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Income Taxes (Tables) | 9 Months Ended
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Sep. 30, 2013
Components of the Company's Deferred Tax Assets (Liabilities) | The significant components of the Company’s deferred tax assets (liabilities) were as follows:
|  | December 31, |
|  | 2011 |  |  | 2012 |
Deferred income tax assets: |  |  |  |  |  |  |  |
Federal U.S. net operating loss carryforward |  | $ | 37,825,639 |  |  | $ | 35,330,167 |
State net operating loss carryforward |  |  | 4,493,151 |  |  |  | 3,521,722 |
Research and development credit, net |  |  | 2,777,899 |  |  |  | 2,777,899 |
Orphan drug credit, net |  |  | 11,507,811 |  |  |  | 19,039,613 |
Deferred rent |  |  | 5,194,408 |  |  |  | 5,218,002 |
Deferred revenue |  |  | 12,924,462 |  |  |  | 9,379,064 |
Depreciation |  |  | 1,515,510 |  |  |  | 1,247,772 |
Other |  |  | 1,551,356 |  |  |  | 1,575,782 |
Gross deferred income tax assets |  |  | 77,790,236 |  |  |  | 78,090,021 |
Valuation allowance |  |  | (77,302,928 | ) |  |  | (78,090,021 | )
Net deferred income tax assets |  |  | 487,308 |  |  |  | — |
Deferred tax liabilities: |  |  |  |  |  |  |  |
Other |  |  | (487,308 | ) |  |  | — |
Gross deferred income tax liabilities |  |  | (487,308 | ) |  |  | — |
Net deferred income tax asset/(liability) |  | $ | — |  |  | $ | — |
Reconciliation of Reported Estimated Income Tax Benefit | The reconciliation of the reported estimated income tax benefit to the amount that would result by applying the U.S. federal statutory tax rate to the net income is as follows:
|  | Year Ended December 31, |
|  | 2011 |  |  | 2012 |
United States federal tax at statutory rate |  | $ | 2,350,992 |  |  | $ | 2,926,615 |
State taxes (net of federal benefit) |  |  | 1,480,185 |  |  |  | 1,460,289 |
Deferred income tax adjustments |  |  | — |  |  |  | (512,375 | )
Orphan drug credit, net |  |  | (7,056,607 | ) |  |  | (4,895,671 | )
Equity based compensation |  |  | 725,811 |  |  |  | 279,165 |
Fair value adjustment of preferred stock warrant liability |  |  | (496,208 | ) |  |  | (52,743 | )
Other permanent items |  |  | 4,696 |  |  |  | 7,627 |
Change in valuation allowance |  |  | 2,991,131 |  |  |  | 787,093 |
Income tax expense/(benefit) |  | $ | — |  |  | $ | — |
Change in Unrecognized Tax Benefits | The change in unrecognized tax benefits, for the years ended December 31, 2011 and 2012, were as follows:
|  | 2011 |  |  | 2012 |
Beginning balance |  | $ | 1,246,025 |  |  | $ | 1,533,986 |
Increases/(decreases) for current year tax positions |  |  | 287,961 |  |  |  | 58,371 |
Increases/(decreases) for prior year tax positions |  |  | — |  |  |  | — |
Decreases as a result of expiration of statute of limitations |  |  | — |  |  |  | — |
Total |  | $ | 1,533,986 |  |  | $ | 1,592,357 |

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- Definition Tabular disclosure of the components of net deferred tax asset or liability recognized in an entity's statement of financial position, including the following: the total of all deferred tax liabilities, the total of all deferred tax assets, the total valuation allowance recognized for deferred tax assets. + References Reference 1: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 50 -Paragraph 2 -URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32537-109319 + Details
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- Definition Tabular disclosure of the reconciliation using percentage or dollar amounts of the reported amount of income tax expense attributable to continuing operations for the year to the amount of income tax expense that would result from applying domestic federal statutory tax rates to pretax income from continuing operations. + References Reference 1: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 50 -Paragraph 12 -URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32687-109319 + Details
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- Definition Tabular disclosure of the change in unrecognized tax benefits. + References Reference 1: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 55 -Paragraph 217 -URI http://asc.fasb.org/extlink&oid=32707879&loc=d3e36027-109320 Reference 2: http://www.xbrl.org/2003/role/presentationRef -Publisher FASB -Name Accounting Standards Codification -Topic 740 -SubTopic 10 -Section 50 -Paragraph 15A -URI http://asc.fasb.org/extlink&oid=6907707&loc=SL6600010-109319 + Details
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