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Income Taxes - Components of the Company's Deferred Tax Assets (Liabilities) (Details) - USD ($)
$ in Thousands
 12 Months Ended
Dec. 31, 2015
Dec. 31, 2014
Dec. 31, 2013
Income Taxes [Abstract]      
Provision for federal or state income taxes $ 0 $ 0 $ 0
Deferred income tax assets [Abstract]      
Federal U.S. net operating loss carryforward 57,949 55,358  
State net operating loss carryforward 3,907 3,723  
Research and development credit, net 10,278 7,177  
Orphan drug credit, net 19,284 19,287  
Deferred rent 2,947 4,069  
Deferred revenue 6,632 3,989  
Depreciation 1,597 1,337  
Other 2,532 962  
Gross deferred income tax assets 105,126 95,902  
Valuation allowance (104,399) (94,297)  
Net deferred income tax assets 727 1,605  
Deferred income tax liabilities [Abstract]      
Prepaid expenditures (727) (1,605)  
Gross deferred income tax liabilities (727) (1,605)  
Net deferred income tax asset/(liability) $ 0 $ 0  
Operating Loss Carryforwards [Line Items]      
Net operating loss carryforwards expiration start year 2020    
Net operating loss carryforward expiration ending year 2035    
Remaining portion of net operating losses $ 152,100    
Net operating losses, recognized as a benefit through additional-paid-in-capital 14,700    
U.S. Federal Government [Member]      
Operating Loss Carryforwards [Line Items]      
Net operating loss carryforwards 165,600    
US Federal Tax credits carry forward $ 29,300    
Federal tax credit expiration start year 2020    
Federal tax credit expiration ending year 2035    
Net operating loss for limited use $ 13,500    
U.S. Federal Government [Member] | Minimum [Member]      
Operating Loss Carryforwards [Line Items]      
Net operating losses limited for year 2016    
Net operating losses limited for use utilized on an annual basis $ 200    
U.S. Federal Government [Member] | Maximum [Member]      
Operating Loss Carryforwards [Line Items]      
Net operating losses limited for year 2028    
Net operating losses limited for use utilized on an annual basis $ 1,400    
State and Local Jurisdiction [Member]      
Operating Loss Carryforwards [Line Items]      
Net operating loss carryforwards $ 165,600