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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 |  |

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