Leases, Licensed Technology and Other Commitments	9 Months Ended
Sep. 30, 2016
Leases [Abstract]
Leases, Licensed Technology and Other Commitments	Leases, Licensed Technology and Other Commitments Facility Leases The Company conducts the majority of its operations in a 100,000 square foot office and laboratory facility under an operating lease that originally extended to July 2019 with two consecutive five-year renewal options. The lease provided the Company with the option to early terminate the lease in July 2017. In July 2016, the Company notified the landlord of the 100,000 square foot office and laboratory facility that the Company was exercising its early termination right under the lease agreement to terminate the lease effective July 2017 (from the original end date of July 2019). As part of the termination, the Company made a payment of $1.7 million related to the termination. The Company maintains an outstanding letter of credit of $1.4 million in accordance with the terms of the amended lease. Future non-cancelable minimum annual rental payments through July 2017 under this lease are $1.6 million remaining in 2016 and $3.5 million in 2017. Binney Street, Cambridge, Massachusetts In January 2013, the Company entered into a lease agreement for approximately 244,000 square feet of laboratory and office space in two adjacent, connected buildings to be constructed in Cambridge, Massachusetts. Under the terms of the original lease, the Company leased all of the rentable space in one of the two buildings and a portion of the available space in the second building. In September 2013, the Company entered into a lease amendment to lease all of the remaining space, approximately 142,000 square feet, in the second building, for an aggregate of 386,000 square feet in both buildings. The terms of the lease amendment were consistent with the terms of the original lease. Construction of the core and shell of the building was completed in March 2015, at which time construction of tenant improvements in the building commenced. In connection with this lease, the landlord is providing a tenant improvement allowance for the costs associated with the design, engineering, and construction of tenant improvements for the leased facility. The tenant improvements will be in accordance with the Company’s plans and include fit-out of the buildings to construct appropriate laboratory and office space, subject to approval by the landlord. To the extent the stipulated tenant allowance provided by the landlord is exceeded, the Company is obligated to fund all costs incurred in excess of the tenant allowance. The scope of the planned tenant improvements do not qualify as “normal tenant improvements” under the lease accounting guidance. Accordingly, for accounting purposes, the Company is the deemed owner of the buildings during the construction period. As construction progresses, the Company records the project construction costs incurred as an asset. To the extent that the cost is incurred by the landlord or incurred by the Company and reimbursed by the landlord, the Company records a corresponding increase to facility lease obligation included in long-term debt on the consolidated balance sheet. As the buildings are completed, the Company is required to determine if the asset and corresponding financing obligation should continue to be carried on its consolidated balance sheet under the relevant accounting guidance. Based on the current terms of the lease, the Company expects to continue to be the deemed owner of the buildings as the construction period is completed. The Company is completing and occupying the building in stages. During the three months ended September 30, 2016, the Company placed approximately 44% of the building into service, or $103.2 million related to the building and $13.3 million related to leasehold improvements. The portion of the building placed in service during the quarter ended September 30, 2016 was occupied by our subtenant described below. The Company expects to substantially complete construction and occupy the remainder of the facility in the fourth quarter of 2016. As of September 30, 2016, the Company has recorded construction in progress of $182.7 million and a facility lease obligation of $284.9 million. The initial term of the lease is for 15 years from substantial completion of the core and shell of the buildings, which occurred in March 2015, with options to renew for three terms of five years each at market-based rates. The base rent is subject to increases over the term of the lease. Based on the original and amended leased space, the future non-cancelable minimum annual lease payments under the lease are $2.2 million remaining in 2016, $25.5 million in 2017, $31.0 million in 2018, $31.5 million in 2019, $32.1 million in 2020, $32.7 million in 2021 and $292.6 million thereafter, plus the Company’s share of the facility operating expenses and other costs that are reimbursable to the landlord under the lease. The Company maintains a letter of credit of $9.2 million as security for the lease, which is supported by restricted cash. In August 2015, the Company entered into a sublease agreement for approximately 160,000 square feet of the total leased space in the Binney Street facility. The sublease has an initial term of 10 years from the rent commencement date, which occurred on July 1, 2016, with an option to extend for the remainder of the initial term of the Company’s underlying lease. The sublease rent is subject to increases over the term of the lease. Based on the agreement, during the initial term the non-cancelable minimum annual sublease payments by calendar year beginning upon the rent commencement date of the sublease are approximately $5.3 million in 2016, $10.7 million in 2017, $10.9 million in 2018, $11.1 million in 2019 and $11.3 million in 2020 and $65.5 million thereafter, plus the subtenant’s share of the facility operating expenses. As managing and subleasing commercial real estate is not part of the Company's core operations, income and expenses associated with the subleased property are included as a component of other income, net, and are excluded from operating expenses. During the three and nine months ended September 30, 2016, the Company recorded $4.6 million of sublease income and $1.8 million of facility costs related to the subleased portion of the facility, including depreciation expense. Total rent expense for the leases described above as well as other Company leases for the three-month periods ended September 30, 2016 and 2015 was $2.7 million and $2.8 million, respectively, and $7.3 million for both the nine-month periods ended September 30, 2016 and 2015, respectively. Contingent rent for the three and nine-month periods ended September 30, 2016 and 2015 was $168,000 and $191,000, respectively, and $537,000 and $574,000, respectively. Total future non-cancelable minimum annual rental payments for the leases described above as well as other Company leases are $3.7 million in 2016, $29.0 million in 2017, $31.0 million in 2018, $31.5 million in 2019, $32.1 million in 2020 and $325.3 million thereafter.

Leases, Licensed Technology and Other Commitments

Facility Leases

The Company conducts the majority of its operations in a 100,000 square foot office and laboratory facility under an operating lease that originally extended to July 2019 with two consecutive five-year renewal options. The lease provided the Company with the option to early terminate the lease in July 2017. In July 2016, the Company notified the landlord of the 100,000 square foot office and laboratory facility that the Company was exercising its early termination right under the lease agreement to terminate the lease effective July 2017 (from the original end date of July 2019). As part of the termination, the Company made a payment of $1.7 million related to the termination. The Company maintains an outstanding letter of credit of $1.4 million in accordance with the terms of the amended lease. Future non-cancelable minimum annual rental payments through July 2017 under this lease are $1.6 million remaining in 2016 and $3.5 million in 2017.

Binney Street, Cambridge, Massachusetts

In January 2013, the Company entered into a lease agreement for approximately 244,000 square feet of laboratory and office space in two adjacent, connected buildings to be constructed in Cambridge, Massachusetts. Under the terms of the original lease, the Company leased all of the rentable space in one of the two buildings and a portion of the available space in the second building. In September 2013, the Company entered into a lease amendment to lease all of the remaining space, approximately 142,000 square feet, in the second building, for an aggregate of 386,000 square feet in both buildings. The terms of the lease amendment were consistent with the terms of the original lease. Construction of the core and shell of the building was completed in March 2015, at which time construction of tenant improvements in the building commenced.

In connection with this lease, the landlord is providing a tenant improvement allowance for the costs associated with the design, engineering, and construction of tenant improvements for the leased facility. The tenant improvements will be in accordance with the Company’s plans and include fit-out of the buildings to construct appropriate laboratory and office space, subject to approval by the landlord. To the extent the stipulated tenant allowance provided by the landlord is exceeded, the Company is obligated to fund all costs incurred in excess of the tenant allowance. The scope of the planned tenant improvements do not qualify as “normal tenant improvements” under the lease accounting guidance. Accordingly, for accounting purposes, the Company is the deemed owner of the buildings during the construction period.

As construction progresses, the Company records the project construction costs incurred as an asset. To the extent that the cost is incurred by the landlord or incurred by the Company and reimbursed by the landlord, the Company records a corresponding increase to facility lease obligation included in long-term debt on the consolidated balance sheet. As the buildings are completed, the Company is required to determine if the asset and corresponding financing obligation should continue to be carried on its consolidated balance sheet under the relevant accounting guidance. Based on the current terms of the lease, the Company expects to continue to be the deemed owner of the buildings as the construction period is completed. The Company is completing and occupying the building in stages. During the three months ended September 30, 2016, the Company placed approximately 44% of the building into service, or $103.2 million related to the building and $13.3 million related to leasehold improvements. The portion of the building placed in service during the quarter ended September 30, 2016 was occupied by our subtenant described below. The Company expects to substantially complete construction and occupy the remainder of the facility in the fourth quarter of 2016. As of September 30, 2016, the Company has recorded construction in progress of $182.7 million and a facility lease obligation of $284.9 million.

The initial term of the lease is for 15 years from substantial completion of the core and shell of the buildings, which occurred in March 2015, with options to renew for three terms of five years each at market-based rates. The base rent is subject to increases over the term of the lease. Based on the original and amended leased space, the future non-cancelable minimum annual lease payments under the lease are $2.2 million remaining in 2016, $25.5 million in 2017, $31.0 million in 2018, $31.5 million in 2019, $32.1 million in 2020, $32.7 million in 2021 and $292.6 million thereafter, plus the Company’s share of the facility operating expenses and other costs that are reimbursable to the landlord under the lease.

The Company maintains a letter of credit of $9.2 million as security for the lease, which is supported by restricted cash.

In August 2015, the Company entered into a sublease agreement for approximately 160,000 square feet of the total leased space in the Binney Street facility. The sublease has an initial term of 10 years from the rent commencement date, which occurred on July 1, 2016, with an option to extend for the remainder of the initial term of the Company’s underlying lease. The sublease rent is subject to increases over the term of the lease. Based on the agreement, during the initial term the non-cancelable minimum annual sublease payments by calendar year beginning upon the rent commencement date of the sublease are approximately $5.3 million in 2016, $10.7 million in 2017, $10.9 million in 2018, $11.1 million in 2019 and $11.3 million in 2020 and $65.5 million thereafter, plus the subtenant’s share of the facility operating expenses.

As managing and subleasing commercial real estate is not part of the Company's core operations, income and expenses associated with the subleased property are included as a component of other income, net, and are excluded from operating expenses. During the three and nine months ended September 30, 2016, the Company recorded $4.6 million of sublease income and $1.8 million of facility costs related to the subleased portion of the facility, including depreciation expense.

Total rent expense for the leases described above as well as other Company leases for the three-month periods ended September 30, 2016 and 2015 was $2.7 million and $2.8 million, respectively, and $7.3 million for both the nine-month periods ended September 30, 2016 and 2015, respectively. Contingent rent for the three and nine-month periods ended September 30, 2016 and 2015 was $168,000 and $191,000, respectively, and $537,000 and $574,000, respectively. Total future non-cancelable minimum annual rental payments for the leases described above as well as other Company leases are $3.7 million in 2016, $29.0 million in 2017, $31.0 million in 2018, $31.5 million in 2019, $32.1 million in 2020 and $325.3 million thereafter.