc.	Sep. 30, 2011 Collaborations AVI BioPharma, Inc., formerly Ercole Biotech, Inc. Pre-specified events USD ($)	Sep. 30, 2011 Collaborations AVI BioPharma, Inc., formerly Ercole Biotech, Inc. Clinical, regulatory and sales milestones USD ($)	Sep. 30, 2011 Collaborations CHDI Foundation, Inc. USD ($)	Sep. 30, 2011 Collaborations CHDI Foundation, Inc. USD ($)	Sep. 30, 2010 Collaborations CHDI Foundation, Inc. USD ($)	Jan. 31, 2009 Collaborations Abbott Molecular Inc. USD ($)	Jan. 31, 2009 Collaborations Abbott Molecular Inc. Minimum USD ($)	Jan. 31, 2009 Collaborations Abbott Molecular Inc. Maximum USD ($)	Dec. 31, 2001 Collaborations Eyetech Pharmaceuticals, Inc. USD ($)	Sep. 30, 2011 Collaborations Eyetech Pharmaceuticals, Inc. USD ($)	Sep. 30, 2010 Collaborations Eyetech Pharmaceuticals, Inc. USD ($)	Sep. 30, 2011 Collaborations Eyetech Pharmaceuticals, Inc. USD ($)	Sep. 30, 2010 Collaborations Eyetech Pharmaceuticals, Inc. USD ($)	Dec. 31, 2004 Collaborations Eyetech Pharmaceuticals, Inc. USD ($)	Sep. 30, 2011 Collaborations Eyetech Pharmaceuticals, Inc. Pre-specified events USD ($)	Dec. 31, 2004 Collaborations Eyetech Pharmaceuticals, Inc. Pre-specified events USD ($)	Sep. 30, 2011 Collaborations Roche Molecular Systems USD ($)	Sep. 30, 2010 Collaborations Roche Molecular Systems USD ($)	Sep. 30, 2011 Collaborations Roche Molecular Systems USD ($)	Sep. 30, 2010 Collaborations Roche Molecular Systems USD ($)	Dec. 31, 2010 Collaborations Roche Molecular Systems USD ($)	Sep. 30, 2011 Collaborations Idera Pharmaceuticals, Inc., formerly Hybridon, Inc. USD ($)	Sep. 30, 2010 Collaborations Idera Pharmaceuticals, Inc., formerly Hybridon, Inc. USD ($)	Sep. 30, 2011 Collaborations Idera Pharmaceuticals, Inc., formerly Hybridon, Inc. USD ($)	Sep. 30, 2010 Collaborations Idera Pharmaceuticals, Inc., formerly Hybridon, Inc. USD ($)	Sep. 30, 2011 Collaborations Integrated DNA Technologies, Inc. USD ($)	Sep. 30, 2011 Collaborations University of Massachusetts USD ($)	Sep. 30, 2011 Collaborations Verva Pharmaceuticals Ltd. Patent, clinical and regulatory milestones USD ($)	Sep. 30, 2011 Collaborations Cold Spring Harbor Laboratory Clinical and regulatory milestones USD ($)	Jun. 30, 2008 Genzyme Corporation USD ($)	Mar. 31, 2011 OncoGenex USD ($)
Collaborations
Milestone payment received and recognized in revenue																															$ 1,250,000						$ 5,000,000															$ 375,000																		$ 6,000,000	$ 2,000,000											$ 5,000,000				$ 15,000,000
Maximum number of programs under strategic alliance (in counts)																																																																			2													6
Amount received from expansion of collaboration																																																																															3,000,000
Collaborative arrangement payment																																																																																													1,000,000
Payment received and recognized in revenue, cash portion																																																																																													500,000
Next prospective milestone																				25,000,000												500,000			750,000			1,200,000	4,000,000																																				2,000,000			5,000,000						2,000,000																			600,000												2,000,000
Amount received from collaboration																																		2,000,000																																																																																			250,000
Upfront fee received																																																										11,000,000			10,000,000		750,000									15,000,000														35,000,000																			1,000,000						500,000																2,000,000																						750,000
Amortization period for amounts received from collaborative arrangements (in years)																																																																															5
Average maximum milestone payments receivable under strategic alliance																																	20,000,000
Maximum amount of license fees and milestone payments receivable under strategic alliance										506,500,000							570,000,000								358,500,000																																																								1,400,000,000			1,400,000,000		1,400,000,000		25,000,000
Revenue recognized throughout arrangement																																																											2,600,000																											48,000,000		4,100,000
Revenue recognized	20,189,000	27,785,000	64,508,000	77,484,000																																																	4,900,000																												2,000,000		6,800,000	10,700,000	8,500,000
Dividend received from collaborative partner																																																																																																408,000
Deferred revenue related to upfront fee																																															44,300,000		44,300,000		94,100,000														750,000																27,200,000			27,200,000		27,200,000	29,800,000												210,000																						203,000	203,000																	150,000
Revenue recognized																																															16,600,000	16,800,000	49,900,000	50,200,000					1,400,000		4,100,000							750,000									575,000	700,000	2,000,000	11,400,000													2,000,000	2,000,000					17,000			210,000		2,000,000							3,000					7,000									997,000	997,000	206,000					195,000	230,000	604,000	378,000				216,000	477,000	630,000	1,400,000		10,000	10,000	10,000	20,000
Equity investment in entity made by strategic alliance partner																																														150,000,000																																																																																																						150,000,000
Stock received as part of collaborative arrangement (in shares)																																																																																																	18,500,000
Equity investment in entity made by strategic alliance partner (in shares)																																														5,000,000																																																																																																						5,000,000
Equity investment in ISIS by strategic alliance partner, price per share (in dollars per share)																																														$ 30																																																																																																						$ 30
Percentage profit																																										30.00%		50.00%
Maximum amount of payments receivable under strategic alliance																																																																																																																				1,500,000			21,000,000														46,300,000	2,800,000
Maximum amount of milestone payments receivable under strategic alliance					750,000,000	2,300,000	4,500,000	2,000,000	195,000,000		8,000,000	1,400,000	40,000,000	40,500,000	150,000,000	825,000,000		12,000,000	120,000,000		1,100,000	1,300,000	1,500,000	50,000,000		5,000,000	7,700,000	7,900,000	30,000,000							1,300,000				5,800,000	3,500,000						1,500,000,000		1,500,000,000							3,400,000																					245,000,000																																47,700,000					48,400,000	300,000,000					21,000,000
Maximum amount of payments payable under strategic alliance																																																								3,400,000																																																															21,000,000																										650,000
Maximum amount of milestone payments payable under strategic alliance																																																																																																																																																		6,100,000	900,000
Eligible milestone payment, high end of range																																																													370,000,000
Maximum contribution in funding for development costs of Mipomersen																																																	125,000,000
Period after which rights to collaborative arrangement are purchased by party (in days)																																																													21
Premium amortized																																														100,000,000
License fee amortized																																														175,000,000																																																																																																						175,000,000
Upfront fee received as a percentage of total revenue																																															80.00%		75.00%																								3.00%		3.00%
Percent of total revenue																																																																																	10.00%			16.00%
Maximum amount of research funding receivable under strategic alliance																																																																								9,000,000
Initial period (in years)																																																	10																							3
Extended period (in years)																																																																				2
Milestone payment received and recognized in form of securities (in shares)																															936,875
Licensing and royalty revenue	524,000	839,000	2,175,000	4,569,000																																																																																																	1,400,000																															4,000,000
Shares purchase in the collaborative party																																																																																																														1,100,000
Ownership interest percentage																																																																																																							12.00%	12.00%								12.00%	12.00%
Ownership interest percentage, high end of range																																																	2.00%																																									10.00%	10.00%			10.00%				10.00%	10.00%							10.00%		10.00%
Percentage of revenue recognized																																																													30.00%
Royalties as percentage of sales																																											3.88%		7.00%
Revenue from research and development under agreement and licensing and royalty revenue	20,713,000	28,624,000	66,683,000	82,053,000
Amount raised by collaborative partner																														1,300,000																																																																					2,400,000
Period after which milestone method payment is receivable (in days)																																																	180
Value of milestone payment received and recognized in form of securities																																																														750,000
Upfront equity investment																																																																																												1,500,000										2,000,000
Payment received in form of securities																																																																																													500,000
Number of shares to be purchased under warrant at an exercise price of $0.1679 per share																																																																																																																						238,228
Number of shares to be purchased under warrant at an exercise price of $3.61 per share																																																																																																																						207,757
Technology access fee																																																						5,000,000		37,100,000
Expenses reimbursed																																																																																																																										1,700,000
Value of equity investment in party to collaborative arrangement																																																						10,000,000																																																																						215,000,000
Collaborative arrangement percentage of sales for earnout payments for sales between $140 million and $2.1 billion, maximum																																																																																																																												5.00%
Collaborative arrangement cumulative sales																																																																																																																													140,000,000	2,100,000,000
Collaborative arrangement percentage of sales for earnout payments for sales over $2.1 billion, maximum																																																																																																																												3.00%
Collaborative arrangement percentage of sales for earnout payments for sales between $140 million and $2.1 billion, minimum																																																																																																																												2.50%
Collaborative arrangement percentage of sales for earnout payments for sales over $2.1 billion, minimum																																																																																																																												1.50%
Upfront fee amortized																																																																					15,000,000
Gain on sale of equity investment in party to collaborative arrangement																																																												6,200,000
License fee paid																																																																																																																																																4,900,000
Proceeds from sale of securities																																																												12,200,000	2,800,000
Payment follow first commercial sale of product																																																																		$ 20,000,000