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Income Taxes - Components of the Company's Deferred Tax Assets (Liabilities) (Details) - USD ($)
 12 Months Ended
Dec. 31, 2017
Dec. 31, 2016
Dec. 31, 2015
Income Tax Disclosure [Abstract]      
Provision for federal or state income taxes $ 0 $ 0 $ 0
Deferred income tax assets:      
Federal U.S. net operating loss carryforward 50,346,000 75,377,000  
State net operating loss carryforward 7,551,000 6,583,000  
Research and development credit, net 21,284,000 12,829,000  
Orphan drug credit, net 21,708,000 19,855,000  
Deferred rent 3,385,000 2,497,000  
Deferred revenue 2,982,000 5,098,000  
Depreciation 155,000 2,926,000  
Other 5,847,000 5,085,000  
Gross deferred income tax assets 113,258,000 130,250,000  
Valuation allowance (112,453,000) (128,844,000)  
Net deferred income tax assets 805,000 1,406,000  
Deferred income tax liabilities:      
Prepaid expenditures (805,000) (1,406,000)  
Gross deferred income tax liabilities (805,000) (1,406,000)  
Net deferred income tax asset/(liability) 0 $ 0  
Operating Loss Carryforwards [Line Items]      
Remaining portion of net operating losses 226,200,000    
Previously unrecognized excess tax benefits 18,600,000    
Previously unrecognized excess tax benefits, tax effected portion 6,500,000    
U.S. Federal and State      
Operating Loss Carryforwards [Line Items]      
Net operating loss carryforwards 239,700,000    
U.S. Federal Government      
Operating Loss Carryforwards [Line Items]      
US Federal tax credits carry forward 42,800,000    
Net operating loss for limited use 13,500,000    
U.S. Federal Government | Minimum      
Operating Loss Carryforwards [Line Items]      
Net operating losses limited for use utilized on an annual basis 200,000    
U.S. Federal Government | Maximum      
Operating Loss Carryforwards [Line Items]      
Net operating losses limited for use utilized on an annual basis $ 1,400,000