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Document and Entity Information - shares	6 Months Ended
Jun. 30, 2016	Jul. 29, 2016
Document and Entity Information
Entity Registrant Name	AMICUS THERAPEUTICS INC
Entity Central Index Key	0001178879
Document Type	10-Q
Document Period End Date	Jun. 30, 2016
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		142,139,451
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	Q2

Consolidated Balance Sheets (Unaudited) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 63,656	$ 69,485
Investments in marketable securities	150,494	144,548
Inventories	194	0
Prepaid expenses and other current assets	3,330	2,568
Total current assets	217,674	216,601
Property and equipment, less accumulated depreciation of $14,284 and $13,353 at June 30, 2016 and December 31, 2015, respectively	10,178	6,178
In-process research & development	486,700	486,700
Goodwill	197,797	197,797
Other non-current assets	1,657	1,108
Total Assets	914,006	908,384
Current liabilities:
Accounts payable and accrued expenses	23,828	32,216
Contingent consideration payable, current portion	56,000	41,400
Other current liabilities	631
Total current liabilities	80,459	73,616
Deferred reimbursements	35,756	35,756
Due to related party	43,443	41,601
Unsecured notes payable	21,851
Contingent consideration payable, less current portion	220,300	232,677
Deferred tax liability	176,219	176,219
Other non-current liabilities	1,735	681
Commitments and contingencies
Stockholders' equity:
Common stock, $.01 per value, 250,000,000 authorized 134,408,526 shares issued and outstanding at June 30, 2016, 250,000,000 shares authorized, 125,027,034 shares issued and outstanding at December 31, 2015	1,399	1,306
Additional paid-in capital	990,032	917,454
Foreign currency translation adjustment, less tax benefit of $453 at June 30, 2016	842
Unrealized gain/(loss) on available-for securities	201	(115)
Warrants	16,076	8,755
Accumulated deficit	(674,307)	(579,566)
Total stockholders' equity	334,243	347,834
Total Liabilities and Stockholders' Equity	$ 914,006	$ 908,384

Consolidated Statements of Operations (Unaudited) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Operating Expenses:
Research and development	$ 18,281	$ 17,234	$ 41,706	$ 33,347
General and administrative	19,300	8,278	35,001	14,705
Changes in fair value of contingent consideration payable	10,186	100	13,338	1,100
Restructuring charges	8	26	58	36
Loss on extinguishment of debt		952		952
Depreciation	767	353	1,440	861
Total operating expenses	48,542	26,943	91,543	51,001
Loss from operations	(48,542)	(26,943)	(91,543)	(51,001)
Other income (expenses):
Interest income	331	158	638	329
Interest expense	(1,055)	(338)	(2,000)	(710)
Other expense	(2,237)	(10)	(2,289)	(39)
Loss before income tax benefit	(51,503)	(27,133)	(95,194)	(51,421)
Income tax benefit	453		453
Net loss	$ (51,050)	$ (27,133)	$ (94,741)	$ (51,421)
Net loss per common shares - basic and diluted	$ (0.40)	$ (0.27)	$ (0.75)	$ (0.53)
Weighted-average common shares outstanding - basic and diluted	129,122,175	99,994,125	127,160,943	97,888,573

Consolidated Statements of Comprehensive Loss (Unaudited) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Consolidated Statements of Comprehensive Loss (Unaudited)
Net loss	$ (51,050)	$ (27,133)	$ (94,741)	$ (51,421)
Other comprehensive gain/(loss)
Foreign currency translation adjustment, net of tax	907		842
Unrealized gain/(loss) on available-for-sale securities	87	(17)	316	80
Other comprehensive gain/(loss)	994	(17)	1,158	80
Comprehensive loss	$ (50,056)	$ (27,150)	$ (93,583)	$ (51,341)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References + Details

Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015
Operating activities
Net loss	$ (94,741)	$ (51,421)
Adjustments to reconcile net loss to net cash used in operating activities:
Non-cash interest expense	1,014	136
Depreciation	1,440	861
Stock-based compensation	8,748	4,191
Restructuring charges	58	36
Loss on extinguishment of debt		952
Loss on disposal of asset	17
Non-cash changes in the fair value of derivative liability	346
Non-cash changes in the fair value of contingent consideration payable	13,338	1,100
Foreign currency remeasurement loss	1,892
Non-cash income tax benefit	(453)
Changes in operating assets and liabilities:
Inventories	(207)
Prepaid expenses and other current assets	(865)	641
Other non-current assets	(549)	(482)
Accounts payable and accrued expenses	(8,244)	459
Non-current liabilities	535	(84)
Net cash used in operating activities	(77,671)	(43,611)
Investing activities
Sale and redemption of marketable securities	121,283	63,163
Purchases of marketable securities	(126,914)	(30,414)
Purchases of property and equipment	(4,608)	(1,429)
Net cash (used in) / provided by investing activities	(10,239)	31,320
Financing activities
Proceeds from issuance of common stock, net of issuance costs	57,818	243,216
Proceeds from unsecured note agreement	30,000
Payments of secured loan agreement		(15,291)
Payment of capital lease	(47)
Payment of contingent consideration	(5,000)
Proceeds from exercise of stock options	647	6,932
Purchase of vested restricted stock units	(657)	(1,617)
Proceeds from exercise of warrants		4,000
Net cash provided by financing activities	82,761	237,240
Effect of exchange rate changes on cash and cash equivalents	(680)
Net (decrease) / increase in cash and cash equivalents	(5,829)	224,949
Cash and cash equivalents at beginning of period	69,485	24,074
Cash and cash equivalents at end of period	63,656	249,023
Supplemental disclosures of cash flow information
Cash paid during the period for interest	276	$ 605
Contingent consideration resolution in shares	6,115
Capital expenditures funded by capital lease borrowings	$ 850

Description of Business	6 Months Ended
Description of Business	Jun. 30, 2016
Description of Business
Description of Business	Note 1. Description of Business Corporate Information, Status of Operations, and Management Plans Amicus Therapeutics, Inc. (the “Company,” “we,” “us,” or “our”) was incorporated on February 4, 2002 in Delaware and is a global patient-focused biotechnology company engaged in the discovery, development, and commercialization of a diverse set of novel treatments for patients living with devastating rare and orphan diseases. The lead product candidate, migalastat HCl is a small molecule that can be used as a monotherapy and in combination with enzyme replacement of therapy (“ERT”) for Fabry disease. SD-101, a product candidate in late-stage development, is a potential first-to-market therapy for the chronic, rare connective tissue disorder Epidermolysis Bullosa (“EB”). The Company is also leveraging its biologics and Chaperone-Advanced Replacement Therapy (“CHART™”) platform technologies to develop novel ERT products for Pompe disease, Fabry disease, and potentially other lysosomal storage disorders (“LSDs”). The Company is also investigating preclinical and discovery programs in other rare and devastating diseases including CDKL5 deficiency. The Company believes that the platform technologies and advanced product pipeline uniquely position the Company at the forefront of advanced therapies to treat a range of devastating rare and orphan diseases. The Company’s Fabry franchise strategy is to develop migalastat HCl (which the Company may refer to as “migalastat”) for all patients with Fabry disease - as a monotherapy for patients with amenable mutations and in combination with ERT for all other patients. In May 2016, the Company announced that the European Commission has granted full approval for the oral small molecule pharmacological chaperone Galafold™ (migalastat) as a first-line therapy for long-term treatment of adults and adolescents aged 16 years and older with a confirmed diagnosis of Fabry disease (alpha-galactosidase A deficiency) and who have an amenable mutation. The approved label includes 269 Fabry-causing mutations which represent up to half of all patients with Fabry disease. The Company began supplying the market in Germany in May 2016 and will commence the reimbursement processes with healthcare authorities in each of the major European countries. In July 2016, the Company expanded its biologics pipeline with a new preclinical program for CDKL5 deficiency, a rare and devastating genetic neurological disease for which there is no currently approved treatment. The Company has obtained the rights and related intellectual property to a preclinical CDKL5 program through its acquisition of MiaMed, Inc. On June 30, 2016, the Company entered into a Joinder to and Amendment of Note and Warrant Purchase Agreement (the “Amended Purchase Agreement”) with Redmile Capital Fund, LP and certain of its affiliates (collectively referred to as “Redmile”). Such amendment joined GCM Grosvenor Special Opportunities Master Fund, Ltd. (“GCM”) to the Note and Warrant Purchase Agreement, dated as of February 19, 2016. At closing, the Company sold (a) $30.0 million principal amount of additional notes and (b) five-year warrants to purchase 42 shares of common stock of the Company, par value $0.01 per share (“Common Stock”) for every $1,000 of the principal amount of Additional Notes purchased by each Purchaser (“Additional Warrants”), for an aggregate of approximately 1.3 million shares of Common Stock issuable under the Additional Warrants. For additional information, see “—Note 7. Debt Instruments and Related Party Transactions.” In February 2016, the Company entered into a sales agreement (“Sales Agreement”) with Cowen and Company, LLC (“Cowen”), to create an at-the-market (“ATM”) equity program under which the Company from time to time may offer and sell shares of its Common Stock having an aggregate offering price of up to $100.0 million through Cowen as sales agent for funds to be received in an escrow, trust or similar arrangement. Cowen will be entitled to compensation at a fixed commission rate up to 3.0% of the gross proceeds per share sold through it as sales agent under the sales agreement. Beginning in April 2016 and through June 30, 2016, the Company sold 8.2 million shares of Common Stock under the ATM sales agreement resulting in net proceeds of $57.8 million, after Cowen’s commission of $1.7 million and other expenses of $0.1 million. In July 2016, the Company sold an additional 6.8 million shares of Common Stock with a net proceeds of $39.3 million. In connection with the July share sales, the Company completed all sales under the ATM equity program. For more details, refer to “— Note 13. Subsequent Events.” The Company had an accumulated deficit of approximately $674.3 million at June 30, 2016 and anticipates incurring losses through the fiscal year ending December 31, 2016 and beyond. The Company has funded its operating losses to date through the sale of its redeemable convertible preferred stock, issuance of convertible notes, net proceeds from its initial public offering and subsequent stock offerings, payments from partners during the terms of the collaboration agreements and other financing arrangements. The Company commenced commercial shipments of Galafold in the EU in the second quarter of 2016 and expects to recognize revenue in the third quarter of 2016. The Company believes that its existing cash and cash equivalents and short-term investments will be sufficient to fund the current operating plan into the second half of 2017.

Summary of Significant Accounting Policies

6 Months Ended

Jun. 30, 2016

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

Note 2. Summary of Significant Accounting Policies

The consolidated financial statements include the accounts of Amicus Therapeutics, Inc. and its wholly-owned subsidiaries, after the elimination of intercompany transactions.

Basis of Presentation

The Company has prepared the accompanying unaudited consolidated financial statements in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) for interim financial information and with the instructions to Form 10-Q and Article 10-01 of Regulations S-X. Accordingly, they do not include all of the information and disclosures required by generally accepted accounting principles for complete financial statements. In the opinion of management, the accompanying unaudited financial statements reflect all adjustments, which include only normal recurring adjustments, necessary to present fairly the Company’s interim financial information.

The accompanying unaudited consolidated financial statements and related notes should be read in conjunction with the Company’s financial statements and related notes as contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015. For a complete description of the Company’s accounting policies, please refer to the Annual Report on Form 10-K for the fiscal year ended December 31, 2015.

Foreign Currency Transactions

The functional currency for most of our foreign subsidiaries is their local currency. For our non-U.S. subsidiaries that transact in a functional currency other than the U.S. dollar, assets and liabilities are translated at current rates of exchange at the balance sheet date. Income and expense items are translated at the average foreign exchange rates for the period. Adjustments resulting from the translation of the financial statements of our foreign operations into U.S. dollars are excluded from the determination of net income and are recorded in accumulated other comprehensive income, a separate component of equity.

Use of Estimates

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates.

Concentration of Credit Risk

The Company’s financial instruments that are exposed to concentration of credit risk consist primarily of cash and cash equivalents and marketable securities. The Company maintains its cash and cash equivalents in bank accounts, which, at times, exceed federally insured limits. The Company invests its marketable securities in high-quality commercial financial instruments. The Company has not recognized any losses from credit risks on such accounts during any of the periods presented. The Company believes it is not exposed to significant credit risk on cash and cash equivalents or its marketable securities.

Significant Accounting Policies

There have been no material changes to the Company’s significant accounting policies during the six months ended June 30, 2016, as compared to the significant accounting policies disclosed in Note 2 of the Consolidated Financial Statements in the Company’s Annual Report on Form 10-K for the year ended December 31, 2015. However, the following accounting policies are the most critical in fully understanding and evaluating the Company’s financial condition and results of operations.

Inventories

Until regulatory approval of migalastat, the Company expensed all of its inventory costs as research and development expense. Upon regulatory approval, the Company began capitalizing costs related to the purchase and manufacture of migalastat. Inventories are stated at the lower of cost or market determined by the first-in, first-out method. The Company will analyze its inventory levels quarterly and will write down inventory that has become obsolete, or has a cost basis in excess of its expected net realizable value and inventory quantities in excess of expected requirements. Expired inventory will be disposed of and the related costs will be recognized as cost of goods sold in the Company’s Consolidated Statements of Operations.

Revenue Recognition

Net Product Sales

The Company recognizes revenue when amounts are realized or realizable and earned. Revenue is considered realizable and earned when the following criteria are met: (1) persuasive evidence of an arrangement exists; (2) delivery has occurred or services have been rendered; (3) the price is fixed or determinable; and (4) collection of the amounts due are reasonably assured.

The Company will record revenue on sales where migalastat is available on a reimbursed expanded access program and typically paid for by a government authority or institution. The Company will recognize revenue for these reimbursed expanded access programs on a cash basis if all other revenue recognition criteria have been met. Once the Company has established a pattern of collectability, revenue will be recognized upon shipment assuming all other revenue recognition criteria are met.

Collaboration Revenue

In multiple element arrangements, revenue is allocated to each separate unit of accounting and each deliverable in an arrangement is evaluated to determine whether it represents separate units of accounting. A deliverable constitutes a separate unit of accounting when it has standalone value and there is no general right of return for the delivered elements. In instances when the aforementioned criteria are not met, the deliverable is combined with the undelivered elements and the allocation of the arrangement consideration and revenue recognition is determined for the combined unit as a single unit of accounting. Allocation of the consideration is determined at arrangement inception on the basis of each unit’s relative selling price. In instances where there is determined to be a single unit of accounting, the total consideration is applied as revenue for the single unit of accounting and is recognized over the period of inception through the date where the last deliverable within the single unit of accounting is expected to be delivered.

The Company’s current revenue recognition policies provide that, when a collaboration arrangement contains multiple deliverables, such as license and research and development services, the Company allocates revenue to each separate unit of accounting based on a selling price hierarchy. The selling price hierarchy for a deliverable is based on (i) its vendor specific objective evidence (“VSOE”) if available, (ii) third party evidence (“TPE”) if VSOE is not available, or (iii) best estimated selling price (“BESP”) if neither VSOE nor TPE is available. The Company would establish the VSOE of selling price using the price charged for a deliverable when sold separately. The TPE of selling price would be established by evaluating largely similar and interchangeable competitor products or services in standalone sales to similarly situated customers. The BESP would be established considering internal factors such as an internal pricing analysis or an income approach using a discounted cash flow model.

The Company also considers the impact of potential future payments it makes in its role as a vendor to its customers and evaluates if these potential future payments could be a reduction of revenue from that customer. If the potential future payments to the customer are:

a payment for an identifiable benefit;

the identifiable benefit is separable from the existing relationship between the Company and its customer;

the identifiable benefit can be obtained from a party other than the customer; and

the Company can reasonably estimate the fair value of the identifiable benefit

then the payments are accounted for separate from the revenue received from that customer. If, however, all these criteria are not satisfied, then the payments are treated as a reduction of revenue from that customer.

If the Company determines that any potential future payments to its customers are to be considered as a reduction of revenue, it must evaluate if the total amount of revenue to be received under the arrangement is fixed and determinable. If the total amount of revenue is not fixed and determinable due to the uncertain nature of the potential future payments to the customer, then any customer payments cannot be recognized as revenue until the total arrangement consideration becomes fixed and determinable.

The reimbursements for research and development costs under collaboration agreements that meet the criteria for revenue recognition are included in Research Revenue and the costs associated with these reimbursable amounts are included in research and development expenses.

In order to determine the revenue recognition for contingent milestones, the Company evaluates the contingent milestones using the criteria as provided by the Financial Accounting Standards Boards (“FASB”) guidance on the milestone method of revenue recognition at the inception of a collaboration agreement. The criteria requires that (i) the Company determines if the milestone is commensurate with either its performance to achieve the milestone or the enhancement of value resulting from the Company’s activities to achieve the milestone, (ii) the milestone be related to past performance, and (iii) the milestone be reasonable relative to all deliverable and payment terms of the collaboration arrangement. If these criteria are met then the contingent milestones can be considered as substantive milestones and will be recognized as revenue in the period that the milestone is achieved.

Fair Value Measurements

The Company records certain asset and liability balances under the fair value measurements as defined by the FASB guidance. Current FASB fair value guidance emphasizes that fair value is a market-based measurement, not an entity-specific measurement. Therefore, a fair value measurement should be determined based on the assumptions that market participants would use in pricing the asset or liability. As a basis for considering market participant assumptions in fair value measurements, current FASB guidance establishes a fair value hierarchy that distinguishes between market participant assumptions based on market data obtained from sources independent of the reporting entity (observable inputs that are classified within Levels 1 and 2 of the hierarchy) and the reporting entity’s own assumptions that market participants assumptions would use in pricing assets or liabilities (unobservable inputs classified within Level 3 of the hierarchy).

Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities that the Company has the ability to access at measurement date. Level 2 inputs are inputs other than quoted prices included in Level 1 that are observable for the asset or liability, either directly or indirectly. Level 2 inputs may include quoted prices for similar assets and liabilities in active markets, as well as inputs that are observable for the asset or liability (other than quoted prices), such as interest rates, foreign exchange rates, and yield curves that are observable at commonly quoted intervals. Level 3 inputs are unobservable inputs for the asset or liability, which is typically based on an entity’s own assumptions, as there is little, if any, related market activity. In instances where the determination of the fair value measurement is based on inputs from different levels of the fair value hierarchy, the level in the fair value hierarchy within which the entire fair value measurement falls is based on the lowest level input that is significant to the fair value measurement in its entirety. The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires judgment, and considers factors specific to the asset or liability.

Contingent Liabilities

On an ongoing basis, the Company may be involved in various claims, and legal proceedings. On a quarterly basis, the Company reviews the status of each significant matter and assesses its potential financial exposure. If the potential loss from any claim, asserted or unasserted, or legal proceeding is considered probable and the amount can be reasonably estimated, the Company will accrue a liability for the estimated loss. Because of uncertainties related to claims and litigation, accruals will be based on the Company’s best estimates based on available information. On a periodic basis, as additional information becomes available, or based on specific events such as the outcome of litigation or settlement of claims, the Company may reassess the potential liability related to these matters and may revise these estimates, which could result in a material adverse adjustments to the Company’s operating results.

New Accounting Pronouncements

In May 2016, the FASB issued ASU 2016-12, Revenue from Contracts with Customers (Topic 606): Narrow-Scope Improvements and Practical Expedients. The amendments address narrow-scope improvements to the guidance on collectability, noncash consideration, and completed contracts at transition. Additionally, the amendments provide a practical expedient for contract modifications at transition and an accounting policy election related to the presentation of sales taxes and other similar taxes collected from customers. These amendments are effective at the same date that Topic 606 is effective. Topic 606 is effective for public entities for annual reporting periods beginning after December 15, 2017, including interim reporting periods therein (i.e., January 1, 2018, for a calendar year entity). This Accounting Standards Update is the final version of Proposed Accounting Standards Update 2015-230—Revenue from Contracts with Customers (Topic 606)—Narrow-Scope Improvements and Practical Expedients, which has been deleted. The Company is currently assessing the impact that this standard will have on its consolidated financial statements.

In April 2016, the FASB issued ASU 2016-10, Revenue from Contracts with Customers (Topic 606): Identifying Performance Obligations and Licensing. The amendments clarify the following two aspects of Topic 606: (a) identifying performance obligations; and (b) the licensing implementation guidance. The amendments do not change the core principle of the guidance in Topic 606. The effective date and transition requirements for the amendments are the same as the effective date and transition requirements in Topic 606. Public entities should apply the amendments for annual reporting periods beginning after December 15, 2017, including interim reporting periods therein (i.e., January 1, 2018, for a calendar year entity). Early application for public entities is permitted only as of annual reporting periods beginning after December 15, 2016, including interim reporting periods within that reporting period. The Company is currently assessing the impact that this standard will have on its consolidated financial statements.

In March 2016, the FASB issued ASU 2016-09, Compensation - Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting. The amendments are intended to improve the accounting for employee share-based payments and affect all organizations that issue share-based payment awards to their employees. Several aspects of the accounting for share-based payment award transactions are simplified, including: (a) income tax consequences; (b) classification of awards as either equity or liabilities; and (c) classification on the statement of cash flows. For public companies, the amendments are effective for annual periods beginning after December 15, 2016, and interim periods within those annual periods. For private companies, the amendments are effective for annual periods beginning after December 15, 2017, and interim periods within annual periods beginning after December 15, 2018. Early adoption is permitted for any organization in any interim or annual period. The Company is currently assessing the impact that this standard will have on its consolidated financial statements.

In March 2016, the FASB issued ASU 2016-08, Revenue from Contracts with Customers (Topic 606): Principal versus Agent Considerations (Reporting Revenue Gross versus Net). The amendments relate to when another party, along with the entity, is involved in providing a good or service to a customer. Topic 606 Revenue from Contracts with Customers requires an entity to determine whether the nature of its promise is to provide that good or service to the customer (i.e., the entity is a principal) or to arrange for the good or service to be provided to the customer by the other party (i.e., the entity is an agent). The amendments are intended to improve the operability and understandability of the implementation guidance on principal versus agent considerations. The effective date and transition of these amendments is the same as the effective date and transition of ASU 2014-09, Revenue from Contracts with Customers (Topic 606). Public entities should apply the amendments in ASU 2014-09 for annual reporting periods beginning after December 15, 2017, including interim reporting periods therein (i.e., January 1, 2018, for a calendar year entity). The Company is currently assessing the impact that this standard will have on its consolidated financial statements.

In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842). This update requires the recognition of lease assets and lease liabilities on the balance sheet for all lease obligations and disclosing key information about leasing arrangements. This update requires the recognition of lease assets and lease liabilities by lessees for those leases classified as operating leases under previous generally accepted accounting principles. This update will be effective for the Company for all annual and interim periods beginning after December 15, 2018, including interim periods within those fiscal years. Early application is permitted for all public business entities and all nonpublic business entities upon issuance. The Company is currently assessing the impact that this standard will have on its consolidated financial statements.

Cash, Money Market Funds and Marketable Securities

6 Months Ended

Jun. 30, 2016

Cash, Money Market Funds and Marketable Securities

Cash, Money Market Funds and Marketable Securities

Note 3. Cash, Money Market Funds and Marketable Securities

As of June 30, 2016, the Company held $63.7 million in cash and cash equivalents and $150.5 million of available-for-sale securities which are reported at fair value on the Company’s balance sheet. Unrealized gains and losses are reported within accumulated other comprehensive income/ (loss) in the statements of comprehensive loss. If a decline in the fair value of a marketable security below the Company’s cost basis is determined to be other than temporary, such marketable security is written down to its estimated fair value as a new cost basis and the amount of the write-down is included in earnings as an impairment charge. To date, only temporary impairment adjustments have been recorded.

The Company regularly invests excess operating cash in deposits with major financial institutions, money market funds, notes issued by the U.S. government, as well as fixed income investments and U.S. bond funds both of which can be readily purchased and sold using established markets. The Company believes that the market risk arising from its holdings of these financial instruments is mitigated as many of these securities are either government backed or of the highest credit rating. Investments that have original maturities or greater than 3 months but less than 1 year are classified as short-term and investments with maturities that are greater than 1 year are classified as long-term.

The Company transacts business in various foreign countries and therefore, is subject to risk of foreign currency exchange rate fluctuations. As such, in June 2016 the Company entered into a forward contract to economically hedge transactional exposure associated with commitments arising from trade accounts payable denominated in a currency other than the functional currency of the respective operating entity. The Company does not designate these forward contracts as hedging instruments under applicable accounting guidance and, therefore, changes in fair value are recorded as other income (expense) in the Consolidated Statements of Operations, with the corresponding liability in current liabilities on the Consolidated Balance Sheet. For the three and six months ended June 30, 2016, the Company recognized a loss of $346 thousand related to the derivative instruments not designated as hedging instruments in other income (expense) in the Consolidated Statements of Operations and the corresponding liability of $346 thousand is recorded as other current liability in the Consolidated Balance Sheets.

Cash and available-for-sale securities are all current unless mentioned otherwise and consisted of the following as of June 30, 2016 and December 31, 2015 (in thousands):

	As of June 30, 2016
	Cost		Unrealized Gain		Unrealized Loss			Fair Value
Cash balances	$	63,656	$	—	$	—		$	63,656
Corporate debt securities	85,475		$	19	$	(23	)	$	85,471
Commercial paper	64,468		$	205	—			$	64,673
Certificate of deposit	350		—		—			350

	$	213,949	$	224	$	(23	)	$	214,150

Included in cash and cash equivalents	$	63,656	$	—	$	—		$	63,656
Included in marketable securities	$	150,293	$	224	$	(23	)	$	150,494

Total cash and marketable securities	$	213,949	$	224	$	(23	)	$	214,150

	As of December 31, 2015
	Cost		Unrealized Gain		Unrealized Loss			Fair Value
Cash balances	$	69,485	$	—	$	—		$	69,485
Corporate debt securities	118,627		1		(154		)	118,474
Commercial paper	25,686		38		—			25,724
Certificate of deposit	350		—		—			350

	$	214,148	$	39	$	(154	)	$	214,033

Included in cash and cash equivalents	$	69,485	—		—			$	69,485
Included in marketable securities	144,663		39		(154		)	144,548

Total cash and marketable securities	$	214,148	$	39	$	(154	)	$	214,033

For the six months ended June 30, 2016 and the year ended December 31, 2015, there were no realized gains or losses. The cost of securities sold is based on the specific identification method.

Unrealized loss positions in the available for sale securities as of June 30, 2016 and December 31, 2015 reflect temporary impairments that have not been recognized and have been in a loss position for less than twelve months and as such are recognized in other comprehensive gain/ (loss). The fair value of these available for sale securities in unrealized loss positions was $50.4 million and $118.5 million as of June 30, 2016 and December 31, 2015, respectively.

The Company holds available-for-sale investment securities which are reported at fair value on the Company’s balance sheet. Unrealized holding gains and losses are reported within accumulated other comprehensive income (“AOCI”) in the Statements of Comprehensive Loss.

Acquisitions	6 Months Ended
Acquisitions	Jun. 30, 2016
Acquisitions
Acquisitions	Note 5. Acquisitions Acquisition of Scioderm, Inc. On September 30, 2015, the Company acquired Scioderm, a privately-held biopharmaceutical company focused on developing innovative therapies for treating the rare disease EB. The acquisition leverages the Scioderm development team’s EB expertise with the Company’s global clinical infrastructure to advance SD-101 toward regulatory approvals and the Company’s commercial, patient advocacy, and medical affairs infrastructure to support a successful global launch. The acquisition of Scioderm was accounted for as a purchase of a business in accordance with FASB Accounting Standard Codification 805 Business Combinations. The Company acquired Scioderm with cash and stock. At closing, the Company paid Scioderm stockholders, option holders, and warrant holders approximately $223.9 million, of which approximately $141.1 million was paid in cash and approximately $82.8 million was paid through the issuance of approximately 5.9 million newly issued shares of the Company. The Company had agreed to pay up to an additional $361 million to Scioderm stockholders, option holders, and warrant holders upon achievement of certain clinical and regulatory milestones, and $257 million to Scioderm stockholders, option holders, and warrant holders upon achievement of certain sales milestones. If SD-101 is approved, EB qualifies as a rare pediatric disease under The Food and Drug Administration Safety and Innovation Act (“FDSIA”) and the Company will request a Priority Review Voucher (“PRV”) under the FDSIA, if available. If the PRV is obtained and subsequently sold, the Company will pay Scioderm stockholders, option holders, and warrant holders the lesser of $100 million in the aggregate or 50% of the proceeds of such sale. If the Company obtains the PRV and has not entered into an agreement to sell or otherwise transfer to a third party the PRV within one year of its receipt, the shareholders’ agent may appoint a financial advisor to conduct a process to sell the PRV. If the Company determines in its sole discretion to use the PRV, the Company shall give the shareholders’ agent written notice thereof and shall pay to the Scioderm stockholders, option holders, and warrant holders $100 million. The inability to sell the PRV after complying with the provisions, shall not give rise to any payment. The fair value of the contingent consideration payments on the acquisition date was $259.0 million. This was an estimate based on significant inputs that are not observable in the market, referred to as Level 3 inputs. Key assumptions included a range of discount rates between 0.4% and 1.1% as interpolated from the U.S. Treasury constant maturity yield curve over the time frame for clinical and regulatory milestones and a range of discount rates between 1.0% and 2.2% for revenue-based milestones. The range of outcomes and assumptions used to develop these estimates have been updated to better reflect the probability of certain milestone outcomes and updated timelines related to clinical development and anticipated approval assumptions as of June 30, 2016 without limitation, the $5 million milestone paid in the second quarter and milestone payments projected for 2017 (See “— Note 9. Assets and Liabilities Measured at Fair Value”, for additional discussion regarding fair value measurements of the contingent acquisition consideration payable). In April 2016, while the total clinical and regulatory approval milestone payments remain unchanged at $361 million, the allocation between the clinical and regulatory approval milestone payments were revised as follows: clinical milestones of up to $81 million and regulatory approval milestones of up to $280 million. The commercial milestone payments of up to $257 million remained unchanged. The Company determined the fair value of the contingent consideration to be $265.8 million at June 30, 2016, of which $56.0 million is payable in the next twelve months, resulting in an increase in the contingent consideration payable and related expense of $13.0 million for the six months ended June 30, 2016. The expense is recorded in the Consolidated Statement of Operations as the change within fair value of contingent consideration payable. See “— Note 9. Assets and Liabilities Measured at Fair Value”, for additional discussion regarding fair value measurements of the contingent acquisition consideration payable. For additional information, see “— Note 6. Goodwill and Intangible Assets.” The purchase price allocation was subject to completion of our analysis of the fair value of the assets and liabilities as of the effective date of the acquisition. The final valuation was completed as of December 31, 2015. A substantial portion of the assets acquired consisted of intangible assets related to SD-101. The Company determined that the estimated acquisition-date fair value of the indefinite lived IPR&D related to the SD-101 was $463.7 million. Acquisition of Callidus Biopharma, Inc. In November 2013, the Company acquired Callidus a privately-held biologics company focused on developing best-in-class ERTs for LSDs with its lead ERT ATB200 for Pompe disease in late preclinical development. The acquisition of the Callidus assets and technology complements the Company’s CHART™ platform for the development of next-generation ERTs. The fair value of the contingent acquisition consideration payments on the acquisition date was $10.6 million and was estimated by applying a probability-based income approach utilizing an appropriate discount rate. This estimation was based on significant inputs that are not observable in the market, referred to as Level 3 inputs. As of June 30, 2016, the range of outcomes and assumptions used to develop these estimates has changed to better reflect the probability of certain milestone outcomes; see “— Note 9. Assets and Liabilities Measured at Fair Value”, for additional discussion regarding fair value measurements of the contingent acquisition consideration payable. The Company determined the fair value of the contingent consideration to be $10.5 million at June 30, 2016, of which $10.1 million relates to ATB-200 Pompe program. The change in fair value of contingent consideration payable is recorded in the Consolidated Statement of Operations. All of the contingent consideration is payable beyond the next twelve months. During the three months ended June 30, 2016, the Company reached the first clinical milestone, which was the dosing of the first patient in a Phase 1 or 2 study. The milestone for this event was $6.0 million which was paid in Company stock during the three months ended June 30, 2016, resulting in $6.1 million impact on stockholder’s equity. For further information, see “— Note 6. Goodwill and Intangible Assets.”

- Definition

The entire disclosure for a business combination (or series of individually immaterial business combinations) completed during the period, including background, timing, and recognized assets and liabilities. The disclosure may include leverage buyout transactions (as applicable).

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+ Details

Goodwill and Intangible Assets

6 Months Ended

Jun. 30, 2016

Goodwill and Intangible Assets

Goodwill and Intangible Assets

Note 6. Goodwill and Intangible Assets

In connection with the acquisitions discussed in “—Note 5. Acquisitions”, the Company has recognized goodwill of $197.8 million. The following table represents the changes in goodwill for the six months ended June 30, 2016:

	( in millions)
Balance at December 31, 2015	$	197.8
Change in goodwill	—

Balance at June 30, 2016	$	197.8

In connection with the acquisitions discussed in “—Note 5. Acquisitions,” the Company recognized IPR&D of $486.7 million. Intangible assets related to IPR&D assets are considered to be indefinite-lived until the completion or abandonment of the associated research and development efforts. During the period the assets are considered indefinite-lived, they will not be amortized but will be tested for impairment on an annual basis and between annual tests if the Company becomes aware of any events occurring or changes in circumstances that would indicate a reduction in the fair value of the IPR&D assets below their respective carrying amounts. The following table represents the changes in IPR&D for the six months ended June 30, 2016:

	( in millions)
Balance at December 31, 2015	$	486.7
Change in IPR&D	—

Balance at June 30, 2016	$	486.7

Goodwill and intangible assets are assessed annually for impairment on October 1 and whenever events or circumstances indicate that the carrying amount of an asset may not be recoverable. If it is determined that the full carrying amount of an asset is not recoverable, an impairment loss is recorded in the amount by which the carrying amount of the asset exceeds its fair value. For the six months ended June 30, 2016, there were no indicators of impairment.

- Definition

The entire disclosure for the aggregate amount of goodwill and a description of intangible assets, which may include (a) for amortizable intangible assets (also referred to as finite-lived intangible assets), the carrying amount, the amount of any significant residual value, and the weighted-average amortization period, (b) for intangible assets not subject to amortization (also referred to as indefinite-lived intangible assets), the carrying amount, and (c) the amount of research and development assets acquired and written off in the period, including the line item in the income statement in which the amounts written off are aggregated, if not readily apparent from the income statement. Also discloses (a) for amortizable intangibles assets in total and by major class, the gross carrying amount and accumulated amortization, the total amortization expense for the period, and the estimated aggregate amortization expense for each of the five succeeding fiscal years, (b) for intangible assets not subject to amortization the carrying amount in total and by major class, and (c) for goodwill, in total and for each reportable segment, the changes in the carrying amount of goodwill during the period (including the aggregate amount of goodwill acquired, the aggregate amount of impairment losses recognized, and the amount of goodwill included in the gain (loss) on disposal of a reporting unit). If any part of goodwill has not been allocated to a reportable segment, discloses the unallocated amount and the reasons for not allocating. For each impairment loss recognized related to an intangible asset (excluding goodwill), discloses: (a) a description of the impaired intangible asset and the facts and circumstances leading to the impairment, (b) the amount of the impairment loss and the method for determining fair value, (c) the caption in the income statement or the statement of activities in which the impairment loss is aggregated, and (d) the segment in which the impaired intangible asset is reported. For each goodwill impairment loss recognized, discloses: (a) a description of the facts and circumstances leading to the impairment, (b) the amount of the impairment loss and the method of determining the fair value of the associated reporting unit, and (c) if a recognized impairment loss is an estimate not finalized and the reasons why the estimate is not final. May also disclose the nature and amount of any significant adjustments made to a previous estimate of an impairment loss.

+ References + Details

Debt Instruments and Related Party Transactions

6 Months Ended

Jun. 30, 2016

Debt Instruments and Related Party Transactions

Debt Instruments and Related Party Transactions

Note 7. Debt Instruments and Related Party Transactions

In October 2015, the Company entered into a Note and Warrant Purchase Agreement (the “October 2015 Purchase Agreement”) with Redmile Capital Fund, LP and certain of its affiliates, whereby it sold, on a private placement basis, (a) $50.0 million aggregate principal amount of its unsecured promissory notes (“Notes”) and (b) five-year warrants (“Warrants”) for approximately 1.3 million shares of Common Stock. The payment terms under the purchase agreement contains two installments, the first $15.0 million in October 2017 and the balance $35.0 million in October 2020. Interest was payable at 4.1% on a monthly basis over the term of the loan. The promissory notes are recorded as due to related party on the consolidated balance sheets. Due to the embedded redemption (put and/or call) features in the note agreement, it was determined that the fair value of the warrants should be bifurcated from the value of the notes payable and recorded as a debt discount. The relative fair value of the warrants and the debt discount as related to the October 2015 purchase agreement was determined to be $8.8 million.

On February 19, 2016, the Company entered into a Note and Warrant Purchase Agreement (the “February 2016 Purchase Agreement”) with Redmile for an aggregate amount of up to $75.0 million. The Company has agreed with Redmile that in full consideration of the purchase price for the notes issued under the February 2016 Purchase Agreement, Redmile surrendered for cancellation all notes and warrants acquired from the October 2015 Purchase Agreement and the Company paid Redmile the interest accrued thereunder. As of June 30, 2016, Redmile beneficially owned approximately 10% of the Company’s outstanding shares of Common Stock and warrants. As such the promissory notes are presented as due to related party on the consolidated balance sheets.

Pursuant to the February 2016 agreement, at closing, it sold, on a private placement basis (a) $50.0 million aggregate principal amount of unsecured promissory notes (“Initial Notes”) and (b) five year warrants to purchase up to 37 shares of the Company’s Common Stock for every $1,000 of the principal amount of Initial Notes purchased (“Initial Warrants”), for an aggregate of up to 1,850,000 shares of Common Stock issuable under the Initial Warrants. The payment terms contain two installments, the first $15.0 million in October 2017 and the balance $35.0 million in October 2021. The interest rate is 3.875% and payable upon of maturity. This transaction was accounted for as a debt modification in accordance with ASC 470-50. The incremental fair value between the warrants that were cancelled and the February issued warrants of $3.5 million was recorded as additional unamortized debt discount on the balance sheet and added to the prior warrant balance within equity. The debt discount will be amortized over the life of the Initial Notes using the effective interest rate method.

On June 30, 2016, following the positive CHMP opinion for migalastat in Europe and the subsequent EC marketing approval, the Company entered into the Amended Purchase Agreement with Redmile, which joined GCM to the February 2016 Purchase Agreement. There was no change to the previously issued debt. Pursuant to the Amended Purchase Agreement, the Company sold an additional $30.0 million unsecured promissory notes and five year warrants to purchase up to 42 shares of the Company’s Common Stock for every $1,000 of the principal amount of additional Notes purchased (“Additional Warrants”), for an aggregate of up to 1,260,000 shares of Common Stock. The $30.0 million payment is due in October 2021. The interest rate is 3.875% and payable upon of maturity.

The fair value of the warrants was determined to be $3.8 million and recorded as a debt discount. The fair value of the warrants were calculated utilizing the Black-Scholes valuation model using the following six inputs: (1) the closing price of the Company’s Common Stock on the day of evaluation of $5.46; (2) the exercise price of the warrants of $7.06; (3) the remaining term of the warrants of 5 years; (4) the volatility of the Company’s Common Stock for the five year term of 86.02%; (5) the annual rate of dividends of 0%; and (6) the risk-free rate of return of 1.01%.

The outstanding debt as of June 30, 2016 between Redmile and GCM as of June 30, 2016 is as follows (in thousands):

Creditor	Gross amount of debt		Net unamortized discount			Net carrying value of debt
RedMile	$	55,000	$	(11,557	)	$	43,443
GCM	25,000		(3,149		)	21,851

Total Debt	$	80,000	$	(14,706	)	$	65,294

The debt discount amortization for the three and six months ended June 30, 2016 was $0.6 million and $1.0 million, respectively.

As of June 30, 2016, the total warrants were recorded at $16.1 million. See “—Note 8. Stockholders’ Equity” for more details.

Stockholders' Equity

6 Months Ended

Jun. 30, 2016

Stockholders' Equity

Stockholders' Equity

Note 8. Stockholders’ Equity

Common Stock and Warrants

As of June 30, 2016, the Company was authorized to issue 250 million shares of Common Stock. Dividends on Common Stock will be paid when, and if, declared by the board of directors. Each stockholder is entitled to vote on all matters that are appropriate for stockholder voting and is entitled to one vote for each share held.

In February 2016, the Company entered into the Sales Agreement with Cowen to create an at-the-market equity program under which the Company from time to time may offer and sell shares of its Common Stock, having an aggregate offering price of up to $100 million through Cowen (the “ATM Facility”). Sales of the shares under the Sales Agreement were to be made in transactions that were deemed to be “at the market offerings” as defined in Rule 415 promulgated under the Securities Act of 1933, as amended, including sales made directly on The NASDAQ Global Market, on any other existing trading market for the Common Stock or to or through a market maker. In addition, with the Company’s prior written approval, Cowen may also sell shares of Common Stock by any other method permitted by law, including in negotiated transactions. Cowen will act as sales agent using its commercially reasonable efforts consistent with its normal trading and sales practices and applicable state and federal laws, rules and regulations and the rules of The NASDAQ Stock Market LLC. There is no arrangement for funds to be received in an escrow, trust or similar arrangement. Cowen will be entitled to compensation at a fixed commission rate up to 3.0% of the gross proceeds per share sold through it as sales agent under the sales agreement. Beginning in April 2016 and through June 30, 2016, the Company sold 8.2 million shares of Common Stock under the ATM sales agreement resulting in net proceeds of $57.8 million, after Cowen’s commission of $1.7 million and other expenses of $0.1 million. In July 2016, the Company sold an additional 6.8 million shares of Common Stock with net proceeds of $39.3 million after Cowen’s commission. In connection with the July share sales, the Company completed all sales under the ATM equity program.

In October 2015, the Company entered into the October 2015 Purchase Agreement with Redmile, whereby the Company sold, on a private placement basis, (a) $50.0 million aggregate principal amount of its Notes and (b) Warrants for 1.3 million shares of Common Stock. On February 19, 2016, the Company entered into the February 2016 Purchase Agreement with Redmile for $50.0 million in unsecured promissory notes and five-year warrants for 1.9 million shares of Common Stock. The Company agreed with Redmile to cancel the $50 million note and warrants issued in October 2015 and pay only the accrued interest due of $0.8 million. In accordance with ASC 470, the transactions qualified as a modification of debt.

On June 30, 2016, following the positive CHMP opinion for migalastat in Europe and the subsequent EC marketing approval, the Company entered into the Amended Purchase Agreement with Redmile. Such amendment joined GCM to the February 2016 Purchase Agreement. Pursuant to the Amended Purchase Agreement, the Company sold an additional $30.0 million unsecured promissory notes and five-year warrants to purchase up to purchase up to 42 shares of the Company’s Common Stock, for every $1,000 of the principal amount of additional Notes purchased (“Additional Warrants”), for an aggregate of up to 1,260,000 shares of Common Stock issuable under the Additional Warrants. The payment is due in October 2021. The interest rate is 3.875% and payable upon of maturity.

The total outstanding warrants as of June 30, 2016 is as follows (in thousands):

Creditor	Warrant shares	Warrant amount
RedMile	2,060	$	12,927
GCM	1,050	3,149

Total warrants	3,110	$	16,076

The closing balance of the warrants was $16.1 million as of June 30, 2016 on the Consolidated Balance Sheet.

Nonqualified Cash Plan

The Company’s Deferral Plan, (the “Deferral Plan”) provides certain key employees and members of the Board of Directors as selected by the Compensation Committee, with an opportunity to defer the receipt of such participant’s base salary, bonus and director’s fees, as applicable. The Deferral Plan is intended to be a nonqualified deferred compensation plan that complies with the provisions of Section 409A of the Internal Revenue Code of 1986, as amended.

Deferred compensation amounts under the Deferral Plan as of June 30, 2016 were approximately $1.2 million, as compared to $0.7 million on December 31, 2015 and are included in other long-term liabilities. Deferral Plan assets as of June 30, 2016 were $1.2 million, as compared to $0.7 million as of December 31, 2015 and are classified as trading securities. The Deferred Plan assets are recorded at fair value with changes in the investments’ fair value recognized in the period they occur. The income from investment and unrealized gain (loss) for the three and six months ended June 30, 2016 and 2015 were deminimis.

Equity Incentive Plan

Stock Option Grants

The fair value of the stock options granted is estimated on the date of grant using a Black-Scholes option pricing model with the following weighted-average assumptions:

	Three months ended June 30,						Six months ended June 30,
	2016			2015			2016			2015
Expected stock price volatility	81.3		%	74.3		%	81.2		%	75.6		%
Risk free interest rate	1.3		%	1.7		%	1.7		%	1.7		%
Expected life of options (years)	6.25			6.25			6.25			6.25
Expected annual dividend per share	$	0.00		$	0.00		$	0.00		$	0.00

A summary of the Company’s stock options for the six months ended June 30, 2016 is as follows:

	Number of Shares ( in thousands)		Weighted Average Exercise Price		Weighted Average Remaining Contractual Life	Aggregate Intrinsic Value ( in millions)

Balance at December 31, 2015	11,729.2		$	7.11
Options granted	2,932.5		$	8.60
Options exercised	(165.8	)	$	3.90
Options forfeited	(224.5	)	$	8.78

Balance at June 30, 2016	14,271.4		$	7.42	7.4 years	$	11.2

Vested and unvested expected to vest June 30, 2016	13,363.2		$	7.31	7.3 years	$	10.9
Exercisable at June 30, 2016	7,049.4		$	6.24	6.0 years	$	7.2

As of June 30, 2016, the total unrecognized compensation cost related to non-vested stock options granted was $32.7 million and is expected to be recognized over a weighted average period of 3 years.

Restricted Stock Units

A summary of non-vested Restricted Stock Units (“RSU”) activity under the Company’s Amended and Restated 2007 Equity Incentive Plan for the six months ended June 30, 2016 is as follows:

	Number of Shares ( in thousands)		Weighted Average Grant Date Fair Value		Weighted Average Remaining Years	Aggregate Intrinsic Value ( in millions)

Non-vested units as of December 31, 2015	478.5		$	10.38
Granted	25.0		$	8.61
Vested	(181.3	)	$	6.55
Forfeited	—		$	—

Non-vested units as of June 30, 2016	322.2		$	12.40	1.88	$	—

Non-vested units expected to vest at June 30, 2016	322.2		$	12.40	1.88	$	—

For the six months ended June 30, 2016, 181,250 of the RSUs vested and all non-vested units are expected to vest over their normal term.

As of June 30, 2016, there was $2.8 million of total unrecognized compensation cost related to unvested RSUs with service-based vesting conditions. These costs are expected to be recognized over a weighted average period of 1.85 year.

Compensation Expense Related to Equity Awards

The following table summarizes information related to compensation expense recognized in the statements of operations related to the equity awards (in thousands):

	Three Months				Six Months
	Ended June 30,				Ended June 30,
	2016		2015		2016		2015
Equity compensation expense recognized in:
Research and development expense	$	1,966	$	1,044	$	3,902	$	1,991
General and administrative expense	2,500		1,187		4,846		2,200

Total equity compensation expense	$	4,466	$	2,231	$	8,748	$	4,191

- Definition

The entire disclosure for shareholders' equity comprised of portions attributable to the parent entity and noncontrolling interest, including other comprehensive income. Includes, but is not limited to, balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings, accumulated balance for each classification of other comprehensive income and amount of comprehensive income.

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Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21475-112644

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Preferred Stock
-URI http://asc.fasb.org/extlink&oid=6521494

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21463-112644

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21564-112644

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
-Section E

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
-Section C

+ Details

Assets and Liabilities Measured at Fair Value

6 Months Ended

Jun. 30, 2016

Assets and Liabilities Measured at Fair Value

Assets and Liabilities Measured at Fair Value

Note 9. Assets and Liabilities Measured at Fair Value

The Company’s financial assets and liabilities are measured at fair value and classified within the fair value hierarchy, which is defined as follows:

Level 1 — Quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the measurement date.

Level 2 — Inputs other than quoted prices in active markets that are observable for the asset or liability, either directly or indirectly.

Level 3 — Inputs that are unobservable for the asset or liability.

A summary of the fair value of the Company’s assets and liabilities aggregated by the level in the fair value hierarchy within which those measurements fall as of June 30, 2016, are identified in the following table (in thousands):

	Level 1		Level 2		Total
Assets:
Cash/ money market funds	$	63,656	$	—	$	63,656
Corporate debt securities	—		$	85,471	$	85,471
Commercial paper	—		$	64,673	$	64,673
Certificate of deposit	—		$	350	$	350
Market exchanged mutual funds	—		$	1,196	1,196

	$	63,656	$	151,690	$	215,346

	Level 2		Level 3		Total
Liabilities:
Contingent consideration payable	—		$	276,300	$	276,300
Derivative liability	346		––		346
Deferred compensation plan liability	$	1,196	—		$	1,196

	$	1,542	$	276,300	$	277,842

A summary of the fair value of the Company’s assets and liabilities aggregated by the level in the fair value hierarchy within which those measurements fall as of December 31, 2015, are identified in the following table (in thousands):

	Level 1		Level 2		Total
Assets:
Cash/ money market funds	$	69,485	$	—	$	69,485
Corporate debt securities	—		118,474		118,474
Commercial paper	—		25,724		25,724
Certificate of deposit	—		350		350
Market exchanged mutual funds			658		658

	$	69,485	$	145,206	$	214,691

	Level 2		Level 3		Total
Liabilities:
Contingent consideration payable	—		274,077		274,077
Deferred compensation plan liability	667		—		667

	$	667	$	274,077	$	274,744

Cash, Money Market Funds and Marketable Securities

The Company classifies its cash and money market funds within the fair value hierarchy as Level 1 as these assets are valued using quoted prices in active market for identical assets at the measurement date. The Company considers its investments in marketable securities as available-for-sale and classifies these assets within the fair value hierarchy as Level 2 primarily utilizing broker quotes in a non-active market for valuation of these securities. No changes in valuation techniques or inputs occurred during the six months ended June 30, 2016. No transfers of assets between Level 1 and Level 2 of the fair value measurement hierarchy occurred during the six months ended June 30, 2016.

Note Payable to Related Party and GCM

In connection with the notes payable to Redmile, as disclosed in “—Note 7. Debt Instruments and Related Party Transactions”, and Warrants as disclosed in “— Note 8. Stockholders’ Equity,” the Company recorded the notes as a liability of $65.3 million on an amortized cost basis.

The warrants issued in connection with the Amended Purchase Agreement were determined to be a component of equity based on the current accounting guidance. As such, these warrants which are considered Level 3 instruments were valued at the issuance date using the Black-Scholes valuation model using the following six inputs: (1) the closing price of the Company’s Common Stock on the day of evaluation of $5.46; (2) the exercise price of the warrants of $7.06; (3) the remaining term of the warrants of 5 years; (4) the volatility of the Company’s Common Stock for the five year term of 86.02%; (5) the annual rate of dividends of 0%; and (6) the risk-free rate of return of 1.01%. The Black-Scholes value of the warrants was $3.8 million.

As of June 30, 2016, the warrants are recorded at $16.1 million and the notes at $65.3 million, net of discount of $14.7 million.

Contingent Consideration Payable

The contingent consideration payable resulted from the acquisitions of Scioderm and Callidus, as discussed in “—Note 5. Acquisitions.” The most recent valuation was determined using a probability weighted discounted cash flow valuation approach. Using this approach, expected future cash flows are calculated over the expected life of the agreement, are discounted, and then exercise scenario probabilities are applied. The valuation is performed quarterly. Gains and losses are included in the statement of operations.

The contingent consideration payable has been classified as a Level 3 recurring liability as its valuation requires substantial judgment and estimation of factors that are not currently observable in the market. If different assumptions were used for the various inputs to the valuation approach the estimated fair value could be significantly higher or lower than the fair value the Company determined. The Company may be required to record losses in future periods. The following significant unobservable inputs were used in the valuation of the contingent consideration payable to former Scioderm stockholders:

Contingent Consideration Liability	Fair value as of June 30, 2016		Valuation Technique	Unobservable Input	Range
Clinical and regulatory milestones	$	239.8 million	Probability weighted discounted cash flow	Discount rate Probability of achievement of milestones Projected year of payments	0.4%-3.2% 66.5% -100.0% 2016-2018

Revenue-based milestones	$	26.0 million	Monte Carlo	Revenue volatility Discount rate Projected year of payments	58% 0.6%-1.6% 2018-2028

The following significant unobservable inputs were used in the valuation of the contingent consideration payable to former Callidus shareholders for the ATB-200 Pompe program:

Contingent
Consideration Liability

Fair value as of
June 30, 2016

Valuation Technique

Unobservable Input

Range

Clinical and regulatory milestones

10.1 million

Probability weighted discounted cash flow

Discount rate

Probability of achievement of milestones

Projected year of payments

10.5%

30%-43%

2018-2021

Contingent consideration liabilities are remeasured to fair value each reporting period using projected revenues, discount rates, probabilities of payment and projected payment dates. Projected contingent payment amounts related to clinical and regulatory based milestones are discounted back to the current period using a discounted cash flow model. Revenue-based payments are valued using a monte-carlo valuation model, which simulates future revenues during the earn-out-period using management’s best estimates. Projected revenues are based on our most recent internal operational budgets and long-range strategic plans. Increases in projected revenues and probabilities of payment may result in higher fair value measurements. Increases in discount rates and the time to payment may result in lower fair value measurements. Increases or decreases in any of those inputs together, or in isolation, may result in a significantly lower or higher fair value measurement. There is no assurance that any of the conditions for the milestone payments will be met.

The following table shows the change in the balance of contingent consideration payable for the six months ended June 30, 2016 and 2015, respectively (in thousands):

	Three months ended June 30,					Six months ended June 30,
	2016			2015		2016			2015

Balance, beginning of the period	$	277,229		$	11,700	$	274,077		$	10,700
Payment of contingent consideration in cash	(5,000		)	—		(5,000		)	—
Payment of contingent consideration in stock	(6,115		)	—		(6,115		)	—
Change in fair value change during the period, included in Statement of Operations	10,186			100		13,338			1,100

Balance, end of the period	$	276,300		$	11,800	$	276,300		$	11,800

Deferred Compensation Plan- Investment and Liability

The Company considers its investments in marketable securities, as available-for-sale and classifies these assets and related liability within the fair value hierarchy as Level 2 primarily utilizing broker quotes in a non-active market for valuation of these securities.

Foreign Currency Exchange Rate Exposure

The Company transacts business in various foreign countries and therefore, is subject to risk of foreign currency exchange rate fluctuations. As such, in June 2016, the Company entered into a forward contract to economically hedge transactional exposure associated with commitments arising from trade accounts payable denominated in a currency other than the functional currency of the respective operating entity. The Company did not designate this forward contract as a hedging instrument under applicable accounting guidance and, therefore, the change in fair value is recorded in the Consolidated Statements of Operations. The forward contract settles in monthly installments with the final installment settlement in May 2017.

There were no outstanding forward contracts at December 31, 2015.

For the three and six months ended June 30, 2016, the Company recognized a loss of $346 thousand related to the derivative instruments not designated as hedging instruments in the Consolidated Statements of Operations and the corresponding liability of $346 thousand is recorded as other current liability in the Consolidated Balance Sheet.

The impact of gains and losses on foreign exchange contracts not designated as hedging instruments related to changes in the fair value of assets and liabilities denominated in foreign currencies are generally offset by net foreign exchange gains and losses, which are also included on the Consolidated Statements of Operations in other income (expense), net for all periods presented. When the Company enters into foreign exchange contracts not designated as hedging instruments to mitigate the impact of exchange rate volatility in the translation of foreign earnings, gains and losses will generally be offset by fluctuations in the U.S. Dollar translated amounts of each Income Statement account in current and/or future periods.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Basic and Diluted Net Loss per Common Share

6 Months Ended

Jun. 30, 2016

Basic and Diluted Net Loss per Common Share

Basic and Diluted Net Loss per Common Share

Note 11. Basic and Diluted Net Loss per Common Share

The Company calculates net loss per share as a measurement of the Company’s performance while giving effect to all dilutive potential common shares that were outstanding during the reporting period. The Company has a net loss for all periods presented; accordingly, the inclusion of Common Stock options and warrants would be anti-dilutive. Therefore, the weighted average shares used to calculate both basic and diluted earnings per share are the same.

The following table provides a reconciliation of the numerator and denominator used in computing basic and diluted net loss per common share:

(In thousands, except per share	Three months Ended June 30,						Six months Ended June 30,
amounts)	2016			2015			2016			2015
Historical
Numerator:

Net loss	$	(51,050	)	$	(27,133	)	$	(94,741	)	$	(51,421	)


Denominator:
Weighted average common shares outstanding — basic and diluted	$	129,122,175		$	99,994,125		$	127,160,943		$	97,888,573

Dilutive common stock equivalents would include the dilutive effect of common stock options, restricted stock units and warrants for common stock equivalents. Potentially dilutive common stock equivalents were excluded from the diluted earnings per share denominator for all periods because of their anti-dilutive effect. The table below presents potential shares of common stock that were excluded from the computation as they were anti-dilutive using the treasury stock method (in thousands):

	As of June 30,
	2016	2015
Options to purchase common stock	14,271	11,663
Outstanding warrants, convertible to common stock	3,110	—
Unvested restricted stock units	322	675

Total number of potentially issuable shares	17,703	12,338

Summary of Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2016

Summary of Significant Accounting Policies

Basis of Presentation

Foreign Currency Transactions

Use of Estimates

Concentration of Credit Risk

Inventories

Revenue Recognition

Net Product Sales

Collaboration Revenue

a payment for an identifiable benefit;

the identifiable benefit is separable from the existing relationship between the Company and its customer;

the identifiable benefit can be obtained from a party other than the customer; and

the Company can reasonably estimate the fair value of the identifiable benefit

Fair Value Measurements

Contingent Liabilities

New Accounting Pronouncements

Cash, Money Market Funds and Marketable Securities (Tables)

6 Months Ended

Jun. 30, 2016

Cash, Money Market Funds and Marketable Securities

Schedule of cash and available-for-sale securities

Cash and available-for-sale securities are all current unless mentioned otherwise and consisted of the following as of June 30, 2016 and December 31, 2015 (in thousands):

	As of June 30, 2016
	Cost		Unrealized Gain		Unrealized Loss			Fair Value
Cash balances	$	63,656	$	—	$	—		$	63,656
Corporate debt securities	85,475		$	19	$	(23	)	$	85,471
Commercial paper	64,468		$	205	—			$	64,673
Certificate of deposit	350		—		—			350

	$	213,949	$	224	$	(23	)	$	214,150

Included in cash and cash equivalents	$	63,656	$	—	$	—		$	63,656
Included in marketable securities	$	150,293	$	224	$	(23	)	$	150,494

Total cash and marketable securities	$	213,949	$	224	$	(23	)	$	214,150

	As of December 31, 2015
	Cost		Unrealized Gain		Unrealized Loss			Fair Value
Cash balances	$	69,485	$	—	$	—		$	69,485
Corporate debt securities	118,627		1		(154		)	118,474
Commercial paper	25,686		38		—			25,724
Certificate of deposit	350		—		—			350

	$	214,148	$	39	$	(154	)	$	214,033

Included in cash and cash equivalents	$	69,485	—		—			$	69,485
Included in marketable securities	144,663		39		(154		)	144,548

Total cash and marketable securities	$	214,148	$	39	$	(154	)	$	214,033

Stockholders' Equity (Tables)

6 Months Ended

Jun. 30, 2016

Stockholders' Equity

Schedule of total outstanding warrants

The total outstanding warrants as of June 30, 2016 is as follows (in thousands):

Creditor	Warrant shares	Warrant amount
RedMile	2,060	$	12,927
GCM	1,050	3,149

Total warrants	3,110	$	16,076

Schedule of fair value weighted-average assumptions

	Three months ended June 30,						Six months ended June 30,
	2016			2015			2016			2015
Expected stock price volatility	81.3		%	74.3		%	81.2		%	75.6		%
Risk free interest rate	1.3		%	1.7		%	1.7		%	1.7		%
Expected life of options (years)	6.25			6.25			6.25			6.25
Expected annual dividend per share	$	0.00		$	0.00		$	0.00		$	0.00

Summary of stock options

	Number of Shares ( in thousands)		Weighted Average Exercise Price		Weighted Average Remaining Contractual Life	Aggregate Intrinsic Value ( in millions)

Balance at December 31, 2015	11,729.2		$	7.11
Options granted	2,932.5		$	8.60
Options exercised	(165.8	)	$	3.90
Options forfeited	(224.5	)	$	8.78

Balance at June 30, 2016	14,271.4		$	7.42	7.4 years	$	11.2

Vested and unvested expected to vest June 30, 2016	13,363.2		$	7.31	7.3 years	$	10.9
Exercisable at June 30, 2016	7,049.4		$	6.24	6.0 years	$	7.2

Summary of non-vested Restricted Stock Units activity

	Number of Shares ( in thousands)		Weighted Average Grant Date Fair Value		Weighted Average Remaining Years	Aggregate Intrinsic Value ( in millions)

Non-vested units as of December 31, 2015	478.5		$	10.38
Granted	25.0		$	8.61
Vested	(181.3	)	$	6.55
Forfeited	—		$	—

Non-vested units as of June 30, 2016	322.2		$	12.40	1.88	$	—

Non-vested units expected to vest at June 30, 2016	322.2		$	12.40	1.88	$	—

Summary of the compensation expense recognized in the statements of operations

The following table summarizes information related to compensation expense recognized in the statements of operations related to the equity awards (in thousands):

	Three Months				Six Months
	Ended June 30,				Ended June 30,
	2016		2015		2016		2015
Equity compensation expense recognized in:
Research and development expense	$	1,966	$	1,044	$	3,902	$	1,991
General and administrative expense	2,500		1,187		4,846		2,200

Total equity compensation expense	$	4,466	$	2,231	$	8,748	$	4,191

- Definition

Tabular disclosure of warrants or rights issued. Warrants and rights outstanding are derivative securities that give the holder the right to purchase securities (usually equity) from the issuer at a specific price within a certain time frame. Warrants are often included in a new debt issue to entice investors by a higher return potential. The main difference between warrants and call options is that warrants are issued and guaranteed by the company, whereas options are exchange instruments and are not issued by the company. Also, the lifetime of a warrant is often measured in years, while the lifetime of a typical option is measured in months. Disclose the title of issue of securities called for by warrants and rights outstanding, the aggregate amount of securities called for by warrants and rights outstanding, the date from which the warrants or rights are exercisable, and the price at which the warrant or right is exercisable.

+ References + Details

Assets and Liabilities Measured at Fair Value (Tables)

6 Months Ended

Jun. 30, 2016

Summary of assets and liabilities subject to fair value measurements

	Level 1		Level 2		Total
Assets:
Cash/ money market funds	$	63,656	$	—	$	63,656
Corporate debt securities	—		$	85,471	$	85,471
Commercial paper	—		$	64,673	$	64,673
Certificate of deposit	—		$	350	$	350
Market exchanged mutual funds	—		$	1,196	1,196

	$	63,656	$	151,690	$	215,346

	Level 2		Level 3		Total
Liabilities:
Contingent consideration payable	—		$	276,300	$	276,300
Derivative liability	346		––		346
Deferred compensation plan liability	$	1,196	—		$	1,196

	$	1,542	$	276,300	$	277,842

	Level 1		Level 2		Total
Assets:
Cash/ money market funds	$	69,485	$	—	$	69,485
Corporate debt securities	—		118,474		118,474
Commercial paper	—		25,724		25,724
Certificate of deposit	—		350		350
Market exchanged mutual funds			658		658

	$	69,485	$	145,206	$	214,691

	Level 2		Level 3		Total
Liabilities:
Contingent consideration payable	—		274,077		274,077
Deferred compensation plan liability	667		—		667

	$	667	$	274,077	$	274,744

Schedule of changes in contingent consideration payable

The following table shows the change in the balance of contingent consideration payable for the six months ended June 30, 2016 and 2015, respectively (in thousands):

	Three months ended June 30,					Six months ended June 30,
	2016			2015		2016			2015

Balance, beginning of the period	$	277,229		$	11,700	$	274,077		$	10,700
Payment of contingent consideration in cash	(5,000		)	—		(5,000		)	—
Payment of contingent consideration in stock	(6,115		)	—		(6,115		)	—
Change in fair value change during the period, included in Statement of Operations	10,186			100		13,338			1,100

Balance, end of the period	$	276,300		$	11,800	$	276,300		$	11,800

Scioderm

Schedule of significant unobservable inputs used in the valuation of the contingent consideration payable

Contingent Consideration Liability	Fair value as of June 30, 2016		Valuation Technique	Unobservable Input	Range
Clinical and regulatory milestones	$	239.8 million	Probability weighted discounted cash flow	Discount rate Probability of achievement of milestones Projected year of payments	0.4%-3.2% 66.5% -100.0% 2016-2018

Revenue-based milestones	$	26.0 million	Monte Carlo	Revenue volatility Discount rate Projected year of payments	58% 0.6%-1.6% 2018-2028

Callidus

Schedule of significant unobservable inputs used in the valuation of the contingent consideration payable

Contingent
Consideration Liability

Fair value as of
June 30, 2016

Valuation Technique

Unobservable Input

Range

Clinical and regulatory milestones

10.1 million

Probability weighted discounted cash flow

Discount rate

Probability of achievement of milestones

Projected year of payments

10.5%

30%-43%

2018-2021

Basic and Diluted Net Loss per Common Share (Tables)

6 Months Ended

Jun. 30, 2016

Basic and Diluted Net Loss per Common Share

Schedule of reconciliation of the numerator and denominator used in computing basic and diluted net loss per common share

(In thousands, except per share	Three months Ended June 30,						Six months Ended June 30,
amounts)	2016			2015			2016			2015
Historical
Numerator:

Net loss	$	(51,050	)	$	(27,133	)	$	(94,741	)	$	(51,421	)


Denominator:
Weighted average common shares outstanding — basic and diluted	$	129,122,175		$	99,994,125		$	127,160,943		$	97,888,573

Schedule of potential shares of common stock that were excluded from the computation as they were anti-dilutive using the treasury stock method

The table below presents potential shares of common stock that were excluded from the computation as they were anti-dilutive using the treasury stock method (in thousands):

	As of June 30,
	2016	2015
Options to purchase common stock	14,271	11,663
Outstanding warrants, convertible to common stock	3,110	—
Unvested restricted stock units	322	675

Total number of potentially issuable shares	17,703	12,338

Description of Business (Details)				1 Months Ended				3 Months Ended	6 Months Ended
Description of Business (Details)	Jun. 30, 2016 USD ($) $ / shares shares	Feb. 26, 2016 USD ($)	Feb. 19, 2016 USD ($) shares	Jul. 31, 2016 USD ($) shares	Jun. 30, 2016 USD ($) $ / shares shares	Feb. 29, 2016 USD ($)	Oct. 31, 2015 USD ($) shares	Jun. 30, 2016 USD ($) $ / shares shares	Jun. 30, 2016 USD ($) $ / shares shares	Jun. 30, 2015 USD ($)	Apr. 01, 2016 item	Dec. 31, 2015 USD ($) $ / shares
Corporate Information, Status of Operations and Management Plans
Number of Fabry causing mutations included in the label approved by the CHMP \| item											269
Common Stock, Par or Stated Value Per Share \| $ / shares	$ 0.01				$ 0.01			$ 0.01	$ 0.01			$ 0.01
Accumulated deficit	$ (674,307,000)				$ (674,307,000)			$ (674,307,000)	$ (674,307,000)			$ (579,566,000)
Proceeds from the issuance of common stock (in dollars)									$ 57,818,000	$ 243,216,000
Cowen and Company, LLC \| Sales Agreement
Corporate Information, Status of Operations and Management Plans
Number of shares issued from ATM transactions (in shares) \| shares				6,800,000				8,200,000
Net proceeds from stock issued at ATM transactions				$ 39,300,000				$ 57,800,000
Commission expenses incurred on issue of common stock								1,700,000
Other expenses paid								$ 100,000
October 2015 Purchase Agreement \| Redmile Group \| Private Placement Purchase Agreement
Corporate Information, Status of Operations and Management Plans
Unsecured notes							$ 50,000,000
Note principal canceled			$ 50,000,000
October 2015 Purchase Agreement \| Warrants \| Redmile Group \| Private Placement Purchase Agreement
Corporate Information, Status of Operations and Management Plans
Warrant term							5 years
Shares issuable for warrants (in shares) \| shares							1,300,000
February 2016 Purchase Agreement \| Redmile Group \| Beneficial Owner \| Private Placement Purchase Agreement
Corporate Information, Status of Operations and Management Plans
Unsecured notes			$ 50,000,000
February 2016 Purchase Agreement \| Warrants \| Redmile Group \| Beneficial Owner \| Private Placement Purchase Agreement
Corporate Information, Status of Operations and Management Plans
Warrant term			5 years
Increment used for debt conversion			$ 1,000
Shares issuable for warrants (in shares) \| shares			1,900,000
Additional Note and Warrant Agreement June 2016 \| Redmile Group \| Beneficial Owner \| Private Placement Purchase Agreement
Corporate Information, Status of Operations and Management Plans
Common Stock, Par or Stated Value Per Share \| $ / shares	$ 0.01				$ 0.01			$ 0.01	$ 0.01
Unsecured notes	$ 30,000,000				$ 30,000,000			$ 30,000,000	$ 30,000,000
Shares issuable for warrants (in shares) \| shares	1,300,000				1,300,000			1,300,000	1,300,000
Additional Note and Warrant Agreement June 2016 \| Warrants \| Redmile Group \| Beneficial Owner \| Private Placement Purchase Agreement
Corporate Information, Status of Operations and Management Plans
Warrant term	5 years				5 years
Increment used for debt conversion	$ 1,000				$ 1,000
Subsequent event \| Cowen and Company, LLC \| Sales Agreement
Corporate Information, Status of Operations and Management Plans
Number of shares issued from ATM transactions (in shares) \| shares				6,800,000
Net proceeds from stock issued at ATM transactions				$ 39,300,000
Maximum
Corporate Information, Status of Operations and Management Plans
Percentage of patients with Fabry disease caused by mutations included in the label approved by the CHMP											0.5
Maximum \| Cowen and Company, LLC \| Sales Agreement
Corporate Information, Status of Operations and Management Plans
Aggregate offering price		$ 100,000,000				$ 100,000,000
Fixed commission rate as a percentage of gross proceeds per Share sold		3.00%				3.00%
Maximum \| February 2016 Purchase Agreement \| Redmile Group \| Beneficial Owner
Corporate Information, Status of Operations and Management Plans
Unsecured notes			$ 75,000,000
Maximum \| February 2016 Purchase Agreement \| Warrants \| Redmile Group \| Beneficial Owner \| Private Placement Purchase Agreement
Corporate Information, Status of Operations and Management Plans
Shares of common stock issued per increment of note principal \| shares			37
Shares issuable for warrants (in shares) \| shares			1,850,000
Maximum \| Additional Note and Warrant Agreement June 2016 \| Warrants \| Redmile Group \| Beneficial Owner \| Private Placement Purchase Agreement
Corporate Information, Status of Operations and Management Plans
Shares of common stock issued per increment of note principal \| shares	42				42
Shares issuable for warrants (in shares) \| shares	1,260,000				1,260,000			1,260,000	1,260,000

Cash, Money Market Funds and Marketable Securities (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended	12 Months Ended
	Jun. 30, 2016	Jun. 30, 2016	Dec. 31, 2015	Jun. 30, 2015	Dec. 31, 2014
Cash, Money Market Funds, and Marketable Securities
Cash and cash equivalents, Amortized Cost	$ 63,656	$ 63,656	$ 69,485	$ 249,023	$ 24,074
Cash and cash equivalents, Fair Value	63,656	63,656	69,485
Marketable securities, Amortized Cost	150,293	150,293	144,663
Unrealized Gain	224	224	39
Unrealized Loss	(23)	(23)	(154)
Marketable securities, Fair Value	150,494	150,494	144,548
Cash and marketable securities, Amortized Cost	213,949	213,949	214,148
Cash and marketable securities, Fair Value	214,150	214,150	214,033
Available-for-sale investments
Realized gain (loss) on securities available-for-sale		0	0
Fair value of available for sale securities in unrealized loss positions	50,400	50,400	118,500
Other current liabilities
Cash, Money Market Funds, and Marketable Securities
Derivative liabilities	346	346		$ 346
Other income (expense)
Cash, Money Market Funds, and Marketable Securities
Loss on derivative instruments	346	346
Corporate debt securities
Cash, Money Market Funds, and Marketable Securities
Marketable securities, Amortized Cost	85,475	85,475	118,627
Unrealized Gain	19	19	1
Unrealized Loss	(23)	(23)	(154)
Marketable securities, Fair Value	85,471	85,471	118,474
Commercial paper
Cash, Money Market Funds, and Marketable Securities
Marketable securities, Amortized Cost	64,468	64,468	25,686
Unrealized Gain	205	205	38
Marketable securities, Fair Value	64,673	64,673	25,724
Certificate of deposit
Cash, Money Market Funds, and Marketable Securities
Marketable securities, Amortized Cost	350	350	350
Marketable securities, Fair Value	$ 350	$ 350	$ 350

Acquisitions (Details) - USD ($) $ / shares in Units, $ in Thousands, shares in Millions			1 Months Ended		3 Months Ended	6 Months Ended
	Jun. 30, 2016	Sep. 30, 2015	Apr. 30, 2016	Nov. 30, 2013	Jun. 30, 2016	Jun. 30, 2016	Jun. 30, 2015	Mar. 31, 2016	Dec. 31, 2015	Mar. 31, 2015	Dec. 31, 2014
Acquisitions
Common stock, par value (in dollars per share)	$ 0.01				$ 0.01	$ 0.01			$ 0.01
Contingent consideration payable upon achievement of milestones	$ 276,300				$ 276,300	$ 276,300	$ 11,800	$ 277,229	$ 274,077	$ 11,700	$ 10,700
Contingent consideration payable, current portion	56,000				56,000	56,000			41,400
Changes in fair value of contingent consideration payable						13,338	1,100
Allocation of the purchase consideration, including the contingent acquisition consideration payable
Contingent acquisition consideration payable	276,300				276,300	276,300	$ 11,800	$ 277,229	274,077	$ 11,700	$ 10,700
Payment of contingent consideration in stock, impact on stockholder's equity					6,115	6,115
Goodwill.	197,797				197,797	197,797			197,797
Scioderm
Acquisitions
Initial amount to Effective Time Holders		$ 223,900
Initial amount cash payment excluding Series B Preferred		141,100
Initial amount paid in shares of Common Stock		82,800
Fair value of the contingent consideration payments	265,800	259,000
Priority Review Voucher sale proceeds shared		$ 100,000
Priority review voucher transfer years		1 year
Contingent consideration payable, current portion	56,000				56,000	56,000
Changes in fair value of contingent consideration payable						13,000
Allocation of the purchase consideration, including the contingent acquisition consideration payable
Fair value of the contingent consideration payments	265,800	$ 259,000
Scioderm \| Series B Preferred Stock
Allocation of the purchase consideration, including the contingent acquisition consideration payable
Upfront equity payments		$ 257,000
Scioderm \| Zorblisa
Allocation of the purchase consideration, including the contingent acquisition consideration payable
Intangible assets-IPR&D									$ 463,700
Scioderm \| Minimum
Acquisitions
Discount rate (as a percent)		0.40%
Scioderm \| Maximum
Acquisitions
Priority Review Voucher sale proceeds shared		$ 100,000
Priority Review Voucher sale proceeds shared (as a percent)		50.00%
Scioderm \| Scioderm \| Series B Preferred Stock
Acquisitions
Consideration paid in common stock		5.9
Allocation of the purchase consideration, including the contingent acquisition consideration payable
Upfront cash payments		$ 361,000
Callidus
Acquisitions
Fair value of the contingent consideration payments				$ 10,600
Contingent consideration payable, current portion	10,500				10,500	10,500
Allocation of the purchase consideration, including the contingent acquisition consideration payable
Fair value of the contingent consideration payments				$ 10,600
Milestone payment, value of shares issued					6,000
Payment of contingent consideration in stock, impact on stockholder's equity					6,100
Callidus \| ATB-200 Pompe program
Acquisitions
Contingent consideration payable, current portion	$ 10,100				$ 10,100	10,100
Clinical and Regulatory Approval milestones \| Scioderm
Acquisitions
Milestone payment						$ 5,000
Clinical and Regulatory Approval milestones \| Scioderm \| Minimum
Acquisitions
Discount rate (as a percent)		0.40%				0.40%
Clinical and Regulatory Approval milestones \| Scioderm \| Maximum
Acquisitions
Discount rate (as a percent)		1.10%				3.20%
Allocation of the purchase consideration, including the contingent acquisition consideration payable
Upfront cash payments			$ 361,000
Revenue-based milestones \| Scioderm \| Minimum
Acquisitions
Discount rate (as a percent)		1.00%
Revenue-based milestones \| Scioderm \| Maximum
Acquisitions
Discount rate (as a percent)		2.20%
Allocation of the purchase consideration, including the contingent acquisition consideration payable
Upfront equity payments						$ 257,000
Clinical milestone \| Scioderm \| Maximum
Allocation of the purchase consideration, including the contingent acquisition consideration payable
Upfront cash payments			81,000
Regulatory Approval milestone \| Scioderm \| Maximum
Allocation of the purchase consideration, including the contingent acquisition consideration payable
Upfront cash payments			$ 280,000

Debt Instruments and Related Party Transactions (Details)			1 Months Ended		3 Months Ended	6 Months Ended
	Jun. 30, 2016 USD ($) item $ / shares shares	Feb. 19, 2016 USD ($) item shares	Jun. 30, 2016 USD ($) item $ / shares shares	Oct. 31, 2015 USD ($) item shares	Jun. 30, 2016 USD ($) $ / shares shares	Jun. 30, 2016 USD ($) $ / shares shares	Dec. 31, 2015 USD ($) $ / shares
Debt Instruments and Related Party Transactions [Line Items]
Debt discount amortization					$ 600,000	$ 1,000,000
Common stock, par value (in dollars per share) \| $ / shares	$ 0.01		$ 0.01		$ 0.01	$ 0.01	$ 0.01
Warrants	$ 16,076,000		$ 16,076,000		$ 16,076,000	$ 16,076,000	$ 8,755,000
Private Placement Purchase Agreement \| Additional Note and Warrant Agreement June 2016
Debt Instruments and Related Party Transactions [Line Items]
Debt discount	14,706,000		14,706,000		14,706,000	14,706,000
Outstanding debt
Gross amount of debt	80,000,000		80,000,000		80,000,000	80,000,000
Net unamortized discount	(14,706,000)		(14,706,000)		(14,706,000)	(14,706,000)
Net carrying value of debt	65,294,000		65,294,000		65,294,000	65,294,000
Redmile Group
Debt Instruments and Related Party Transactions [Line Items]
Warrants	12,927,000		12,927,000		12,927,000	12,927,000
Redmile Group \| Private Placement Purchase Agreement \| October 2015 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Proceeds from note and warrant purchase agreement				$ 50,000,000
Number of installments for repayment of debt \| item				2
Fixed interest rate (as a percent)				4.10%
Redmile Group \| Private Placement Purchase Agreement \| Additional Note and Warrant Agreement June 2016
Debt Instruments and Related Party Transactions [Line Items]
Debt discount	11,557,000		11,557,000		11,557,000	11,557,000
Outstanding debt
Gross amount of debt	55,000,000		55,000,000		55,000,000	55,000,000
Net unamortized discount	(11,557,000)		(11,557,000)		(11,557,000)	(11,557,000)
Net carrying value of debt	43,443,000		43,443,000		43,443,000	43,443,000
Redmile Group \| Private Placement Purchase Agreement \| October 2017 payment \| October 2015 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Installment payment				$ 15,000,000
Redmile Group \| Private Placement Purchase Agreement \| October 2020 payment \| October 2015 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Installment payment				$ 35,000,000
Redmile Group \| Warrants \| Private Placement Purchase Agreement \| October 2015 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Warrant Term				5 years
Shares issuable for warrants (in shares) \| shares				1,300,000
Debt discount	8,800,000		8,800,000		8,800,000	8,800,000
Outstanding debt
Net unamortized discount	$ (8,800,000)		$ (8,800,000)		$ (8,800,000)	$ (8,800,000)
Redmile Group \| Beneficial Owner \| February 2016 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Ownership position in the company (as a percent)	10.00%		10.00%		10.00%	10.00%
Redmile Group \| Beneficial Owner \| Private Placement Purchase Agreement \| February 2016 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Proceeds from note and warrant purchase agreement		$ 50,000,000
Number of installments for repayment of debt \| item		2
Fixed interest rate (as a percent)		3.875%
Redmile Group \| Beneficial Owner \| Private Placement Purchase Agreement \| Additional Note and Warrant Agreement June 2016
Debt Instruments and Related Party Transactions [Line Items]
Proceeds from note and warrant purchase agreement	$ 30,000,000		$ 30,000,000		$ 30,000,000	$ 30,000,000
Shares issuable for warrants (in shares) \| shares	1,300,000		1,300,000		1,300,000	1,300,000
Fixed interest rate (as a percent)	3.875%		3.875%		3.875%	3.875%
Common stock, par value (in dollars per share) \| $ / shares	$ 0.01		$ 0.01		$ 0.01	$ 0.01
Redmile Group \| Beneficial Owner \| Private Placement Purchase Agreement \| October 2017 payment \| February 2016 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Installment payment		$ 15,000,000
Redmile Group \| Beneficial Owner \| Private Placement Purchase Agreement \| October 2021 payment \| February 2016 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Installment payment		$ 35,000,000
Redmile Group \| Beneficial Owner \| Warrants \| Private Placement Purchase Agreement \| February 2016 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Warrant Term		5 years
Shares issuable for warrants (in shares) \| shares		1,900,000
Increment used for debt conversion		$ 1,000
Incremental fair value of warrant liability		3,500,000
Offering price (in dollars per share) \| $ / shares	$ 5.46		$ 5.46		5.46	5.46
Redmile Group \| Beneficial Owner \| Warrants \| Private Placement Purchase Agreement \| Additional Note and Warrant Agreement June 2016
Debt Instruments and Related Party Transactions [Line Items]
Warrant Term	5 years		5 years
Increment used for debt conversion	$ 1,000		$ 1,000
Number of inputs used in fair value classification \| item			6
Offering price (in dollars per share) \| $ / shares	$ 5.46		$ 5.46		5.46	5.46
Exercise price of warrants (in dollars per share) \| $ / shares	$ 7.06		$ 7.06		$ 7.06	$ 7.06
Remaining term of the warrants			5 years
Volatility (as a percent)			86.02%
Annual rate of dividends (as a percent)			0.00%
Risk-free rate of return (as a percent)			1.01%
Value of the warrants						$ 3,800,000
Fair value of the warrant liability	$ 3,800,000		$ 3,800,000		$ 3,800,000	$ 3,800,000
Redmile Group \| Beneficial Owner \| Warrants \| Private Placement Purchase Agreement \| June 2016 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Number of inputs used in fair value classification \| item	6
Exercise price of warrants (in dollars per share) \| $ / shares	$ 7.06		$ 7.06		$ 7.06	$ 7.06
Volatility (as a percent)	86.02%
Annual rate of dividends (as a percent)	0.00%
Risk-free rate of return (as a percent)	1.01%
Fair value of the warrant liability	$ 3,800,000		$ 3,800,000		$ 3,800,000	$ 3,800,000
GCM
Debt Instruments and Related Party Transactions [Line Items]
Warrants	3,149,000		3,149,000		3,149,000	3,149,000
GCM \| Private Placement Purchase Agreement \| Additional Note and Warrant Agreement June 2016
Debt Instruments and Related Party Transactions [Line Items]
Debt discount	3,149,000		3,149,000		3,149,000	3,149,000
Outstanding debt
Gross amount of debt	25,000,000		25,000,000		25,000,000	25,000,000
Net unamortized discount	(3,149,000)		(3,149,000)		(3,149,000)	(3,149,000)
Net carrying value of debt	$ 21,851,000		$ 21,851,000		$ 21,851,000	$ 21,851,000
Maximum \| Redmile Group \| Beneficial Owner \| February 2016 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Proceeds from note and warrant purchase agreement		$ 75,000,000
Maximum \| Redmile Group \| Beneficial Owner \| Warrants \| Private Placement Purchase Agreement \| February 2016 Purchase Agreement
Debt Instruments and Related Party Transactions [Line Items]
Shares issuable for warrants (in shares) \| shares		1,850,000
Shares of common stock issued per increment of note principal \| shares		37
Maximum \| Redmile Group \| Beneficial Owner \| Warrants \| Private Placement Purchase Agreement \| Additional Note and Warrant Agreement June 2016
Debt Instruments and Related Party Transactions [Line Items]
Shares issuable for warrants (in shares) \| shares	1,260,000		1,260,000		1,260,000	1,260,000
Shares of common stock issued per increment of note principal \| shares	42		42

Stockholders' Equity - Common Stock and Warrants (Details)				1 Months Ended				3 Months Ended	6 Months Ended
	Jun. 30, 2016 USD ($) item $ / shares shares	Feb. 26, 2016 USD ($)	Feb. 19, 2016 USD ($) shares	Jul. 31, 2016 USD ($) shares	Jun. 30, 2016 USD ($) item $ / shares shares	Feb. 29, 2016 USD ($)	Oct. 31, 2015 USD ($) shares	Jun. 30, 2016 USD ($) item $ / shares shares	Jun. 30, 2016 USD ($) item $ / shares shares	Jun. 30, 2015 USD ($)	Dec. 31, 2015 USD ($) $ / shares shares
Collaborative Agreements
Authorized number of shares of common stock \| shares	250,000,000				250,000,000			250,000,000	250,000,000		250,000,000
Voting right for each share held, number \| item	1				1			1	1
Common stock, par value (in dollars per share) \| $ / shares	$ 0.01				$ 0.01			$ 0.01	$ 0.01		$ 0.01
Net proceeds from the issuance of common stock									$ 57,818,000	$ 243,216,000
Proceeds from Warrant Exercises										$ 4,000,000
Warrants outstanding (in shares) \| shares	3,110,000				3,110,000			3,110,000	3,110,000
Warrant liability	$ 16,076,000				$ 16,076,000			$ 16,076,000	$ 16,076,000		$ 8,755,000
Cowen and Company, LLC \| Sales Agreement
Collaborative Agreements
Number of shares issued from ATM transactions (in shares) \| shares				6,800,000				8,200,000
Net proceeds from stock issued at ATM transactions				$ 39,300,000				$ 57,800,000
Commission expenses incurred on issue of common stock								1,700,000
Other Expenses								$ 100,000
Cowen and Company, LLC \| Sales Agreement \| Maximum
Collaborative Agreements
Aggregate offering price		$ 100,000,000				$ 100,000,000
Fixed commission rate as a percentage of gross proceeds per Share sold		3.00%				3.00%
Redmile Group
Collaborative Agreements
Warrants outstanding (in shares) \| shares	2,060,000				2,060,000			2,060,000	2,060,000
Warrant liability	$ 12,927,000				$ 12,927,000			$ 12,927,000	$ 12,927,000
GCM
Collaborative Agreements
Warrants outstanding (in shares) \| shares	1,050,000				1,050,000			1,050,000	1,050,000
Warrant liability	$ 3,149,000				$ 3,149,000			$ 3,149,000	$ 3,149,000
October 2015 Purchase Agreement \| Redmile Group \| Private Placement Purchase Agreement
Collaborative Agreements
Proceeds from note and warrant purchase agreement							$ 50,000,000
Debt Instrument, Interest Rate, Stated Percentage							4.10%
Fixed interest rate (as a percent)							4.10%
Note principal canceled			$ 50,000,000
Accrued interest due			800,000
October 2015 Purchase Agreement \| Redmile Group \| Private Placement Purchase Agreement \| Warrants
Collaborative Agreements
Warrant term							5 years
Shares issuable for warrants (in shares) \| shares							1,300,000
February 2016 Purchase Agreement \| Beneficial Owner \| Redmile Group \| Maximum
Collaborative Agreements
Proceeds from note and warrant purchase agreement			75,000,000
February 2016 Purchase Agreement \| Beneficial Owner \| Redmile Group \| Private Placement Purchase Agreement
Collaborative Agreements
Proceeds from note and warrant purchase agreement			$ 50,000,000
Debt Instrument, Interest Rate, Stated Percentage			3.875%
Fixed interest rate (as a percent)			3.875%
February 2016 Purchase Agreement \| Beneficial Owner \| Redmile Group \| Private Placement Purchase Agreement \| Warrants
Collaborative Agreements
Warrant term			5 years
Increment used for debt conversion			$ 1,000
Shares issuable for warrants (in shares) \| shares			1,900,000
Offering price (in dollars per share) \| $ / shares	$ 5.46				$ 5.46			$ 5.46	$ 5.46
Incremental fair value of warrant liability			$ 3,500,000
February 2016 Purchase Agreement \| Beneficial Owner \| Redmile Group \| Private Placement Purchase Agreement \| Maximum \| Warrants
Collaborative Agreements
Shares of common stock issued per increment of note principal \| shares			37
Shares issuable for warrants (in shares) \| shares			1,850,000
Additional Note and Warrant Agreement June 2016 \| Beneficial Owner \| Redmile Group \| Private Placement Purchase Agreement
Collaborative Agreements
Common stock, par value (in dollars per share) \| $ / shares	$ 0.01				$ 0.01			$ 0.01	$ 0.01
Proceeds from note and warrant purchase agreement	$ 30,000,000				$ 30,000,000			$ 30,000,000	$ 30,000,000
Shares issuable for warrants (in shares) \| shares	1,300,000				1,300,000			1,300,000	1,300,000
Debt Instrument, Interest Rate, Stated Percentage	3.875%				3.875%			3.875%	3.875%
Fixed interest rate (as a percent)	3.875%				3.875%			3.875%	3.875%
Additional Note and Warrant Agreement June 2016 \| Beneficial Owner \| Redmile Group \| Private Placement Purchase Agreement \| Warrants
Collaborative Agreements
Warrant term	5 years				5 years
Increment used for debt conversion	$ 1,000				$ 1,000
Number of inputs used in fair value classification \| item					6
Offering price (in dollars per share) \| $ / shares	$ 5.46				$ 5.46			$ 5.46	$ 5.46
Exercise price of warrants (in dollars per share) \| $ / shares	$ 7.06				$ 7.06			$ 7.06	$ 7.06
Remaining term of the warrants					5 years
Volatility (as a percent)					86.02%
Annual rate of dividends (as a percent)					0.00%
Risk-free rate of return (as a percent)					1.01%
Value of the warrants									$ 3,800,000
Fair value of the warrant liability	$ 3,800,000				$ 3,800,000			$ 3,800,000	$ 3,800,000
Additional Note and Warrant Agreement June 2016 \| Beneficial Owner \| Redmile Group \| Private Placement Purchase Agreement \| Maximum \| Warrants
Collaborative Agreements
Shares of common stock issued per increment of note principal \| shares	42				42
Shares issuable for warrants (in shares) \| shares	1,260,000				1,260,000			1,260,000	1,260,000

Stockholders' Equity - Equity Incentive Plan (Details) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Dec. 31, 2015
Nonqualified Cash Plan
Stockholders' Equity
Deferred compensation liability, noncurrent	$ 1,200,000		$ 1,200,000		$ 700,000
Trading securities	$ 1,200,000		$ 1,200,000		$ 700,000
Amended and Restated 2007 Equity Incentive Plan
Fair value weighted-average assumptions:
Expected life of options			1 year 10 months 17 days
Weighted Average Remaining Contractual Life
Vested and unvested expected to vest at the end of the period			1 year 10 months 17 days
Common stock options
Fair value weighted-average assumptions:
Expected stock price volatility (as a percent)	81.30%	74.30%	81.20%	75.60%
Risk free interest rate (as a percent)	1.30%	1.70%	1.70%	1.70%
Expected life of options	6 years 3 months	6 years 3 months	6 years 3 months	6 years 3 months
Expected annual dividend per share (in dollars per share)	$ 0.00	$ 0.00	$ 0.00	$ 0.00
Number of Shares
Balance at the beginning of the period (in shares)			11,729,200
Options granted (in shares)			2,932,500
Options exercised (in shares)			(165,800)
Options forfeited (in shares)			(224,500)
Balance at the end of the period (in shares)	14,271,400		14,271,400
Vested and unvested expected to vest at the end of the period (in shares)	13,363,200		13,363,200
Exercisable at the end of the period (in shares)	7,049,400		7,049,400
Weighted Average Exercise Price
Balance at the beginning of the period (in dollars per share)			$ 7.11
Options granted (in dollars per share)			8.60
Options exercised (in dollars per share)			3.90
Options forfeited (in dollars per share)			8.78
Balance at the end of the period (in dollars per share)	$ 7.42		7.42
Vested and unvested expected to vest at the end of the period (in dollars per share)	7.31		7.31
Exercisable at the end of the period (in dollars per share)	$ 6.24		$ 6.24
Weighted Average Remaining Contractual Life
Balance at the end of the period			7 years 4 months 24 days
Vested and unvested expected to vest at the end of the period			7 years 3 months 18 days
Exercisable at the end of the period			6 years
Aggregate Intrinsic Value
Aggregate intrinsic value of options outstanding (in dollars)	$ 11,200		$ 11,200
Aggregate intrinsic value of options vested and unvested expected to vest (in dollars)	10,900		10,900
Aggregate intrinsic value of options exercisable (in dollars)	7,200		7,200
Total unrecognized compensation cost related to non-vested stock options granted (in dollars)	$ 32,700,000		$ 32,700,000
Period of recognition compensation cost			3 years
Restricted stock units (RSUs) \| Amended and Restated 2007 Equity Incentive Plan
Fair value weighted-average assumptions:
Options vested (in shares)			181,300
Number of Shares
Balance at the beginning of the period (in shares)			478,500
Options granted (in shares)			25,000
Options vested (in shares)			181,300
Balance at the end of the period (in shares)	322,200		322,200
Vested and unvested expected to vest at the end of the period (in shares)	322,200		322,200
Weighted Average Exercise Price
Balance at the beginning of the period (in dollars per share)			$ 10.38
Options granted (in dollars per share)			8.61
Share-based Compensation Arrangement by Share-based Payment Award, Options, Vested, Weighted Average Grant Date Fair Value			6.55
Balance at the end of the period (in dollars per share)	$ 12.40		12.40
Vested and unvested expected to vest at the end of the period (in dollars per share)	$ 12.40		$ 12.40
Aggregate Intrinsic Value
Period of recognition compensation cost			1 year 10 months 6 days
Unrecognized compensation cost related to unvested restricted stock awards (in dollars)	$ 2,800,000		$ 2,800,000

Assets and Liabilities Measured at Fair Value (Details) $ / shares in Units, $ in Thousands			1 Months Ended	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2016 USD ($) item	Sep. 30, 2015	Jun. 30, 2016 USD ($) item	Jun. 30, 2016 USD ($)	Jun. 30, 2015 USD ($)	Jun. 30, 2016 USD ($) item	Jun. 30, 2015 USD ($)	Dec. 31, 2015 USD ($) item	Jun. 30, 2016 USD ($) $ / shares	Feb. 19, 2016 USD ($)	Dec. 31, 2015 USD ($)	Oct. 31, 2015 USD ($)	Jun. 30, 2015 USD ($)	Dec. 31, 2014 USD ($)
Financial assets and liabilities subject to fair value measurements
Transfer of assets from Level 1 to Level 2									$ 0
Transfer of assets from Level 2 to Level 1									0
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Warrant liability									16,076		$ 8,755
Contingent consideration payable
Balance at the beginning of the period				$ 277,229	$ 11,700	$ 274,077	$ 10,700	$ 10,700
Payment of contingent consideration in cash				(5,000)		(5,000)
Payment of contingent consideration in stock				(6,115)		(6,115)
Change in fair value change during the period, included in Statement of Operations				10,186	100	13,338	1,100
Balance at the end of the period	$ 276,300		$ 276,300	276,300	11,800	276,300	11,800	274,077
Assets:
Cash/money market funds									63,656		69,485		$ 249,023	$ 24,074
Fair value of assets									215,346		214,691
Liabilities:
Contingent consideration payable upon achievement of milestones	276,300		276,300	277,229	$ 11,700	$ 274,077	$ 10,700	$ 10,700	276,300		274,077		11,800	$ 10,700
Derivative liability									346
Deferred compensation plan liability									1,196		667
Fair value of liabilities									277,842		274,744
Note payable to related party									21,851
Foreign Currency Exchange Rate Exposure
Number of forward contracts \| item						1		0
Non-cash changes in the fair value of derivative liability				346		$ 346
Other current liabilities
Foreign Currency Exchange Rate Exposure
Derivative liabilities									346				$ 346
Callidus
Contingent consideration payable
Payment of contingent consideration in stock				(6,100)
Clinical and Regulatory Approval milestones \| Callidus
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Fair value of contingent payment						10,100
Clinical and Regulatory Approval milestones \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Fair value of contingent payment						239,800
Revenue-based milestones \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Fair value of contingent payment						$ 26,000
Minimum \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Discount rate (as a percent)		0.40%
Minimum \| Clinical and Regulatory Approval milestones \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Discount rate (as a percent)		0.40%				0.40%
Minimum \| Revenue-based milestones \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Discount rate (as a percent)		1.00%
Maximum \| Clinical and Regulatory Approval milestones \| Callidus
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Probability of achievement of milestones (as a percent)						43.00%
Maximum \| Clinical and Regulatory Approval milestones \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Discount rate (as a percent)		1.10%				3.20%
Maximum \| Revenue-based milestones \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Discount rate (as a percent)		2.20%
Cash/money market funds
Assets:
Cash/money market funds									63,656		69,485
Corporate debt securities
Assets:
Fair value of assets									85,471		118,474
Commercial paper
Assets:
Fair value of assets									64,673		25,724
Certificate of deposit
Assets:
Fair value of assets									350		350
Market exchanged mutual funds
Assets:
Fair value of assets									1,196		658
Level 1
Assets:
Fair value of assets									63,656		69,485
Level 1 \| Cash/money market funds
Assets:
Cash/money market funds									63,656		69,485
Level 2
Assets:
Fair value of assets									151,690		145,206
Liabilities:
Derivative liability									346
Deferred compensation plan liability									1,196		667
Fair value of liabilities									1,542		667
Level 2 \| Corporate debt securities
Assets:
Fair value of assets									85,471		118,474
Level 2 \| Commercial paper
Assets:
Fair value of assets									64,673		25,724
Level 2 \| Certificate of deposit
Assets:
Fair value of assets									350		350
Level 2 \| Market exchanged mutual funds
Assets:
Fair value of assets									1,196		658
Level 3
Contingent consideration payable
Balance at the beginning of the period						$ 274,077
Balance at the end of the period	276,300		276,300	276,300		276,300		$ 274,077
Liabilities:
Contingent consideration payable upon achievement of milestones	$ 276,300		$ 276,300	$ 276,300		$ 274,077		$ 274,077	276,300		274,077
Fair value of liabilities									276,300		$ 274,077
Level 3 \| Clinical and Regulatory Approval milestones \| Probability weighted discounted cash flow \| Callidus
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Discount rate (as a percent)						10.50%
Level 3 \| Revenue-based milestones \| Monte Carlo \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Revenue Volatility (as a percent)						58.00%
Level 3 \| Minimum \| Clinical and Regulatory Approval milestones \| Probability weighted discounted cash flow \| Callidus
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Probability of achievement of milestones (as a percent)						30.00%
Level 3 \| Minimum \| Clinical and Regulatory Approval milestones \| Probability weighted discounted cash flow \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Probability of achievement of milestones (as a percent)						66.50%
Level 3 \| Minimum \| Revenue-based milestones \| Monte Carlo \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Discount rate (as a percent)						0.60%
Level 3 \| Maximum \| Clinical and Regulatory Approval milestones \| Probability weighted discounted cash flow \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Probability of achievement of milestones (as a percent)						100.00%
Level 3 \| Maximum \| Revenue-based milestones \| Monte Carlo \| Scioderm
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Discount rate (as a percent)						1.60%
Additional Note and Warrant Agreement June 2016 \| Private Placement Purchase Agreement
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Notes payable									65,294
Debt discount									14,706
Redmile Group
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Warrant liability									12,927
Redmile Group \| October 2015 Purchase Agreement \| Private Placement Purchase Agreement
Financial assets and liabilities subject to fair value measurements
Proceeds from note and warrant purchase agreement												$ 50,000
Redmile Group \| October 2015 Purchase Agreement \| Warrants \| Private Placement Purchase Agreement
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Debt discount									$ 8,800
Redmile Group \| February 2016 Purchase Agreement \| Beneficial Owner \| Maximum
Financial assets and liabilities subject to fair value measurements
Proceeds from note and warrant purchase agreement										$ 75,000
Redmile Group \| February 2016 Purchase Agreement \| Beneficial Owner \| Private Placement Purchase Agreement
Financial assets and liabilities subject to fair value measurements
Proceeds from note and warrant purchase agreement										$ 50,000
Redmile Group \| February 2016 Purchase Agreement \| Beneficial Owner \| Warrants \| Private Placement Purchase Agreement
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Share Price \| $ / shares									$ 5.46
Redmile Group \| Additional Note and Warrant Agreement June 2016 \| Private Placement Purchase Agreement
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Notes payable									$ 43,443
Debt discount									11,557
Redmile Group \| Additional Note and Warrant Agreement June 2016 \| Beneficial Owner \| Private Placement Purchase Agreement
Financial assets and liabilities subject to fair value measurements
Proceeds from note and warrant purchase agreement									$ 30,000
Redmile Group \| Additional Note and Warrant Agreement June 2016 \| Beneficial Owner \| Warrants \| Private Placement Purchase Agreement
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Number of inputs used in fair value classification \| item			6
Share Price \| $ / shares									$ 5.46
Exercise price of warrants (in dollars per share) \| $ / shares									$ 7.06
Remaining term of the warrants			5 years
Expected stock price volatility (as a percent)			86.02%
Expected annual dividend per share (as a percent)			0.00%
Risk free interest rate (as a percent)			1.01%
Value of the warrants						$ 3,800
Fair value of the warrant liability									$ 3,800
Redmile Group \| June 2016 Purchase Agreement \| Beneficial Owner \| Warrants \| Private Placement Purchase Agreement
Weighted average assumptions used in the Black-Scholes valuation model for the warrants
Number of inputs used in fair value classification \| item	6
Exercise price of warrants (in dollars per share) \| $ / shares									$ 7.06
Expected stock price volatility (as a percent)	86.02%
Expected annual dividend per share (as a percent)	0.00%
Risk free interest rate (as a percent)	1.01%
Fair value of the warrant liability									$ 3,800
Redmile Group and GCM \| October 2015 Purchase Agreement
Financial assets and liabilities subject to fair value measurements
Proceeds from note and warrant purchase agreement												$ 65,300

Commitments and Contingencies	6 Months Ended
Commitments and Contingencies	Jun. 30, 2016
Commitments and Contingencies.
Commitments and Contingencies	Note 12. Commitments and Contingencies Since October 1, 2015, three purported securities class action lawsuits have been commenced in the United States District Court for New Jersey, naming as defendants the Company, its Chairman and Chief Executive Officer, and in one of the actions, its Chief Medical Officer. The lawsuits allege violations of the Securities Exchange Act of 1934 in connection with allegedly false and misleading statements made by the Company related to the regulatory approval path for migalastat. The plaintiffs seek, among other things, damages for purchasers of the Company’s Common Stock during different periods, all of which fall between March 19, 2015 and October 1, 2015. It is possible that additional suits will be filed, or allegations received from stockholders, with respect to similar matters and also naming the Company and/or its officers and directors as defendants. On May 26, 2016, the Court consolidated these lawsuits into a single action and appointed a lead plaintiff. The lead plaintiff filed a Consolidated Amended Complaint on July 11, 2016. Defendants’ response is due on August 25, 2016. The Company believes that it has meritorious defenses and intends to defend the lawsuits vigorously. These lawsuits and any other related lawsuits are subject to inherent uncertainties, and the actual cost will depend upon many unknown factors. The outcome of the litigation is necessarily uncertain, the Company could be forced to expend significant resources in the defense of these lawsuits and it may not prevail. On or about November 2, 2015, a derivative lawsuit was filed by an Amicus shareholder purportedly on Amicus’ behalf in the Superior Court of New Jersey, Middlesex County, Chancery Division, against the individuals who serve on the Amicus Board of Directors. Amicus itself was named as a nominal defendant. The derivative lawsuit alleged claims for breach of state law fiduciary duties, waste of corporate assets, and unjust enrichment based on allegedly false and misleading statements made by Amicus related to the regulatory approval path for migalastat HCl. On February 19, 2016, the complaint was dismissed by the Court and plaintiffs have not refiled. On or about March 3, 2016, a derivative lawsuit was filed by an Amicus shareholder purportedly on Amicus’ behalf in the Superior Court of New Jersey, Middlesex County, Chancery Division, against various officers and directors of the Company. Amicus itself is named as a nominal defendant. The derivative lawsuit alleges similar facts and circumstances as the three purported securities class action lawsuits described above and further alleges claims for breach of state law fiduciary duties, waste of corporate assets, unjust enrichment, abuse of control, and gross mismanagement based on allegedly false and misleading statements made by Amicus related to the regulatory approval path for migalastat HCl. The plaintiff seeks, among other things, to require the Amicus Board to take certain actions to reform its corporate governance procedures, including greater shareholder input and a provision to permit shareholders to nominate candidates for election to the Board, along with restitution, costs of suit and attorney’s fees. The parties have entered into a stipulation to stay the time to respond to the derivative complaint until the resolution of any motion to dismiss in the above-referenced securities action. This lawsuit and any other related lawsuits are subject to inherent uncertainties and the actual cost will depend upon many unknown factors. The outcome of the litigation is necessarily uncertain and the Company could be forced to expend significant resources in the defense of this suit, and the Company may not prevail. The Company is not currently able to estimate the possible cost to it from this matter, as this lawsuit is currently at an early stage and the Company cannot ascertain how long it may take to resolve this matter.

Subsequent Events	6 Months Ended
Subsequent Events	Jun. 30, 2016
Subsequent Events
Subsequent Events	Note 13. Subsequent Events On July 5, 2016, the Company entered into a Plan of Merger (the “Merger Agreement”) with MiaMed, Inc., (“MiaMed”). MiaMed is a pre-clinical biotechnology company focused on developing protein replacement therapy for CDKL5 and related diseases. Under the terms of the Merger Agreement, the former holders of MiaMed’s capital stock received an aggregate of $6.5 million, comprised of (i) approximately $1.8 million in cash (plus MiaMed’s cash and cash equivalents at closing and less any of MiaMed’s unpaid third-party fees and expenses related to the transaction), and (ii) 825,603 shares of the Company’s Common Stock. In addition, the Company also agreed to pay up to an additional $ 83.0 million in connection with the achievement of certain clinical, regulatory and commercial milestones, for a potential aggregate deal value of $89.5 million. The Company is currently assessing the accounting impact of the merger with MiaMed. In July 2016, as mentioned in “—Note 1. Description of Business,” the Company sold through the ATM program, an additional 6.8 million shares of Common Stock with a net proceeds of $39.3 million. In connection with the July share sales, the Company completed all sales under the ATM equity program.

Inventories (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Inventories
Work-in-process	$ 137
Finished goods	57
Total inventories	194	$ 0
Inventories expected to remain on-hand beyond one year	$ 0

Goodwill and Intangible Assets (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Changes in goodwill
Goodwill	$ 197,797	$ 197,797
Business Acquisitions
Changes in goodwill
Goodwill	$ 197,800	$ 197,800

Goodwill and Intangible Assets - IPR&D (Details) $ in Millions	6 Months Ended
	Jun. 30, 2016 USD ($) item
Changes in IPR&D
Indicators of impairment \| item	0
IPR&D
Changes in IPR&D
Balance at beginning of the period	$ 486.7
Balance at end of the period	486.7
Business Acquisitions \| IPR&D
Changes in IPR&D
Balance at end of the period	$ 486.7

Restructuring Charges (Details) $ in Thousands	1 Months Ended	3 Months Ended		6 Months Ended
Restructuring Charges (Details) $ in Thousands	Dec. 31, 2013 USD ($) item	Jun. 30, 2016 USD ($)	Jun. 30, 2015 USD ($)	Jun. 30, 2016 USD ($)	Jun. 30, 2015 USD ($)
Summary of restructuring charges and utilization
Charges		$ (8)	$ (26)	$ (58)	$ (36)
Facilities consolidation
Restructuring charges
Number of subleased locations that were closed in consolidation \| item	1
Lease payments	$ 700
Summary of restructuring charges and utilization
Balance at the beginning of the period				118
Cash payments				(135)
Adjustments				58
Balance at the end of the period		$ 41		$ 41

Commitments and Contingencies (Details)	Jun. 30, 2016 lawsuit
Commitments and Contingencies.
Number of purported securities class action lawsuits	3
Number of purported securities class action lawsuits naming additional company officers as defendants	1

Subsequent Events (Details) - USD ($) $ in Millions		1 Months Ended	3 Months Ended
Subsequent Events (Details) - USD ($) $ in Millions	Jul. 05, 2016	Jul. 31, 2016	Jun. 30, 2016
Subsequent event \| MiaMed Inc
Total consideration, stock and cash	$ 6.5
Cash consideration paid	1.8
Contingent consideration payable upon achievement of milestones	83.0
Potential aggregate deal value	$ 89.5
Subsequent event \| Amicus
Consideration paid in common stock	825,603
Sales Agreement \| Cowen and Company, LLC
Number of shares issued from ATM transactions (in shares)		6,800,000	8,200,000
Net proceeds from stock issued at ATM transactions		$ 39.3	$ 57.8
Sales Agreement \| Subsequent event \| Cowen and Company, LLC
Number of shares issued from ATM transactions (in shares)		6,800,000
Net proceeds from stock issued at ATM transactions		$ 39.3