Alnylam Pharmaceuticals (ALNY) 10-K13 Feb 152014 FY Annual reportFinancial data

Company Profile

Document_and_Entity_Informatio

Document and Entity Information (USD $)	12 Months Ended
Document and Entity Information (USD $)	Dec. 31, 2014	Jan. 30, 2015	Jun. 30, 2014
Document Information [Line Items]
Document Type	10-K
Amendment Flag	FALSE
Document Period End Date	31-Dec-14
Document Fiscal Year Focus	2014
Document Fiscal Period Focus	FY
Trading Symbol	ALNY
Entity Registrant Name	ALNYLAM PHARMACEUTICALS, INC.
Entity Central Index Key	1178670
Current Fiscal Year End Date	-19
Entity Well-known Seasoned Issuer	Yes
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		83,760,143
Entity Public Float			$4,772,901,068

CONSOLIDATED_BALANCE_SHEETS

CONSOLIDATED BALANCE SHEETS (USD $)	Dec. 31, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013
Current assets:
Cash and cash equivalents	$75,179	$53,169
Marketable securities	526,929	192,701
Investment in equity securities of Regulus Therapeutics Inc	94,583
Billed and unbilled collaboration receivables	39,937	4,248
Prepaid expenses and other current assets	9,739	3,910
Total current assets	746,367	254,028
Marketable securities	279,821	104,602
Deferred tax assets	31,667
Investment in equity securities of Regulus Therapeutics Inc.		45,452
Property and equipment, net	21,740	16,448
Total assets	1,079,595	420,530
Current liabilities:
Accounts payable	15,111	5,896
Accrued expenses	23,680	14,160
Deferred tax liabilities	31,667
Deferred rent	1,005	1,112
Deferred revenue	23,871	32,696
Total current liabilities	95,334	53,864
Deferred rent, net of current portion	5,011	2,925
Deferred revenue, net of current portion	42,983	93,394
Total liabilities	143,328	150,183
Commitments and contingencies (Note 7)
Stockholders' equity:
Preferred stock, $0.01 par value per share, 5,000,000 shares authorized and no shares issued and outstanding at December 31, 2014 and 2013
Common stock, $0.01 par value per share, 125,000,000 shares authorized; 77,202,753 shares issued and outstanding at December 31, 2014; 63,741,573 shares issued and outstanding at December 31, 2013	772	637
Additional paid-in capital	1,843,362	846,228
Accumulated other comprehensive income	48,763	19,717
Accumulated deficit	-956,630	-596,235
Total stockholders' equity	936,267	270,347
Total liabilities and stockholders' equity	$1,079,595	$420,530

CONSOLIDATED_BALANCE_SHEETS_Pa

CONSOLIDATED BALANCE SHEETS (Parenthetical) (USD $)	Dec. 31, 2014	Dec. 31, 2013
Preferred stock, par value	$0.01	$0.01
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value	$0.01	$0.01
Common stock, shares authorized	125,000,000	125,000,000
Common stock, shares issued	77,202,753	63,741,573
Common stock, shares outstanding	77,202,753	63,741,573

CONSOLIDATED_STATEMENTS_OF_COM

CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2014		Dec. 31, 2013		Dec. 31, 2012
Net revenues from collaborators	$50,561		$47,167		$66,725
Operating expenses:
Research and development	190,249	[1]	112,957	[1]	86,569	[1]
In-process research and development	220,766
General and administrative	44,526	[1]	27,152	[1]	44,612	[1]
Restructuring of Tekmira license agreement					65,000
Total operating expenses	455,541		140,109		196,181
Loss from operations	-404,980		-92,942		-129,456
Other income (expense):
Equity in loss of joint venture (Regulus Therapeutics Inc.)					-4,522
Gain on issuance of stock by Regulus Therapeutics Inc.					16,084
Interest income	2,559		1,069		977
Other income (expense)	1,817		-47		331
Total other income	4,376		1,022		12,870
Loss before income taxes	-400,604		-91,920		-116,586
Benefit from income taxes	40,209		2,695		10,572
Net loss	-360,395		-89,225		-106,014
Net loss per common share - basic and diluted	($4.85)		($1.45)		($2.11)
Weighted-average common shares used to compute basic and diluted net loss per common share	74,278		61,551		50,286
Comprehensive loss:
Net loss	-360,395		-89,225		-106,014
Unrealized gain on marketable securities, net of tax	31,127		4,055		15,827
Reclassification adjustment for realized gain on marketable securities included in net loss	-2,081
Comprehensive loss	($331,349)		($85,170)		($90,187)

[1]	Non-cash stock-based compensation expenses included in operating expenses are as follows: Research and development $ 18,233 $ 14,369 $ 8,041 General and administrative 14,828 6,334 4,319

CONSOLIDATED_STATEMENTS_OF_COM1

CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS (Parenthetical) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Non-cash stock-based compensation expenses included in operating expenses are as follows:
Non-cash stock-based compensation	$33,061	$20,703	$12,360
Research and Development Expense
Non-cash stock-based compensation expenses included in operating expenses are as follows:
Non-cash stock-based compensation	18,233	14,369	8,041
General and Administrative Expense
Non-cash stock-based compensation expenses included in operating expenses are as follows:
Non-cash stock-based compensation	$14,828	$6,334	$4,319

CONSOLIDATED_STATEMENTS_OF_STO

CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY (USD $)	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
In Thousands, except Share data	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
Balance at Dec. 31, 2011	$117,997	$427	$518,731	($165)	($400,996)
Balance (in shares) at Dec. 31, 2011		42,721,942
Exercise of common stock options (in shares)		661,909
Exercise of common stock options	6,402	7	6,395
Issuance of common stock under other types of equity plans (in shares)		97,459
Issuance of common stock under other types of equity plans	879	1	878
Issuance of restricted stock, net of cancellations and tax withholdings (in shares)		383,626
Issuance of restricted stock, net of cancellations and tax withholdings	-519	4	-523
Issuance of common stock, net of offering costs (in shares)		8,625,000
Issuance of common stock, net of offering costs	86,800	86	86,714
Stock-based compensation expense	12,360		12,360
Joint venture stock-based compensation expense (Regulus Therapeutics Inc.)	321		321
Other comprehensive income	15,827			15,827
Net loss	-106,014				-106,014
Balance at Dec. 31, 2012	134,053	525	624,876	15,662	-507,010
Balance (in shares) at Dec. 31, 2012		52,489,936
Exercise of common stock options (in shares)		2,031,916
Exercise of common stock options	27,994	20	27,974
Issuance of common stock under other types of equity plans (in shares)		60,180
Issuance of common stock under other types of equity plans	1,184	1	1,183
Tax withholdings and cancellations of restricted stock, net of issuances of new awards, shares		-40,459
Tax withholdings and cancellations of restricted stock, net of issuances of new awards	-1,989	-1	-1,988
Issuance of common stock, net of offering costs (in shares)		9,200,000
Issuance of common stock, net of offering costs	173,572	92	173,480
Stock-based compensation expense	20,703		20,703
Other comprehensive income	4,055			4,055
Net loss	-89,225				-89,225
Balance at Dec. 31, 2013	270,347	637	846,228	19,717	-596,235
Balance (in shares) at Dec. 31, 2013		63,741,573
Exercise of common stock options (in shares)	1,982,000	1,972,204
Exercise of common stock options	28,449	20	28,429
Issuance of common stock under other types of equity plans (in shares)		31,122
Issuance of common stock under other types of equity plans	1,581	1	1,580
Tax withholdings and cancellations of restricted stock, net of issuances of new awards, shares		-172,976
Tax withholdings and cancellations of restricted stock, net of issuances of new awards	-15,392	-2	-15,390
Issuance of common stock, net of offering costs (in shares)		9,110,786
Issuance of common stock, net of offering costs	774,487	91	774,396
Issuance of common stock in connection with an asset acquisition (in shares)		2,520,044
Issuance of common stock in connection with an asset acquisition	195,766	25	195,741
Stock-based compensation expense	33,061		33,061
Tax provision associated with intraperiod tax allocation	-20,683		-20,683
Other comprehensive income	31,127			31,127
Reclassification adjustment for realized gain on marketable securities included in net loss	-2,081			-2,081
Net loss	-360,395				-360,395
Balance at Dec. 31, 2014	$936,267	$772	$1,843,362	$48,763	($956,630)
Balance (in shares) at Dec. 31, 2014		77,202,753

CONSOLIDATED_STATEMENTS_OF_CAS

CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Cash flows from operating activities:
Net loss	($360,395)	($89,225)	($106,014)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	11,926	10,229	9,035
Non-cash stock-based compensation	33,061	20,703	12,360
Charge for 401(k) company stock match	692	449	364
Equity in loss of joint venture (Regulus Therapeutics Inc.)			4,522
Realized gain on sale of marketable securities	-2,081		-255
Gain on issuance of stock by joint venture			-16,084
Benefit from intraperiod tax allocation	-40,209	-2,695	-10,572
In-process research and development	220,766
Changes in operating assets and liabilities:
Proceeds from landlord tenant improvements	1,941	204	1,780
Billed and unbilled collaboration receivables	-35,689	-4,144	1,364
Prepaid expenses and other assets	-5,829	-1,356	1,780
Accounts payable	8,840	1,832	-1,736
Accrued expenses and other	9,122	1,547	-3,591
Deferred revenue	-7,786	-6,201	-8,562
Net cash used in operating activities	-165,641	-68,657	-115,609
Cash flows from investing activities:
Purchases of property and equipment	-8,961	-4,006	-8,348
Increase in restricted cash			-162
Purchases of marketable securities	-977,775	-364,305	-277,129
Sales and maturities of marketable securities	462,922	237,806	289,013
Payment for asset acquisition	-25,000
Net cash (used in) provided by investing activities	-548,814	-130,505	3,374
Cash flows from financing activities:
Proceeds from exercise of stock options and other types of equity	29,420	28,743	6,971
Proceeds from issuance of common stock, net of offering costs		173,572	86,800
Proceeds from issuance of common stock to Genzyme	723,037
Payments for repurchase of common stock for employee tax withholding	-15,992	-1,389	-359
Net cash provided by financing activities	736,465	200,926	93,412
Net increase (decrease) in cash and cash equivalents	22,010	1,764	-18,823
Cash and cash equivalents, beginning of period	53,169	51,405	70,228
Cash and cash equivalents, end of period	75,179	53,169	51,405
Supplemental disclosure of cash flows:
Net cash proceeds from income tax refunds (cash paid for income taxes)	517	-11	-17
Supplemental disclosure of noncash investing and financing activities:
Fixed asset expenditures included in accounts payable and accrued expenses	1,526	161	1,441
Fair value of common stock issued for asset acquisition	195,766
Receipt of common stock for exercises of stock options	1,219
Difference in fair value of common stock issued to Genzyme less cash proceeds received	51,450
Repurchase of common stock for employee tax withholding in accrued expenses		$600

NATURE_OF_BUSINESS

NATURE OF BUSINESS	12 Months Ended
	Dec. 31, 2014
NATURE OF BUSINESS	1	NATURE OF BUSINESS
	We commenced operations on June 14, 2002 as a biopharmaceutical company seeking to develop and commercialize novel therapeutics based on RNA interference, or RNAi. We are focused on discovering, developing and commercializing RNAi therapeutics by establishing strategic alliances with leading pharmaceutical and life sciences companies, establishing and maintaining a strong intellectual property position in the RNAi field, generating revenues through licensing agreements, and ultimately developing and commercializing RNAi therapeutics for our own account. We have devoted substantially all of our efforts to business planning, research and development, acquiring, filing and expanding intellectual property rights, recruiting management and technical staff, and raising capital.

SUMMARY_OF_SIGNIFICANT_ACCOUNT

SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

12 Months Ended

Dec. 31, 2014

SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES

Basis of Presentation and Principles of Consolidation

The accompanying consolidated financial statements reflect the operations of Alnylam and our wholly-owned subsidiaries. All intercompany accounts and transactions have been eliminated.

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America, or GAAP, requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.

Concentrations of Credit Risk and Significant Customers

Financial instruments that potentially expose us to concentrations of credit risk consist primarily of cash, cash equivalents and fixed income marketable securities. At December 31, 2014 and 2013, substantially all of our cash, cash equivalents and fixed income marketable securities were invested in money market mutual funds, certificates of deposit, commercial paper, corporate notes, municipal debt securities, U.S. government-sponsored enterprise securities and U.S. treasury securities through highly rated financial institutions. Investments are restricted, in accordance with our investment policy, to a concentration limit per issuer.

In recent periods, our revenues from collaborations have been generated from primarily F. Hoffmann-La Roche Ltd and certain of its affiliates, collectively, Roche, which assigned its rights and obligations to Arrowhead Research Corporation, or Arrowhead, in 2011, Takeda Pharmaceutical Company Limited, or Takeda, Cubist Pharmaceuticals, Inc., or Cubist, Monsanto Company, or Monsanto, and The Medicines Company, or MDCO. For the year ended December 31, 2014, our billed and unbilled collaboration receivables were composed primarily of amounts due from Genzyme Corporation, a Sanofi company, or Genzyme, and MDCO based upon the achievement of certain milestones and, also with respect to MDCO, expense reimbursement. For the year ended December 31, 2013, our billed and unbilled collaboration receivables were composed primarily of an amount due from Genzyme based upon the initiation of a Phase 3 clinical trial.

The following table summarizes customers that represent greater than 10% of our net revenues from collaborators, for the periods indicated:

Year Ended

December 31,

2014

2013

2012

Takeda

Monsanto

MDCO

Cubist

Roche/Arrowhead

The following table summarizes customers with amounts due that represent greater than 10% of our billed and unbilled collaboration receivables balance, at the periods indicated:

At December 31,

2014

2013

Genzyme

MDCO

Represents 10% or less

Fair Value Measurements

The fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are observable, such as quoted prices (adjusted), interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points for the asset or liability, and include situations where there is little, if any, market activity for the asset or liability. The fair value hierarchy level is determined by the lowest level of significant input.

Investments in Marketable Securities

We invest our excess cash balances in short-term and long-term marketable debt and equity securities. We classify our investments in marketable debt securities as either held-to-maturity or available-for-sale based on facts and circumstances present at the time we purchased the securities. At each balance sheet date presented, we classified all of our investments in debt and equity securities as available-for-sale. We report available-for-sale investments at fair value at each balance sheet date and include any unrealized holding gains and losses (the adjustment to fair value) in accumulated other comprehensive income (loss), a component of stockholders’ equity. At December 31, 2014, the balance in our accumulated other comprehensive income was composed solely of activity related to our available-for-sale marketable securities, including our investment in equity securities of Regulus Therapeutics Inc., or Regulus. Realized gains and losses are determined using the specific identification method and are included in other income. We recognized $2.1 million of realized gains from sales of our Regulus available-for-sale securities as other income on our consolidated statements of comprehensive loss during the year ended December 31, 2014. If any adjustment to fair value reflects a decline in the value of the investment, we consider all available evidence to evaluate the extent to which the decline is “other than temporary,” including our intention to sell and, if so, mark the investment to market through a charge to our consolidated statements of comprehensive loss. We did not record any impairment charges related to our fixed income marketable securities during the years ended December 31, 2014, 2013 or 2012. Our marketable securities are classified as cash equivalents if the original maturity, from the date of purchase, is 90 days or less, and as marketable securities if the original maturity, from the date of purchase, is in excess of 90 days. Our cash equivalents are composed of money market funds.

In the fourth quarter of 2012, we began accounting for our investment in Regulus as an available-for-sale marketable security. Intraperiod tax allocation rules require us to allocate our provision for income taxes between continuing operations and other categories of earnings, such as other comprehensive income. In periods in which we have a year-to-date pre-tax loss from continuing operations and pre-tax income in other categories of earnings, such as other comprehensive income, we must allocate the tax provision to the other categories of earnings. We then record a related tax benefit in continuing operations. Upon sales of our available-for-sale marketable securities, we apply the aggregate portfolio approach. As a result, the disproportionate tax effect remains in accumulated other comprehensive income as long as we maintain an investment portfolio.

Estimated Liability for Development Costs

We record accrued liabilities related to expenses for which service providers have not yet billed us with respect to products we have received or services that we have incurred, specifically related to ongoing pre-clinical studies and clinical trials. These costs primarily relate to third-party clinical management costs, laboratory and analysis costs, toxicology studies and investigator fees. We have multiple product candidates in concurrent pre-clinical studies and clinical trials at multiple clinical sites throughout the world. In order to ensure that we have adequately provided for ongoing pre-clinical and clinical development costs during the period in which we incur such costs, we maintain an accrual to cover these expenses. We update the estimate for this accrual on at least a quarterly basis. The assessment of these costs is a subjective process that requires judgment. Upon settlement, these costs may differ materially from the amounts accrued in our consolidated financial statements. Our historical accrual estimates have not been materially different from our actual costs.

Revenue Recognition

We have entered into collaboration agreements with leading pharmaceutical and life sciences companies, including Novartis Pharma AG and one of its affiliates, together, Novartis, Roche, Takeda, Kyowa Hakko Kirin Co., Ltd., or Kyowa Hakko Kirin, Cubist, Monsanto, Genzyme and MDCO. The terms of our collaboration agreements typically include non-refundable license fees, funding of research and development, payments based upon achievement of clinical and pre-clinical development milestones, regulatory milestones, manufacturing services, sales milestones and royalties on product sales.

In January 2011, we adopted new authoritative guidance on revenue recognition for multiple element arrangements. The guidance, which applied to multiple element arrangements entered into or materially modified on or after January 1, 2011, amended the criteria for separating and allocating consideration in a multiple element arrangement by modifying the fair value requirements for revenue recognition and eliminating the use of the residual method. The fair value of deliverables under the arrangement may be derived using a “best estimate of selling price” if vendor specific objective evidence and third-party evidence is not available. Deliverables under the arrangement could be considered separate units of accounting provided that (i) a delivered item has value to the customer on a standalone basis and (ii) if the arrangement includes a general right of return relative to the delivered item, delivery or performance of the undelivered item is considered probable and substantially in the control of the vendor. The new guidance did not change the criteria for standalone value. As a biotechnology entity with unique and specialized delivered and undelivered performance obligations, we have been unable to demonstrate standalone value in our multiple element arrangements. For example, we applied the new rules to collaborations executed with Monsanto and Genzyme during 2012, but we were unable to demonstrate standalone value for the delivered license element. In addition, we have not materially modified any of our multiple element arrangements entered into prior to 2011.

Non-refundable license fees are recognized as revenue upon delivery of the license only if we have a contractual right to receive such payment, the contract price is fixed or determinable, the collection of the resulting receivable is reasonably assured and we have no further performance obligations under the license agreement. Multiple element arrangements, such as license and development arrangements, are analyzed to determine whether the deliverables, which often include a license and performance obligations such as research and steering committee services, can be separated or whether they must be accounted for as a single unit of accounting. We recognize upfront license payments as revenue upon delivery of the license only if the license has standalone value and the fair value of the undelivered performance obligations, typically including research and/or steering committee services, can be determined. If the fair value of the undelivered performance obligations can be determined, such obligations are accounted for separately as such obligations are fulfilled. If the license is considered to either not have standalone value or have standalone value but the fair value of any of the undelivered performance obligations cannot be determined, the arrangement would then be accounted for as a single unit of accounting and the license payments and payments for performance obligations are recognized as revenue over the estimated period of when the performance obligations are performed and or deferred indefinitely until the undelivered performance obligation can be determined.

Whenever we determine that an arrangement should be accounted for as a single unit of accounting, we determine the period over which the performance obligations will be performed and revenue will be recognized. Revenue is recognized using either a proportional performance or straight-line method. We recognize revenue using the proportional performance method when the level of effort required to complete our performance obligations under an arrangement can be reasonably estimated and such performance obligations are provided on a best-efforts basis. Direct labor hours or full-time equivalents are typically used as the measure of performance. The amount of revenue recognized under the proportional performance method is determined by multiplying the total payments under the contract, excluding royalties and payments contingent upon achievement of milestones, by the ratio of level of effort incurred to date to estimated total level of effort required to complete our performance obligations under the arrangement. Revenue is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the proportional performance method, as of the period ending date.

If we cannot reasonably estimate the level of effort to complete our performance obligations under an arrangement, we recognize revenue under the arrangement on a straight-line basis over the period we are expected to complete our performance obligations. Revenue is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the straight-line method, as of the period ending date.

Significant management judgment is required in determining the level of effort required under an arrangement and the period over which we are expected to complete our performance obligations under an arrangement. Steering committee services that are not inconsequential or perfunctory and that are determined to be performance obligations are combined with other research services or performance obligations required under an arrangement, if any, in determining the level of effort required in an arrangement and the period over which we expect to complete our aggregate performance obligations.

Many of our collaboration agreements entitle us to additional payments upon the achievement of performance-based milestones. These milestones are generally categorized into three types; development milestones which are generally based on the advancement of our pipeline and initiation of clinical trials, regulatory milestones which are generally based on the submission, filing or approval of regulatory applications such as a new drug application in the United States, and commercialization milestones which are generally based on meeting specific thresholds of sales in certain geographic areas. If the achievement of a milestone is considered probable at the inception of the collaboration, the related milestone payment is included with other collaboration consideration, such as upfront fees and research funding, in our revenue model. Milestones that are tied to regulatory approval are not considered probable of being achieved until such approval is received. Milestones tied to counter-party performance are not included in our revenue model until the performance conditions are met. Upfront and ongoing development milestones are not subject to refund if the development activities are not successful.

We perform an assessment to determine whether a substantive milestone exists at the inception of our collaborative arrangements. In evaluating if a milestone is substantive, we consider whether uncertainty exists as to the achievement of the milestone event at the inception of the arrangement, the achievement of the milestone involves substantive effort and can only be achieved based in whole or part on the performance or the occurrence of a specific outcome resulting from our performance, the amount of the milestone payment appears reasonable either in relation to the effort expected to be expended or to the projected enhancement of the value of the delivered items, there is any future performance required to earn the milestone, and the consideration is reasonable relative to all deliverables and payment terms in the arrangement. When a substantive milestone is achieved, the accounting rules permit us to recognize revenue related to the milestone payment in its entirety.

To date, we have not recorded any substantive milestones under our collaborations because we have not identified any milestones that meet the required criteria listed above. We have deferred recognition of payments for achievement of non-substantive milestones and recognized revenue over the estimated period of performance applicable to each collaborative arrangement. As these milestones are achieved, we will recognize as revenue a portion of the milestone payment, which is equal to the percentage of the performance period completed when the milestone is achieved, multiplied by the amount of the milestone payment, upon achievement of such milestone. We will recognize the remaining portion of the milestone payment over the remaining performance period under the proportional performance method or on a straight-line basis.

For revenue generating arrangements where we, as a vendor, provide consideration to a licensor or collaborator, as a customer, we apply the accounting standard that governs such transactions. This standard addresses the accounting for revenue arrangements where both the vendor and the customer make cash payments to each other for services and/or products. A payment to a customer is presumed to be a reduction of the selling price unless we receive an identifiable benefit for the payment and it can reasonably estimate the fair value of the benefit received. Payments to a customer that are deemed a reduction of selling price are recorded first as a reduction of revenue, to the extent of both cumulative revenue recorded to date and probable future revenues, which include any unamortized deferred revenue balances, under all arrangements with such customer, and then as an expense. Payments that are not deemed to be a reduction of selling price are recorded as an expense.

We evaluate our collaborative agreements for proper classification in our consolidated statements of comprehensive loss based on the nature of the underlying activity. Transactions between collaborators recorded in our consolidated statements of comprehensive loss are recorded on either a gross or net basis, depending on the characteristics of the collaborative relationship. We generally reflect amounts due under our collaborative agreements related to cost-sharing of development activities as revenue.

Amounts received prior to satisfying the above revenue recognition criteria are recorded as deferred revenue in the accompanying consolidated balance sheets. Although we follow detailed guidelines in measuring revenue, certain judgments affect the application of our revenue policy. For example, in connection with our existing collaboration agreements, we have recorded on our balance sheet short-term and long-term deferred revenue based on our best estimate of when such revenue will be recognized. Short-term deferred revenue consists of amounts that are expected to be recognized as revenue in the next 12 months. Amounts that we expect will not be recognized within the next 12 months are classified as long-term deferred revenue. However, this estimate is based on our current operating plan and, if our operating plan should change in the future, we may recognize a different amount of deferred revenue over the next 12-month period.

The estimate of deferred revenue also reflects management’s estimate of the periods of our involvement in certain of our collaborations. Our performance obligations under these collaborations consist of participation on steering committees and the performance of other research and development services. In certain instances, the timing of satisfying these obligations can be difficult to estimate. Accordingly, our estimates may change in the future. Such changes to estimates would result in a change in revenue recognition amounts. If these estimates and judgments change over the course of these agreements, it may affect the timing and amount of revenue that we recognize and record in future periods. At December 31, 2014, we had short-term and long-term deferred revenue of $23.9 million and $43.0 million, respectively, related to our collaborations.

Income Taxes

We use the asset and liability method of accounting for income taxes. Under the asset and liability method, deferred tax assets and liabilities reflect the impact of temporary differences between amounts of assets and liabilities for financial reporting purposes and such amounts as measured under enacted tax laws. A valuation allowance is required to offset any net deferred tax assets if, based upon the available evidence, it is more likely than not that some or all of the deferred tax asset will not be realized.

We account for uncertain tax positions using a “more-likely-than-not” threshold for recognizing and resolving uncertain tax positions. The evaluation of uncertain tax positions is based on factors that include, but are not limited to, changes in tax law, the measurement of tax positions taken or expected to be taken in tax returns, the effective settlement of matters subject to audit, new audit activity and changes in facts or circumstances related to a tax position. Our policy is to accrue interest and penalties related to unrecognized tax positions in income tax expense. As of December 31, 2014, we have not recorded significant interest and penalty expense related to uncertain tax positions.

Research and Development Costs

We expense research and development costs as incurred. Included in research and development costs are wages, benefits and other operating costs, facilities, supplies, external services, clinical trial and manufacturing costs, and overhead directly related to our research and development operations, as well as costs to acquire technology licenses.

We have entered into several license agreements for rights to utilize certain technologies. The terms of the licenses may provide for upfront payments, annual maintenance payments, milestone payments based upon certain specified events being achieved and royalties on product sales. We charge costs to acquire and maintain licensed technology that has not reached technological feasibility and does not have alternative future use to research and development expense as incurred. During the years ended December 31, 2014, 2013 and 2012, we charged to research and development expense costs associated with license fees of $12.1 million, $8.0 million and $5.7 million, respectively.

Accounting for Stock-Based Compensation

We have stock incentive plans and an employee stock purchase plan under which we grant equity instruments. We account for all stock-based awards granted to employees at their fair value and generally recognize compensation expense over the vesting period of the award. Determining the amount of stock-based compensation to be recorded requires us to develop estimates of fair values of stock options as of the grant date. We calculate the grant date fair values using the Black-Scholes valuation model. Our expected stock price volatility assumption is based on the historical volatility of our publicly traded stock.

For stock-based awards granted to non-employees, we generally recognize compensation expense over the vesting period of the award, which is generally the period during which services are rendered by such non-employees. At the end of each financial reporting period prior to vesting, we re-measure the value of these stock-based awards (as calculated using the Black-Scholes option-pricing model) using the then-current fair value of our common stock. Stock options granted by us to non-employees, other than members of our Board of Directors and Scientific Advisory Board members, generally vest over the service period.

The fair value of restricted stock awards granted to employees is based upon the quoted closing market price per share on the date of grant, adjusted for assumed forfeitures. Expense is recognized over the vesting period, commencing when we determine that it is probable that the awards will vest.

For performance-based stock awards, expense is first recorded when we determine that the achievement of such performance conditions is deemed probable. This determination requires significant judgment by management. At the probable date, we record a cumulative expense catch-up, with remaining expense amortized over the remaining service period.

Comprehensive Loss

Comprehensive loss is comprised of net loss and certain changes in stockholders’ equity that are excluded from net loss. We include foreign currency translation adjustments in other comprehensive loss for Alnylam Europe AG, or Alnylam Europe, as the functional currency is not the United States dollar. We include unrealized gains and losses on certain marketable securities in other comprehensive loss.

Net Loss Per Common Share

We compute basic net loss per common share by dividing net loss by the weighted-average number of common shares outstanding. We compute diluted net loss per common share by dividing net loss by the weighted-average number of common shares and dilutive potential common share equivalents then outstanding. Potential common shares consist of shares issuable upon the exercise of stock options (using the treasury stock method), and unvested restricted stock awards. Because the inclusion of potential common shares would be anti-dilutive for all periods presented, diluted net loss per common share is the same as basic net loss per common share.

The following table sets forth for the periods presented the potential common shares (prior to consideration of the treasury stock method) excluded from the calculation of net loss per common share because their inclusion would be anti-dilutive, in thousands:

At December 31,

2014

2013

2012

Options to purchase common stock

8,169

8,713

8,932

Unvested restricted common stock

500

604

8,199

9,213

9,536

Segment Information

We operate in a single reporting segment, the discovery, development and commercialization of RNAi therapeutics.

Subsequent Events

We did not have any material recognized subsequent events. However, we did have the following nonrecognized subsequent events, which are more fully described in Notes 3 and 8:

•

In January 2015, we sold an aggregate of 5,447,368 shares of our common stock through an underwritten public offering at a price to the public of $95.00 per share. See Note 8.

•

In January 2015, in connection with our public offering, we sold an aggregate of 744,566 shares of our common stock to Genzyme through concurrent private placements at the public offering price of $95.00 per share. See Note 3.

Recent Accounting Pronouncements

In May 2014, the Financial Accounting Standards Board, or FASB, issued a new revenue recognition standard which amends revenue recognition principles and provides a single, comprehensive set of criteria for revenue recognition within and across all industries. The new standard provides a five step framework whereby revenue is recognized when promised goods or services are transferred to a customer at an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. The standard also requires enhanced disclosures pertaining to revenue recognition in both interim and annual periods. For public companies, the standard is effective for interim and annual reporting periods beginning after December 15, 2016. Early adoption is not permitted. The standard allows for adoption using a full retrospective method or a modified retrospective method. We are currently evaluating the method of adoption and the expected impact that the standard could have on our consolidated financial statements and related disclosures.

In June 2014, the FASB issued guidance that share-based payment awards with performance targets that affect vesting and could be achieved after the requisite service period should be accounted for as performance conditions. As a result, performance targets are not reflected in estimating the award’s grant date fair value. Stock-based compensation expense is recognized over the requisite service period if the achievement of the performance condition is probable. The standard is effective for interim and annual reporting periods beginning after December 15, 2015. Early adoption is permitted. We do not expect the standard will have an impact on our consolidated financial statements and related disclosures since our accounting for share-based payment awards with performance targets is consistent with this guidance.

SIGNIFICANT_AGREEMENTS

SIGNIFICANT AGREEMENTS

12 Months Ended

Dec. 31, 2014

SIGNIFICANT AGREEMENTS

The following table summarizes our total consolidated net revenues from collaborators, for the periods indicated, in thousands:

Year Ended December 31,

2014

2013

2012

Takeda

21,973

Monsanto

14,985

5,640

1,954

MDCO

10,753

4,604

—

Roche/Arrowhead

1,000

—

37,318

Cubist

—

9,721

2,777

Other

1,850

5,229

2,703

Total net revenues from collaborators

50,561

47,167

66,725

Product Alliances

Genzyme Collaboration

In January 2014, we entered into a global, strategic collaboration with Genzyme to discover, develop and commercialize RNAi therapeutics as Genetic Medicines to treat orphan diseases. The 2014 Genzyme collaboration superseded and replaced the previous collaboration between us and Genzyme entered into in October 2012 to develop and commercialize RNAi therapeutics targeting transthyretin, or TTR, for the treatment of TTR-mediated amyloidosis, or ATTR, including patisiran and revusiran, in Japan and the Asia-Pacific region.

2012 Genzyme Agreement

Under the 2012 Genzyme agreement, Genzyme paid us an upfront cash payment of $22.5 million. We were also entitled to receive certain milestone payments under the 2012 Genzyme agreement. In the fourth quarter of 2013, we earned a milestone of $7.0 million based upon the completion of a successful patisiran Phase 2 clinical trial and a milestone of $4.0 million based upon the initiation of the Phase 3 clinical trial for patisiran.

Under the 2012 Genzyme agreement, the parties agreed to collaborate in the development and commercialization of licensed products, with Genzyme assuming primary responsibility in the Genzyme territory, which included Japan and the Asia-Pacific region, and us retaining primary responsibility in the rest of the world.

We determined that the deliverables under the 2012 Genzyme agreement included the license, a joint steering committee and any additional TTR-specific RNAi therapeutic compounds that comprised the ALN-TTR program. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and undelivered joint steering committee and any additional TTR-specific RNAi therapeutic compounds did not have standalone value due to the specialized nature of the services to be provided by us. In addition, while Genzyme had the ability to grant sublicenses, it could not sublicense all or substantially all of its rights under the 2012 Genzyme agreement. The uniqueness of our services and the limited sublicense right were indicators that standalone value was not present in the arrangement. Therefore the deliverables were not separable and, accordingly, the license and undelivered services were treated as a single unit of accounting. We were unable to reasonably estimate the period of performance under the 2012 Genzyme agreement, as we were unable to estimate the timeline of our deliverables related to the deliverable for any additional TTR-specific RNAi therapeutic compounds. Through December 31, 2013, we had deferred all revenue, or $33.5 million, under the 2012 Genzyme agreement.

2014 Genzyme Collaboration

In January 2014, we entered into the 2014 Genzyme collaboration. As noted above, the 2014 Genzyme collaboration superseded and replaced the 2012 Genzyme agreement.

The 2014 Genzyme collaboration is structured as an exclusive relationship for the worldwide development and commercialization of RNAi therapeutics in the field of Genetic Medicines, which includes our current and future Genetic Medicine programs that reach Human Proof-of-Principle Study Completion (as defined in the Genzyme master agreement), or Human POP, by the end of 2019, subject to extension to the end of 2021 in various circumstances. We will retain product rights in North America and Western Europe, referred to as the Alnylam Territory, while Genzyme will obtain exclusive rights to develop and commercialize collaboration products in the rest of the world, referred to as the Genzyme Territory, together with certain broader co-development/co-promote or worldwide rights for certain products. Genzyme’s rights, described in detail below, are structured as an opt-in that is triggered upon achievement of Human POP. We maintain development control for all programs prior to Genzyme’s opt-in and maintain development and commercialization control after Genzyme’s opt-in for all programs in the Alnylam Territory.

Specifically, in addition to its regional rights for our current and future Genetic Medicine programs in the Genzyme Territory, Genzyme has the right to either (i) co-develop and co-promote ALN-AT3 for the treatment of hemophilia and other rare bleeding disorders in the Alnylam Territory, with us maintaining development and commercialization control, or (ii) obtain a global license to ALN-AS1 for the treatment of hepatic porphyrias. Genzyme may exercise this selection right upon the completion of Human POP for both the ALN-AT3 and ALN-AS1 programs. Finally, Genzyme has the right for a global license to a single, future Genetic Medicine program that was not one of our defined Genetic Medicine programs as of the effective date of the 2014 Genzyme collaboration. We will retain global rights to any RNAi therapeutic Genetic Medicine program that does not reach Human POP by the end of 2019, subject to certain limited exceptions. We retain full rights to all current and future RNAi therapeutic programs outside of the field of Genetic Medicines, including the right to form new collaborations.

Under the 2014 Genzyme collaboration, Genzyme’s specific license rights include the following:

•

Regional license terms — Upon opt-in, we will retain product rights in the Alnylam Territory, while Genzyme will obtain exclusive rights to develop and commercialize the product in the Genzyme Territory. Genzyme can elect this license for any of our current and future Genetic Medicine programs that complete Human POP by the end of 2019, subject to limited extension. Development costs for products once Genzyme exercises an option will be shared between Genzyme and us, with Genzyme responsible for twenty percent of the global development costs. Upon the effective date of the 2014 Genzyme collaboration, Genzyme expanded the scope of its regional license and collaboration for patisiran, an investigational RNAi therapeutic currently in a Phase 3 clinical trial, which was originally established under the 2012 Genzyme agreement. Genzyme will be required to make payments totaling up to $50.0 million upon the achievement of certain patisiran development milestones. In addition, Genzyme will be required to make payments totaling up to $75.0 million per product other than patisiran, including up to $55.0 million in development milestones and $20.0 million in commercial milestones. We could potentially earn the next patisiran milestone payment, ranging between $5.0 million and $20.0 million based on the geographic region, upon the achievement of specified events in connection with a regulatory filing or approval. Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for each regional product based on annual net sales, if any, of such regional product by Genzyme, its affiliates and sublicensees.

•

Co-development/co-promote license terms — Upon opt-in, we will retain product rights in the Alnylam Territory, while Genzyme will obtain exclusive rights to develop and commercialize the product in the Genzyme Territory, and will co-promote the product in the Alnylam Territory. Upon the effective date of the 2014 Genzyme collaboration, Genzyme expanded its regional rights for revusiran, an investigational RNAi therapeutic currently in a Phase 3 clinical trial, which were originally granted under the 2012 Genzyme agreement, to include a co-development/co-promote license and collaboration. Genzyme also has the right to elect a co-development/co-promote license and collaboration for ALN-AT3, if it does not elect a global license and collaboration for ALN-AS1. Development costs for co-development/co-promote products, once Genzyme exercises an option, will be shared between Genzyme and us, with Genzyme responsible for fifty percent of the global development costs. Genzyme will be required to make payments totaling up to $75.0 million in development milestones for each of revusiran and ALN-AT3, if selected. In December 2014, we earned a development milestone payment of $25.0 million based upon the initiation of the first global Phase 3 clinical trial for revusiran. We could potentially earn the next revusiran milestone payment, ranging between $5.0 million and $25.0 million based on the geographic region, upon the achievement of specified events in connection with regulatory approval. Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for each co-development/co-promote product based on annual net sales, if any, in the Genzyme Territory for such co-development/co-promote product by Genzyme, its affiliates and sublicensees. The parties will share profits equally and we expect to book product sales in the Alnylam Territory.

•

Global license terms — Global license terms – Upon opt-in, Genzyme will obtain a worldwide license to develop and commercialize the product. Genzyme can elect a global license for ALN-AS1, if it does not elect a co-development/co-promote license for ALN-AT3. Genzyme will also have one right to a global license through 2019, subject to limited extension, for a future Genetic Medicine program that was not one of our defined Genetic Medicine programs as of the effective date of the 2014 Genzyme collaboration. Genzyme shall be responsible for one hundred percent of global development costs. Genzyme will be required to make payments totaling up to $200.0 million per global product, including up to $60.0 million in development milestones and $140.0 million in commercial milestones. Genzyme will also be required to pay tiered double-digit royalties up to twenty percent for each global product based on annual net sales, if any, of each global product by Genzyme, its affiliates and sublicensees.

Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Genzyme under the 2014 Genzyme collaboration.

Under the master agreement, the parties will collaborate in the development of option products, with us leading development for all programs prior to Genzyme’s opt-in and also leading development and commercialization for all programs in the Alnylam Territory after Genzyme’s opt-in. If Genzyme does not exercise its option to license rights to a particular program, we will retain the exclusive right to develop and commercialize such program throughout the world, including the right to sublicense to third parties.

The 2014 Genzyme collaboration is governed by an alliance joint steering committee that is comprised of an equal number of representatives from each party. There will also be additional committees to manage various aspects of each regional, co-developed/co-promoted and global program. We and Genzyme intend to enter into supply agreements to provide for supply of collaboration products to Genzyme for clinical studies, and, at Genzyme’s request, commercial sales. Genzyme also has certain rights to manufacture collaboration products. Additionally, Genzyme has certain limited opt-out rights, as specified in the master agreement, upon which products revert fully back to us with no further obligations to Genzyme.

The master agreement (including the license terms appended thereto) contains certain termination provisions, including for material breach by the other party. Unless terminated earlier pursuant to its terms, the master agreement will terminate upon the last to expire of any of the option periods under the master agreement or the license terms appended thereto.

Upon the closing of the equity transaction in February 2014, we sold to Genzyme 8,766,338 shares of our common stock and Genzyme paid $700.0 million in aggregate cash consideration to us. As a condition to the closing of the equity transaction, Genzyme entered into an investor agreement with us. Under the investor agreement, until the earlier of the fifth anniversary of the expiration or earlier termination of the 2014 Genzyme collaboration and the date on which Genzyme and its affiliates cease to beneficially own at least 5% of our outstanding common stock, Genzyme and its affiliates are bound by certain “standstill” provisions. The standstill provisions include agreements not to acquire more than 30% of our outstanding common stock, call stockholder meetings, nominate directors other than those approved by our board of directors, subject to certain limited exceptions, or propose or support a proposal to acquire us. Further, Genzyme has agreed to vote, and cause its affiliates to vote, all shares of our voting securities they are entitled to vote, up to a maximum of 20% of our outstanding common stock, in a manner either as recommended by our board of directors or proportionally with the votes cast by our other stockholders, except with respect to certain change of control transactions or our liquidation or dissolution. Until Genzyme owns less than 7.5% of our outstanding common stock, subject to Genzyme’s limited right to maintain its ownership percentage as described below, if we issue common stock or securities convertible into or exercisable for common stock to a third party that holds at least 30% of our outstanding common stock or, in connection with a collaboration or license transaction, to a third party that will initially hold at least the percentage of our outstanding common stock represented by the shares purchased by Genzyme at the closing of the equity transaction, we will offer Genzyme an opportunity to amend the standstill and voting provisions in the investor agreement to be consistent with the terms provided to such third party.

Under the investor agreement, Genzyme has also agreed not to dispose of any shares of common stock beneficially owned by it immediately after the closing of the stock purchase until the earlier of (i) December 31, 2019 (subject to extension by up to two years if Genzyme’s option to select additional compounds under the master agreement is extended beyond December 31, 2019) and (ii) six months after the expiration or earlier valid termination of the collaboration, in each case subject to earlier termination in the event certain clinical activities under the collaboration fail to occur. Following the expiration of this lock-up period, Genzyme will be permitted to sell such shares of common stock subject to certain limitations, including volume and manner of sale restrictions. Notwithstanding the foregoing, following the two-year anniversary of the closing of the stock purchase, in the event that the market price per share of our common stock is at least 100% higher than the market price per share of our common stock at closing of the stock purchase (in each case based upon a ten-day trailing average), Genzyme may sell up to 25% of its initial shares, subject to certain restrictions on post-lock-up period dispositions as described above.

Under the investor agreement, following the lock-up period, Genzyme will have three demand rights to require us to conduct a registered underwritten public offering with respect to the shares of common stock beneficially owned by Genzyme immediately after the closing of the stock purchase. In addition, following the lock-up period, subject to certain conditions, Genzyme will be entitled to participate in registered underwritten public offerings by us if other selling stockholders are included in the registration.

The investor agreement provides that, until Genzyme owns less than 7.5% of our outstanding common stock, subject to Genzyme’s limited right to maintain its ownership percentage as described herein, in connection with new issuances of common stock, subject to certain exceptions, Genzyme will be entitled to a right of first offer to participate proportionally to maintain its then-current ownership percentage of our common stock. If Genzyme is not entitled to a right of first offer with respect to a new issuance, Genzyme will have the opportunity, on a post-transaction basis, to purchase additional shares sufficient to maintain its pre-transaction ownership percentage of our common stock (subject to the same 7.5% ownership threshold).

Finally, in the event Genzyme and its affiliates acquire at least 20% or more of our outstanding common stock, Genzyme will be entitled to appoint one individual to our board of directors. Genzyme will also be entitled to certain information rights, including with respect to financial information in the event Genzyme or its affiliates require such information for its own financial reporting purposes. The rights and restrictions under the investor agreement are subject to termination upon the occurrence of certain events.

We recorded the issuance of 8,766,338 shares of our common stock under the stock purchase agreement using the price of our common stock on the date the shares were issued to Genzyme. Based on the common stock price of $85.72, the fair value of the shares issued was $751.5 million, which was $51.5 million in excess of the proceeds received from Genzyme for the issuance of our common stock. This $51.5 million is being amortized on a straight-line basis over the performance period, which is currently approximately six years as described below. In addition, due to intraperiod tax allocation rules, upon closing of the equity transaction we recorded a benefit from income taxes of $15.2 million due to the Genzyme equity purchase being recorded in additional paid-in capital, net of tax. For the year ended December 31, 2014, we recorded a cumulative benefit from income taxes of $20.7 million.

In accordance with the investor agreement, as a result of our issuance of shares in connection with our acquisition of Sirna Therapeutics, Inc., or Sirna, in March 2014, Genzyme exercised its right to purchase an additional 344,448 shares of our common stock for approximately $23.0 million. In addition, in January 2015, in connection with our public offering, Genzyme exercised its right to purchase directly from us, in concurrent private placements, 744,566 shares of common stock at the public offering price resulting in approximately $70.7 million in proceeds to us. The sales of common stock to Genzyme were not registered as part of the public offering, though they were consummated simultaneously with the public offering.

In addition, as part of these rights under our investor agreement with Genzyme, Genzyme has the right each January to purchase a number of shares of our common stock based on the number of shares we issued during the previous year for compensatory purposes. Genzyme exercised this right to purchase directly from us 196,251 shares of our common stock on January 22, 2015 for approximately $18.3 million. The sale of these shares to Genzyme was consummated as a private placement. In each instance, the purchase by Genzyme described above allowed Genzyme to maintain its ownership level of our common stock of approximately 12%.

We determined that the deliverables for the programs Genzyme is currently collaborating with us on include the licenses to our patisiran and revusiran clinical programs, which licenses were delivered to Genzyme upon the closing date of the transaction, and the associated development activities, joint steering committee participation and information exchange for these clinical programs. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and associated undelivered development activities, joint steering committee participation and information exchange activities did not have standalone value due to the specialized nature of the services to be provided by us. In addition, while Genzyme has the ability to grant sublicenses, it cannot sublicense all or substantially all of its rights under the 2014 Genzyme collaboration. The uniqueness of our services and the limited sublicense rights are indicators that standalone value is not present in the arrangement. Therefore the deliverables are not separable and, accordingly, the license and undelivered services were treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, we base our revenue recognition model on the final deliverable. Under the 2014 Genzyme collaboration, the last deliverables for patisiran and revusiran are expected to be completed within approximately six years.

We determined that the total cash received from Genzyme under the now superseded 2012 Genzyme agreement reflects consideration for certain of the performance obligations for ALN-TTR programs included in the 2014 Genzyme collaboration. Therefore we are recognizing the $33.5 million of deferred revenue under the 2012 Genzyme agreement on a straight-line basis over the period of performance of the ALN-TTR programs, which, as noted above, is currently approximately six years. In addition, during the fourth quarter of 2014, we recognized as revenue a portion of the $25.0 million milestone payment earned in December 2014 equal to the percentage of the performance period completed when the milestone was earned. As future consideration, including any milestones or reimbursement for development activities, are achieved, we will recognize as revenue a portion of these payments equal to the percentage of the performance period completed when the milestone or activities have been satisfied, multiplied by the amount of the payment. We will recognize the remaining portion of consideration received over the remaining performance period on a straight-line basis. At December 31, 2014, deferred revenue under the 2014 Genzyme collaboration was $6.7 million.

We determined that the opt-in rights that Genzyme has for future Genetic Medicine programs represent separate and additional deliverables that Genzyme may receive from us in future periods. Upon each opt-in by Genzyme, we have determined that each program and the related activities will represent a single unit of accounting and, consistent with our accounting policies, we will base our revenue recognition period on the final deliverable associated with each future opt-in, if any.

The Medicines Company Alliance

In February 2013, we and MDCO entered into a license and collaboration agreement pursuant to which we granted to MDCO an exclusive, worldwide license to develop, manufacture and commercialize RNAi therapeutics targeting PCSK9 for the treatment of hypercholesterolemia and other human diseases, including ALN-PCSsc. MDCO paid us an upfront cash payment of $25.0 million. Upon achievement of certain events, we will be entitled to receive milestone payments, up to an aggregate of $180.0 million, including up to $30.0 million in specified development milestones, $50.0 million in specified regulatory milestones and $100.0 million in specified commercialization milestones. In addition, we will be entitled to royalties ranging from the low- to high- teens based on annual worldwide net sales, if any, of licensed products by MDCO, its affiliates and sublicensees, subject to reduction under specified circumstances. In December 2014, we earned a development milestone payment of $10.0 million under the MDCO agreement based upon the initiation of our Phase 1 clinical trial for ALN-PCSsc. In addition, in December 2014, we earned $4.8 million for reimbursement of costs incurred for certain development activities. We could potentially earn the next development milestone payment of $20.0 million based upon the initiation of a pivotal study for ALN-PCSsc. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from MDCO.

Under the MDCO agreement, we and MDCO will collaborate in the further development of ALN-PCSsc. We will retain responsibility for the development of ALN-PCSsc until Phase 1 Completion, as defined in the MDCO agreement, at our cost, up to an agreed upon initial development cost cap. MDCO will assume all other responsibility for the development and commercialization of ALN-PCSsc, at its sole cost. The collaboration between us and MDCO is governed by a joint steering committee comprised of an equal number of representatives from each party.

We are solely responsible for obtaining supply of finished product reasonably required for the conduct of our obligations under the initial development plan through Phase 1 Completion, and supplying MDCO with finished product reasonably required for the first Phase 2 clinical trial of ALN-PCSsc conducted by MDCO, at our expense, provided such costs do not exceed the development costs cap, subject to certain exceptions. After such time, MDCO will have the sole right and responsibility to manufacture and supply ALN-PCSsc for development and commercialization under the MDCO development plan, subject to the terms of the MDCO agreement. We and MDCO intend to enter into a supply and technical transfer agreement to provide for supply of ALN-PCSsc to MDCO within a specified time following the effective date of the MDCO agreement.

Unless terminated earlier in accordance with the terms of the agreement, the MDCO Agreement expires on a licensed product-by-licensed product and country-by-country basis upon expiration of the last royalty term for any licensed product in any country, where a royalty term is defined as the latest to occur of (1) the expiration of the last valid claim of patent rights covering a licensed product, (2) the expiration of the Regulatory Exclusivity, as defined in the MDCO Agreement, and (3) the twelfth anniversary of the first commercial sale of the licensed product in such country. We estimate that our fundamental RNAi patents covering licensed products under the MDCO Agreement will expire both in and outside of the United States generally between 2015 and 2028. We also estimate that our ALN-PCS product-specific patents covering licensed products under the MDCO Agreement in the United States and elsewhere will expire at the end of 2033. These patent rights are subject to potential patent term extensions and/or supplemental protection certificates extending such terms in countries where such extensions may become available. In addition, more patent filings relating to the collaboration may be made in the future.

Either party may terminate the MDCO Agreement in the event the other party fails to cure a material breach or upon patent-related challenges by the other party. In addition, MDCO has the right to terminate the agreement without cause at any time upon four months’ prior written notice.

During the term of the MDCO agreement, neither party will, alone or with an affiliate or third party, research, develop or commercialize, or grant a license to any third party to research, develop or commercialize, in any country, any product directed to the PCSK9 gene, other than a licensed product, without the prior written agreement of the other party, subject to the terms of the MDCO agreement.

We have determined that the significant deliverables under the MDCO agreement include the license, the joint steering committee, technology transfer obligations, development activities through Phase 1 Completion and supply of product for a Phase 2 clinical trial. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and collective undelivered activities and services do not have standalone value due to the specialized nature of the activities and services to be provided by us. In addition, while MDCO has the ability to grant sublicenses, it must receive our prior written consent to sublicense all or substantially all of its rights. The uniqueness of our services and the limited sublicense right are indicators that standalone value is not present in the arrangement. Therefore the deliverables are not separable and, accordingly, the license and undelivered services are being treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, we base our revenue recognition pattern on the final deliverable. Under the MDCO agreement, all deliverables are expected to be completed within five years. We are recognizing revenue under the MDCO agreement on a straight-line basis over five years. We are not utilizing a proportional performance model since we are unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the effort required under the development activities is largely unknown.

We received the upfront payment of $25.0 million from MDCO in February 2013, which was initially recorded as deferred revenue. During the fourth quarter of 2014, we recognized as revenue a portion of the $10.0 million milestone payment earned in December 2014 equal to the percentage of the performance period completed when the milestone was earned. During the fourth quarter of 2014, we also recognized as revenue a portion of the $4.8 million expense reimbursement due to us under the terms of the MDCO agreement equal to the percentage of the performance period completed upon invoice date. As future consideration, including any milestones or reimbursement for development activities, are earned, we will recognize as revenue a portion of these payments equal to the percentage of the performance period completed when the milestone or service has been satisfied, multiplied by the amount of the payment. We will recognize the remaining portion of consideration received over the remaining performance period on a straight-line basis. At December 31, 2014, deferred revenue under the MDCO agreement was $24.7 million.

Platform Alliances

Monsanto Alliance

In August 2012, we and Monsanto entered into a license and collaboration agreement, pursuant to which we granted to Monsanto a worldwide, exclusive, royalty bearing right and license, including the right to grant sublicenses, to our RNAi platform technology and intellectual property controlled by us as of the date of the Monsanto agreement or during the 30 months thereafter, in the field of agriculture. The Monsanto agreement also includes the transfer of technology from us to Monsanto and initially included a collaborative research project. Under the Monsanto agreement, Monsanto will be our exclusive collaborator in the agriculture field for a ten-year period.

Monsanto paid us $29.2 million in upfront cash payments, and was also required to make near-term milestone payments to us upon the achievement of specified technology transfer and patent-related milestones. We were also entitled to receive additional funding for collaborative research efforts. In the aggregate, we had the ability to earn up to $5.0 million in milestone payments and research funding under the Monsanto alliance. We received a total of $4.0 million in milestone payments from Monsanto based upon the achievement of a specified patent-related event and the completion of technology transfer activities. In September 2014, we and Monsanto mutually determined not to pursue the discovery collaboration originally contemplated under the terms of the Monsanto agreement. Accordingly, Monsanto will not be required to pay us the final milestone of $1.0 million. There are no remaining milestones under the Monsanto agreement. Monsanto is required to pay to us a percentage of specified fees from certain sublicense agreements Monsanto may enter into that include access to our intellectual property, as well as low single-digit royalty payments on worldwide, net sales by Monsanto, its affiliates and sublicensees of certain licensed products, as defined in the Monsanto agreement, if any. Due to the uncertainty of the application of RNAi technology in the field of agriculture, we may not receive any license fees or royalty payments from Monsanto.

The term of the Monsanto agreement generally ends upon the expiration of the last-to-expire patent licensed under the agreement. We estimate that our fundamental RNAi patents licensed under the Monsanto agreement will expire both in and outside the United States generally between 2016 and 2025, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. Monsanto may terminate the Monsanto agreement in its entirety upon 30-days’ prior written notice to us, provided, however, that Monsanto is required to continue to make royalty payments to us if any royalties were payable on net sales of a licensed product during the previous 24 months. The Monsanto agreement may also be terminated by either party in the event the other party fails to cure a material breach under the Monsanto agreement.

Under the terms of the Monsanto agreement, in the event that during the exclusivity period we cease to own or otherwise exclusively control certain licensed patent rights in the agriculture field, for any reason other than Monsanto’s breach of the Monsanto agreement or its negligence or willful misconduct, resulting in the loss of exclusivity with respect to Monsanto’s rights to such patent rights, and such loss of exclusivity has a material adverse effect on the licensed products, then we would be required to pay Monsanto up to $5.0 million as liquidated damages, and Monsanto’s royalty obligations to us under the Monsanto agreement would be reduced or, under certain circumstances, terminated. We have the right to cure any such loss of patent rights under the Monsanto agreement.

Under the Monsanto agreement, the last deliverable expected to be completed was the discovery collaboration, which was originally to be completed within five years. Therefore, prior to the September 2014 amendment, we were recognizing revenue under the Monsanto agreement on a straight-line basis over five years. However, as a result of the September 2014 amendment, we have determined that the final deliverable in the collaboration is the technology transfer activities, know-how exchange and access to intellectual property controlled by us as of the date of the Monsanto agreement or during the 30 months thereafter, in the field of agriculture. Consequently, we are now recognizing the remaining deferred revenue of $16.8 million at the date of the amendment on a prospective basis from September 2014 through February 2015, the date which is the end of the 30 month obligation, which excludes $5.0 million related to a potential refund due to Monsanto under certain circumstances pursuant to the original terms of the Monsanto agreement. We will continue to recognize this revenue on a straight-line basis over the remaining obligation period. We cannot use a proportional performance model since we are unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the potential effort required is unknown. At December 31, 2014, deferred revenue under the Monsanto agreement was $10.6 million, of which $5.6 million will be recognized through February 2015 and $5.0 million will be recognized when the potential refund obligation ceases and can be considered fixed or determinable.

Takeda Alliance

In May 2008, we entered into a license and collaboration agreement with Takeda to pursue the development and commercialization of RNAi therapeutics. Under the Takeda agreement, we granted to Takeda a non-exclusive, worldwide, royalty-bearing license to our intellectual property, including delivery-related intellectual property, controlled by us as of the date of the Takeda agreement or during the five years thereafter, to develop, manufacture, use and commercialize RNAi therapeutics, subject to our existing contractual obligations to third parties. The license initially is limited to the fields of oncology and metabolic disease and may be expanded at Takeda’s option to include other therapeutic areas, subject to specified conditions.

Takeda paid us an upfront payment of $100.0 million and an additional $50.0 million upon achievement of specified technology transfer milestones. In addition, for each RNAi therapeutic product developed by Takeda, its affiliates and sublicensees, we are entitled to receive specified development, regulatory and commercialization milestone payments, totaling up to $171.0 million per product, together with a double-digit percentage royalty payment based on worldwide annual net sales, if any. The potential future milestone payments per product include up to $26.0 million for the achievement of specified development milestones, up to $40.0 million for the achievement of specified regulatory milestones and up to $105.0 million for the achievement of specified commercialization milestones. We could potentially earn the next milestone payment of $2.0 million based upon the achievement of a specified pre-clinical event by Takeda for an RNAi therapeutic product. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any additional milestone payments or any royalty payments from Takeda.

Pursuant to the Takeda agreement, we and Takeda also agreed to collaborate on the research of RNAi therapeutics directed to one or two disease targets agreed to by the parties, subject to our existing contractual obligations with third parties. The collaboration is governed by a joint technology transfer committee, a joint research collaboration committee and a joint delivery collaboration committee, each of which is comprised of an equal number of representatives from each party. The term of the Takeda agreement generally ends upon the later of (i) the expiration of our last-to-expire patent covering a licensed product and (ii) the last-to-expire term of a profit sharing agreement in the event we elect to enter into such an agreement. We estimate that our fundamental RNAi patents covered under the Takeda agreement will expire both in and outside the United States generally between 2016 and 2025, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. The Takeda agreement may be terminated by either party in the event the other party fails to cure a material breach under the agreement. In addition, Takeda may terminate the agreement on a licensed product-by-licensed product or country-by-country basis upon 180-days’ prior written notice to us, provided, however, that Takeda is required to continue to make royalty payments to us for the duration of the royalty term with respect to a licensed product.

We have determined that the deliverables under the Takeda agreement include the license, the joint committees, the technology transfer activities and the services that we were obligated to perform under the research collaboration. We also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and undelivered services (i.e., the joint committees and the research collaboration) are not separable and, accordingly, the license and services are being treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, we base our revenue recognition pattern on the final deliverable. Under the Takeda agreement, the last elements to be delivered are the joint technology transfer committee and joint delivery collaboration committee services, each of which has a life of no more than seven years.

We are recognizing the upfront payment of $100.0 million and the technology transfer milestones of $50.0 million, the receipt of which we believed was probable at the commencement of the collaboration, on a straight-line basis over seven years because we are unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the effort required under the research collaboration is largely unknown, and therefore, cannot utilize a proportional performance model. As future milestones are achieved, if any, we will recognize as revenue a portion of the milestone payment equal to the percentage of the performance period completed when the milestone is achieved, multiplied by the amount of the milestone payment. At December 31, 2014, deferred revenue under the Takeda agreement was $8.9 million. This remaining deferred revenue will be recognized in full through May 30, 2015.

Other Strategic License Agreements

Isis Collaboration and License Agreement

In January 2015, we and Isis entered into a second amended and restated strategic collaboration and license agreement. The 2015 Isis agreement provides for certain new exclusive target cross-licenses of intellectual property on four disease targets, providing each company with exclusive RNA therapeutic license rights for two programs, and extends the parties’ existing non-exclusive technology cross-license, which was originally entered into in 2004 and was amended and restated in 2009, through April 2019.

Pursuant to the 2015 Isis agreement, Isis granted to us an exclusive, low single-digit royalty-bearing license to its chemistry, motif, mechanism and target-specific intellectual property for oligonucleotide therapeutics against two targets: antithrombin and aminolevulinic acid synthase-1. In exchange, we granted to Isis an exclusive, low single-digit royalty-bearing license to our chemistry, motif, mechanism and target-specific intellectual property for oligonucleotide therapeutics against two targets: Factor XI and apolipoprotein (a).

In addition, under the 2015 Isis agreement, the parties agreed to extend the existing non-exclusive technology cross-license through April 2019. Specifically, Isis granted us a low single-digit royalty-bearing, non-exclusive license to new platform technology arising from May 2014 through April 2019 for double-stranded RNAi therapeutics. In turn, we granted Isis a low single-digit royalty-bearing, non-exclusive license to new platform technology arising from May 2014 through April 2019 for single-stranded antisense therapeutics. This broad, non-exclusive cross-license includes chemistry, motif and mechanism patents, but excludes patent claims on formulations, manufacturing and specific targets.

Under the original 2004 agreement, Isis licensed to us its patent estate related to antisense motifs and mechanisms and oligonucleotide chemistry for double-stranded RNAi products in exchange for a previously disclosed technology access fee, participation in fees for our partnering programs and future milestone and royalty payments from us for programs that incorporate Isis’ intellectual property. We have the right to use Isis’ intellectual property in our development programs or in collaborations and Isis agreed not to grant licenses under these patents to any other organization for the discovery, development and commercialization of double-stranded RNA products designed to work through an RNAi mechanism, except in the context of a collaboration in which Isis plays an active role.

In turn, under the original 2004 agreement, we non-exclusively licensed to Isis our patent estate relating to antisense motifs and mechanisms and oligonucleotide chemistry to research, develop and commercialize single-stranded antisense therapeutics, single stranded RNAi therapeutics and to research double-stranded RNAi compounds. Isis also received a license to develop and commercialize double-stranded RNAi drugs targeting a limited number of therapeutic targets on a non-exclusive basis. We granted these licenses for RNAi therapeutics in exchange for option fees, and future milestone and royalty payments from Isis for RNAi programs that incorporate certain of our intellectual property.

In August 2012, we and Isis amended the agreement to provide certain terms for the discovery, development and commercialization of double-stranded RNA products by us or our sublicensees in the field of agriculture.

As set forth in the 2015 Isis agreement, under the original 2004 agreement, we paid Isis an upfront license fee of $5.0 million and we agreed to pay Isis milestone payments, totaling up to approximately $3.4 million, upon the occurrence of specified development and regulatory events, and low single-digit royalties on sales, if any, for each product that we or a collaborator develop using Isis intellectual property. In addition, we agreed to pay to Isis a percentage of specified fees from strategic collaborations we may enter into that include access to Isis’ intellectual property.

Isis has the right to elect up to ten non-exclusive target licenses under the agreement and has the right to purchase one additional non-exclusive target per year during the term of the collaboration. Isis agreed to pay us, per therapeutic target, a license fee of $0.5 million, milestone payments for double-stranded RNAi products totaling approximately $3.4 million, payable upon the occurrence of specified development and regulatory events, and low single-digit royalties on sales, if any, for each double-stranded RNAi or single-stranded RNAi product developed by Isis or a collaborator that utilizes our intellectual property. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, we may not receive any milestone or royalty payments from Isis.

The term of 2015 Isis agreement generally ends upon the expiration of the last-to-expire patent licensed thereunder, whether such patent is a patent licensed by us to Isis, or vice versa. Either party may terminate the 2015 Isis agreement on 90 days’ prior written notice if the other party materially breaches the agreement and fails to cure the breach within the 90-day notice period and no substantial steps have otherwise been taken to cure the breach, provided, however, that neither party may terminate licenses granted to the other party to the extent necessary to develop or sell products that have at least reached investigational new drug-enabling studies (except for a party’s uncured failure of its payment obligations). Either party may also terminate the agreement in the event the other party undergoes specified bankruptcy events.

During the years ended December 31, 2014, 2013 and 2012, as result of certain payments received by us in connection with the Genzyme, MDCO and Monsanto alliances, we paid $7.7 million, $0.7 million and $2.5 million to Isis, respectively. In addition, as of December 31, 2014, we owed Isis $1.8 million for amounts incurred but not yet paid. These license fees were charged to research and development expense.

Asset acquisition

In-process research and development

In March 2014, we purchased from Merck Sharp & Dohme Corp., or Merck, all of Merck’s right, title and interest in and to all of the outstanding shares of common stock of Sirna. Sirna possesses intellectual property and RNAi assets including early-stage pre-clinical therapeutic candidates, chemistry, and siRNA-conjugate and other delivery technologies that we intend to integrate into our platform for delivery of RNAi therapeutics.

At the closing of the transaction, we paid Merck $25.0 million in cash and issued 2,142,037 shares of our common stock. We recorded this issuance using the price of our common stock on March 5, 2014, the date that these shares were issued to Merck. Based on the common stock price of $81.36, the fair value of the shares issued was $174.3 million. As a result of the cash payment and issuance of shares to Merck, we recorded a total of $199.3 million to in-process research and development expense. We issued an additional 378,007 shares of common stock to Merck on May 19, 2014 upon the completion of certain technology transfer activities during the second quarter of 2014. In the first quarter of 2014, we recorded a liability of $25.4 million associated with the then future obligation to issue these shares, based on the then current price of our common stock, which was also charged to in-process research and development expense. Upon completion of these technology transfer activities in the second quarter of 2014, we re-measured the expense recorded in connection with these shares using the then current price of our common stock, resulting in a credit of $3.9 million. We recorded an expense of $220.8 million to in-process research and development for the year ended December 31, 2014 as a result of this asset acquisition. In future periods, there will be no additional charges recorded to in-process research and development related to the purchase of the Sirna RNAi assets from Merck.

We accounted for this transaction as an acquisition of in-process research and development assets and recorded the entire amount to in-process research and development expense as we did not acquire any employees, manufacturing or other facilities, developed processes or clinical-stage assets as part of our acquisition of Sirna.

Pursuant to the Sirna agreement, Merck is also eligible to receive the following consideration from us: (i) up to an aggregate of $10.0 million upon the achievement by us or our related parties of specified regulatory milestones for RNAi products covered by Sirna intellectual property, and (ii) up to an aggregate of $105.0 million upon the achievement by us or our related parties of specified development and regulatory ($40.0 million) and commercial ($65.0 million) milestones associated with the clinical development progress of certain pre-clinical candidates discovered by Sirna, together with low single-digit royalties for our products and single-digit royalties for Sirna products, in each case based on annual worldwide net sales, if any, by us and our related parties of any such products. These amounts will be recorded as research and development expenses as incurred based on our accounting for this transaction as an asset acquisition.

Under the Sirna agreement, Merck also agreed not to dispose of (i) any shares of our common stock beneficially owned for a period of six months following the closing date, subject to certain limited exceptions, and (ii) 50% of the shares of our common stock beneficially owned for a period of six additional months following the termination of the initial lock-up, referred to as the Subsequent Lock-Up. During and following the expiration of the Subsequent Lock-Up, Merck will be permitted to sell such shares of our common stock subject to certain limitations, including certain volume and manner of sale restrictions.

FAIR_VALUE_MEASUREMENTS

FAIR VALUE MEASUREMENTS	12 Months Ended
FAIR VALUE MEASUREMENTS	Dec. 31, 2014
FAIR VALUE MEASUREMENTS	4	FAIR VALUE MEASUREMENTS
	The following tables present information about our assets that are measured at fair value on a recurring basis at December 31, 2014 and 2013, and indicate the fair value hierarchy of the valuation techniques we utilized to determine such fair value, in thousands:


	Description		At		Quoted		Significant		Significant
			December 31,		Prices in		Observable		Unobservable
			2014		Active		Inputs		Inputs
					Markets		(Level 2)		(Level 3)
					(Level 1)
	Cash equivalents		$	56,203	$	56,203	$	—	$	—
	Marketable securities (fixed income):
	Certificates of deposit			24,300		—		24,300		—
	Commercial paper			40,796		—		40,796		—
	Corporate notes			662,545		—		662,545		—
	Municipal debt securities			9,005		—		9,005		—
	U.S. government-sponsored enterprise securities			64,856		—		64,856		—
	U.S. treasury securities			5,248		—		5,248		—
	Marketable securities (Regulus equity holdings)			94,583		94,583		—		—

	Total		$	957,536	$	150,786	$	806,750	$	—



	Description		At		Quoted		Significant		Significant
			December 31,		Prices in		Observable		Unobservable
			2013		Active		Inputs		Inputs
					Markets		(Level 2)		(Level 3)
					(Level 1)
	Cash equivalents		$	32,571	$	32,571	$	—	$	—
	Marketable securities (fixed income):
	Corporate notes			228,462		—		228,462		—
	U.S. government-sponsored enterprise securities			56,863		—		56,863		—
	Commercial paper			11,978		—		11,978		—
	Marketable securities (Regulus equity holdings)			45,452		45,452		—		—

	Total		$	375,326	$	78,023	$	297,303	$	—

	For the year ended December 31, 2014, there were no transfers between Level 1 and Level 2 financial assets. For the year ended December 31, 2013, we transferred $45.5 million of marketable securities (equity holdings in Regulus) from Level 2 to Level 1 due to the increased volume in average daily trading on the NASDAQ stock market for these instruments. The carrying amounts reflected in our consolidated balance sheets for cash, billed and unbilled collaboration receivables, other current assets, accounts payable and accrued expenses approximate fair value due to their short-term maturities.

MARKETABLE_SECURITIES

MARKETABLE SECURITIES	12 Months Ended
MARKETABLE SECURITIES	Dec. 31, 2014
MARKETABLE SECURITIES	5	MARKETABLE SECURITIES
	The following tables summarize the fair value, accumulated other comprehensive income and intraperiod tax allocation regarding our investment in Regulus available-for-sale marketable securities at December 31, 2014 and 2013, and for the activity recorded in the year, in thousands:


	Description		At				Sales of Regulus				All Other				Balance at
			December 31,				Shares During				Activity During				December 31,
			2013				Year Ended				Year Ended				2014
							December 31,				December 31,
							2014				2014
	Carrying value		$	12,449			$	(514	)		$	—			$	11,935
	Accumulated other comprehensive income, before tax			33,003				(2,081	)			51,726				82,648

	Investment in equity securities of Regulus Therapeutics Inc., as reported		$	45,452			$	(2,595	)		$	51,726			$	94,583

	Accumulated other comprehensive income, before tax		$	33,003			$	(2,081	)		$	51,726			$	82,648
	Intraperiod tax allocation recorded as a benefit from income taxes			(13,267	)			—				(19,525	)			(32,792	)

	Accumulated other comprehensive income, net of tax		$	19,736			$	(2,081	)		$	32,201			$	49,856


	Description		At				Sales of Regulus				All Other				Balance at
			December 31,				Shares During				Activity During				December 31,
			2012				year Ended				Year Ended				2013
							December 31,				December 31,
							2013				2013
	Carrying value		$	12,449			$	—			$	—			$	12,449
	Accumulated other comprehensive income, before tax			26,299				—				6,704				33,003

	Investment in equity securities of Regulus Therapeutics Inc., as reported		$	38,748			$	—			$	6,704			$	45,452

	Accumulated other comprehensive income, before tax		$	26,299			$	—			$	6,704			$	33,003
	Intraperiod tax allocation recorded as a benefit from income taxes			(10,572	)			—				(2,695	)			(13,267	)

	Accumulated other comprehensive income, net of tax		$	15,727			$	—			$	4,009			$	19,736

	We obtain fair value measurement data for our marketable securities from independent pricing services. We perform validation procedures to ensure the reasonableness of this data. This includes meeting with the independent pricing services to understand the methods and data sources used. Additionally, we perform our own review of prices received from the independent pricing services by comparing these prices to other sources and confirming those securities are trading in active markets.

	The following tables summarize our marketable securities, other than our holdings in Regulus noted above, at December 31, 2014 and 2013, in thousands:


			December 31, 2014
			Amortized				Gross				Gross				Fair Value
			Cost				Unrealized				Unrealized
							Gains				Losses
	Certificates of deposit (Due within 1 year)		$	24,300			$	—			$	—			$	24,300
	Commercial paper (Due within 1 year)			40,785				11				—				40,796
	Corporate notes (Due within 1 year)			449,044				14				(293	)			448,765
	Corporate notes (Due after 1 year through 2 years)			214,510				—				(730	)			213,780
	Municipal debt securities (Due after 1 year through 2 years)			9,002				3				—				9,005
	U.S. government-sponsored enterprise securities (Due within 1 year)			13,069				—				(1	)			13,068
	U.S. government-sponsored enterprise securities (Due after 1 year through 2 years)			51,879				—				(91	)			51,788
	U.S. treasury securities (Due after 1 year through 2 years)			5,254				—				(6	)			5,248

	Total		$	807,843			$	28			$	(1,121	)		$	806,750



			December 31, 2013
			Amortized				Gross				Gross				Fair Value
			Cost				Unrealized				Unrealized
							Gains				Losses
	Commercial paper (Due within 1 year)		$	11,983			$	—			$	(5	)		$	11,978
	Corporate notes (Due within 1 year)			154,175				33				(46	)			154,162
	Corporate notes (Due after 1 year through 2 years)			74,312				23				(35	)			74,300
U.S. government-sponsored enterprise securities (Due within 1 year)			26,553				8				—				26,561
U.S. government-sponsored enterprise securities (Due after 1 year through 2 years)			30,300				2				—				30,302

Total		$	297,323			$	66			$	(86	)		$	297,303

PROPERTY_AND_EQUIPMENT_NET

PROPERTY AND EQUIPMENT, NET	12 Months Ended
PROPERTY AND EQUIPMENT, NET	Dec. 31, 2014
PROPERTY AND EQUIPMENT, NET	6	PROPERTY AND EQUIPMENT, NET
	Property and equipment consist of the following at December 31, 2014 and 2013, in thousands:


					December 31,
			Useful Life		2014			2013
	Laboratory equipment			5 years	$	28,559		$	22,729
	Computer equipment and software			3 years		4,440			4,261
	Furniture and fixtures			5 years		1,999			1,793
	Leasehold improvements			*		30,853			28,953
	Construction in progress			—		1,982			28

						67,833			57,764
	Less: accumulated depreciation					(46,093	)		(41,316	)

					$	21,740		$	16,448


	*	Shorter of asset life or lease term

	During the years ended December 31, 2014, 2013 and 2012, we recorded $5.0 million, $6.1 million and $4.6 million, respectively, of depreciation expense related to our property and equipment.

COMMITMENTS_AND_CONTINGENCIES

COMMITMENTS AND CONTINGENCIES	12 Months Ended
	Dec. 31, 2014
COMMITMENTS AND CONTINGENCIES	7	COMMITMENTS AND CONTINGENCIES

	Purchase Commitments

	We have future purchase commitments totaling $104.5 million at December 31, 2014, of which $59.3 million is expected to be incurred in 2015 and $45.2 million is expected to be incurred past 2015. These commitments are related to purchase orders, clinical and pre-clinical agreements, and other purchase commitments for goods or services that we are likely to continue, regardless of the fact that they were cancelable at December 31, 2014.

	Technology License Commitments

	We have licensed from third parties the rights to use certain technologies in our research processes as well as in any products we may develop including these licensed technologies. In accordance with the related license agreements, we are required to make certain fixed payments to the licensor or a designee of the licensor over various agreement terms. Many of these agreement terms are consistent with the remaining lives of the underlying intellectual property that we have licensed. At December 31, 2014, we were committed to make the following fixed, estimated and cancelable payments under existing license agreements, in thousands:



	Year Ending December 31,
	2015		$	7,379
	2016			724
	2017			744
	2018			754
	2019			762
	Thereafter			8,592

	Total		$	18,955


	Operating Leases

	We lease office and laboratory space located at 300 Third Street, Cambridge, Massachusetts, for our corporate headquarters and primary research facility under a non-cancelable real property lease agreement, or the Third Street Lease, with ARE-MA Region No. 28 LLC, or the Landlord. Under the Third Street Lease, we lease a total of approximately 129,000 square feet of office and laboratory space. The term of the Third Street Lease was set to expire in September 2016. In March 2014, we and the Landlord amended the Third Street Lease to extend the term for an additional five years, through September 30, 2021. Under the amended Third Street Lease, we have the option to extend the term for one additional five-year period. As a result of the extension of the term of the Third Street Lease, our operating lease obligations through 2021 increased by $37.8 million.

	On February 10, 2012, we entered into a non-cancelable real property lease agreement, or the BMR Lease, with BMR-Fresh Pond Research Park LLC, or BMR, for our manufacturing facility. Under the BMR Lease, we lease approximately 15,000 square feet of office and laboratory space located at 665 Concord Avenue, Cambridge, Massachusetts. The term of the BMR Lease expires August 31, 2017. We have the option to extend the BMR Lease for two successive five-year periods.

	We received $1.9 million, $0.2 million and $1.8 million in leasehold improvement incentives from BMR during the years ended December 31, 2014, 2013 and 2012, respectively. These leasehold improvement incentives are being accounted for as a reduction in rent expense ratably over the BMR Lease term. The balance from these leasehold improvement incentives is included in current portion of deferred rent and deferred rent, net of current portion, in the consolidated balance sheets at December 31, 2014 and 2013.

	Total rent expense, including operating expenses, under our real property leases was $8.9 million, $4.9 million and $6.4 million for the years ended December 31, 2014, 2013 and 2012, respectively.



	Future minimum payments under our non-cancelable leases are approximately as follows, in thousands:



	Year Ending December 31,
	2015		$	6,810
	2016			6,994
	2017			7,535
	2018			7,387
	2019			7,608
	Thereafter			13,845

	Total		$	50,179


	Litigation

	University of Utah Litigation

	On March 22, 2011, The University of Utah, or Utah, filed a civil complaint in the United States District Court for the District of Massachusetts against us, Max Planck Gesellschaft Zur Foerderung Der Wissenschaften e.V. and Max Planck Innovation GmbH, together, Max Planck, the Whitehead Institute for Biomedical Research, or Whitehead, the Massachusetts Institute of Technology, or MIT, and the University of Massachusetts, or UMass, claiming a professor at Utah is the sole inventor or, in the alternative, a joint inventor, of the Tuschl patents. On October 31, 2011, we, Max Planck, Whitehead, MIT and UMass filed a motion to dismiss. Also on October 31, 2011, UMass filed a motion to dismiss on separate grounds, which we, Max Planck, Whitehead and MIT have joined. On December 31, 2011, Utah filed a second amended complaint dropping UMass as a defendant and adding as defendants several UMass officials. In June 2012, the Court denied both motions to dismiss. We, Max Planck, Whitehead, MIT and UMass filed an appeal of the Court’s ruling on the motion to dismiss for lack of jurisdiction and a motion requesting that the Court stay the case pending the outcome of the appeal. In July 2012, the Court stayed discovery in the case pending the outcome of the defendants’ appeal. In August 2013, the United States Court of Appeals for the Federal Circuit, or CAFC, affirmed the lower Court’s ruling, in a split decision. In September 2013, we filed a petition with the CAFC for rehearing or rehearing en banc. In November 2013, the CAFC denied our petition for rehearing or rehearing en banc and remanded the case back to the lower Court. In February 2014, we filed a petition for writ of certiorari from the Supreme Court and a motion to stay the lower Court proceedings pending a decision from the Supreme Court on our petition. The lower Court granted our motion to stay the proceedings, however, in June 2014 the Supreme Court denied our petition for certiorari and remanded the case back to the United States District Court for the District of Massachusetts for trial, which is now scheduled to begin on November 2, 2015.

	Although we believe we have meritorious defenses and intend to vigorously defend ourselves in this matter, litigation is subject to inherent uncertainty and a court could ultimately rule against us. In addition, the defense of litigation and related matters are costly and may divert the attention of our management and other resources that would otherwise be engaged in other activities. We have not recorded an estimate of the possible loss associated with this legal proceeding due to the uncertainties related to both the likelihood and the amount of any possible loss or range of loss.

	Our accounting policy for accrual of legal costs is to recognize such expenses as incurred.

	Tekmira Settlement Agreement

	On November 12, 2012, we, Tekmira Pharmaceuticals Corporation, or TPC, Protiva Biotherapeutics, Inc., a wholly owned subsidiary of TPC, or Protiva, and together with TPC, Tekmira, and Acuitas Therapeutics Inc. (formerly AlCana Technologies, Inc.), or Acuitas, entered into a settlement agreement and general release resolving all ongoing litigation, as well as a patent interference proceeding between us and Protiva. The terms of the settlement agreement include mutual releases and dismissal with prejudice of all claims and counterclaims between the parties. In addition, as part of the settlement agreement, the parties agreed to a covenant not to sue one another in the future on matters released under the settlement agreement, as well as substantial liquidated damages to be paid by any party that breaches such covenant. The parties also agreed to resolve any future disputes that may arise over the three years following the settlement through binding arbitration.

Pursuant to the settlement agreement, we and Tekmira also agreed to resolve the interference proceeding declared by the United States Board of Patent Appeals and Interferences between us and Protiva, captioned Protiva Biotherapeutics, Inc. v. Alnylam Pharmaceuticals, Inc., Patent Interference No. 105792.

Contemporaneously with the execution of the settlement agreement, we and Tekmira restructured our contractual relationship and entered into a cross-license agreement that superseded the prior license and manufacturing agreements among us, TPC and Protiva. In connection with this restructuring, we incurred a $65.0 million charge to operating expenses for the year ended December 31, 2012. Specifically, we made a one-time payment of $30.0 million to Tekmira for the termination of, and our release from, all of our obligations under the manufacturing agreement with TPC, including without limitation the obligations to obtain materials and/or services from TPC. Further, we elected to buy-down certain future potential milestone and royalty payments due to Tekmira for certain of our RNAi therapeutics, formulated using lipid nanoparticle, or LNP, technology. Specifically, pursuant to the cross-license agreement, we made a one-time payment of $35.0 million to Tekmira, which amount constituted payment for the termination of the 2008 license agreements with TPC and Protiva and the parties’ rights and obligations thereunder, as well as the buy-down of certain milestone payments and the significant reduction of royalty rates for ALN-VSP, ALN-PCS02 and patisiran. In addition, under the 2012 cross-license agreement, we were obligated to pay TPC an aggregate of $10.0 million in contingent milestone payments related to advancement of ALN-VSP and patisiran, which now represent the only potential milestones due to Tekmira for ALN-VSP, ALN-PCS02 and patisiran LNP-based RNAi therapeutics. In the fourth quarter of 2013, we paid TPC $5.0 million in connection with the initiation of the patisiran Phase 3 clinical trial. With respect to the second $5.0 million milestone, in August 2013, we initiated binding arbitration proceedings to resolve a disagreement with TPC regarding the achievement by TPC of this milestone under the parties cross-license agreement relating to the manufacture of ALN-VSP clinical trial material for use in China. We currently expect that the Tekmira arbitration hearing will be held in the second quarter of 2015. Our policy is to expense these potential milestones when incurred and record them as research and development expense. A description of our cross-license agreement with Tekmira is included in Part I, Item 1, “— Delivery-Related Licenses and Collaborations — Tekmira,” of this annual report on Form 10-K.

Indemnifications

Licensor indemnification — In connection with our license agreements with Max Planck relating to the Tuschl I and Tuschl II patent applications, we are required to indemnify Max Planck for certain damages arising in connection with the intellectual property rights licensed under the agreements. Under the Max Planck indemnification agreement, we are responsible for paying the costs of any litigation relating to the license agreements or the underlying intellectual property rights, including the costs associated with certain litigation regarding the Tuschl patents, which was settled during 2011, as well as certain costs associated with defending the University of Utah litigation described above. In connection with our research agreement with Acuitas, we agreed to indemnify Acuitas for certain legal costs, subject to certain exceptions and limitations, associated with the Tekmira litigation described above. These indemnification costs were charged to general and administrative expense. We are also a party to a number of agreements entered into in the ordinary course of business, which contain typical provisions that obligate us to indemnify the other parties to such agreements upon the occurrence of certain events. Such indemnification obligations are usually in effect from the date of execution of the applicable agreement for a period equal to the applicable statute of limitations.

Our maximum potential future liability under any such indemnification provisions is uncertain. However, to date, other than certain costs associated with certain previously settled litigation related to the Tuschl patents and the Tekmira litigation described above, and certain ongoing defense costs related to the University of Utah litigation also described above, we have not incurred material costs to defend lawsuits or settle claims related to these indemnification provisions. We have determined that the estimated aggregate fair value of our potential liabilities under all such indemnification provisions is minimal and have not recorded any liability related to such indemnification provisions at December 31, 2014 or 2013.

STOCKHOLDERS_EQUITY

STOCKHOLDERS' EQUITY	12 Months Ended
	Dec. 31, 2014
STOCKHOLDERS' EQUITY	8	STOCKHOLDERS’ EQUITY
	Preferred Stock
	We have authorized up to 5,000,000 shares of preferred stock, $0.01 par value per share, for issuance. The preferred stock will have such rights, preferences, privileges and restrictions, including voting rights, dividend rights, conversion rights, redemption privileges and liquidation preferences, as shall be determined by our Board of Directors upon its issuance. At December 31, 2014 and 2013, there were no shares of preferred stock outstanding.
	Stockholder Rights Agreement
	On July 13, 2005, our Board of Directors declared a dividend of one right, or collectively, the Rights, to buy one one-thousandth of a share of newly designated Series A Junior Participating Preferred Stock, or Series A Junior Preferred Stock, for each outstanding share of our common stock to stockholders of record at the close of business on July 26, 2005. Initially, the Rights are not exercisable and will be attached to all certificates representing outstanding shares of common stock. The Rights will expire at the close of business on July 13, 2015 unless earlier redeemed or exchanged. Until a Right is exercised, the holder thereof will have no rights as a stockholder of Alnylam, including the right to vote or to receive dividends. Subject to the terms and conditions of the rights agreement, or the Rights Agreement, the Rights will become exercisable upon the earlier of (1) ten business days following the later of (a) the first date of a public announcement that a person or group (an “Acquiring Person”) acquires, or obtained the right to acquire, beneficial ownership of 20% or more of our outstanding shares of common stock or (b) the first date on which an executive officer of Alnylam has actual knowledge that an Acquiring Person has become such or (2) ten business days following the commencement of a tender offer or exchange offer that would result in a person or group beneficially owning more than 20% of our outstanding shares of common stock. Each Right entitles the holder to purchase one one-thousandth of a share of Series A Junior Preferred Stock at an initial purchase price of $80.00 in cash, subject to adjustment. In the event that any person or group becomes an Acquiring Person, unless the event causing the 20% threshold to be crossed is a Permitted Offer (as defined in the Rights Agreement), each Right not owned by the Acquiring Person will entitle its holder to receive, upon exercise, that number of shares of common stock of the Company (or in certain circumstances, cash, property or our other securities) which equals the exercise price of the Right divided by 50% of the current market price (as defined in the Rights Agreement) per share of such common stock at the date of the occurrence of the event. In the event that, at any time after any person or group becomes an Acquiring Person, (i) Alnylam is consolidated with, or merged with and into, another entity and we are not the surviving entity of such consolidation or merger (other than a consolidation or merger which follows a Permitted Offer) or if we are the surviving entity, but shares of our outstanding common stock are changed or exchanged for stock or securities (of any other person) or cash or any other property, or (ii) more than 50% of our assets or earning power is sold or transferred, each holder of a Right (except Rights which previously have been voided as set forth in the Rights Agreement) shall thereafter have the right to receive, upon exercise, that number of shares of common stock of the acquiring company which equals the exercise price of the Right divided by 50% of the current market price of such common stock at the date of the occurrence of the event.
	Public Offerings
	In February 2012, we sold an aggregate of 8,625,000 shares of our common stock through an underwritten public offering at a price to the public of $10.75 per share. As a result of this offering, we received aggregate net proceeds of approximately $86.8 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $5.9 million.
	In January 2013, we sold an aggregate of 9,200,000 shares of our common stock through an underwritten public offering at a price to the public of $20.13 per share. As a result of this offering, we received aggregate net proceeds of approximately $173.6 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $11.6 million.
	In January 2015, we sold an aggregate of 5,447,368 shares of our common stock through an underwritten public offering at a price to the public of $95.00 per share. As a result of the offering, which included the full exercise of the underwriters’ option to purchase additional shares, we received aggregate net proceeds of approximately $496.4 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $21.1 million.

STOCK_INCENTIVE_PLANS

STOCK INCENTIVE PLANS	12 Months Ended
STOCK INCENTIVE PLANS	Dec. 31, 2014
STOCK INCENTIVE PLANS	9	STOCK INCENTIVE PLANS

	Stock Plans

	In June 2009, our stockholders approved an amendment and restatement of our 2004 Stock Incentive Plan, or the Amended and Restated 2004 Plan, which replaced our 2004 Stock Incentive Plan, as amended, or the 2004 Plan. At December 31, 2014, the Amended and Restated 2004 Plan provided for the granting of stock options to purchase up to 12,366,485 shares of common stock. Prior to the adoption of the Amended and Restated 2004 Plan, we were authorized to grant both stock options and restricted stock awards under the 2004 Plan. As of the effective date of the Amended and Restated 2004 Plan, we may only grant stock options under the Amended and Restated 2004 Plan, provided that the terms and conditions of any restricted stock awards outstanding under the 2004 Plan will continue to be governed by the Amended and Restated 2004 Plan.

	In June 2009, our stockholders also approved our 2009 Stock Incentive Plan, or the 2009 Plan. The 2009 Plan provides for the granting of stock options, restricted stock awards and units, stock appreciation rights and other stock-based awards. In June 2013, our stockholders approved an amendment to the 2009 Plan, which increased the number of shares of common stock authorized for issuance from 2,200,000 to 5,900,000. The 2009 Plan has a fungible share pool. Any award that is not a full value award is counted against the authorized share limits specified in the 2009 Plan as one share for each share of common stock subject to the award, and all full value awards, defined in the 2009 Plan as restricted stock awards or other stock-based awards, are counted as one and a half shares for each one share of common stock subject to such full value award. In addition, the 2009 Plan includes a non-employee director stock option program under which each eligible non-employee director is entitled to (1) a grant of an option to purchase 30,000 shares of common stock upon his or her initial appointment to the Board of Directors, or such other amount as the Board of Directors deems appropriate, and (2) a subsequent annual grant of an option to purchase 15,000 shares of common stock based on continued service, provided the non-employee director has served as a director for at least six months and is serving as a director immediately prior to and following such annual grant. Stock options granted by us to non-employee directors upon their appointment to the Board of Directors vest as to one-third of such shares on each of the first, second and third anniversaries of the date of grant, and those granted annually thereafter vest in full on the first anniversary of the date of grant. During 2014, the Compensation Committee of our Board of Directors approved an amendment to the 2009 Plan to provide that upon retirement or resignation, non-employee Directors would have three months to exercise any outstanding stock option awards, unless such non-employee Director has five or more years of service, in which case such non-employee Director will have the lesser of five years or the remainder of the stock option term post-retirement or resignation to exercise such awards.

	At December 31, 2014, an aggregate of 9,317,147 shares of common stock were reserved for issuance under our stock plans, including outstanding stock options to purchase 8,168,533 shares of common stock, 941,583 of common stock available for additional equity awards and 207,031 shares available for future grant under our 2004 Employee Stock Purchase Plan, or the 2004 ESPP, excluding 612,085 shares of common stock granted in December 2014 that are subject to and contingent upon receiving stockholder approval of an amendment and restatement of our 2009 Plan in connection with our 2015 annual stockholder meeting. Each option shall expire within ten years of issuance. Stock options granted by us to employees generally vest as to 25% of the shares on the first anniversary of the grant date and 6.25% of the shares at the end of each successive three-month period until fully vested. Performance-based stock options granted to employees vest as to one-third of the shares upon the achievement of each of three specific clinical development and regulatory events, as approved by our compensation committee.



	Stock-Based Compensation

	The following table summarizes stock-based compensation expense by type of award during the three years ended December 31, 2014, in thousands:



			2014				2013				2012
	Stock-based compensation expense by type of award:
	Stock options		$	24,603			$	13,839			$	8,739
	Performance-based stock options			4,960				—				—
	Restricted stock awards			1,068				3,420				2,436
	ESPP share issuances			392				261				241
	Non-employee stock options			2,038				3,183				944

			$	33,061			$	20,703			$	12,360


	The following table summarizes our unrecognized stock-based compensation expense, net of estimated forfeitures, at December 31, 2014 by type of awards, excluding performance-based stock options, and the weighted-average period over which that expense is expected to be recognized:



			At December 31, 2014
			Unrecognized Expense,				Weighted-average
			Net of				Recognition
			Estimated Forfeitures				Period
			(in thousands)				(in years)
	Type of award:
	Stock options		$	59,854				2.62
	Restricted stock awards			1,571				3.46
	ESPP share issuances			197				0.33

	Valuation Assumptions for Stock Options

	The fair value of stock options, at date of grant, based on the following assumptions, was estimated using the Black-Scholes option-pricing model. Our expected stock-price volatility assumption is based on the historical volatility of our publicly traded stock. The expected life assumption is based on our historical data. The dividend yield assumption is based on the fact that we have never paid cash dividends and have no present intention to pay cash dividends. The risk-free interest rate used for each grant is equal to the zero coupon rate for instruments with a similar expected life.



			2014				2013				2012
	Risk-free interest rate			1.7-2.3	%			1.0-2.0	%			0.8-1.0	%
	Expected dividend yield			—				—				—
	Expected option life			5.5-7.5 years				5.6 years				5.6-5.9 years
	Expected volatility			53-57	%			55-56	%			57	%



	Stock Option Activity

	The following table summarizes the activity of our stock option plans, excluding stock options granted in December 2014, subject to and contingent upon stockholder approval of an amendment and restatement of our 2009 Plan, and performance-based stock options:



			Number of				Weighted-				Weighted-				Aggregate
Options			average				average				Intrinsic
(in thousands)			Exercise				Remaining				Value
			Price				Contractual				(in thousands)
							Term (in years)
Outstanding, December 31, 2013				8,245			$	22.06
Granted				1,352				75.77
Exercised				(1,982	)			14.83
Cancelled				(85	)			35.32

Outstanding, December 31, 2014			7,530			$	33.46				6.32			$	478,506

Exercisable at December 31, 2014			4,736			$	21.44				4.86			$	357,891
Vested or expected to vest at December 31, 2014			7,292			$	32.53				6.23			$	470,149

The weighted-average fair value of stock options granted was $39.08, $26.33 and $8.68 per share for the years ended December 31, 2014, 2013 and 2012, respectively. The intrinsic value of stock options exercised was $126.5 million, $57.9 million and $4.8 million for the years ended December 31, 2014, 2013 and 2012, respectively. We satisfy stock option exercises with newly issued shares of our common stock.

Performance-Based Stock Options

During 2013, we began granting performance-based stock options to employees that vest as to one-third of the shares upon the achievement of each of three specific clinical development and regulatory events, as approved by our Compensation Committee. The following table summarizes the activity of our performance-based stock options, excluding stock options granted in December 2014 subject to and contingent upon stockholder approval of an amendment and restatement of our 2009 Plan:



		Number of				Weighted-				Weighted-				Aggregate
		Options				average				average				Intrinsic
		(in thousands)				Exercise				Remaining				Value
						Price				Contractual				(in thousands)
										Term (in years)
Outstanding, December 31, 2013			468			$	63
Granted			194				96.45
Exercised			(5	)			63
Cancelled			(18	)			63

Outstanding, December 31, 2014			639			$	73.15				9.05			$	15,237

Exercisable at December 31, 2014			150			$	63				8.4			$	5,100

On December 12, 2014, we achieved the first performance criteria of the December 18, 2013 grant of performance-based stock options and the stock option was vested as one-third of the performance-based portion of the grant. The weighted-average grant date fair value of the first tranche of the December 18, 2013 performance-based stock option was $32.26 per share. During the fourth quarter of 2014, we determined the first performance criteria of the December 18, 2013 grant was probable and began to record expense, which was recognized in full as of December 12, 2014. As of the grant date and December 31, 2014, we have determined that the remaining performance criteria of all outstanding performance-based stock options reflected in the table above are not probable. As a result, we have not recorded stock-based compensation expense for these performance-based stock options. The intrinsic value of performance-based stock options exercised was $0.1 million for the year ended December 31, 2014. We satisfy performance-based stock option exercises with newly issued shares of our common stock.

Contingent Stock Option Awards

On December 17, 2014, the Compensation Committee of our Board of Directors approved the grant of stock options to purchase 612,085 shares of our common stock, at an exercise price of $96.45 per share, to members of our management team. These stock option grants were approved subject to and contingent upon approval by our stockholders at our 2015 annual meeting of an amendment and restatement of our 2009 Plan, to, among other things, increase the shares authorized for issuance thereunder. One-half of the contingent stock options granted are time-based stock options and one-half are performance-based stock options. In no event will the contingent stock options be exercised before approval of the amended and restated 2009 Plan by our stockholders; and in the event that the amended and restated 2009 Plan is not approved by the stockholders at the 2015 annual meeting, the contingent stock options shall immediately terminate and be of no further force or effect. If the stockholders approve the amended and restated 2009 Plan, the grant-date fair value of the contingent stock options would be based on a Black-Scholes valuation model based on the fair market value of the stock on the date of such stockholder approval. No stock-based compensation expense was recorded in 2014 relating to this contingent stock option grant.

Restricted Stock Awards

In October 2010, we granted 113,370 shares of our restricted stock to certain employees. These restricted stock awards were valued at $1.4 million on the grant date. These restricted stock awards vested ratably over an approximate three-year period. In May 2011, we granted an aggregate of 229,806 shares of performance-based restricted stock awards to our employees, excluding our leadership team. These restricted stock awards were valued at $2.3 million on the grant date and had a contractual term of five years. The vesting of these awards was predicated on our achievement of certain clinical development goals. These awards have vested in full due to the achievement of these goals in 2011 and 2013.

In January 2012, as part of our post-restructuring retention program, we granted an aggregate of 508,928 shares of restricted stock to our retained employees, excluding our chief executive officer and president and chief operating officer. These restricted stock awards were valued at $5.3 million on the grant date and vested in full on the second anniversary of the grant date.

The following table summarizes the activity of our restricted stock awards, including restricted stock and restricted stock units:



		Number of				Weighted-
		Restricted				average
		Stock Awards				Grant Date
		(in thousands)				Fair Value
Unvested at December 31, 2013			500			$	10.69
Granted			29				68.28
Vested			(499	)			10.59
Forfeited			—				—

Unvested at December 31, 2014			30			$	68.02


The total fair value of restricted stock awards that vested during the years ended December 31, 2014, 2013 and 2012 (measured on the date of vesting) was $44.4 million, $5.8 million and $1.5 million, respectively.

Employee Stock Purchase Plan

In 2004, we adopted the 2004 ESPP with 315,789 shares authorized for issuance. In June 2010, our stockholders approved an amendment to the 2004 ESPP, which increased the shares authorized for issuance from 315,789 shares to 715,789 shares. Under the 2004 ESPP, each offering period is six months, at the end of which employees may purchase shares of common stock through payroll deductions made over the term of the offering. The per-share purchase price at the end of each offering period is equal to the lesser of 85% of the closing price of our common stock at the beginning or end of the offering period. We issued 21,938, 45,141 and 73,590 shares during the years ended December 31, 2014, 2013 and 2012, respectively, and at December 31, 2014, 207,031 shares were available for issuance under the 2004 ESPP.

The weighted-average fair value of stock purchase rights granted as part of the 2004 ESPP was $17.03, $11.49 and $2.82 per share for the years ended December 31, 2014, 2013 and 2012, respectively. The fair value was estimated using the Black-Scholes option-pricing model. During the three years ended December 31, 2014, we used a weighted-average stock-price volatility of 55%, expected option life assumption of six months and a risk-free interest rate of 0.1%.

INCOME_TAXES

INCOME TAXES	12 Months Ended
INCOME TAXES	Dec. 31, 2014
INCOME TAXES	10	INCOME TAXES

	The domestic and foreign components of loss before income taxes are as follows, in thousands:



			2014				2013				2012
	Domestic		$	(372,137	)		$	(81,109	)		$	(116,400	)
	Foreign			(28,467	)			(10,811	)			(186	)

	Loss before income taxes		$	(400,604	)		$	(91,920	)		$	(116,586	)


	Deferred income taxes reflect the tax effects of temporary differences between the carrying amounts of assets and liabilities for financial reporting and income tax purposes. We establish a valuation allowance when uncertainty exists as to whether all or a portion of the net deferred tax assets will be realized. We have allocated the valuation allowance between current and non-current deferred tax assets and liabilities. As a result of this allocation, we have recorded a long term deferred tax asset of $31.7 million and a corresponding short term deferred tax liability of $31.7 million on the balance sheet. Components of the net deferred tax (liability) asset at December 31, 2014 and 2013 are as follows, in thousands:



			2014				2013
	Deferred tax assets:
	Net operating loss carryforwards		$	176,789			$	124,797
	Research and development credits			38,204				23,902
	AMT credits			788				788
	Foreign tax credits			3,196				3,196
	Capitalized research and development and start-up costs			19,246				16,214
	Deferred revenue			14,273				37,273
	Deferred compensation			24,516				21,706
	Intangible assets			17,637				2,210
	Partnership interest			689				689
	Other			5,871				4,885

	Total deferred tax assets			301,209				235,660
	Deferred tax liabilities:
	Intangible assets			—				(7	)
	Unrealized gain on available-for-sale securities			(32,793	)			(13,267	)
	Deferred tax asset valuation allowance			(268,416	)			(222,393	)

	Net deferred tax liability		$	—			$	(7	)




	The benefit from income taxes for the years ended December 31, 2014, 2013 and 2012 are as follows, in thousands:



			2014				2013				2012
	U.S.:
	Current		$	—			$	34			$	52
	Deferred			(40,209	)			(2,695	)			(10,572	)

	Total U.S.			(40,209	)			(2,661	)			(10,520	)

	Foreign:
	Current			—				—				—
	Deferred			—				(34	)			(52	)

	Total Foreign			—				(34	)			(52	)

	Benefit from income taxes		$	(40,209	)		$	(2,695	)		$	(10,572	)


	Our effective income tax rate differs from the statutory federal income tax rate as follows for the years ended December 31, 2014, 2013 and 2012:



		2014				2013				2012
At U.S. federal statutory rate			35	%			35	%			35	%
State taxes, net of federal effect			1.8				4.3				4.9
Stock-based compensation			(0.2	)			0.8				(0.7	)
Tax credits			3.5				8.5				4.2
Orphan drug credit addback			(0.6	)			(2.7	)			—
Other permanent items			—				(0.3	)			(1.6	)
Foreign rate differential			(2.5	)			(4.1	)			(0.1	)
In-process research and development			(19.4	)			—				—
Tax basis in intangible assets as a result of Sirna transaction			4.2				—				—
Valuation allowance			(11.8	)			(38.5	)			(32.6	)

Effective income tax rate			10	%			3	%			9.1	%


We have evaluated the positive and negative evidence bearing upon the realizability of our deferred tax assets. We have concluded, in accordance with the applicable accounting standards, that it is more likely than not that we may not realize the benefit of all of our deferred tax assets. Accordingly, we have recorded a valuation allowance against the deferred tax assets that management believes will not be realized. We reevaluate the positive and negative evidence on a quarterly basis. The valuation allowance increased by $46.0 million, $29.7 million and $38.3 million for the years ended December 31, 2014, 2013 and 2012 respectively, due primarily to additional operating losses. Increases to the valuation allowance were partially offset by decreases related to the recognition of deferred revenue.

For the years ended December 31, 2014, 2013 and 2012, we recorded a tax benefit of $40.2 million, $2.7 million and $10.6 million, respectively. For the years ended December 31, 2014, 2013 and 2012, we recorded unrealized gains on our investments in available-for-sale securities in other comprehensive income and additional paid-in capital. The benefit of $19.5 million, $2.7 million and $10.6 million for the years ended December 31, 2014, 2013 and 2012, respectively, is due to the recognition of corresponding income tax expense associated with the increase in the value of our investment in Regulus that we carried at fair market value during the same period. In addition, for the year ended December 31, 2014, we recorded a benefit of $20.7 million due to the difference between the fair value of stock and the cash proceeds received from Genzyme for the issuance of our common stock calculated at the closing date of the transaction. The corresponding income tax expense has been recorded in other comprehensive income and additional paid-in capital, respectively. Intraperiod tax allocation rules require us to allocate our provision for income taxes between continuing operations and other categories of earnings, such as other comprehensive income and additional paid-in capital. In periods in which we have a year-to-date pre-tax loss from continuing operations and pre-tax income in other categories of earnings, such as other comprehensive income and additional paid-in capital, we must allocate the tax provision to the other categories of earnings. We then record a related tax benefit in continuing operations.

The deferred tax assets above exclude $83.5 million of net operating losses and $0.4 million of federal and state research and development credits related to tax deductions from the exercise of stock options subsequent to the adoption of the 2006 accounting standard on stock-based compensation. This amount represents an excess tax benefit and has not been included in the gross deferred tax assets.

At December 31, 2014, we had federal and state net operating loss carryforwards of $639.3 million and $701.8 million, respectively. These amounts will reduce future taxable income that will expire at various dates through 2034. At December 31, 2014, federal and state research and development credit carryforwards were $32.3 million and $10.1 million, respectively, available to reduce future tax liabilities that expire at various dates through 2034. At December 31, 2014, foreign tax credit carryforwards were $3.2 million available to reduce future tax liabilities that expire in 2017. At December 31, 2014, alternative minimum tax credits of $0.8 million are available to reduce future regular tax liabilities to the extent such regular tax less other non-refundable credits exceeds the tentative minimum tax. Ownership changes, as defined in the Internal Revenue Code, including those resulting from the issuance of common stock in connection with our public offerings, may limit the amount of net operating loss that can be utilized to offset future taxable income or tax liability. We have determined that based on the value of Alnylam, in the event there was an annual limitation under Section 382, all net operating loss and tax credit carryforwards would still be available to offset taxable income.

At December 31, 2014, 2013 and 2012, we had no unrecognized tax benefits that, if recognized, would favorably impact our effective income tax rate in future periods.

The tax years 2010 through 2014 remain open to examination by major taxing jurisdictions to which we are subject, which are primarily in the United States, as carryforward attributes generated in years past may still be adjusted upon examination by the Internal Revenue Service or state tax authorities if they have or will be used in a future period. We have not recorded any interest and penalties on any unrecognized tax benefits since its inception.

REGULUS

REGULUS	12 Months Ended
REGULUS	Dec. 31, 2014
REGULUS	11	REGULUS

	In September 2007, we and Isis established Regulus, a company focused on the discovery, development and commercialization of microRNA therapeutics, a potential new class of drugs to treat the pathways of human disease. Regulus, which initially was established as a limited liability company, converted to a C corporation in January 2009 and changed its name to Regulus Therapeutics Inc. Regulus operates as an independent company with a separate board of directors, scientific advisory board and management team. We currently own approximately 12% of Regulus’ outstanding common stock.

	In consideration for our and Isis’ initial interests in Regulus, each party granted Regulus exclusive licenses to its intellectual property for certain microRNA therapeutic applications as well as certain patents in the microRNA field. In addition, we made an initial cash contribution to Regulus of $10.0 million, resulting in us and Isis making approximately equal aggregate initial capital contributions to Regulus. In March 2009, we and Isis each purchased $10.0 million of Series A preferred stock of Regulus.

	From the formation of Regulus in September 2007 to October 2012, we accounted for our interest in Regulus using the equity method of accounting. We reviewed the consolidation guidance that defines a variable interest entity, or VIE, and concluded that Regulus qualified as a VIE during such time period. We did not consolidate Regulus as we lacked the power to direct the activities that could significantly impact the economic success of this entity.



	Summary results of Regulus’ statements of comprehensive loss for the nine months ended September 30, 2012 are presented in the tables below, in thousands:



			Nine months ended
			September 30,
			2012
	Statements of Comprehensive Loss Data:
	Net revenues		$	9,462
	Operating expenses			17,733

	Loss from operations			(8,271	)
	Other expense			(2,289	)
	Income tax benefit			28

	Net loss		$	(10,532	)


	Under the equity method of accounting, we were required to recognize losses up to the amount of Regulus’ debt, which was guaranteed by us. This resulted in a negative carrying amount. In October 2012, Regulus completed an initial public offering, resulting in our ownership percentage decreasing from approximately 44% to 17% of Regulus’ outstanding common stock. Upon the completion of the Regulus’ initial public offering, our debt guarantee was terminated.

	Based upon our ownership percentage of 17% after the initial public offering, as well as a review of qualitative factors, we did not believe that we had the ability to exercise significant influence over the operating decisions and financial policies of Regulus and therefore discontinued the equity method of accounting for Regulus at September 30, 2012. We determined that the period between September 30, 2012 and the date on which Regulus’ closed its initial public offering was immaterial for additional equity method accounting. Accordingly, beginning in October , 2012, we accounted for our investment in Regulus as an available-for-sale marketable security due to its readily determinable fair value. As a result of the issuance of additional common stock by Regulus, we recognized a gain of $16.1 million. This amount was recorded as other income in our consolidated statements of comprehensive loss for the year ended December 31, 2012. Our carrying amount in Regulus increased to $12.4 million following the initial public offering, which became the initial basis of our investment in Regulus under the accounting standard for marketable securities. In addition, we recorded $15.7 million as an unrealized gain in other comprehensive income, net of an intraperiod tax benefit of $10.6 million during the year ended December 31, 2012. After sales of our investment in Regulus during 2014, our carrying amount in Regulus decreased to $11.9 million at December 31, 2014.

ACCRUED_EXPENSES

ACCRUED EXPENSES	12 Months Ended
ACCRUED EXPENSES	Dec. 31, 2014
ACCRUED EXPENSES	12	ACCRUED EXPENSES
	Accrued expenses consist of the following at December 31, 2014 and 2013, in thousands:


			At December 31,
			2014		2013
	Compensation and related		$	7,357	$	4,822
	Clinical trial and manufacturing			5,548		2,933
	Consulting and professional services			3,886		2,135
	Pre-clinical			3,081		1,004
	Other			3,808		3,266

			$	23,680	$	14,160

RESTRUCTURING

RESTRUCTURING	12 Months Ended
	Dec. 31, 2014
RESTRUCTURING	13	RESTRUCTURING

	In January 2012, our Board of Directors approved, and we implemented, a strategic corporate restructuring pursuant to which we reduced our overall workforce by approximately 33%, to approximately 115 employees. During the three months ended March 31, 2012, we substantially completed the implementation of the strategic corporate restructuring and recorded $3.9 million of restructuring-related costs in operating expenses, including employee severance, benefits and related costs. We paid substantially all of these restructuring costs during 2012. We did not incur any additional significant costs associated with this restructuring and do not expect to incur any additional significant costs in the future.

QUARTERLY_FINANCIAL_DATA

QUARTERLY FINANCIAL DATA	12 Months Ended
QUARTERLY FINANCIAL DATA	Dec. 31, 2014
QUARTERLY FINANCIAL DATA	14. QUARTERLY FINANCIAL DATA (UNAUDITED)

	The following information has been derived from unaudited consolidated financial statements that, in the opinion of management, include all recurring adjustments necessary for a fair statement of such information.



		Three Months Ended
		March 31,			June 30,			September 30,			December 31,
		2014			2014			2014			2014
		(In thousands, except per share data)
	Revenues	$	8,275		$	7,295		$	10,972		$	24,019
	Operating expenses		277,339			52,300			56,171			69,731
	Net loss		(250,943	)		(44,074	)		(43,989	)		(21,389	)
	Net loss per common share — basic and diluted	$	(3.70	)	$	(0.58	)	$	(0.58	)	$	(0.28	)
	Weighted-average common shares — basic and diluted		67,786			75,835			76,408			76,957



		Three Months Ended
		March 31,			June 30,			September 30,			December 31,
		2013			2013			2013			2013
		(In thousands, except per share data)
	Revenues	$	18,642		$	8,687		$	8,991		$	10,847
	Operating expenses		28,446			29,999			41,225			40,439
	Net loss		(9,013	)		(18,169	)		(29,686	)		(32,357	)
	Net loss per common share — basic and diluted	$	(0.15	)	$	(0.29	)	$	(0.48	)	$	(0.51	)
	Weighted-average common shares — basic and diluted		59,173			61,661			62,416			62,909

	The increase in operating expenses for the three months ended March 31, 2014 resulted from a $224.7 million charge to in-process research and development expense in connection with the purchase of the Sirna RNAi assets from Merck. During the three months ended June 30, 2014, we recorded a credit of $3.9 million to in-process research and development expense, resulting in $220.8 million in-process research and development expense recorded for the year ended December 31, 2014 as a result of this asset acquisition. See Note 3, “Significant Agreements,” for further information.

SUMMARY_OF_SIGNIFICANT_ACCOUNT1

SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Policies)

12 Months Ended

Dec. 31, 2014

Basis of Presentation and Principles of Consolidation

The accompanying consolidated financial statements reflect the operations of Alnylam and our wholly-owned subsidiaries. All intercompany accounts and transactions have been eliminated.

Use of Estimates

Concentrations of Credit Risk and Significant Customers

The following table summarizes customers that represent greater than 10% of our net revenues from collaborators, for the periods indicated:

Year Ended

December 31,

2014

2013

2012

Takeda

Monsanto

MDCO

Cubist

Roche/Arrowhead

The following table summarizes customers with amounts due that represent greater than 10% of our billed and unbilled collaboration receivables balance, at the periods indicated:

At December 31,

2014

2013

Genzyme

MDCO

Represents 10% or less

Fair Value Measurements

Investments in Marketable Securities

Estimated Liability for Development Costs

Revenue Recognition

Income Taxes

Research and Development Costs

Accounting for Stock-Based Compensation

Comprehensive Loss

Net Loss Per Common Share

At December 31,

2014

2013

2012

Options to purchase common stock

8,169

8,713

8,932

Unvested restricted common stock

500

604

8,199

9,213

9,536

Segment Information

We operate in a single reporting segment, the discovery, development and commercialization of RNAi therapeutics.

Subsequent Events

We did not have any material recognized subsequent events. However, we did have the following nonrecognized subsequent events, which are more fully described in Notes 3 and 8:

•

In January 2015, we sold an aggregate of 5,447,368 shares of our common stock through an underwritten public offering at a price to the public of $95.00 per share. See Note 8.

•

Recent Accounting Pronouncements

SUMMARY_OF_SIGNIFICANT_ACCOUNT2

SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Tables)	12 Months Ended
SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Tables)	Dec. 31, 2014
Concentrations of Credit Risk and Significant Customers	The following table summarizes customers that represent greater than 10% of our net revenues from collaborators, for the periods indicated:


			Year Ended
			December 31,
			2014			2013			2012
	Takeda			43	%		47	%		33	%
	Monsanto			30	%		12	%		*
	MDCO			21	%		*			*
	Cubist			*			21	%		*
	Roche/Arrowhead			*			*			56	%
	The following table summarizes customers with amounts due that represent greater than 10% of our billed and unbilled collaboration receivables balance, at the periods indicated:


			At December 31,
			2014			2013
	Genzyme			63	%		94	%
	MDCO			37	%		*

	*	Represents 10% or less
Common Shares Excluded from the Calculation of Net Loss Per Common Share	The following table sets forth for the periods presented the potential common shares (prior to consideration of the treasury stock method) excluded from the calculation of net loss per common share because their inclusion would be anti-dilutive, in thousands:


			At December 31,
			2014			2013			2012
	Options to purchase common stock			8,169			8,713			8,932
	Unvested restricted common stock			30			500			604

				8,199			9,213			9,536

SIGNIFICANT_AGREEMENTS_Tables

SIGNIFICANT AGREEMENTS (Tables)	12 Months Ended
SIGNIFICANT AGREEMENTS (Tables)	Dec. 31, 2014
Revenue from Collaborators	The following table summarizes our total consolidated net revenues from collaborators, for the periods indicated, in thousands:


		Year Ended December 31,
		2014		2013		2012
	Takeda	$	21,973	$	21,973	$	21,973
	Monsanto		14,985		5,640		1,954
	MDCO		10,753		4,604		—
	Roche/Arrowhead		1,000		—		37,318
	Cubist		—		9,721		2,777
	Other		1,850		5,229		2,703

	Total net revenues from collaborators	$	50,561	$	47,167	$	66,725

FAIR_VALUE_MEASUREMENTS_Tables

FAIR VALUE MEASUREMENTS (Tables)	12 Months Ended
FAIR VALUE MEASUREMENTS (Tables)	Dec. 31, 2014
Fair Value of Assets Measured on a Recurring Basis	The following tables present information about our assets that are measured at fair value on a recurring basis at December 31, 2014 and 2013, and indicate the fair value hierarchy of the valuation techniques we utilized to determine such fair value, in thousands:


	Description	At		Quoted		Significant		Significant
		December 31,		Prices in		Observable		Unobservable
		2014		Active		Inputs		Inputs
				Markets		(Level 2)		(Level 3)
				(Level 1)
	Cash equivalents	$	56,203	$	56,203	$	—	$	—
	Marketable securities (fixed income):
	Certificates of deposit		24,300		—		24,300		—
	Commercial paper		40,796		—		40,796		—
	Corporate notes		662,545		—		662,545		—
	Municipal debt securities		9,005		—		9,005		—
	U.S. government-sponsored enterprise securities		64,856		—		64,856		—
	U.S. treasury securities		5,248		—		5,248		—
	Marketable securities (Regulus equity holdings)		94,583		94,583		—		—

	Total	$	957,536	$	150,786	$	806,750	$	—



	Description	At		Quoted		Significant		Significant
		December 31,		Prices in		Observable		Unobservable
		2013		Active		Inputs		Inputs
				Markets		(Level 2)		(Level 3)
				(Level 1)
	Cash equivalents	$	32,571	$	32,571	$	—	$	—
	Marketable securities (fixed income):
	Corporate notes		228,462		—		228,462		—
	U.S. government-sponsored enterprise securities		56,863		—		56,863		—
	Commercial paper		11,978		—		11,978		—
	Marketable securities (Regulus equity holdings)		45,452		45,452		—		—

	Total	$	375,326	$	78,023	$	297,303	$	—

MARKETABLE_SECURITIES_Tables

MARKETABLE SECURITIES (Tables)	12 Months Ended
MARKETABLE SECURITIES (Tables)	Dec. 31, 2014
Summary of Fair Value Accumulated Other Comprehensive Income and Intraperiod Tax Allocation in Regulus Available-for-Sale Marketable Securities	The following tables summarize the fair value, accumulated other comprehensive income and intraperiod tax allocation regarding our investment in Regulus available-for-sale marketable securities at December 31, 2014 and 2013, and for the activity recorded in the year, in thousands:


	Description	At			Sales of Regulus			All Other			Balance at
		December 31,			Shares During			Activity During			December 31,
		2013			Year Ended			Year Ended			2014
					December 31,			December 31,
					2014			2014
	Carrying value	$	12,449		$	(514	)	$	—		$	11,935
	Accumulated other comprehensive income, before tax		33,003			(2,081	)		51,726			82,648

	Investment in equity securities of Regulus Therapeutics Inc., as reported	$	45,452		$	(2,595	)	$	51,726		$	94,583

	Accumulated other comprehensive income, before tax	$	33,003		$	(2,081	)	$	51,726		$	82,648
	Intraperiod tax allocation recorded as a benefit from income taxes		(13,267	)		—			(19,525	)		(32,792	)

	Accumulated other comprehensive income, net of tax	$	19,736		$	(2,081	)	$	32,201		$	49,856


	Description	At			Sales of Regulus			All Other			Balance at
		December 31,			Shares During			Activity During			December 31,
		2012			year Ended			Year Ended			2013
					December 31,			December 31,
					2013			2013
	Carrying value	$	12,449		$	—		$	—		$	12,449
	Accumulated other comprehensive income, before tax		26,299			—			6,704			33,003

	Investment in equity securities of Regulus Therapeutics Inc., as reported	$	38,748		$	—		$	6,704		$	45,452

	Accumulated other comprehensive income, before tax	$	26,299		$	—		$	6,704		$	33,003
	Intraperiod tax allocation recorded as a benefit from income taxes		(10,572	)		—			(2,695	)		(13,267	)

	Accumulated other comprehensive income, net of tax	$	15,727		$	—		$	4,009		$	19,736

Summary of Company's Marketable Securities Excluding Regulus	The following tables summarize our marketable securities, other than our holdings in Regulus noted above, at December 31, 2014 and 2013, in thousands:


		December 31, 2014
		Amortized			Gross			Gross			Fair Value
		Cost			Unrealized			Unrealized
					Gains			Losses
	Certificates of deposit (Due within 1 year)	$	24,300		$	—		$	—		$	24,300
	Commercial paper (Due within 1 year)		40,785			11			—			40,796
	Corporate notes (Due within 1 year)		449,044			14			(293	)		448,765
	Corporate notes (Due after 1 year through 2 years)		214,510			—			(730	)		213,780
	Municipal debt securities (Due after 1 year through 2 years)		9,002			3			—			9,005
	U.S. government-sponsored enterprise securities (Due within 1 year)		13,069			—			(1	)		13,068
	U.S. government-sponsored enterprise securities (Due after 1 year through 2 years)		51,879			—			(91	)		51,788
	U.S. treasury securities (Due after 1 year through 2 years)		5,254			—			(6	)		5,248

	Total	$	807,843		$	28		$	(1,121	)	$	806,750



		December 31, 2013
		Amortized			Gross			Gross			Fair Value
		Cost			Unrealized			Unrealized
					Gains			Losses
	Commercial paper (Due within 1 year)	$	11,983		$	—		$	(5	)	$	11,978
	Corporate notes (Due within 1 year)		154,175			33			(46	)		154,162
	Corporate notes (Due after 1 year through 2 years)		74,312			23			(35	)		74,300
	U.S. government-sponsored enterprise securities (Due within 1 year)		26,553			8			—			26,561
	U.S. government-sponsored enterprise securities (Due after 1 year through 2 years)		30,300			2			—			30,302

	Total	$	297,323		$	66		$	(86	)	$	297,303

PROPERTY_AND_EQUIPMENT_NET_Tab

PROPERTY AND EQUIPMENT, NET (Tables)	12 Months Ended
PROPERTY AND EQUIPMENT, NET (Tables)	Dec. 31, 2014
Property and Equipment, Net	Property and equipment consist of the following at December 31, 2014 and 2013, in thousands:


					December 31,
			Useful Life		2014			2013
	Laboratory equipment			5 years	$	28,559		$	22,729
	Computer equipment and software			3 years		4,440			4,261
	Furniture and fixtures			5 years		1,999			1,793
	Leasehold improvements			*		30,853			28,953
	Construction in progress			—		1,982			28

						67,833			57,764
	Less: accumulated depreciation					(46,093	)		(41,316	)

					$	21,740		$	16,448


	*	Shorter of asset life or lease term

COMMITMENTS_AND_CONTINGENCIES_

COMMITMENTS AND CONTINGENCIES (Tables)	12 Months Ended
COMMITMENTS AND CONTINGENCIES (Tables)	Dec. 31, 2014
Fixed, Estimated and Cancelable Payments under Existing License Agreements	At December 31, 2014, we were committed to make the following fixed, estimated and cancelable payments under existing license agreements, in thousands:


	Year Ending December 31,
	2015	$	7,379
	2016		724
	2017		744
	2018		754
	2019		762
	Thereafter		8,592

	Total	$	18,955

Future Minimum Lease Payments under Non-Cancelable Lease	Future minimum payments under our non-cancelable leases are approximately as follows, in thousands:


	Year Ending December 31,
	2015	$	6,810
	2016		6,994
	2017		7,535
	2018		7,387
	2019		7,608
	Thereafter		13,845

	Total	$	50,179

STOCK_INCENTIVE_PLANS_Tables

STOCK INCENTIVE PLANS (Tables)	12 Months Ended
STOCK INCENTIVE PLANS (Tables)	Dec. 31, 2014
Summary of Stock-Based Compensation Expense by Type of Award	The following table summarizes stock-based compensation expense by type of award during the three years ended December 31, 2014, in thousands:


		2014			2013			2012
	Stock-based compensation expense by type of award:
	Stock options	$	24,603		$	13,839		$	8,739
	Performance-based stock options		4,960			—			—
	Restricted stock awards		1,068			3,420			2,436
	ESPP share issuances		392			261			241
	Non-employee stock options		2,038			3,183			944

		$	33,061		$	20,703		$	12,360

Summary of Unrecognized Stock-Based Compensation Expense, Net of Estimated Forfeitures	The following table summarizes our unrecognized stock-based compensation expense, net of estimated forfeitures, at December 31, 2014 by type of awards, excluding performance-based stock options, and the weighted-average period over which that expense is expected to be recognized:


		At December 31, 2014
		Unrecognized Expense,			Weighted-average
		Net of			Recognition
		Estimated Forfeitures			Period
		(in thousands)			(in years)
	Type of award:
	Stock options	$	59,854			2.62
	Restricted stock awards		1,571			3.46
	ESPP share issuances		197			0.33
Valuation Assumptions for Stock Options
		2014			2013			2012
	Risk-free interest rate		1.7-2.3	%		1.0-2.0	%		0.8-1.0	%
	Expected dividend yield		—			—			—
	Expected option life		5.5-7.5 years			5.6 years			5.6-5.9 years
	Expected volatility		53-57	%		55-56	%		57	%
Stock Option Activity	The following table summarizes the activity of our stock option plans, excluding stock options granted in December 2014 subject to and contingent upon stockholder approval of an amendment and restatement of our 2009 Plan and performance-based stock options:


		Number of			Weighted-			Weighted-			Aggregate
		Options			average			average			Intrinsic
		(in thousands)			Exercise			Remaining			Value
					Price			Contractual			(in thousands)
								Term (in years)
	Outstanding, December 31, 2013		8,245		$	22.06
	Granted		1,352			75.77
	Exercised		(1,982	)		14.83
	Cancelled		(85	)		35.32

	Outstanding, December 31, 2014		7,530		$	33.46			6.32		$	478,506

	Exercisable at December 31, 2014		4,736		$	21.44			4.86		$	357,891
	Vested or expected to vest at December 31, 2014		7,292		$	32.53			6.23		$	470,149
Restricted Stock Awards Activity	The following table summarizes the activity of our restricted stock awards, including restricted stock and restricted stock units:


		Number of			Weighted-
		Restricted			average
		Stock Awards			Grant Date
		(in thousands)			Fair Value
	Unvested at December 31, 2013		500		$	10.69
	Granted		29			68.28
	Vested		(499	)		10.59
	Forfeited		—			—

	Unvested at December 31, 2014		30		$	68.02

Performance-based Stock Options
Stock Option Activity	The following table summarizes the activity of our performance-based stock options, excluding stock options granted in December 2014 subject to and contingent upon stockholder approval of an amendment and restatement of our 2009 Plan:


		Number of			Weighted-			Weighted-			Aggregate
		Options			average			average			Intrinsic
		(in thousands)			Exercise			Remaining			Value
					Price			Contractual			(in thousands)
								Term (in years)
	Outstanding, December 31, 2013		468		$	63
	Granted		194			96.45
	Exercised		(5	)		63
	Cancelled		(18	)		63

	Outstanding, December 31, 2014		639		$	73.15			9.05		$	15,237

	Exercisable at December 31, 2014		150		$	63			8.4		$	5,100

INCOME_TAXES_Tables

INCOME TAXES (Tables)	12 Months Ended
INCOME TAXES (Tables)	Dec. 31, 2014
Components of Loss before Income Tax, Domestic and Foreign	The domestic and foreign components of loss before income taxes are as follows, in thousands:


		2014			2013			2012
	Domestic	$	(372,137	)	$	(81,109	)	$	(116,400	)
	Foreign		(28,467	)		(10,811	)		(186	)

	Loss before income taxes	$	(400,604	)	$	(91,920	)	$	(116,586	)

Schedule of Deferred Tax Assets and Liabilities	Components of the net deferred tax (liability) asset at December 31, 2014 and 2013 are as follows, in thousands:


		2014			2013
	Deferred tax assets:
	Net operating loss carryforwards	$	176,789		$	124,797
	Research and development credits		38,204			23,902
	AMT credits		788			788
	Foreign tax credits		3,196			3,196
	Capitalized research and development and start-up costs		19,246			16,214
	Deferred revenue		14,273			37,273
	Deferred compensation		24,516			21,706
	Intangible assets		17,637			2,210
	Partnership interest		689			689
	Other		5,871			4,885

	Total deferred tax assets		301,209			235,660
	Deferred tax liabilities:
	Intangible assets		—			(7	)
	Unrealized gain on available-for-sale securities		(32,793	)		(13,267	)
	Deferred tax asset valuation allowance		(268,416	)		(222,393	)

	Net deferred tax liability	$	—		$	(7	)

Benefit from Income Taxes	The benefit from income taxes for the years ended December 31, 2014, 2013 and 2012 are as follows, in thousands:


		2014			2013			2012
	U.S.:
	Current	$	—		$	34		$	52
	Deferred		(40,209	)		(2,695	)		(10,572	)

	Total U.S.		(40,209	)		(2,661	)		(10,520	)

	Foreign:
	Current		—			—			—
	Deferred		—			(34	)		(52	)

	Total Foreign		—			(34	)		(52	)

	Benefit from income taxes	$	(40,209	)	$	(2,695	)	$	(10,572	)

Effective Income Tax Rate	Our effective income tax rate differs from the statutory federal income tax rate as follows for the years ended December 31, 2014, 2013 and 2012:


		2014			2013			2012
	At U.S. federal statutory rate		35	%		35	%		35	%
	State taxes, net of federal effect		1.8			4.3			4.9
	Stock-based compensation		(0.2	)		0.8			(0.7	)
	Tax credits		3.5			8.5			4.2
	Orphan drug credit addback		(0.6	)		(2.7	)		—
	Other permanent items		—			(0.3	)		(1.6	)
	Foreign rate differential		(2.5	)		(4.1	)		(0.1	)
	In-process research and development		(19.4	)		—			—
	Tax basis in intangible assets as a result of Sirna transaction		4.2			—			—
	Valuation allowance		(11.8	)		(38.5	)		(32.6	)

	Effective income tax rate		10	%		3	%		9.1	%

REGULUS_Tables

REGULUS (Tables)	12 Months Ended
REGULUS (Tables)	Dec. 31, 2014
Summary Results of Regulus' Operation	Summary results of Regulus’ statements of comprehensive loss for the nine months ended September 30, 2012 are presented in the tables below, in thousands:


		Nine months ended
		September 30,
		2012
	Statements of Comprehensive Loss Data:
	Net revenues	$	9,462
	Operating expenses		17,733

	Loss from operations		(8,271	)
	Other expense		(2,289	)
	Income tax benefit		28

	Net loss	$	(10,532	)

ACCRUED_EXPENSES_Tables

ACCRUED EXPENSES (Tables)	12 Months Ended
ACCRUED EXPENSES (Tables)	Dec. 31, 2014
Accrued Expenses	Accrued expenses consist of the following at December 31, 2014 and 2013, in thousands:



		At December 31,
		2014		2013
	Compensation and related	$	7,357	$	4,822
	Clinical trial and manufacturing		5,548		2,933
	Consulting and professional services		3,886		2,135
	Pre-clinical		3,081		1,004
	Other		3,808		3,266

		$	23,680	$	14,160

QUARTERLY_FINANCIAL_DATA_Table

QUARTERLY FINANCIAL DATA (Tables)	12 Months Ended
QUARTERLY FINANCIAL DATA (Tables)	Dec. 31, 2014
Schedule of Quarterly Financial Information	The following information has been derived from unaudited consolidated financial statements that, in the opinion of management, include all recurring adjustments necessary for a fair statement of such information.



		Three Months Ended
		March 31,			June 30,			September 30,			December 31,
		2014			2014			2014			2014
		(In thousands, except per share data)
	Revenues	$	8,275		$	7,295		$	10,972		$	24,019
	Operating expenses		277,339			52,300			56,171			69,731
	Net loss		(250,943	)		(44,074	)		(43,989	)		(21,389	)
	Net loss per common share — basic and diluted	$	(3.70	)	$	(0.58	)	$	(0.58	)	$	(0.28	)
	Weighted-average common shares — basic and diluted		67,786			75,835			76,408			76,957



		Three Months Ended
		March 31,			June 30,			September 30,			December 31,
		2013			2013			2013			2013
		(In thousands, except per share data)
	Revenues	$	18,642		$	8,687		$	8,991		$	10,847
	Operating expenses		28,446			29,999			41,225			40,439
	Net loss		(9,013	)		(18,169	)		(29,686	)		(32,357	)
	Net loss per common share — basic and diluted	$	(0.15	)	$	(0.29	)	$	(0.48	)	$	(0.51	)
	Weighted-average common shares — basic and diluted		59,173			61,661			62,416			62,909

Customers_that_Represent_Great

Customers that Represent Greater than Ten Percent of Net Revenues from Collaborators (Detail) (Revenue from Rights Concentration Risk, Net Revenues)	12 Months Ended
	Dec. 31, 2014		Dec. 31, 2013		Dec. 31, 2012
Takeda
Concentration Risk [Line Items]
Concentration risk percentage	43.00%		47.00%		33.00%
Monsanto
Concentration Risk [Line Items]
Concentration risk percentage	30.00%		12.00%			[1]
MDCO
Concentration Risk [Line Items]
Concentration risk percentage	21.00%			[1]		[1]
Cubist
Concentration Risk [Line Items]
Concentration risk percentage		[1]	21.00%			[1]
Roche/Arrowhead
Concentration Risk [Line Items]
Concentration risk percentage		[1]		[1]	56.00%

[1]	Represents 10% or less

Customers_that_Represent_Great1

Customers that Represent Greater than Ten Percent of Billed and Unbilled Collaboration Receivables (Detail) (Accounts Receivable, Credit Concentration Risk [Member])	12 Months Ended
	Dec. 31, 2014	Dec. 31, 2013
Genzyme
Concentration Risk [Line Items]
Concentration risk percentage	63.00%	94.00%
MDCO
Concentration Risk [Line Items]
Concentration risk percentage	37.00%		[1]

[1]	Represents 10% or less

Recovered_Sheet1

Summary of Significant Accounting Policies - Additional Information (Detail) (USD $)	1 Months Ended		12 Months Ended		1 Months Ended			12 Months Ended
	Jan. 31, 2013	Feb. 29, 2012	Dec. 31, 2014	Dec. 31, 2012	Mar. 31, 2014	Feb. 28, 2014	Jan. 31, 2015	Dec. 31, 2013	Jan. 11, 2014
Significant Accounting Policies [Line Items]
Gain on sale of available for sale securities			$2,081,000	$255,000
Marketable securities classified as cash equivalents, original maturity			90 days
Policy for marketable securities			90 days
Deferred revenue, current			23,871,000					32,696,000
Deferred revenue, net of current portion			42,983,000					93,394,000
Issuance of common stock, net of offering costs (in shares)	9,200,000	8,625,000
Underwritten public offering amount per share	$20.13	$10.75
Genzyme
Significant Accounting Policies [Line Items]
Issuance of common stock, net of offering costs (in shares)					344,448	8,766,338
Underwritten public offering amount per share									$85.72
Subsequent Event
Significant Accounting Policies [Line Items]
Issuance of common stock, net of offering costs (in shares)							5,447,368
Underwritten public offering amount per share							$95
Subsequent Event \| Genzyme
Significant Accounting Policies [Line Items]
Issuance of common stock, net of offering costs (in shares)							744,566
Underwritten public offering amount per share							$95
Regulus Therapeutics Inc
Significant Accounting Policies [Line Items]
Gain on sale of available for sale securities			2,100,000
Research and Development Expense
Significant Accounting Policies [Line Items]
License fee			$12,100,000	$5,700,000				$8,000,000

Potential_Common_Shares_Common

Potential Common Shares Common Shares Excluded from Calculation of Net Loss Per Common Share (Detail)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from computation of earnings	8,199	9,213	9,536
Options to Purchase Common Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from computation of earnings	8,169	8,713	8,932
Restricted stock awards
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from computation of earnings	30	500	604

Revenue_from_Collaborators_Det

Revenue from Collaborators (Detail) (USD $)	3 Months Ended								12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2014	Sep. 30, 2014	Jun. 30, 2014	Mar. 31, 2014	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total net revenues from collaborators	$24,019	$10,972	$7,295	$8,275	$10,847	$8,991	$8,687	$18,642	$50,561	$47,167	$66,725
Takeda
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total net revenues from collaborators									21,973	21,973	21,973
Monsanto
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total net revenues from collaborators									14,985	5,640	1,954
MDCO
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total net revenues from collaborators									10,753	4,604
Roche/Arrowhead
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total net revenues from collaborators									1,000		37,318
Cubist
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total net revenues from collaborators										9,721	2,777
Other
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Total net revenues from collaborators									$1,850	$5,229	$2,703

Significant_Agreements_Additio

Significant Agreements - Additional Information (Detail) (USD $)

0 Months Ended

1 Months Ended

3 Months Ended

12 Months Ended

1 Months Ended

3 Months Ended

1 Months Ended

0 Months Ended

1 Months Ended

3 Months Ended

0 Months Ended

3 Months Ended

0 Months Ended

1 Months Ended

Mar. 05, 2014

Jan. 31, 2013

Feb. 29, 2012

Jun. 30, 2014

Dec. 31, 2014

Dec. 31, 2013

Dec. 31, 2012

Jan. 31, 2014

Mar. 31, 2014

Jan. 31, 2015

Jan. 11, 2014

Mar. 31, 2014

Feb. 28, 2014

Dec. 31, 2014

Oct. 31, 2012

Dec. 31, 2013

Jan. 14, 2014

Jan. 22, 2015

Jun. 30, 2008

Feb. 28, 2013

Sep. 30, 2014

Aug. 31, 2012

Mar. 31, 2004

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Issuance of common stock, net of offering costs (in shares)

9,200,000

8,625,000

Proceeds from issuance of common stock to Genzyme

$723,037,000

Benefit from income taxes

-40,209,000

-2,695,000

-10,572,000

Common stock price

$20.13

$10.75

Fair value of shares issued

1,581,000

1,184,000

879,000

Asset acquisition cash consideration

25,000,000

Issuance of common stock in connection with an asset acquisition

195,766,000

Liability for stock issuance

3,808,000

3,266,000

3,808,000

3,266,000

In-process research and development

199,300,000

220,766,000

In-process research and development credit

3,900,000

Research and Development Expense

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

License fee

12,100,000

8,000,000

5,700,000

Sirna Therapeutics

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Common stock price

$81.36

Asset acquisition cash consideration

25,000,000

Issuance of common stock in connection with an asset acquisition (in shares)

2,142,037

378,007

Issuance of common stock in connection with an asset acquisition

174,300,000

Liability for stock issuance

25,400,000

In-process research and development

220,800,000

224,700,000

In-process research and development credit

3,900,000

Asset acquisition consideration upon achievement of milestones

105,000,000

Lock up period

6 months

Subsequent lock up period stock holding percentage

50.00%

Sirna Therapeutics | Intellectual Property

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Asset acquisition consideration upon achievement of milestones

10,000,000

Sirna Therapeutics | Additional

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Lock up period

6 months

Platform Alliances | Joint Technology Transfer Committee

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Maximum life of collaboration committee

7 years

Platform Alliances | Joint Delivery Collaboration Committee

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Maximum life of collaboration committee

7 years

Clinical Development and Regulatory Milestone | Sirna Therapeutics

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Asset acquisition consideration upon achievement of milestones

40,000,000

Commercial Milestones | Sirna Therapeutics

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Asset acquisition consideration upon achievement of milestones

65,000,000

Subsequent Event

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Issuance of common stock, net of offering costs (in shares)

5,447,368

Common stock price

$95

Genzyme

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Amount earned upon achievement of milestone

25,000,000

Issuance of common stock, net of offering costs (in shares)

344,448

8,766,338

Proceeds from issuance of common stock to Genzyme

23,000,000

700,000,000

Voting percentage

20.00%

Minimum percentage of ownership interest terminate

7.50%

Percentage of acquired outstanding common stock for Genzyme to appoint individual to board of directors

20.00%

Benefit from income taxes

20,700,000

15,200,000

Common stock price

$85.72

Fair value of shares issued

751,500,000

Excess of fair value over cash received for stock issuance

51,500,000

Performance period

6 years

Percentage ownership interest owned by noncontrolling owners

12.00%

Genzyme | Minimum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Agreement to acquire outstanding shares of common stock percentage

5.00%

Percentage of ownership interest

30.00%

Genzyme | Maximum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Agreement to acquire outstanding shares of common stock percentage

30.00%

Genzyme | Product Alliances

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Upfront fee received

22,500,000

Deferred revenue

6,700,000

33,500,000

6,700,000

33,500,000

Performance period

6 years

Genzyme | Product Alliances | Phase Two Clinical Trial ALN-TTR

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Amount earned upon achievement of milestone

7,000,000

Genzyme | Product Alliances | Phase Three Clinical Trial

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Amount earned upon achievement of milestone

4,000,000

Genzyme | Regional Collaboration Product

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Percentage of sharing in development cost

20.00%

Potential future payment for the achievement of certain development milestones

55,000,000

Maximum number of potential future milestones

75,000,000

Potential future payment for the achievement of specified commercialization milestones

20,000,000

Royalty rate

20.00%

Genzyme | Regional Collaboration Product | Minimum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Potential milestone payments to be earned

5,000,000

Genzyme | Regional Collaboration Product | Maximum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Potential milestone payments to be earned

20,000,000

Genzyme | Regional Collaboration Product | Milestone One

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Potential future payment for the achievement of certain development milestones

50,000,000

Genzyme | Co-developed/ Co-promoted Collaboration Product

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Percentage of sharing in development cost

50.00%

Maximum number of potential future milestones

75,000,000

Royalty rate

20.00%

Genzyme | Co-developed/ Co-promoted Collaboration Product | Minimum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Potential milestone payments to be earned

5,000,000

Genzyme | Co-developed/ Co-promoted Collaboration Product | Maximum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Potential milestone payments to be earned

25,000,000

Genzyme | Co-developed/ Co-promoted Collaboration Product | Phase Three Clinical Trial

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Next potential milestone payment

25,000,000

Genzyme | Global Collaboration Product

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Percentage of sharing in development cost

100.00%

Potential future payment for the achievement of certain development milestones

60,000,000

Maximum number of potential future milestones

200,000,000

Potential future payment for the achievement of specified commercialization milestones

140,000,000

Royalty rate

20.00%

Genzyme | Investors [Member]

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Number of demand rights to conduct registered underwritten public offering

Genzyme | Following the two-year anniversary

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Number of trailing days on which average is calculated

10 days

Genzyme | Following the two-year anniversary | Minimum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Percentage of market price per share of common stock compared to share of common stock at closing of stock purchase

100.00%

Genzyme | Following the two-year anniversary | Maximum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Percentage of sale of initial shares

25.00%

Genzyme | Subsequent Event

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Issuance of common stock, net of offering costs (in shares)

744,566

Common stock price

$95

Genzyme | Subsequent Event | Concurrent Private Placement

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Issuance of common stock, net of offering costs (in shares)

744,566

Proceeds from issuance of common stock to Genzyme

70,700,000

Genzyme | Subsequent Event | Compensatory Purposes

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Issuance of common stock, net of offering costs (in shares)

196,251

Proceeds from issuance of common stock to Genzyme

18,300,000

Takeda | Platform Alliances

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Upfront fee received

100,000,000

Deferred revenue

8,900,000

Potential future payment for the achievement of certain development milestones

26,000,000

Maximum number of potential future milestones

171,000,000

Potential future payment for the achievement of specified commercialization milestones

105,000,000

Next potential milestone payment

2,000,000

Potential future payment for the achievement of specified regulatory milestones

40,000,000

Granted period of royalty bearing license

5 years

Milestone fees to company upon achievement of specified technology transfer milestones

50,000,000

License and collaborations agreements, prior written notice period before termination

180 days

Takeda | Platform Alliances | Minimum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Estimated range of expiration for fundamental patents

2016

Takeda | Platform Alliances | Maximum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Estimated range of expiration for fundamental patents

2025

MDCO | Product Alliances

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Upfront fee received

25,000,000

Amount earned upon achievement of milestone

10,000,000

Deferred revenue

24,700,000

Potential future payment for the achievement of certain development milestones

30,000,000

Maximum number of potential future milestones

180,000,000

Potential future payment for the achievement of specified commercialization milestones

100,000,000

Next potential milestone payment

20,000,000

Potential future payment for the achievement of specified regulatory milestones

50,000,000

Revenue recognizing period

5 years

MDCO | Product Alliances | Licensing Agreements

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenue from reimbursement of costs incurred

4,800,000

MDCO | Product Alliances | Minimum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Estimated range of expiration for fundamental patents

2015

MDCO | Product Alliances | Maximum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Estimated range of expiration for fundamental patents

2023

Monsanto Alliance | Minimum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Estimated range of expiration for fundamental patents

2016

Monsanto Alliance | Maximum

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Estimated range of expiration for fundamental patents

2025

Monsanto Alliance | Platform Alliances

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Upfront fee received

29,200,000

Amount earned upon achievement of milestone

4,000,000

Deferred revenue

10,600,000

Maximum number of potential future milestones

5,000,000

Next potential milestone payment

Revenue recognizing period

5 years

Period of exclusivity in the collaboration

10 years

Final required milestone payment cancelled

1,000,000

Deferred revenue, potential refundable amount

5,000,000

Period for services under contract

5 years

Monsanto Alliance | Platform Alliances | Recognized through February 2015

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Deferred revenue

5,600,000

Monsanto Alliance | Platform Alliances | Recognized when the potential refund obligation ceases

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Deferred revenue

5,000,000

Monsanto Alliance | Platform Alliances | Amended Agreement

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Deferred revenue

16,800,000

Isis | Discovery and Development Alliances

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Upfront fee received

500,000

Potential future payment upon the occurrence of achievement of specified development and regulatory milestones

3,400,000

Number of licensed products

Additional number of licensed products

Isis | Discovery and Development Alliances | Research and Development Expense

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

License fee

8,300,000

700,000

2,500,000

License fees incurred but not yet paid

1,800,000

Isis | Discovery and Development Alliances | Up Front Payment | Research and Development Expense

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

License fee

5,000,000

Isis | Discovery and Development Alliances | Milestone Payments | Research and Development Expense

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

License fee

$3,400,000

Isis | Subsequent Event | Discovery and Development Alliances

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Number of programs Providing exclusive RNA therapeutic license rights

Fair_Value_Measured_on_Recurri

Fair Value Measured on Recurring Basis (Detail) (USD $)	Dec. 31, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	$806,750	$297,303
Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	56,203	32,571
Available for sale equity securities, Fair value disclosure	94,583	45,452
Total	957,536	375,326
Recurring \| Corporate notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	662,545	228,462
Recurring \| U.S. government-sponsored enterprise securities
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	64,856	56,863
Recurring \| Commercial paper
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	40,796	11,978
Recurring \| Certificates of deposit
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	24,300
Recurring \| Municipal debt securities
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	9,005
Recurring \| U.S. treasury securities
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	5,248
Quoted Prices in Active Markets (Level 1) \| Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	56,203	32,571
Available for sale equity securities, Fair value disclosure	94,583	45,452
Total	150,786	78,023
Significant Observable Inputs (Level 2) \| Recurring
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total	806,750	297,303
Significant Observable Inputs (Level 2) \| Recurring \| Corporate notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	662,545	228,462
Significant Observable Inputs (Level 2) \| Recurring \| U.S. government-sponsored enterprise securities
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	64,856	56,863
Significant Observable Inputs (Level 2) \| Recurring \| Commercial paper
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	40,796	11,978
Significant Observable Inputs (Level 2) \| Recurring \| Certificates of deposit
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	24,300
Significant Observable Inputs (Level 2) \| Recurring \| Municipal debt securities
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	9,005
Significant Observable Inputs (Level 2) \| Recurring \| U.S. treasury securities
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Available for sale debt securities, Fair value disclosure	$5,248

Fair_Value_Measurements_Additi

Fair Value Measurements - Additional Information (Detail) (Regulus Therapeutics Inc, USD $)	Dec. 31, 2013
In Millions, unless otherwise specified	Dec. 31, 2013
Regulus Therapeutics Inc
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Marketable securities transferred from Level 2 to Level 1	$45.50

Summary_of_Fair_Value_Accumula

Summary of Fair Value Accumulated Other Comprehensive Income and Intraperiod Tax Allocation in Available-for-Sale Marketable Securities (Detail) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Schedule of Available-for-sale Securities [Line Items]
Carrying value	$11,900		$12,400
Intraperiod tax allocation recorded as a benefit from income taxes	-32,793	-13,267
Accumulated other comprehensive income, net of tax			15,700
Intraperiod tax allocation recorded as a benefit from income taxes			10,600
Accumulated other comprehensive income, net of tax	31,127	4,055	15,827
Regulus Therapeutics Inc
Schedule of Available-for-sale Securities [Line Items]
Carrying value	11,935	12,449	12,449
Accumulated other comprehensive income, before tax	82,648	33,003	26,299
Investment in equity securities of Regulus Therapeutics Inc., as reported	94,583	45,452	38,748
Accumulated other comprehensive income, before tax	82,648	33,003	26,299
Intraperiod tax allocation recorded as a benefit from income taxes	-32,792	-13,267	-10,572
Accumulated other comprehensive income, net of tax	49,856	19,736	15,727
Regulus Therapeutics Inc \| Sales of Regulus Shares
Schedule of Available-for-sale Securities [Line Items]
Carrying value	-514
Accumulated other comprehensive income, before tax	-2,081
Investment in equity securities of Regulus Therapeutics Inc., as reported	-2,595
Accumulated other comprehensive income, before tax	-2,081
Accumulated other comprehensive income, net of tax	-2,081
Regulus Therapeutics Inc \| All Other Activity
Schedule of Available-for-sale Securities [Line Items]
Accumulated other comprehensive income, before tax	51,726	6,704
Investment in equity securities of Regulus Therapeutics Inc., as reported	51,726	6,704
Accumulated other comprehensive income, before tax	51,726	6,704
Intraperiod tax allocation recorded as a benefit from income taxes	-19,525	-2,695
Accumulated other comprehensive income, net of tax	$32,201	$4,009

Summary_of_Companys_Marketable

Summary of Company's Marketable Securities (Detail) (USD $)	Dec. 31, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$807,843	$297,323
Gross Unrealized Gains	28	66
Gross Unrealized Losses	-1,121	-86
Fair Value	806,750	297,303
Certificates of deposit (Due within 1 year)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	24,300
Fair Value	24,300
Commercial paper (Due within 1 year)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	40,785	11,983
Gross Unrealized Gains	11
Gross Unrealized Losses		-5
Fair Value	40,796	11,978
Corporate notes (Due within 1 year)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	449,044	154,175
Gross Unrealized Gains	14	33
Gross Unrealized Losses	-293	-46
Fair Value	448,765	154,162
Corporate notes (Due after 1 year through 2 years)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	214,510	74,312
Gross Unrealized Gains		23
Gross Unrealized Losses	-730	-35
Fair Value	213,780	74,300
Municipal debt securities (Due after 1 year through 2 years)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	9,002
Gross Unrealized Gains	3
Fair Value	9,005
U.S. government-sponsored enterprise securities (Due within 1 year)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	13,069	26,553
Gross Unrealized Gains		8
Gross Unrealized Losses	-1
Fair Value	13,068	26,561
U.S. government-sponsored enterprise securities (Due after 1 year through 2 years)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	51,879	30,300
Gross Unrealized Gains		2
Gross Unrealized Losses	-91
Fair Value	51,788	30,302
U.S. treasury securities (Due after 1 year through 2 years)
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	5,254
Gross Unrealized Losses	-6
Fair Value	$5,248

Property_and_Equipment_Detail

Property and Equipment (Detail) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2014		Dec. 31, 2013
Property, Plant and Equipment [Line Items]
Laboratory equipment	28,559		$22,729
Computer equipment and software	4,440		4,261
Furniture and fixtures	1,999		1,793
Leasehold improvements	30,853		28,953
Construction in progress	1,982		28
Property and Equipment Gross	67,833		57,764
Less: accumulated depreciation	-46,093		-41,316
Property and Equipment Net	21,740		$16,448
Laboratory equipment
Property, Plant and Equipment [Line Items]
Property, and equipment, useful life	5 years
Computer equipment and software
Property, Plant and Equipment [Line Items]
Property, and equipment, useful life	3 years
Furniture and Fixtures
Property, Plant and Equipment [Line Items]
Property, and equipment, useful life	5 years
Leasehold improvements
Property, Plant and Equipment [Line Items]
Property, and equipment, useful life		[1]

[1]	Shorter of asset life or lease term

Property_and_Equipment_Net_Add

Property and Equipment Net - Additional Information (Detail) (USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Property, Plant and Equipment [Line Items]
Depreciation expense	$5	$6.10	$4.60

Recovered_Sheet2

Commitments and Contingencies - Additional Information (Detail) (USD $)	1 Months Ended	3 Months Ended								12 Months Ended
	Mar. 31, 2014	Dec. 31, 2014	Sep. 30, 2014	Jun. 30, 2014	Mar. 31, 2014	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Commitments and Contingencies [Line Items]
Future purchase commitments		$104,500,000								$104,500,000
Future purchase commitments expected to be incurred in 2015		59,300,000								59,300,000
Future purchase commitments expected to be incurred past 2015		45,200,000								45,200,000
Lease extension period	5 years
Lease extended expiration date	30-Sep-21
Operating lease obligation through 2021		18,955,000								18,955,000
Lease expiration date											2016-09
Rent expense										8,900,000	4,900,000	6,400,000
Operating expenses		69,731,000	56,171,000	52,300,000	277,339,000	40,439,000	41,225,000	29,999,000	28,446,000	455,541,000	140,109,000	196,181,000
One time settlement payment												65,000,000
Tekmira Restructured Cross-License Agreement
Commitments and Contingencies [Line Items]
Operating expenses												65,000,000
Future milestone payments											5,000,000
Milestone paid						5,000,000
Tekmira Restructured Cross-License Manufacturing Contracts and Service Agreement
Commitments and Contingencies [Line Items]
One time settlement payment												30,000,000
Tekmira Restructured Cross-License Buy-Down
Commitments and Contingencies [Line Items]
One time settlement payment												35,000,000
Contingent milestone payments												10,000,000
Bmr Fresh Pond Research Park Llc
Commitments and Contingencies [Line Items]
Lease extension period										5 years
Area of office and laboratory space held under operating lease		15,000								15,000
Lease expiration date										31-Aug-17
Number 0f lease extension options										2
Lease incentive received		1,900,000				200,000				1,900,000	200,000	1,800,000
Third Street
Commitments and Contingencies [Line Items]
Operating lease obligation through 2021	37,800,000				$37,800,000
Area of office and laboratory space held under operating lease		129,000								129,000
Operating Lease Amendment \| Third Street \| Optional
Commitments and Contingencies [Line Items]
Lease extension period	5 years

Future_Fixed_Cancelable_Paymen

Future Fixed Cancelable Payments under Existing License Agreements (Detail) (USD $)	Dec. 31, 2014
In Thousands, unless otherwise specified	Dec. 31, 2014
Licenses Agreements [Line Items]
2015	$7,379
2016	724
2017	744
2018	754
2019	762
Thereafter	8,592
Total	$18,955

Future_Minimum_Lease_Payments_

Future Minimum Lease Payments under Non-Cancelable Lease (Detail) (USD $)	Dec. 31, 2014
In Thousands, unless otherwise specified	Dec. 31, 2014
Schedule of Operating Leases [Line Items]
2015	$6,810
2016	6,994
2017	7,535
2018	7,387
2019	7,608
Thereafter	13,845
Total	$50,179

Stockholders_Equity_Additional

Stockholders Equity - Additional Information (Detail) (USD $)	0 Months Ended	1 Months Ended			12 Months Ended			1 Months Ended
	Jul. 13, 2005	Jan. 31, 2013	Feb. 29, 2012	Jul. 31, 2005	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012	Jan. 31, 2015
Stockholders Equity [Line Items]
Preferred stock, shares authorized					5,000,000	5,000,000
Preferred stock, par value					$0.01	$0.01
Preferred stock, shares outstanding					0	0
Right to buy Series A Junior Preferred stock declared as dividend	0.001
Date on which rights expire	13-Jul-15
Acquisition of outstanding common stock that trigger exercise of right				50.00%
Tender or exchange offer for outstanding common stock that trigger exercise of right				20.00%
Cash purchase price of Series A Junior Preferred stock	$80
Issuance of common stock, net of offering costs (in shares)		9,200,000	8,625,000
Underwritten public offering amount per share		$20.13	$10.75
Issuance of common stock, net of offering costs		$173,600,000	$86,800,000		$774,487,000	$173,572,000	$86,800,000
Underwriting discounts and commissions and other estimated offering expenses		11,600,000	5,900,000
Subsequent Event
Stockholders Equity [Line Items]
Issuance of common stock, net of offering costs (in shares)								5,447,368
Underwritten public offering amount per share								$95
Issuance of common stock, net of offering costs								496,400,000
Underwriting discounts and commissions and other estimated offering expenses								$21,100,000

Stock_Incentive_Plans_Addition

Stock Incentive Plans - Additional Information (Detail) (USD $)	1 Months Ended		12 Months Ended			1 Months Ended	0 Months Ended	1 Months Ended
In Millions, except Share data, unless otherwise specified	31-May-11	Oct. 31, 2010	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012	Jan. 31, 2012	Dec. 17, 2014	Jun. 30, 2009	Jun. 30, 2013	Jun. 30, 2010	Dec. 31, 2004
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock incentive plan, shares available for future grant			9,317,147
Option vesting percentage on the first anniversary of grant date			25.00%
Option vesting percentage at the end of each successive three-month period			6.25%
Stock options granted			1,352,000
Weighted average fair value of stock options granted			$8.68	$8.68	$8.68
Aggregate intrinsic value of stock option exercised			$126.50	$57.90	$4.80
Stock options granted, exercise price			$75.77
Restricted Stock Awards Granted			29,000
Fair value of equity awards granted	2.3	1.4
Employee stock purchase plan, offering period			6 months
Weighted average fair value awards granted			$68.28
Expected volatility					57.00%
Expected option life				5 years 7 months 6 days
Current Employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Fair value of equity awards granted						5.3
Stock Incentive Plan 2004
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock incentive plan, shares authorized			12,366,485
Performance Contingent Options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options granted			612,085				612,085
Stock options granted, exercise price							$96.45
Restricted stock awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted Stock Awards Granted		113,370
Stock awards vesting period		3 years
Total fair value of restricted stock awards vested during period			44.4	5.8	1.5
Restricted stock awards \| Current Employees
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted Stock Awards Granted						508,928
Stock awards vesting period						2 years
Stock Incentive Plan 2009
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock incentive plan, shares authorized								2,200,000	5,900,000
Stock incentive plan, non-employee directors award vest on each first, second and third anniversary of grant date								33.33%
Stock Incentive Plan 2009 \| Board of Directors
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock incentive plan, non-employee directors required service period								6 months
Stock Incentive Plan 2009 \| Board of Directors \| Initial Appointment
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock incentive plan, shares authorized for non-employee directors								30,000
Stock Incentive Plan 2009 \| Board of Directors \| On Date Of Annual Meeting Of Shareholders
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock incentive plan, shares authorized for non-employee directors								15,000
Stock Incentive Plan 2009 \| If non-employee Director has less than five years of service \| Amendment \| Board of Directors
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Exercise period on any outstanding stock option awards			3 months
Stock Incentive Plan 2009 \| If non-employee Director has five or more years of service \| Amendment \| Board of Directors
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Exercise period on any outstanding stock option awards			5 years
Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock incentive plan, shares available for future grant			8,168,533
Equity awards, term			10 years
Additional Equity Awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock incentive plan, shares available for future grant			941,583
Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock incentive plan, shares authorized										715,789	315,789
Stock incentive plan, shares available for future grant			207,031
Employee stock purchase plan, purchase price as a percentage of common stock closing price			85.00%
Employee stock purchase plan, shares issued			21,938	45,141	73,590
Weighted average fair value awards granted			$17.03	$11.49	$2.82
Expected volatility			55.00%	55.00%	55.00%
Expected option life			6 months	6 months	6 months
Risk-free interest rate			0.10%	0.10%	0.10%
Performance-based Stock Options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options granted			194,000
Weighted average fair value of stock options granted				$32.26
Aggregate intrinsic value of stock option exercised			$0.10
Stock options granted, exercise price			$96.45
Performance Based Restricted Stock Awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Equity awards, term	5 years
Restricted Stock Awards Granted	229,806

Summary_of_StockBased_Compensa

Summary of Stock-Based Compensation Expense by Type of Award (Detail) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Non-cash stock-based compensation	$33,061	$20,703	$12,360
Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Non-cash stock-based compensation	24,603	13,839	8,739
Performance-based Stock Options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Non-cash stock-based compensation	4,960
Restricted stock awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Non-cash stock-based compensation	1,068	3,420	2,436
Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Non-cash stock-based compensation	392	261	241
Non Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Non-cash stock-based compensation	$2,038	$3,183	$944

Summary_of_Unrecognized_StockB

Summary of Unrecognized Stock-Based Compensation Expense, Net of Estimated Forfeitures (Detail) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2014
Employee Stock Option
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized Expense, Net of Estimated Forfeitures	$59,854
Weighted-average Recognition Period	2 years 7 months 13 days
Restricted stock awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized Expense, Net of Estimated Forfeitures	1,571
Weighted-average Recognition Period	3 years 5 months 16 days
Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized Expense, Net of Estimated Forfeitures	$197
Weighted-average Recognition Period	3 months 29 days

Valuation_Assumptions_for_Stoc

Valuation Assumptions for Stock Options (Detail)	12 Months Ended
Valuation Assumptions for Stock Options (Detail)	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate, minimum	1.70%	1.00%	0.80%
Risk-free interest rate, maximum	2.30%	2.00%	1.00%
Expected dividend yield	0.00%	0.00%	0.00%
Expected option life		5 years 7 months 6 days
Expected volatility			57.00%
Expected volatility, minimum	53.00%	55.00%
Expected volatility, maximum	57.00%	56.00%
Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected option life	5 years 6 months		5 years 7 months 6 days
Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected option life	7 years 6 months		5 years 10 months 24 days

Stock_Option_Activity_Detail

Stock Option Activity (Detail) (USD $)	12 Months Ended
In Thousands, except Share data, unless otherwise specified	Dec. 31, 2014
Number of Options
Outstanding, beginning balance	8,245,000
Granted	1,352,000
Exercised	-1,982,000
Cancelled	-85,000
Outstanding, ending balance	7,530,000
Exercisable at December 31, 2014	4,736,000
Vested or expected to vest at December 31, 2014	7,292,000
Weighted Average Exercise Price
Outstanding, beginning balance	$22.06
Granted	$75.77
Exercised	$14.83
Cancelled	$35.32
Outstanding, ending balance	$33.46
Exercisable at December 31, 2014	$21.44
Vested or expected to vest at December 31, 2014	$32.53
Weighted Average Remaining Contractual Term
Outstanding, December 31, 2014	6 years 3 months 26 days
Exercisable at December 31, 2014	4 years 10 months 10 days
Vested or expected to vest at December 31, 2014	6 years 2 months 23 days
Aggregate Intrinsic Value
Outstanding, December 31, 2014	$478,506
Exercisable at December 31, 2014	357,891
Vested or expected to vest at December 31, 2014	470,149
Performance-based Stock Options
Number of Options
Outstanding, beginning balance	468,000
Granted	194,000
Exercised	-5,000
Cancelled	-18,000
Outstanding, ending balance	639,000
Exercisable at December 31, 2014	150,000
Weighted Average Exercise Price
Outstanding, beginning balance	$63
Granted	$96.45
Exercised	$63
Cancelled	$63
Outstanding, ending balance	$73.15
Exercisable at December 31, 2014	$63
Weighted Average Remaining Contractual Term
Outstanding, December 31, 2014	9 years 18 days
Exercisable at December 31, 2014	8 years 4 months 24 days
Aggregate Intrinsic Value
Outstanding, December 31, 2014	15,237
Exercisable at December 31, 2014	$5,100

Restricted_Stock_Awards_Detail

Restricted Stock Awards (Detail) (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2014
Number of awards
Unvested at beginning of year	500
Granted	29
Vested	-499
Forfeited	0
Unvested at end of year	30
Weighted Average Grant Date Fair Value
Unvested at beginning of year	$10.69
Granted	$68.28
Vested	$10.59
Forfeited	$0
Unvested at end of year	$68.02

Components_of_Loss_before_Inco

Components of Loss before Income Tax, Domestic and Foreign (Detail) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Schedule of Income Before Income Tax [Line Items]
Domestic	($372,137)	($81,109)	($116,400)
Foreign	-28,467	-10,811	-186
Loss before income taxes	($400,604)	($91,920)	($116,586)

Income_Taxes_Additional_Inform

Income Taxes - Additional Information (Detail) (USD $)	12 Months Ended
Income Taxes - Additional Information (Detail) (USD $)	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Income Taxes [Line Items]
Deferred tax assets	$31,667,000
Deferred tax liabilities	31,667,000
Increase in valuation allowance due to increase in operating losses and tax credit carryforwards	46,000,000	29,700,000	38,300,000
Benefit from (provision for) income taxes	-40,209,000	-2,695,000	-10,572,000
Net operating loss carryforwards expiration year	2034
Regulus Therapeutics Inc
Income Taxes [Line Items]
Benefit from (provision for) income taxes	-19,500,000	-2,700,000	-10,600,000
Genzyme
Income Taxes [Line Items]
Benefit from (provision for) income taxes	-20,700,000
Research and development tax credit
Income Taxes [Line Items]
Excess tax benefit from exercise of stock options	400,000
Tax credit carryforwards expiration year	2034
Alternative minimum tax
Income Taxes [Line Items]
Tax credit carryforwards	800,000
Net operating loss carryforwards
Income Taxes [Line Items]
Excess tax benefit from exercise of stock options	83,500,000
Federal
Income Taxes [Line Items]
Net operating loss carryforward	639,300,000
Federal \| Research and development tax credit
Income Taxes [Line Items]
Tax credit carryforwards	32,300,000
State and local jurisdiction
Income Taxes [Line Items]
Net operating loss carryforward	701,800,000
State and local jurisdiction \| Research and development tax credit
Income Taxes [Line Items]
Tax credit carryforwards	10,100,000
Foreign tax authority
Income Taxes [Line Items]
Tax credit carryforwards	$3,200,000
Tax credit carryforwards expiration year	2017

Deferred_Tax_Assets_and_Liabil

Deferred Tax Assets and Liabilities (Detail) (USD $)	Dec. 31, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013
Deferred tax assets:
Net operating loss carryforwards	$176,789	$124,797
Research and development credits	38,204	23,902
AMT credits	788	788
Foreign tax credits	3,196	3,196
Capitalized research and development and start-up costs	19,246	16,214
Deferred revenue	14,273	37,273
Deferred compensation	24,516	21,706
Intangible assets	17,637	2,210
Partnership interest	689	689
Other	5,871	4,885
Total deferred tax assets	301,209	235,660
Deferred tax liabilities:
Intangible assets		-7
Unrealized gain on available-for-sale securities	-32,793	-13,267
Deferred tax asset valuation allowance	-268,416	-222,393
Net deferred tax liability		($7)

Benefit_for_Income_Taxes_Detai

Benefit for Income Taxes (Detail) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Schedule Of Income Taxes [Line Items]
Current		$34	$52
Deferred	-40,209	-2,695	-10,572
Total U.S.	-40,209	-2,661	-10,520
Current	0	0	0
Deferred		-34	-52
Total Foreign		-34	-52
Benefit from income taxes	($40,209)	($2,695)	($10,572)

Effective_Income_Tax_Rate_Deta

Effective Income Tax Rate (Detail)	12 Months Ended
Effective Income Tax Rate (Detail)	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Reconciliation of Provision of Income Taxes [Line Items]
At U.S. federal statutory rate	35.00%	35.00%	35.00%
State taxes, net of federal effect	1.80%	4.30%	4.90%
Stock-based compensation	-0.20%	0.80%	-0.70%
Tax credits	3.50%	8.50%	4.20%
Orphan drug credit addback	-0.60%	-2.70%
Other permanent items		-0.30%	-1.60%
Foreign rate differential	-2.50%	-4.10%	-0.10%
In-process research and development	-19.40%
Tax basis in intangible assets as a result of Sirna transaction	4.20%
Valuation allowance	-11.80%	-38.50%	-32.60%
Effective income tax rate	10.00%	3.00%	9.10%

Regulus_Additional_Information

Regulus - Additional Information (Detail) (USD $)	1 Months Ended	3 Months Ended	12 Months Ended
Regulus - Additional Information (Detail) (USD $)	Mar. 31, 2009	Dec. 31, 2012	Dec. 31, 2012	Dec. 31, 2014	Sep. 30, 2012
Schedule Of Equity Method Investments Joint Ventures [Line Items]
Company ownership percentage				12.00%	44.00%
Equity method investments	$10,000,000
Company ownership percentage		17.00%
Gain on issuance of stock by Regulus Therapeutics Inc.			16,084,000
Carrying value in Regulus Therapeutics Inc.		12,400,000	12,400,000	11,900,000
Unrealized gain in other comprehensive income		15,700,000	15,700,000
Intraperiod tax benefit			-10,600,000
Isis
Schedule Of Equity Method Investments Joint Ventures [Line Items]
Equity method investments	$10,000,000

Summary_Results_of_Regulus_Ope

Summary Results of Regulus Operation (Detail) (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2012
Statements of Comprehensive Loss Data:
Net revenues	$9,462
Operating expenses	17,733
Loss from operations	-8,271
Other expense	-2,289
Income tax benefit	28
Net loss	($10,532)

Accrued_Expenses_Detail

Accrued Expenses (Detail) (USD $)	Dec. 31, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified	Dec. 31, 2014	Dec. 31, 2013
Schedule of Accrued Liabilities [Line Items]
Compensation and related	$7,357	$4,822
Clinical trial and manufacturing	5,548	2,933
Consulting and professional services	3,886	2,135
Pre-clinical	3,081	1,004
Other	3,808	3,266
Accrued expenses	$23,680	$14,160

Restructuring_Additional_Infor

Restructuring - Additional Information (Detail) (USD $)	1 Months Ended	3 Months Ended
In Millions, unless otherwise specified	Jan. 31, 2012	Mar. 31, 2012
	Employee	Mar. 31, 2012
Restructuring Cost and Reserve [Line Items]
Percentage of workforce reduced by company	33.00%
Number of employees remaining	115
Restructuring-related costs		$3.90

Quarterly_Financial_Data_Detai

Quarterly Financial Data (Detail) (USD $)	3 Months Ended								12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2014	Sep. 30, 2014	Jun. 30, 2014	Mar. 31, 2014	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2014	Dec. 31, 2013	Dec. 31, 2012
Selected Quarterly Financial Information [Abstract]
Revenues	$24,019	$10,972	$7,295	$8,275	$10,847	$8,991	$8,687	$18,642	$50,561	$47,167	$66,725
Operating expenses	69,731	56,171	52,300	277,339	40,439	41,225	29,999	28,446	455,541	140,109	196,181
Net loss	($21,389)	($43,989)	($44,074)	($250,943)	($32,357)	($29,686)	($18,169)	($9,013)	($360,395)	($89,225)	($106,014)
Net loss per common share - basic and diluted	($0.28)	($0.58)	($0.58)	($3.70)	($0.51)	($0.48)	($0.29)	($0.15)	($4.85)	($1.45)	($2.11)
Weighted-average common shares - basic and diluted	76,957	76,408	75,835	67,786	62,909	62,416	61,661	59,173	74,278	61,551	50,286

Quarterly_Financial_Data_Addit

Quarterly Financial Data - Additional Information (Detail) (USD $)	0 Months Ended	3 Months Ended	12 Months Ended	3 Months Ended
	Mar. 05, 2014	Jun. 30, 2014	Dec. 31, 2014	Mar. 31, 2014
Quarterly Financial Information [Line Items]
In-process research and development	$199,300,000		$220,766,000
In-process research and development credit		3,900,000
Sirna Therapeutics
Quarterly Financial Information [Line Items]
In-process research and development			220,800,000	224,700,000
In-process research and development credit		$3,900,000