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Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Sep. 30, 2016	Nov. 03, 2016
Document Information [Line Items]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Sep. 30, 2016
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	Q3
Trading Symbol	ZIOP
Entity Registrant Name	ZIOPHARM ONCOLOGY INC
Entity Central Index Key	0001107421
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		131,732,423

BALANCE SHEETS - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 94,683	$ 140,717
Receivables	25	446
Prepaid expenses and other current assets	20,969	11,358
Total current assets	115,677	152,521
Property and equipment, net	825	581
Deposits	128	128
Other non-current assets	492	494
Total assets	117,122	153,724
Current liabilities:
Accounts payable	1,814	2,008
Accrued expenses	7,364	8,906
Deferred rent - current portion	177	348
Deferred revenue - current portion	6,389	6,861
Total current liabilities	15,744	18,123
Deferred rent, net of current portion	163	313
Deferred revenue, net of current portion	43,125	47,917
Derivative liabilities	694
Total liabilities	59,726	66,353
Commitments and contingencies (Note 5)
Stockholders' equity (deficit):
Preferred stock, $0.001 par value; 30,000,000 shares authorized, 250,000 designated as Series 1; 29,750,000 undesignated, no shares issued and outstanding at September 30, 2016 and December 31, 2015, respectively
Common stock, $0.001 par value; 250,000,000 shares authorized; 131,732,423 and 131,718,579 shares issued and outstanding at September 30, 2016 and December 31, 2015, respectively	132	132
Additional paid-in capital - common stock	582,225	579,939
Accumulated deficit	(646,773)	(492,700)
Total stockholders' equity (deficit)	(64,416)	87,371
Total liabilities, preferred stock, and stockholders' equity (deficit)	117,122	$ 153,724
Series 1 Preferred Stock
Current liabilities:
Series 1 preferred stock, $1,200 stated value; 250,000 designated; 103,063 and 0 shares issued and outstanding at September 30, 2016 and December 31, 2015, respectively	121,812
Stockholders' equity (deficit):
Total stockholders' equity (deficit)	$ 121,812

BALANCE SHEETS (Parenthetical) - $ / shares	Sep. 30, 2016	Dec. 31, 2015
Preferred stock, par value	$ 0.001	$ 0.001
Preferred stock, shares authorized	30,000,000	30,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value	$ 0.001	$ 0.001
Common stock, shares authorized	250,000,000	250,000,000
Common stock, shares issued	131,732,423	131,718,579
Common stock, shares outstanding	131,732,423	131,718,579
Series 1 Preferred Stock
Preferred stock, stated value	$ 1,200	$ 1,200
Preferred stock, shares authorized	250,000	250,000
Preferred stock, shares issued	103,063	0
Preferred stock, shares outstanding	103,063	0
Preferred stock, shares authorized	250,000	250,000
Undesignated Preferred Stock
Preferred stock, shares authorized	29,750,000	29,750,000

STATEMENTS OF OPERATIONS - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
STATEMENTS OF OPERATIONS - USD ($) $ in Thousands	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Collaboration revenue	$ 1,598	$ 1,869	$ 5,264	$ 2,413
Operating expenses:
Research and development, including costs of contracts	8,975	16,970	148,402	98,643
General and administrative	3,537	3,065	11,058	14,388
Total operating expenses	12,512	20,035	159,460	113,031
Loss from operations	(10,914)	(18,166)	(154,196)	(110,618)
Other income (expense), net	39	(4)	102	6
Change in derivative liabilities	21		21
Net loss	(10,854)	(18,170)	(154,073)	(110,612)
Preferred stock dividends	(3,591)		(3,591)
Net loss applicable to common stockholders	$ (14,445)	$ (18,170)	$ (157,664)	$ (110,612)
Net loss per common share - basic and diluted	$ (0.11)	$ (0.14)	$ (1.21)	$ (0.89)
Weighted average common shares outstanding used to compute net loss per share - basic and diluted	130,496,035	129,732,356	130,347,370	123,911,796

STATEMENT OF STOCKHOLDERS' EQUITY (DEFICIT) - 9 months ended Sep. 30, 2016 - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-In Capital Common Stock	Accumulated Deficit	Series 1 Preferred Stock
Beginning Balance (in shares) at Dec. 31, 2015		131,718,579
Beginning Balance at Dec. 31, 2015	$ 87,371	$ 132	$ 579,939	$ (492,700)
Stock-based compensation	$ 6,094		6,094
Exercise of employee stock options (in shares)	169,000	137,346
Exercise of employee stock options	$ 551	$ 1	550
Repurchase of common stock (in shares)		(168)
Repurchase of common stock	(2)		(2)
Restricted stock buy-back at vesting to cover taxes (in shares)		(123,334)
Restricted stock buy-back at vesting to cover taxes	(853)	$ (1)	(852)
Issuance of stock in a license agreement	87		87		$ 118,241
Issuance of stock in a license agreement (in shares)					100,000
Issuance of stock in a license agreement	87		87		$ 118,241
Issuance of preferred stock dividends (in shares)					3,063
Issuance of preferred stock dividends	(3,591)		(3,591)		$ 3,571
Net loss	(154,073)			(154,073)
Ending Balance (in shares) at Sep. 30, 2016		131,732,423			103,063
Ending Balance at Sep. 30, 2016	$ (64,416)	$ 132	$ 582,225	$ (646,773)	$ 121,812

STATEMENT OF STOCKHOLDERS' EQUITY (DEFICIT) (Parenthetical) $ in Thousands	9 Months Ended
	Sep. 30, 2016 USD ($)
Issuance of preferred stock in a license agreement with Intrexon, issuance costs	$ 109

STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	9 Months Ended
STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	Sep. 30, 2016	Sep. 30, 2015
Cash flows from operating activities:
Net loss	$ (154,073)	$ (110,612)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	227	295
Stock-based compensation	6,094	6,054
Common stock issued in exchange for MD Anderson license agreement		67,285
Preferred stock issued in exchange for 2016 ECP amendment	118,936
Change in fair value of derivative liability	(21)
Issuance of common stock in a license agreement	87
Loss on disposal of fixed assets		(1)
(Increase) decrease in:
Receivables	421	(224)
Prepaid expenses and other current assets	(9,611)	(7,129)
Other noncurrent assets	1
Increase (decrease) in:
Accounts payable	(194)	2,150
Accrued expenses	(1,542)	10,956
Deferred revenue	(5,264)	55,087
Deferred rent	(322)	(69)
Net cash provided by (used in) operating activities	(45,261)	23,792
Cash flows from investing activities:
Purchases of property and equipment	(469)	(25)
Net cash provided by (used in) investing activities	(469)	(25)
Cash flows from financing activities:
Proceeds from exercise of stock options	551	3,366
Repurchase of restricted common stock	(853)	(379)
Repurchase of common stock	(2)	(34)
Proceeds from issuance of common stock, net		94,320
Net cash provided by (used in) financing activities	(304)	97,273
Net increase (decrease) in cash and cash equivalents	(46,034)	121,040
Cash and cash equivalents, beginning of period	140,717	42,803
Cash and cash equivalents, end of period	94,683	163,843
Supplementary disclosure of cash flow information:
Cash paid for interest	0	0
Cash paid for income taxes	0	0
Common Stock
Supplementary disclosure of noncash investing and financing activities:
Issuance of stock		$ 67,285
Series 1 Preferred Stock
Supplementary disclosure of noncash investing and financing activities:
Issuance of stock	119,045
Payment of dividends in preferred stock	$ 3,591

Business

9 Months Ended

Sep. 30, 2016

Business

1. Business

Overview

ZIOPHARM Oncology, Inc., which is referred to herein as “ZIOPHARM” or the “Company,” is a biopharmaceutical company seeking to acquire, develop and commercialize, on its own or with partners, a diverse portfolio of cancer therapies that address unmet medical needs.

The Company’s operations to date have consisted primarily of raising capital and conducting research and development. The Company’s fiscal year ends on December 31.

The Company has operated at a loss since its inception in 2003 and has minimal revenues. The Company anticipates that its losses will continue for the foreseeable future. At September 30, 2016, the Company’s accumulated deficit was approximately $646.8 million. The Company’s ability to continue operations after its current cash resources are exhausted depends on its ability to obtain additional financing or to achieve profitable operations, as to which no assurances can be given. Cash requirements may vary materially from those now planned because of changes in the Company’s focus and direction of its research and development programs, competitive and technical advances, patent developments, regulatory changes or other developments. Additional financing will be required to continue operations after the Company exhausts its current cash resources and to continue its long-term plans for clinical trials and new product development. There can be no assurance that any such financing can be obtained by the Company, or if obtained, what the terms thereof may be, or that any amount that the Company is able to raise will be adequate to support the Company’s working capital requirements until it achieves profitable operations.

Basis of Presentation

The accompanying unaudited interim financial statements have been prepared in accordance with the instructions to Form 10-Q pursuant to the rules and regulations of the Securities and Exchange Commission, or the SEC. Certain information and note disclosures required by generally accepted accounting principles in the United States have been condensed or omitted pursuant to such rules and regulations.

It is management’s opinion that the accompanying unaudited interim financial statements reflect all adjustments (which are normal and recurring) that are necessary for a fair statement of the results for the interim periods. The unaudited interim financial statements should be read in conjunction with the audited financial statements and the notes thereto for the year ended December 31, 2015, included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2015 filed with the SEC on February 24, 2016, or the Form 10-K.

The year-end balance sheet data was derived from the audited financial statements but does not include all disclosures required by generally accepted accounting principles in the United States.

The results disclosed in the statements of operations for the three and nine months ended September 30, 2016 are not necessarily indicative of the results to be expected for the full fiscal year.

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenues and expenses during the reporting period. Although the Company regularly assesses these estimates, actual results could differ from those estimates. Changes in estimates are recorded in the period in which they become known.

The Company’s most significant estimates and judgments used in the preparation of its financial statements are:

•

Clinical trial expenses;

•

Collaboration agreements;

•

Fair value measurements for stock-based compensation and Series 1 preferred stock; and

•

Income taxes.

Subsequent Events

The Company evaluated all events and transactions that occurred after the balance sheet date through the date of this filing. During this period, the Company did not have any material subsequent events that impacted its financial statements or disclosures.

Summary of Significant Accounting Policies	9 Months Ended
Summary of Significant Accounting Policies	Sep. 30, 2016
Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies The Company’s significant accounting policies were identified in the Company’s Form 10-K. There have been no material changes in those policies since the filing of its Form 10-K.

Fair Value Measurements

9 Months Ended

Sep. 30, 2016

Fair Value Measurements

3. Fair Value Measurements

The Company accounts for its financial assets and liabilities using fair value measurements. The authoritative accounting guidance defines fair value, establishes a framework for measuring fair value under generally accepted accounting principles and enhances disclosures about fair value measurements. Fair value is defined as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. Valuation techniques used to measure fair value must maximize the use of observable inputs and minimize the use of unobservable inputs. The fair value hierarchy is based on three levels of inputs, of which the first two are considered observable and the last unobservable, that may be used to measure fair value as follows:

•

Level 1 - Quoted prices in active markets for identical assets or liabilities.

•

Level 2 - Inputs other than Level 1 that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.

•

Level 3 - Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

Assets and liabilities measured at fair value on a recurring basis as of September 30, 2016 and December 31, 2015 were as follows:


($ in thousands)				Fair Value Measurements at Reporting Date Using
Description	Balance as of September 30, 2016			Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Cash equivalents	$	91,372		$	91,372	$	—	$	—

Derivative liabilities	$	(694	)	$	—	$	—	$	(694	)


($ in thousands)			Fair Value Measurements at Reporting Date Using
Description	Balance as of December 31, 2015		Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Cash equivalents	$	137,405	$	137,405	$	—	$	—

The cash equivalents represent deposits in a short term United States treasury money market mutual fund quoted in an active market and classified as a Level 1 asset.

As discussed further in Notes 5 and 8, the Company issued Intrexon Corporation, or Intrexon, 100,000 shares of the Company’s Series 1 preferred stock, a new class of preferred stock authorized by the Company’s board of directors, in consideration of the parties entering into a Third Amendment to Exclusive Channel Partner Agreement, or the 2016 ECP Amendment, amending their existing Exclusive Channel Partner Agreement, effective January 6, 2011 and as amended to date, which the Company refers to as the Channel Agreement, and an Amendment to Exclusive Channel Collaboration Agreement, or the 2016 GvHD Amendment, amending their existing Exclusive Channel Collaboration Agreement, effective September 28, 2015, which the Company refers to as the GvHD Agreement.

At June 30, 2016, the Company’s Series 1 preferred stock was valued using a probability-weighted approach and a Monte Carlo simulation model. Additionally, the monthly dividends issued on the outstanding Series 1 preferred stock are valued using a similar probability-weighted approach and a Monte Carlo simulation model. However, there is no adjustment or further revaluation after the initial valuation.

The Company’s Level 3 financial liabilities consist of a conversion option and a redemption feature associated with the Company’s Series 1 preferred stock issued in connection with the 2016 ECP Amendment and 2016 GvHD Amendment with Intrexon amending the Channel Agreement entered into on June 29, 2016 that have been bifurcated from the Series 1 preferred stock and are accounted for as derivative liabilities at fair value. The preferred stock derivative liabilities were valued using a probability-weighted approach and a Monte Carlo simulation model. The fair value of the embedded derivatives was estimated using the “with” and “without” method where the preferred stock was first valued with all of its features (“with” scenario) and then without derivatives subject to the valuation analysis (“without” scenario). The fair value of the derivatives was then estimated as the difference between the fair value of the preferred stock in the “with” scenario and the preferred stock in the “without” scenario. See Note 5 for additional disclosures on the 2016 ECP and 2016 GvHD Amendments and Note 8 for additional disclosure on the rights and preferences of the Series 1 preferred stock and valuation methodology.

Net Loss per Share

9 Months Ended

Sep. 30, 2016

Net Loss per Share

4. Net Loss per Share

Basic net loss per share is computed by dividing net loss by the weighted average number of shares of common stock outstanding for the period. The Company’s potential dilutive shares, which include outstanding common stock options, unvested restricted stock and preferred stock, have not been included in the computation of diluted net loss per share for any of the periods presented as the result would be anti-dilutive. Such potential shares of common stock at September 30, 2016 and 2015 consisted of the following:


	September 30,
	2016		2015
Stock options		3,448,070		3,655,135
Unvested restricted common stock		1,236,388		1,127,703
Series 1 preferred stock		22,564,685		—

		27,249,143		4,782,838

The Series 1 preferred stock automatically converts into shares of common stock upon the date the first approval in the United States of (i) a ZIOPHARM Product, as defined in and developed under the Exclusive Channel Partner Agreement dated as of January 6, 2011 and as amended from time to time, by and between the Company and Intrexon, or (ii) a Product, as defined in and developed under the Exclusive Channel Collaboration Agreement dated September 28, 2015 and as amended from time to time, by and between the Company and Intrexon, or (iii) a Product as defined in and developed under the License and Collaboration Agreement dated March 27, 2015 and as amended from time to time, by and among Intrexon, ARES TRADING, S.A. and the Company, is publicly announced. Assuming a conversion event date of September 30, 2016, the Series 1 preferred stock would convert into 22,564,685 shares of common stock using the greater of (i) the volume weighted average closing price of the Company’s Common Stock as reported by the Nasdaq Stock Market, LLC over previous the 20 trading days ending on the conversion event date or (ii) $1.00 per share. See Note 5 and Note 8 for additional disclosure regarding the 2016 ECP and 2016 GvHD Amendments, valuation methodology and significant assumptions.

Commitments and Contingencies

9 Months Ended

Sep. 30, 2016

Commitments and Contingencies

5. Commitments and Contingencies

Operating Leases

Prior to December 31, 2012, the Company entered into an operating lease in New York, NY for office space. In accordance with this agreement, the Company entered into a letter of credit in the amount of $388 thousand, naming the Company’s landlord as beneficiary. In January 2012, the Company amended the lease agreement, adding additional office space. The collateral for the letter of credit is restricted cash and recorded in other non-current assets on the balance sheet as of September 30, 2016 and December 31, 2015. The lease for office space in New York, NY expires in October 2018.

On October 17, 2013, the Company entered into a sublease agreement to lease all of its New York office space to a subtenant. The Company remains primarily liable to pay rent on the original lease. The Company recorded a loss on the sublease in the amount of $729 thousand for the year ended December 31, 2013, representing the remaining contractual obligation of $2.3 million, less $1.6 million in payments from its subtenant. The Company retired assets as a result of this sublease with a net book value of $392 thousand, and recorded a loss on disposal of fixed assets for the same amount for the year ended December 31, 2013. The Company continues to maintain the $388 thousand letter of credit in respect of the New York office space and recorded in other non-current assets on the balance sheets.

Prior to December 31, 2012, the Company entered into separate operating lease agreements for various spaces in a building in Boston, MA. In June 2012, the Company re-negotiated a master lease for the entire Boston office space that incorporated all three lease agreements under the same master agreement which originally expired in August 2016. On December 21, 2015 and April 15, 2016, the Company renewed the sublease for the Company’s corporate headquarters in Boston, MA through August 31, 2021. As of September 30, 2016 and December 31, 2015, a total security deposit of $128 thousand is included in deposits on the balance sheet.

Total rent expense was approximately $109 thousand and $231 thousand for the three and nine months ended September 30, 2016, respectively and $104 thousand and $581 thousand for the three and nine months ended September 30, 2015, respectively.

The Company records rent expense on a straight-line basis over the term of the lease. Accordingly, the Company has recorded a liability for deferred rent at September 30, 2016 and December 31, 2015 of $340 thousand ($177 thousand current and $163 thousand long-term) and $661 thousand ($348 thousand current and $313 thousand long-term), respectively, which is recorded in deferred rent on the balance sheets.

License Agreements

Exclusive Channel Partner Agreement with Intrexon Corporation for the Cancer Programs

On January 6, 2011, the Company entered into the Channel Agreement with Intrexon that governs a “channel partnering” arrangement in which the Company uses Intrexon’s technology to research, develop and commercialize products in which DNA is administered to humans for expression of anti-cancer effectors for the purpose of treatment or prophylaxis of cancer, which the Company collectively refers to as the Cancer Program. This Channel Agreement establishes committees comprised of representatives of the Company and Intrexon that govern activities related to the Cancer Program in the areas of project establishment, chemistry, manufacturing and controls, clinical and regulatory matters, commercialization efforts and intellectual property.

The Channel Agreement grants the Company a worldwide license to use patents and other intellectual property of Intrexon in connection with the research, development, use, importing, manufacture, sale, and offer for sale of products involving DNA administered to humans for expression of anti-cancer effectors for the purpose of treatment or prophylaxis of cancer, which is collectively referred to as the ZIOPHARM Products. Such license is exclusive with respect to any clinical development, selling, offering for sale or other commercialization of ZIOPHARM Products, and otherwise is non-exclusive. Subject to limited exceptions, the Company may not sublicense these rights without Intrexon’s written consent.

Under the Channel Agreement, and subject to certain exceptions, the Company is responsible for, among other things, the performance of the Cancer Program, including the development, commercialization and certain aspects of manufacturing of ZIOPHARM Products. Intrexon is responsible for establishing manufacturing capabilities and facilities for the bulk manufacture of products developed under the Cancer Program, certain other aspects of manufacturing and costs of discovery-stage research with respect to platform improvements and costs of filing, prosecution and maintenance of Intrexon’s patents.

Subsequent to the Third Amendment to the Exclusive Channel Partner Agreement, or the 2016 ECP Amendment, discussed below, and subject to certain expense allocations and other offsets provided in the Channel Agreement, the Company is obligated to pay Intrexon on a quarterly basis 20% of net profits derived in that quarter from the sale of ZIOPHARM Products, calculated on a ZIOPHARM Product-by- ZIOPHARM Product basis. The Company likewise agreed to pay Intrexon on a quarterly basis 50% of revenue obtained in that quarter from a sublicensor in the event of a sublicensing arrangement. In addition, in partial consideration for each party’s execution and delivery of the Channel Agreement, the Company entered into a stock purchase agreement with Intrexon.

Upon termination of the Channel Agreement, the Company may continue to develop and commercialize any ZIOPHARM Product that, at the time of termination:

•

Is being commercialized by the Company;

•

Has received regulatory approval;

•

Is a subject of an application for regulatory approval that is pending before the applicable regulatory authority; or

•

Is the subject of at least an ongoing Phase 2 clinical trial (in the case of a termination by Intrexon due to an uncured breach or a voluntary termination by the Company), or an ongoing Phase 1 clinical trial in the field (in the case of a termination by the Company due to an uncured breach or a termination by Intrexon following an unconsented assignment by the Company or its election not to pursue development of a Superior Therapy (as defined in the Channel Agreement)).

The Company’s obligation to pay 20% of net profits or revenue described above with respect to these “retained” products will survive termination of the Channel Agreement.

Exclusive Channel Collaboration Agreement with Intrexon Corporation for Graft-Versus-Host Disease (GvHD)

On September 28, 2015, the Company entered into the GvHD Agreement with Intrexon, whereby the Company will use Intrexon’s technology directed towards in vivo expression of effectors to research, develop and commercialize products for use in the treatment or prevention of graft-versus-host disease, or GvHD. GVHD may occur after a bone marrow or stem cell transplant in which someone receives bone marrow tissue or cells from a donor. The new, transplanted cells regard the recipient’s body as foreign. When this happens, the newly transplanted cells attack the recipient’s body.

The exclusive collaboration, or the GvHD Program, will focus on the pursuit of the following engineered cell therapy strategies, used either separately or in combination, for the targeted treatment of GvHD: (i) the infusion of regulatory T cells expressing membrane-bound and/or soluble interleukin-2 and (ii) the deployment of orally delivered, genetically modified L. lactis that express interleukin-2 to modulate immune function. The GvHD Agreement establishes committees comprised of Company and Intrexon representatives that will govern activities related to the GvHD Program in the areas of project establishment, chemistry, manufacturing and controls, clinical and regulatory matters, commercialization activities and intellectual property.

The GvHD Agreement grants the Company a worldwide license to use specified patents and other intellectual property of Intrexon in connection with the research, development, use, importing, manufacture, sale, and offer for sale of products developed under the GvHD Program, or the Products. Such license is exclusive with respect to any clinical development, selling, offering for sale or other commercialization of the Products, and otherwise is non-exclusive. Subject to limited exceptions, the Company may not sublicense the rights described without Intrexon’s written consent.

Under the GvHD Agreement, and subject to certain exceptions, the Company is responsible for, among other things, the performance of the GvHD Program including development, commercialization and certain aspects of manufacturing of the Products. Among other things, Intrexon is responsible for the costs of establishing manufacturing capabilities and facilities for the bulk manufacture of the Products, certain other aspects of manufacturing, costs of discovery-stage research with respect to platform improvements and costs of filing, prosecution and maintenance of Intrexon’s patents.

The Company paid Intrexon a technology access fee of $10.0 million in cash in October 2015 and will reimburse Intrexon for all research and development costs. Subject to certain expense allocations and other offsets provided in the GvHD Agreement, the GvHD Agreement also provides for equal sharing of the profits derived from the sale of the Products.

The Company has determined that the rights acquired in the GvHD Agreement represent in-process research and development with no alternative future use. Accordingly, the Company recorded a charge of $10.0 million to research and development expense in September 2015.

During the first 24 months after September 28, 2015, the GvHD Agreement may be terminated by (i) either party in the event of a material breach by the other, except for the failure of the other party to use diligent efforts or to comply with any diligence obligations set forth in the GvHD Agreement and (ii) Intrexon under certain circumstances if the Company assigns its rights under the GvHD Agreement without Intrexon’s consent. Following such twenty-four-month period, Intrexon may also terminate the GvHD Agreement if the Company elects not to pursue the development of the GvHD Program identified by Intrexon that is a “Superior Therapy,” as such term is defined in the GvHD Agreement. Also following such period, the Company may voluntarily terminate the GvHD Agreement upon 90 days’ written notice to Intrexon.

Upon termination of the GvHD Agreement, the Company may continue to develop and commercialize any Product that, at the time of termination:

•

is being commercialized by the Company,

•

has received regulatory approval,

•

is a subject of an application for regulatory approval that is pending before the applicable regulatory authority, or

•

is the subject of at least an ongoing Phase 2 clinical trial (in the case of a termination by Intrexon due to a Company uncured breach or a voluntary termination by the Company), or an ongoing Phase 1 clinical trial (in the case of a termination by the Company due to an Intrexon uncured breach or a termination by Intrexon following an unconsented assignment by the Company or the Company’s election not to pursue development of a Superior Therapy).

The Company’s obligation to pay 20% of net profits or revenue with respect to these “retained” products will survive termination of the GvHD Agreement.

Amendment of Collaborations with Intrexon

On March 27, 2015, the Company and Intrexon entered into an Exclusive Channel Partner Amendment, or ECP Amendment, amending the Channel Agreement. The ECP Amendment modifies the scope of the parties’ collaboration under the Channel Agreement in connection with the Ares Trading Agreement discussed below. Pursuant to the ECP Amendment, the chimeric antigen receptor T cell products to be developed and commercialized pursuant to the Ares Trading Agreement shall be included within the Intrexon/ZIOPHARM collaboration under the Channel Agreement. The ECP Amendment provides that Intrexon will pay to the Company fifty percent of all payments Intrexon receives for upfronts, milestones and royalties under the Ares Trading Agreement.

On June 29, 2016, the Company entered into (1) the 2016 ECP Amendment with Intrexon amending the Channel Agreement, and (2) the 2016 GvHD Amendment, amending the GvHD Agreement. The 2016 ECP Amendment reduced the royalty percentage that the Company will pay to Intrexon under the Channel Agreement on a quarterly basis from 50% to 20% of net profits derived in that quarter from the sale of ZIOPHARM Products, calculated on a ZIOPHARM Product-by-ZIOPHARM Product basis, subject to certain expense allocations and other offsets provided in the Channel Agreement. The 2016 GvHD Amendment reduced the royalty percentage that the Company will pay to Intrexon under the GvHD Agreement on a quarterly basis from 50% to 20% of net profits derived in that quarter from the sale of Products (as defined in the GvHD Agreement), subject to certain expense allocations and other offsets provided in the GvHD Agreement. The reductions in the royalty percentages provided by the 2016 ECP Amendment and the 2016 GvHD Amendment do not apply to sublicensing revenue or royalties under the Channel Agreement and GvHD Agreement, nor do they apply to any royalties or other payments made with respect to sublicensing revenue from the Company’s existing collaboration Ares Trading S.A., or Ares Trading, a subsidiary of the biopharmaceutical business of Merck KGaA, Darmstadt, Germany.

In consideration for the execution and delivery of the 2016 ECP Amendment and the 2016 GvHD Amendment, the Company agreed to issue to Intrexon 100,000 shares of its Series 1 preferred stock. Each share of the Company’s Series 1 preferred stock has a stated value of $1,200, subject to appropriate adjustment in the event of any stock dividend, stock split, combination or other recapitalization, and certain other rights, preferences, privileges and obligations (Note 8).

License Agreement—The University of Texas MD Anderson Cancer Center

On January 13, 2015, the Company, together with Intrexon, entered into a License Agreement, or the MD Anderson License, with The University of Texas MD Anderson Cancer Center, or MD Anderson. Pursuant to the MD Anderson License, the Company and Intrexon hold an exclusive, worldwide license to certain technologies owned and licensed by MD Anderson including technologies relating to novel chimeric antigen receptor (CAR) T cell therapies, non-viral gene transfer systems, genetic modification and/or propagation of immune cells and other cellular therapy approaches, Natural Killer, or NK Cells and T-cell receptors, or TCR’s arising from the laboratory of Laurence Cooper, M.D., Ph.D., who became the Chief Executive Officer of the Company on May 7, 2015 and was formerly a tenured professor of pediatrics at MD Anderson and now currently a visiting scientist under that institution’s policies, as well as either co-exclusive or non-exclusive licenses under certain related technologies.

Pursuant to the terms of the MD Anderson License, MD Anderson received consideration consisting of $50.0 million in shares of the Company’s common stock (or 10,124,561 shares), and $50.0 million in shares of Intrexon’s common stock, in each case based on a trailing 20 day volume weighted average of the closing price of the Company’s and Intrexon’s common stock ending on the date prior to the announcement of the entry into the MD Anderson License, collectively referred to as the License Shares, pursuant to the terms of the License Shares Securities Issuance Agreement described below. The License Shares were issued to MD Anderson on March 11, 2015 pursuant to the terms of the MD Anderson License.

On January 9, 2015, in order to induce MD Anderson to enter into the MD Anderson License on an accelerated schedule, the Company and Intrexon entered into a letter agreement, or the Letter Agreement, pursuant to which MD Anderson received consideration of $7.5 million in shares of the Company’s common stock (or 1,597,602 shares), and $7.5 million in shares of Intrexon’s common stock, in each case based on a trailing 20 day volume weighted average of the closing price of the Company’s and Intrexon’s common stock ending on the date prior to the execution of the Letter Agreement, collectively referred to as the Incentive Shares, in the event that the MD Anderson License was entered into on or prior to 8:00 am Pacific Time on January 14, 2015. The Incentive Shares were issued to MD Anderson on March 11, 2015 pursuant to the terms of the Incentive Shares Securities Issuance Agreement described below.

On August 17, 2015, the Company, Intrexon and MD Anderson entered into a research and development agreement, or the Research and Development Agreement, to formalize the scope and process for the transfer by MD Anderson, pursuant to the terms of the MD Anderson License, of certain existing research programs and related technology rights, as well as the terms and conditions for future collaborative research and development of new and ongoing research programs.

Pursuant to the Research and Development Agreement, the Company, Intrexon and MD Anderson have agreed to form a joint steering committee that will oversee and manage the new and ongoing research programs. As provided under the MD Anderson License, the Company will provide funding for research and development activities in support of the research programs under the Research and Development Agreement for a period of three years and in an amount of no less than $15.0 million and no greater than $20.0 million per year. During the quarter ended September 30, 2016, the Company made one quarterly payment of $3.8 million and has paid an aggregate of $22.5 million under this arrangement. As of September 30, 2016, MD Anderson has used $2.7 million to offset costs incurred pursuant to the MD Anderson License and the Research and Development Agreement. The net balance of $19.8 million is included in other current assets at September 30, 2016.

The term of the MD Anderson License expires on the last to occur of (a) the expiration of all patents licensed thereunder, or (b) the twentieth anniversary of the date of the License; provided, however, that following the expiration of the term of the MD Anderson License, the Company and Intrexon shall then have a fully-paid up, royalty free, perpetual, irrevocable and sublicensable license to use the licensed intellectual property thereunder. After ten years from the date of the MD Anderson License and subject to a 90-day cure period, MD Anderson will have the right to convert the MD Anderson License into a non-exclusive license if the Company and Intrexon are not using commercially reasonable efforts to commercialize the licensed intellectual property on a case-by-case basis. After five years from the date of the MD Anderson License and subject to a 180-day cure period, MD Anderson will have the right to terminate the MD Anderson License with respect to specific technology(ies) funded by the government or subject to a third party contract if the Company and Intrexon are not meeting the diligence requirements in such funding agreement or contract, as applicable. MD Anderson may also terminate the agreement with written notice upon material breach by the Company and Intrexon, if such breach has not been cured within 60 days of receiving such notice. In addition, the MD Anderson License will terminate upon the occurrence of certain insolvency events for both the Company and Intrexon and may be terminated by the mutual written agreement of the Company, Intrexon and MD Anderson.

In connection with the License and the issuance of the License Shares and the Incentive Shares, on January 13, 2015, the Company and MD Anderson entered into a Registration Rights Agreement, or the Registration Rights Agreement, pursuant to which the Company agreed to file a “resale” registration statement, or the Registration Statement, registering the resale of the License Shares, the Incentive Shares and any other shares of the Company’s common stock held by MD Anderson on the date that the Registration Statement is filed Under the Registration Rights Agreement, the Company is obligated to maintain the effectiveness of the Registration Statement until all securities therein are sold or are otherwise can be sold pursuant to Rule 144, without any restrictions. A prospectus supplement under the Company’s already effective registration statement on Form S-3 (File No. 333-201826) was filed on April 1, 2015 in satisfaction of the Company’s obligations under the Registration Rights Agreement.

The Company has determined that the rights acquired in the MD Anderson License represent in process research and development with no alternative future use. Accordingly, the Company recorded a charge of $67.3 million to research and development expense in 2015, representing the fair value of the 11,722,163 shares of its common stock on the date the MD Anderson License was executed.

Ares Trading License and Collaboration Agreement

On March 27, 2015, the Company and Intrexon signed a worldwide License and Collaboration Agreement, or the Ares Trading Agreement, with Ares Trading S.A., or Ares Trading, a subsidiary of the biopharmaceutical business of Merck KGaA, Darmstadt, Germany, through which the parties established a collaboration for the research and development and commercialization of certain products for the prophylactic, therapeutic, palliative or diagnostic use for cancer in humans.

Under the collaboration, Ares Trading has elected two CAR⁺ T targets for which the Company will perform certain research activities that will, in part, be funded by Ares Trading. Once these candidates reach investigational new drug (IND) stage, the programs will be transferred to Ares Trading for clinical development and commercialization. The Company expects to perform multiple preclinical development programs, each consisting of the development of one product candidate, pursuant to the agreement. The Company and Intrexon will also independently conduct research and development on other CAR⁺ T candidates, with Ares Trading having the opportunity during clinical development to opt-in to these candidates for additional payments to the Company and Intrexon.

Intrexon is entitled to receive $5.0 million payable in equal quarterly installments over two years for each identified product candidate, which will be used to fund discovery work. The Company will be responsible for costs exceeding the quarterly installments and all other costs of the preclinical research and development.

Ares Trading paid a non-refundable upfront fee of $115.0 million to Intrexon as consideration for entry into the Ares Trading Agreement. Pursuant to the ECP Amendment, the Company was entitled to receive 50% of the upfront fee, or $57.5 million, which the Company received from Intrexon in July 2015.

The Ares Trading Agreement provides for up to $413.0 million of potential payments for certain development and commercial milestones for each product candidate, and royalties ranging from the lower-single digits to the low-teens of net sales derived from the sale of products developed under agreement. The Ares Trading Agreement also provides for up to $50.0 million of payments upon the achievement of certain technical milestones. Intrexon will pay 50% of all milestone and royalty payments that it receives under the Ares Trading Agreement to the Company pursuant to the ECP Amendment.

The term of the Ares Trading Agreement commenced in May 2015 and may be terminated by either party in the event of a material breach as defined in the agreement and may be terminated voluntarily by Ares Trading upon 90 days written notice to the Company.

The Company considered FASB Accounting Standards Codification 605-25, Multiple-Element Arrangements, in evaluating the appropriate accounting for the Ares Trading Agreement. In accordance with this guidance, the Company identified the license and research and development services as the Company’s deliverables in the arrangement. The Company concluded that the license does not have standalone value independent from the research and development services. Accordingly, the Ares Trading Agreement is accounted for by the Company as a single unit of accounting. The $57.5 million upfront payment received by the Company was recorded as deferred revenue and is being recognized over the estimated period of performance of the research and development services which are currently estimated to be 9 years, beginning with the commencement of the research and development services. During the three and nine months ended September 30, 2016, the Company recognized $1.6 million and $4.8 million, respectively, of revenue related to the Ares Trading Agreement. The remaining balance of deferred revenue associated with the upfront payment was $49.5 million, of which $6.4 million is current and $43.1 million is classified as long term at September 30, 2016.

Patent and Technology License Agreement—The University of Texas MD Anderson Cancer Center and the Texas A&M University System.

On August 24, 2004, the Company entered into a patent and technology license agreement with The University of Texas MD Anderson Cancer Center and the Texas A&M University System, which the Company refers to, collectively, as the Licensors. Under this agreement, the Company was granted an exclusive, worldwide license to rights (including rights to U.S. and foreign patent and patent applications and related improvements and know-how) for the manufacture and commercialization of two classes of organic arsenicals (water- and lipid-based) for human and animal use. The class of water-based organic arsenicals includes darinaparsin.

The Company issued options to purchase 50,222 shares outside of the Company’s stock option plans following the successful completion of certain clinical milestones, of which 37,666 have vested. The remaining 12,556 shares vested upon enrollment of the first patient in a multi-center pivotal clinical trial i.e. a human clinical trial intended to provide the substantial evidence of efficacy necessary to support the filing of an approvable New Drug Application, or NDA. An expense of $87 thousand was charged to research and development expense for the vesting event which occurred in March 2016. This trial was initiated by Solasia Pharma K.K., or Solasia, on March 28, 2016 and triggered a $1.0 million milestone payment to the Company from Solasia which was received in May 2016. An equivalent milestone payment of $1.0 million was made to MD Anderson. In addition, the Licensors are entitled to receive certain milestone payments. The Company may be required to make additional payments upon achievement of certain other milestones in varying amounts which on a cumulative basis could total up to an additional $4.5 million. In addition, the Licensors are entitled to receive single digit percentage royalty payments on sales from a licensed product and will also be entitled to receive a portion of any fees that the Company may receive from a possible sublicense under certain circumstances.

Collaboration Agreement with Solasia Pharma K.K.

On March 7, 2011, the Company entered into a License and Collaboration Agreement with Solasia. Pursuant to the License and Collaboration Agreement, the Company granted Solasia an exclusive license to develop and commercialize darinaparsin in both IV and oral forms and related organic arsenic molecules, in all indications for human use in a pan-Asian/Pacific territory comprised of Japan, China, Hong Kong, Macau, Republic of Korea, Taiwan, Singapore, Australia, New Zealand, Malaysia, Indonesia, Philippines and Thailand.

As consideration for the license, the Company received an upfront payment of $5.0 million to be used exclusively for further clinical development of darinaparsin outside of the pan-Asian/Pacific territory, and will be entitled to receive additional payments of up to $32.5 million in development-based milestones and up to $53.5 million in sales-based milestones. The Company will also be entitled to receive double digit royalty payments from Solasia based upon net sales of licensed products in the applicable territories, once commercialized, and a percentage of sublicense revenues generated by Solasia. The $5.0 million upfront payment received in March 2011 was amortized over the period of the Company’s research and development effort, which was completed in March 2016.

On July 31, 2014, the Company entered into an amendment and restatement of the License and Collaboration Agreement granting Solasia an exclusive worldwide license to develop and commercialize darinaparsin, and related organoarsenic molecules, in both intravenous and oral forms in all indications for human use. In exchange, the Company will be eligible to receive from Solasia development-and sales-based milestones, a royalty on net sales of darinaparsin, once commercialized, and a percentage of any sublicense revenues generated by Solasia.

Solasia will be responsible for all costs related to the development, manufacturing and commercialization of darinaparsin. The Company’s Licensors, as defined in the agreement, will receive a portion of all milestone and royalty payments made by Solasia to the Company in accordance with the terms of the Company’s license agreement with the Licensors.

On March 28, 2016, Solasia initiated a multi-center pivotal clinical trial intended to provide substantial evidence of efficacy necessary to support the filing of an application for an NDA for darinaparsin in certain of the territories assigned to Solasia. The initiation of the trial on March 28, 2016 triggered a $1.0 million milestone payment from Solasia to the Company which was received in May 2016. The Company subsequently made an equivalent payment to MD Anderson as the ultimate licensor of darinaparsin.

License Agreement with Baxter Healthcare S.A.

On November 3, 2006, the Company entered into a definitive Asset Purchase Agreement for indibulin and a License Agreement to proprietary nanosuspension technology with affiliates of Baxter Healthcare S.A. The purchase included the entire indibulin intellectual property portfolio as well as existing drug substance and capsule inventories. Additional payments of $250 thousand each are due in November 2016 and 2017. The terms of the Asset Purchase Agreement included an upfront cash payment and an additional payment for existing inventory. No payments were made during the nine months ended September 30, 2016 and 2015. The Company is not actively pursuing the development of indibulin.

Related Party Transactions

9 Months Ended

Sep. 30, 2016

Related Party Transactions

6. Related Party Transactions

Collaborations with Intrexon

On January 6, 2011, the Company entered into the Channel Agreement with Intrexon (see Note 5). A director of the Company, Randal J. Kirk, is the CEO, a director, and the largest stockholder of Intrexon.

On February 3, 2015, Intrexon purchased 1,440,000 shares of common stock in the Company’s public offering upon the same terms as others that participated in the offering.

On March 27, 2015, the Company and Intrexon entered into a Second Amendment to Exclusive Channel Partner Agreement amending the Channel Agreement, which is referred to as the ECP Amendment. The ECP Amendment modified the scope of the parties’ collaboration under the Channel Agreement in connection with the worldwide License and Collaboration Agreement, or the Ares Trading Agreement, which the Company and Intrexon entered into with Ares Trading S.A., or Ares Trading, on March 27, 2015. The ECP Amendment provided that Intrexon will pay to the Company fifty percent of all payments that Intrexon receives for upfronts, milestones and royalties under the Ares Trading Agreement (see Note 5). The Amendment also reduces Intrexon’s aggregate commitment under a Stock Purchase Agreement that the parties executed in connection with the initial Channel Agreement to purchase the Company’s common stock from $50.0 million to $43.5 million, which has been satisfied.

On June 29, 2015, the Company re-purchased 3,711 shares of common stock from Intrexon, at a discount of 5% to the closing price of the Company’s common stock on the date of purchase, which represented fractional shares that resulted from Intrexon’s special stock dividend of the Company’s shares to Intrexon’s shareholders, for $34 thousand. On January 8, 2016, the Company re-purchased an additional 168 shares of common stock from Intrexon for $2 thousand at the same terms as the previous share purchase.

On September 28, 2015, the Company entered into the GvHD Agreement with Intrexon, whereby the Company will use Intrexon’s technology directed towards in vivo expression of biologics to research, develop and commercialize products for use in the treatment or prevention of graft-versus-host disease, or GvHD (see Note 5). The Company paid Intrexon a technology access fee of $10.0 million in cash in October 2015 and will reimburse Intrexon for all research and development costs. Subject to certain expense allocations and other offsets provided in the ECC Agreement, the ECC Agreement also provides for equal sharing of the profits derived from the sale of the Products.

On June 29, 2016, the Company entered into a Third Amendment to Exclusive Channel Partner Agreement, or the 2016 ECP Amendment, with Intrexon, amending the Channel Agreement, and an Amendment to Exclusive Channel Collaboration Agreement, or the 2016 GvHD Amendment, amending their existing Exclusive Channel Collaboration Agreement, effective September 28, 2015, which the Company refers to as the GvHD Agreement. The 2016 ECP Amendment reduced the royalty percentage that the Company will pay to Intrexon under the Channel Agreement on a quarterly basis from 50% to 20% of net profits derived in that quarter from the sale of ZIOPHARM Products (as defined in the Channel Agreement), calculated on a ZIOPHARM Product-by-ZIOPHARM Product basis, subject to certain expense allocations and other offsets provided in the Channel Agreement. The 2016 GvHD Amendment reduced the royalty percentage that the Company will pay to Intrexon under the GvHD Agreement on a quarterly basis from 50% to 20% of net profits derived in that quarter from the sale of Products (as defined in the GvHD Agreement), subject to certain expense allocations and other offsets provided in the GvHD Agreement. The reductions in the royalty percentages provided by the 2016 ECP Amendment and the 2016 GvHD Amendment do not apply to sublicensing revenue or royalties under the Channel Agreement and GvHD Agreement, nor do they apply to any royalties or other payments made with respect to sublicensing revenue from the Company’s existing collaboration with Merck Serono, the biopharmaceutical business of Merck KGaA.

In consideration for the execution and delivery of the 2016 ECP Amendment and the 2016 GvHD Amendment, the Company issued Intrexon 100,000 shares of its Series 1 preferred stock. Each share of the Company’s Series 1 preferred stock has a stated value of $1,200, subject to appropriate adjustment in the event of any stock dividend, stock split, combination or other recapitalization, and certain other rights, preferences, privileges and obligations (Note 8). The holders of the shares of Series 1 preferred stock are entitled to receive a monthly dividend, payable in additional shares of Series 1 preferred stock, equal to $12.00 per preferred share held by such holder per month divided by the stated value of the preferred shares, rounded down to the nearest whole share.

During the three months ended September 30, 2016, the Company issued an aggregate of 3,063 shares of Series 1 preferred stock to Intrexon, the holder of all of the outstanding shares of the Company’s Series 1 preferred stock, as monthly dividend payments. The Company recorded $21 thousand for the fair value of the derivatives as a liability and $3.6 million for the fair value of the Series 1 preferred stock as a component of temporary equity. See Notes 3, 8 and 9 for additional discussion regarding the accounting for and valuation of these derivative financial instruments.

During the nine months ended September 30, 2016, the Company expensed $17.0 million for services performed by Intrexon, of which $3.4 million is included within current liabilities on the balance sheet. During the nine months ended September 30, 2015 the Company expensed $11.7 million for services performed by Intrexon, of which $5.7 million is included within current liabilities on the balance sheet.

Collaboration with Intrexon and MD Anderson

On January 13, 2015, the Company, together with Intrexon, entered into a license agreement with MD Anderson, which is referred to as the MD Anderson License. Pursuant to the MD Anderson License, the Company and Intrexon hold an exclusive, worldwide license to certain technologies owned and licensed by MD Anderson including technologies relating to novel CAR⁺ T cell therapies arising from the laboratory of Laurence Cooper, M.D., Ph.D., who is now the Company’s Chief Executive Officer and was formerly a professor of pediatrics at MD Anderson and now currently a visiting scientist under that institution’s policies, as well as either co-exclusive or non-exclusive licenses under certain related technologies. In partial consideration for entering into the MD Anderson License, the Company issued MD Anderson an aggregate of 11,722,163 shares of common stock for which the Company incurred a $67.3 million charge. The Company has determined that the rights acquired in the MD Anderson License represent in-process research and development with no alternative future use. During the nine months ending September 30, 2016, the Company made three quarterly payments of $3.8 million bringing the total aggregate payments to $22.5 million under this arrangement.

Stock-Based Compensation

9 Months Ended

Sep. 30, 2016

Stock-Based Compensation

7. Stock-Based Compensation

The Company recognized stock-based compensation expense on all employee and non-employee awards as follows:


	For the three months				For the nine months
	ended September 30,				ended September 30,
(in thousands)	2016		2015		2016		2015
Research and development	$	505	$	264	$	1,398	$	874
General and administrative		1,514		1,213		4,696		5,180

Stock-based compensation expense	$	2,019	$	1,477	$	6,094	$	6,054

The Company granted an aggregate of 21,300 and 157,300 stock options during the three and nine months ended September 30, 2016 with a weighted-average grant date fair value of $3.71 and $5.36 per share, respectively. The Company granted an aggregate of 203,000 and 254,800 stock options during the three and nine months ended September 30, 2015 with a weighted-average grant date fair value of $8.49 and $8.10 per share, respectively.

For the three months ended September 30, 2016 and 2015, the fair value of stock options was estimated on the date of grant using a Black-Scholes option valuation model with the following assumptions:


	For the nine months ended September 30,
	2016	2015
Risk-free interest rate	1.27 - 1.37%	1.66 - 1.93%
Expected life in years	6	6
Expected volatility	79.26 - 79.34%	80.01 - 81.7%
Expected dividend yield	0	0

Stock option activity under the Company’s stock option plan for the nine months ended September 30, 2016 is as follows:


(in thousands, except share and per share data)	Number of Shares			Weighted- Average Exercise Price		Weighted- Average Contractual Term (Years)		Aggregate Intrinsic Value
Outstanding, December 31, 2015		3,481,469		$	4.96
Granted		157,300			7.76
Exercised		(169,000	)		4.81
Cancelled		(21,699	)		6.18

Outstanding, September 30, 2016		3,448,070		$	5.08		6.52	$	4,319

Vested and unvested expected to vest at September 30, 2016		3,357,976		$	4.25		5.57	$	4,206

Options exercisable, September 30, 2016		2,317,935		$	4.25		5.57	$	3,755

Options exercisable, December 31, 2015		2,120,834		$	4.24		5.84	$	8,622

Options available for future grant		2,632,629

At September 30, 2016, total unrecognized compensation costs related to unvested stock options outstanding amounted to $3.6 million. The cost is expected to be recognized over a weighted-average period of 1.46 years.

A summary of the status of unvested restricted stock for the nine months ended September 30, 2016 is as follows:


	Number of Shares			Weighted-Average Grant Date Fair Value
Non-vested, December 31, 2015		1,586,388		$	9.00
Granted		—			—
Vested		(350,000	)		9.35
Cancelled		—			—

Non-vested, September 30, 2016		1,236,388		$	9.00

At September 30, 2016, total unrecognized compensation costs related to unvested restricted stock outstanding amounted to $8.0 million. The cost is expected to be recognized over a weighted-average period of 1.45 years.

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

+ References + Details

Preferred Stock

9 Months Ended

Sep. 30, 2016

Preferred Stock

8. Preferred Stock

The Company has 30,000,000 shares of preferred stock authorized, of which, 250,000 shares are designated as Series 1 preferred stock.

On June 29, 2016, the Company entered into the 2016 ECP Amendment and 2016 GvHD Amendment with Intrexon (Note 5). In consideration for the execution and delivery of the 2016 ECP Amendment and the 2016 GvHD Amendment, the Company issued to Intrexon 100,000 shares of its newly designated Series 1 preferred stock. Each share of the Company’s Series 1 preferred stock has a stated value of $1,200, subject to appropriate adjustment in the event of any stock dividend, stock split, combination or other recapitalization. The Series 1 preferred stock has the following rights and preferences and certain other rights, preferences, privileges and obligations.

Conversion

All shares of Series 1 preferred stock shall automatically convert into shares of common stock upon the public announcement of the first approval in the United States of (i) a ZIOPHARM Product under the Channel Agreement, (ii) a Product under the GvHD Agreement or (iii) a Product under the Ares Trading Agreement, which the Company refers to as the Conversion Event Date. On the second business day following the Conversion Event Date, each of Series 1 preferred stock shall convert into a number of shares of common stock equal to the stated value of such Series 1 preferred stock, divided by the greater of (i) the volume weighted average closing price of common stock as reported by The Nasdaq Stock Market, LLC over the 20 trading days ending on the Conversion Event Date or (ii) $1.00 per share; however, without shareholder approval in accordance with the NASDAQ Listing Rules, the Company will not affect any conversion of the Series 1 preferred stock into shares of common stock in excess of 19.9% of the lesser of (i) the pre-transaction outstanding shares of common stock or (ii) the outstanding shares of common stock at the time of conversion. In addition, without shareholder approval in accordance with the NASDAQ Listing Rules, the Company will not affect any conversion of the Series 1 preferred stock into common stock to the extent that the number of shares of common stock issued in such conversion would constitute a change of control under the NASDAQ Listing Rules.

Dividends

A monthly dividend, payable in additional shares of Series 1 preferred stock, equal to $12.00 per share, per month divided by the stated value per share, or the PIK Dividend; provided, that if any shares of Series 1 preferred stock are not converted on the Conversion Event Date (discussed below), then the rate of the PIK Dividend on all remaining unconverted shares of Series 1 preferred stock shall automatically increase from $12.00 to $24.00 per share, per month.

Liquidation Preference

In the event of any voluntary or involuntary liquidation, dissolution or winding up of the Company or a change of control or sale, lease transfer or exclusive license of all or substantially all of the Company’s assets prior to the conversion of the Series 1 preferred stock into shares of common stock, then the Series 1 preferred stock will participate in the proceeds of the transaction on a pro rata basis along with common stock, treating the Series 1 preferred stock as if it had been converted into a number of shares of common stock equal to the aggregate stated value of the Series 1 preferred stock, divided by the volume weighted average closing price of common stock over the 20 trading days ending on the public announcement of such voluntary or involuntary liquidation, dissolution or winding up of the Company or change of control or sale, lease transfer or exclusive license of all or substantially all of the Company’s assets. Alternatively, the Company may redeem the Series 1 preferred stock at a redemption price equal to the pro rata amount that the Series 1 preferred stock would have received if it had been converted using the same formula.

Voting Rights

The Series 1 preferred stock does not have any voting rights except that the Company may not, without the consent of the holders of a majority of the outstanding shares of the Series 1 preferred stock, voting as a separate class, (i) amend, alter or repeal any provision of its Certificate of Incorporation in a manner that adversely affects the powers, preferences or rights of the Series 1 preferred stock in a manner that is more adverse than the effect on any other class or series of the Company’s capital stock; (ii) (A) create, or authorize the creation of, or issue or obligate itself to issue shares of, any additional class or series of the Company’s capital stock unless the same ranks junior or pari passu to the Series 1 preferred stock with respect to the distribution of assets on the liquidation, dissolution or winding up of the Company, the payment of dividends and rights of redemption, or (B) reclassify, alter or amend any existing security that is junior or pari passu to the Series 1 preferred stock with respect to the distribution of assets on the liquidation, dissolution or winding up of the Company, the payment of dividends or rights of redemption, if such reclassification, alteration or amendment would render such other security senior to the Series 1 preferred in respect of any such right, preference or privilege; or (iii) enter into any transaction (or series of related transactions) the effect of which would adversely affect the holders of the Series 1 preferred stock in a manner that is more adverse than the effect on any other class or series of capital stock.

Analysis

The Company analyzed the features of the Series 1 preferred stock and determined that the conversion option and the Company’s right to redeem the shares at liquidation are embedded derivatives that required bifurcation from the Series 1 preferred stock in accordance with FASB ASC 815, Derivatives and Hedging. The embedded derivatives were valued as described below at $0.7 million. Upon issuance of the shares on July 1, 2016 the Company recorded the fair value of the derivatives as a liability and the fair value of the Series 1 preferred stock of $118.4 million as a component of temporary equity. Furthermore, because of the temporary equity classification, the carrying value of the Series 1 preferred stock will not be accreted to redemption value unless or until its redemption becomes probable.

During the three months ended September 30, 2016, the Company issued an aggregate of 3,063 shares of Series 1 preferred stock to Intrexon, the holder of all of the outstanding shares of its Series 1 preferred stock, as monthly dividend payments. The Company recorded Series 1 preferred stock at a fair value of $3.6 million, which is a component of temporary equity and recorded a gain on the change of the derivative liabilities in the amount of $21 thousand (Note 9).

The fair value of the Series 1 preferred stock was estimated using a probability-weighted approach and a Monte Carlo simulation model. The fair value of the embedded derivatives was estimated using the “with” and “without” method where the preferred stock was first valued with all of its features (“with” scenario) and then without derivatives subject to the valuation analysis (“without” scenario). The fair value of the derivatives was then estimated as the difference between the fair value of the preferred stock in the “with” scenario and the preferred stock in the “without” scenario. The model also takes into account, management estimates of clinical success/failure based upon market studies and probability of potential conversion and liquidation events. If these estimates were different, the valuations would change and that change could be material. Inputs to the models included the following:


Risk-free interest rate		1.04	%
Expected dividend rate		0
Expected volatility		70.50	%
Preferred stock conversion limit - percentage of outstanding common stock		19.90	%
Preferred conversion floor price	$	1.00

Derivative Financial Instruments

9 Months Ended

Sep. 30, 2016

Derivative Financial Instruments

9. Derivative Financial Instruments

The Company determined that certain embedded features related to the Series 1 preferred stock are derivative financial instruments.

Fair values of derivative instruments to be classified as derivative liabilities on the balance sheet consist of the following:


($ in thousands)
Liability derivates:	Balance Sheet Location		Fair Value
September 30, 2016:
Derivative liabilities		Liabilities	$	694

The change in the derivative liability for the three months ended September 30, 2016 consists of the following:


($ in thousands)
	Fair Value
Balance, June 30, 2016	$	694
Dividends		21
Mark-to-market		(21	)

Balance, September 30, 2016	$	694

See Notes 3 and 8 for additional discussion regarding the accounting for and valuation of these derivative financial instruments.

- Definition

The entire disclosure for derivative instruments and hedging activities including, but not limited to, risk management strategies, non-hedging derivative instruments, assets, liabilities, revenue and expenses, and methodologies and assumptions used in determining the amounts.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 30
-Section 45
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6441202&loc=d3e80720-113993

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 815
-SubTopic 10
-Section 50
-Paragraph 4C
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+ Details

Fair Value Measurements (Tables)

9 Months Ended

Sep. 30, 2016

Assets and Liabilities Measured at Fair Value on Recurring Basis

Assets and liabilities measured at fair value on a recurring basis as of September 30, 2016 and December 31, 2015 were as follows:


($ in thousands)				Fair Value Measurements at Reporting Date Using
Description	Balance as of September 30, 2016			Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Cash equivalents	$	91,372		$	91,372	$	—	$	—

Derivative liabilities	$	(694	)	$	—	$	—	$	(694	)


($ in thousands)			Fair Value Measurements at Reporting Date Using
Description	Balance as of December 31, 2015		Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)
Cash equivalents	$	137,405	$	137,405	$	—	$	—

Net Loss per Share (Tables)

9 Months Ended

Sep. 30, 2016

Potential Dilutive Shares Excluded from Computation of Diluted Net Loss Per Share

The Company’s potential dilutive shares, which include outstanding common stock options, unvested restricted stock and preferred stock, have not been included in the computation of diluted net loss per share for any of the periods presented as the result would be anti-dilutive. Such potential shares of common stock at September 30, 2016 and 2015 consisted of the following:


	September 30,
	2016		2015
Stock options		3,448,070		3,655,135
Unvested restricted common stock		1,236,388		1,127,703
Series 1 preferred stock		22,564,685		—

		27,249,143		4,782,838

Stock-Based Compensation (Tables)

9 Months Ended

Sep. 30, 2016

Stock-Based Compensation Expense on All Employee and Non-Employee Awards

The Company recognized stock-based compensation expense on all employee and non-employee awards as follows:


	For the three months				For the nine months
	ended September 30,				ended September 30,
(in thousands)	2016		2015		2016		2015
Research and development	$	505	$	264	$	1,398	$	874
General and administrative		1,514		1,213		4,696		5,180

Stock-based compensation expense	$	2,019	$	1,477	$	6,094	$	6,054

Fair Value of Stock Options Assumptions Using Black-Scholes Option Valuation Model

For the three months ended September 30, 2016 and 2015, the fair value of stock options was estimated on the date of grant using a Black-Scholes option valuation model with the following assumptions:


	For the nine months ended September 30,
	2016	2015
Risk-free interest rate	1.27 - 1.37%	1.66 - 1.93%
Expected life in years	6	6
Expected volatility	79.26 - 79.34%	80.01 - 81.7%
Expected dividend yield	0	0

Stock Option Activity Under Stock Option Plan

Stock option activity under the Company’s stock option plan for the nine months ended September 30, 2016 is as follows:


(in thousands, except share and per share data)	Number of Shares			Weighted- Average Exercise Price		Weighted- Average Contractual Term (Years)		Aggregate Intrinsic Value
Outstanding, December 31, 2015		3,481,469		$	4.96
Granted		157,300			7.76
Exercised		(169,000	)		4.81
Cancelled		(21,699	)		6.18

Outstanding, September 30, 2016		3,448,070		$	5.08		6.52	$	4,319

Vested and unvested expected to vest at September 30, 2016		3,357,976		$	4.25		5.57	$	4,206

Options exercisable, September 30, 2016		2,317,935		$	4.25		5.57	$	3,755

Options exercisable, December 31, 2015		2,120,834		$	4.24		5.84	$	8,622

Options available for future grant		2,632,629

Summary of Unvested Restricted Stock

A summary of the status of unvested restricted stock for the nine months ended September 30, 2016 is as follows:


	Number of Shares			Weighted-Average Grant Date Fair Value
Non-vested, December 31, 2015		1,586,388		$	9.00
Granted		—			—
Vested		(350,000	)		9.35
Cancelled		—			—

Non-vested, September 30, 2016		1,236,388		$	9.00

Preferred Stock (Tables)

9 Months Ended

Sep. 30, 2016

Fair Value Assumptions Used in Probability Weighted Approach and Monte Carlo Simulation Model


Risk-free interest rate		1.04	%
Expected dividend rate		0
Expected volatility		70.50	%
Preferred stock conversion limit - percentage of outstanding common stock		19.90	%
Preferred conversion floor price	$	1.00

Derivative Financial Instruments (Tables)

9 Months Ended

Sep. 30, 2016

Fair Values of Derivative Instruments to be classified as Derivative Liabilities on Balance Sheet

Fair values of derivative instruments to be classified as derivative liabilities on the balance sheet consist of the following:


($ in thousands)
Liability derivates:	Balance Sheet Location		Fair Value
September 30, 2016:
Derivative liabilities		Liabilities	$	694

Change in Derivative Liability

The change in the derivative liability for the three months ended September 30, 2016 consists of the following:


($ in thousands)
	Fair Value
Balance, June 30, 2016	$	694
Dividends		21
Mark-to-market		(21	)

Balance, September 30, 2016	$	694

Business - Additional Information (Detail) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Nature Of Operations [Line Items]
Accumulated deficit	$ 646,773	$ 492,700

Assets and Liabilities Measured at Fair Value on Recurring Basis (Detail) - Fair Value, Measurements, Recurring - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	$ 91,372	$ 137,405
Derivative liabilities	(694)
Quoted Prices in Active Markets for Identical Assets/Liabilities (Level 1)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	91,372	$ 137,405
Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Derivative liabilities	$ (694)

Fair Value Measurements - Additional Information (Detail) - Series 1 Preferred Stock - shares	Sep. 30, 2016	Jun. 29, 2016	Dec. 31, 2015
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Preferred stock, shares issued	103,063		0
Intrexon Corporation
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Preferred stock, shares issued	3,063	100,000

Potential Dilutive Shares Excluded from Computation of Diluted Net Loss Per Share (Detail) - shares	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	27,249,143	4,782,838
Stock Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	3,448,070	3,655,135
Restricted Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	1,236,388	1,127,703
Series 1 Preferred Stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	22,564,685

Net Loss per Share - Additional Information (Detail) - Intrexon Corporation	9 Months Ended
	Sep. 30, 2016 $ / shares shares
Earnings Loss Per Share [Line Items]
Agreement start date	Jan. 06, 2011
Series 1 Preferred Stock
Earnings Loss Per Share [Line Items]
Number of shares converted into common stock \| shares	22,564,685
Preferred stock, conversion rate \| $ / shares	$ 1.00

Commitments and Contingencies - Additional Information (Detail)								1 Months Ended				3 Months Ended		9 Months Ended		12 Months Ended
	Jun. 29, 2016 $ / shares shares	Sep. 28, 2015 USD ($)	Jan. 13, 2015 USD ($) shares	Jan. 09, 2015 USD ($) shares	Mar. 07, 2011 USD ($)	Jan. 06, 2011	Aug. 24, 2004 Patent	Nov. 30, 2017 USD ($)	Nov. 30, 2016 USD ($)	Sep. 30, 2015 USD ($)	Jul. 31, 2015 USD ($)	Sep. 30, 2016 USD ($) $ / shares shares	Sep. 30, 2015 USD ($)	Sep. 30, 2016 USD ($) $ / shares shares	Sep. 30, 2015 USD ($)	Dec. 31, 2015 USD ($) $ / shares shares	Dec. 31, 2013 USD ($)	Dec. 31, 2012	Dec. 31, 2011 USD ($)	Mar. 31, 2016 USD ($)	May 31, 2015 USD ($)	Dec. 31, 2014 USD ($) shares
Commitments and Contingencies Disclosure [Line Items]
Loss on disposal of fixed assets															$ 1,000
Total rent Expense												$ 109,000	$ 104,000	$ 231,000	581,000
Deferred rent - current portion												177,000		177,000		$ 348,000
Deferred rent-non-current portion												163,000		163,000		313,000
Deferred rent liability net												340,000		340,000		661,000
Research and Development Expense												8,975,000	$ 16,970,000	$ 148,402,000	98,643,000
Research and development arrangement Terms														Pursuant to the Research and Development Agreement, the Company, Intrexon and MD Anderson have agreed to form a joint steering committee that will oversee and manage the new and ongoing research programs. As provided under the MD Anderson License, the Company will provide funding for research and development activities in support of the research programs under the Research and Development Agreement for a period of three years and in an amount of no less than $15.0 million and no greater than $20.0 million per year.
Research and Development Service Agreement Aggregate Quarterly Payments														$ 3,800,000
Offset costs in research and development expense														2,700,000
Research and Development Service Agreement Aggregate Payments														22,500,000
Deferred revenue - current portion												6,389,000		6,389,000		6,861,000
Deferred Revenue, long term												43,125,000		$ 43,125,000		47,917,000
Issuance of common stock in a license agreement															67,285,000
The University of Texas MD Anderson Cancer Center and The Texas A & M University System
Commitments and Contingencies Disclosure [Line Items]
Milestone maximum payment																						$ 4,500,000
Number of products \| Patent							2
Options to purchase common stock \| shares														50,222
Shares vested \| shares																						37,666
The University of Texas MD Anderson Cancer Center and The Texas A & M University System \| Research and Development Expense
Commitments and Contingencies Disclosure [Line Items]
Issuance of common stock in a license agreement														$ 87,000
The University of Texas MD Anderson Cancer Center and The Texas A & M University System \| Upon enrollment of the first patient in a multi-center pivotal clinical trial
Commitments and Contingencies Disclosure [Line Items]
Shares vested \| shares																						12,556
Solasia
Commitments and Contingencies Disclosure [Line Items]
Upfront payment received					$ 5,000,000
Milestone payment received																				$ 1,000,000
Milestone Payments Payable																				$ 1,000,000
Solasia \| Development-based milestones
Commitments and Contingencies Disclosure [Line Items]
Expected Additional milestone payments to be received														32,500,000
Solasia \| Sales-based milestones
Commitments and Contingencies Disclosure [Line Items]
Expected Additional milestone payments to be received														53,500,000
Baxter Healthcare Corporation \| Upon the successful U.S. IND application for indibulin
Commitments and Contingencies Disclosure [Line Items]
Installment payments														0	$ 0
Baxter Healthcare Corporation \| Upon the successful U.S. IND application for indibulin \| Scenario, Forecast
Commitments and Contingencies Disclosure [Line Items]
Additional payment payable amount								$ 250,000	$ 250,000
License Agreement
Commitments and Contingencies Disclosure [Line Items]
Research and Development Expense														$ 67,300,000		$ 67,300,000
Issuance of common stock in licensing agreement, shares \| shares														11,722,163		11,722,163
ARES Trading License
Commitments and Contingencies Disclosure [Line Items]
Agreement termination, notice period														90 days
Payments for development and commercial milestones per Product														$ 413,000,000
Milestone payments, percentage														50.00%
Agreement commencement date														2015-05
Deferred revenue, revenue recognized												1,600,000		$ 4,800,000
Deferred revenue, upfront payment												$ 49,500,000		$ 49,500,000							$ 57,500,000
Minimum
Commitments and Contingencies Disclosure [Line Items]
Research and Development Expense			$ 15,000,000
Maximum
Commitments and Contingencies Disclosure [Line Items]
Research and Development Expense			20,000,000
Series 1 Preferred Stock
Commitments and Contingencies Disclosure [Line Items]
Preferred stock, shares issued \| shares												103,063		103,063		0
Preferred stock, stated value \| $ / shares												$ 1,200		$ 1,200		$ 1,200
Issuance of common stock in licensing agreement, shares \| shares														100,000
Prepaid Expenses and Other Current Assets
Commitments and Contingencies Disclosure [Line Items]
Pre paid research and development expenses												$ 19,800,000		$ 19,800,000
Intrexon Corporation
Commitments and Contingencies Disclosure [Line Items]
Contract termination description														The Company's obligation to pay 20% of net profits or revenue described above with respect to these "retained" products will survive termination of the Channel Agreement.
Licensing fee		$ 10,000,000									$ 115,000,000
Milestone payment receivable														$ 5,000,000
Milestone payment receivable period														2 years
Upfront payment received											$ 57,500,000
Percentage of upfront fee Payable											50.00%
Milestone maximum payment												$ 50,000,000		$ 50,000,000
Intrexon Corporation \| 2016 GvHD Amendment
Commitments and Contingencies Disclosure [Line Items]
Royalty percentage of net profit														20.00%
Contract termination description														The Company's obligation to pay 20% of net profits or revenue with respect to these "retained" products will survive termination of the GvHD Agreement.
Licensing fee		$ 10,000,000
Research and Development Expense										$ 10,000,000
Agreement termination period		24 months
Agreement termination, notice period		90 days
Intrexon Corporation \| License Agreement
Commitments and Contingencies Disclosure [Line Items]
Cash consideration for license agreement			$ 50,000,000
Intrexon Corporation \| Letter Agreement
Commitments and Contingencies Disclosure [Line Items]
Cash consideration for license agreement				$ 7,500,000
Intrexon Corporation \| Quarterly Payment
Commitments and Contingencies Disclosure [Line Items]
Royalty percentage of net profit						20.00%
Percentage of revenue agreed to pay which is obtained from sublicensor						50.00%
Intrexon Corporation \| Quarterly Payment \| 2016 GvHD Amendment \| After Amendment
Commitments and Contingencies Disclosure [Line Items]
Royalty percentage of net profit	20.00%
Intrexon Corporation \| Quarterly Payment \| 2016 GvHD Amendment \| Before Amendment
Commitments and Contingencies Disclosure [Line Items]
Royalty percentage of net profit	50.00%
Intrexon Corporation \| Quarterly Payment \| ECP Channel Agreement \| After Amendment
Commitments and Contingencies Disclosure [Line Items]
Royalty percentage of net profit	20.00%
Intrexon Corporation \| Quarterly Payment \| ECP Channel Agreement \| Before Amendment
Commitments and Contingencies Disclosure [Line Items]
Royalty percentage of net profit	50.00%
Intrexon Corporation \| Series 1 Preferred Stock
Commitments and Contingencies Disclosure [Line Items]
Preferred stock, shares issued \| shares	100,000											3,063		3,063
Preferred stock, stated value \| $ / shares	$ 1,200
ZIOPHARM \| License Agreement
Commitments and Contingencies Disclosure [Line Items]
Common stock issued for cash \| shares			10,124,561
Cash consideration for license agreement			$ 50,000,000
ZIOPHARM \| Letter Agreement
Commitments and Contingencies Disclosure [Line Items]
Common stock issued for cash \| shares				1,597,602
Cash consideration for license agreement				$ 7,500,000
New York, NY
Commitments and Contingencies Disclosure [Line Items]
Letter of credit												$ 388,000		$ 388,000					$ 388,000
Operating lease expiration month and year																		2018-10
Loss on sublease																	$ 729,000
Remaining contractual obligation																	2,300,000
Sublease revenue from subtenant																	1,600,000
Loss on disposal of fixed assets																	$ (392,000)
Boston, MA
Commitments and Contingencies Disclosure [Line Items]
Operating lease expiration month and year																			2016-08
Security deposits												$ 128,000		$ 128,000		$ 128,000
Sublease term amendment														Aug. 31, 2021

Related Party Transactions - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Thousands								1 Months Ended		3 Months Ended		9 Months Ended		12 Months Ended
	Jun. 29, 2016	Jan. 08, 2016	Sep. 28, 2015	Jun. 29, 2015	Mar. 27, 2015	Feb. 03, 2015	Jan. 06, 2011	Sep. 30, 2015	Jul. 31, 2015	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015
Related Party Transaction [Line Items]
Commitment to purchase common stock												$ 2	$ 34
Stock buy back												2
Change in fair value of derivative liability										$ 21		21
Research and Development Expense										$ 8,975	$ 16,970	148,402	98,643
Research and Development Service Agreement Aggregate Quarterly Payments												3,800
Research and Development Service Agreement Aggregate Payments												$ 22,500
Series 1 Preferred Stock
Related Party Transaction [Line Items]
Preferred stock, shares issued										103,063		103,063		0
Preferred stock, stated value										$ 1,200		$ 1,200		$ 1,200
Temporary equity, fair value										$ 3,600		$ 3,600
Issuance of common stock in licensing agreement (in shares)												100,000
License Agreement
Related Party Transaction [Line Items]
Research and Development Expense												$ 67,300		$ 67,300
Issuance of common stock in licensing agreement (in shares)												11,722,163		11,722,163
Intrexon Corporation
Related Party Transaction [Line Items]
Stock issued during period						1,440,000
Commitment to purchase common stock					$ 43,500		$ 50,000
Percentage of commitment for payments from receipts of upfronts, milestones and royalties					50.00%
Stock buy back (Shares)				3,711
Stock buy back				$ 34
Share buy back discount on closing price				5.00%
Company re-purchased additional shares		168
Company re-purchased additional shares Value		$ 2
Licensing fee			$ 10,000						$ 115,000
Amounts expensed for services incurred												$ 17,000	11,700
Amount due to related party, current								$ 5,700		$ 3,400	$ 5,700	$ 3,400	$ 5,700
Intrexon Corporation \| Series 1 Preferred Stock
Related Party Transaction [Line Items]
Preferred stock, shares issued	100,000									3,063		3,063
Preferred stock, stated value	$ 1,200
Dividends, preferred stock	$ 12.00
Intrexon Corporation \| 2016 GvHD Amendment
Related Party Transaction [Line Items]
Licensing fee			$ 10,000
Royalty percentage of net profit												20.00%
Research and Development Expense								$ 10,000
Intrexon Corporation \| Quarterly Payment
Related Party Transaction [Line Items]
Royalty percentage of net profit							20.00%
Intrexon Corporation \| Quarterly Payment \| ECP Channel Agreement \| After Amendment
Related Party Transaction [Line Items]
Royalty percentage of net profit	20.00%
Intrexon Corporation \| Quarterly Payment \| ECP Channel Agreement \| Before Amendment
Related Party Transaction [Line Items]
Royalty percentage of net profit	50.00%
Intrexon Corporation \| Quarterly Payment \| 2016 GvHD Amendment \| After Amendment
Related Party Transaction [Line Items]
Royalty percentage of net profit	20.00%
Intrexon Corporation \| Quarterly Payment \| 2016 GvHD Amendment \| Before Amendment
Related Party Transaction [Line Items]
Royalty percentage of net profit	50.00%

Stock-Based Compensation Expense Included in Statement of Operations (Detail) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	$ 2,019	$ 1,477	$ 6,094	$ 6,054
Research and Development Expense
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	505	264	1,398	874
General and Administrative Expense
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	$ 1,514	$ 1,213	$ 4,696	$ 5,180

Stock-Based Compensation - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Millions	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options, granted	21,300	203,000	157,300	254,800
Weighted-average grant date fair value	$ 3.71	$ 8.49	$ 5.36	$ 8.10
Unvested Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized compensation costs related to unvested restricted stock outstanding	$ 3.6		$ 3.6
Expected recognition period			1 year 5 months 16 days
Unvested Restricted Common Stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected recognition period			1 year 5 months 12 days
Unrecognized stock-based compensation expense related to unvested restricted stock	$ 8.0		$ 8.0

Fair Value of Stock Options Assumptions Using Black-Scholes Option Valuation Model (Detail)	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate, Minimum	1.27%	1.66%
Risk-free interest rate, Maximum	1.37%	1.93%
Expected life in years	6 years	6 years
Expected volatility, Minimum	79.26%	80.01%
Expected volatility, Maximum	79.34%	81.70%
Expected dividend yield	0.00%	0.00%

Stock Option Activity Under Stock Option Plan (Detail) - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2016	Dec. 31, 2015
Number of Shares
Beginning Balance	3,481,469
Granted	157,300
Exercised	(169,000)
Cancelled	(21,699)
Ending Balance	3,448,070	3,481,469
Vested and unvested expected to vest at end of period	3,357,976
Options exercisable, at end of period	2,317,935	2,120,834
Options available for future grant	2,632,629
Weighted Average Exercise Price
Beginning Balance	$ 4.96
Granted	7.76
Exercised	4.81
Cancelled	6.18
Ending Balance	5.08	$ 4.96
Vested and unvested expected to vest at end of period	4.25
Options exercisable, at end of period	$ 4.25	$ 4.24
Weighted Average Contractual Term (Years)
Outstanding, at end of period	6 years 6 months 7 days
Vested and unvested expected to vest at end of period	5 years 6 months 26 days
Options exercisable, at end of period	5 years 6 months 26 days	5 years 10 months 2 days
Aggregate Intrinsic Value
Outstanding, at end of period	$ 4,319
Vested and unvested expected to vest at end of period	4,206
Options exercisable, at end of period	$ 3,755	$ 8,622

Summary of Unvested Restricted Stock (Detail) - Unvested Restricted Common Stock	9 Months Ended
	Sep. 30, 2016 $ / shares shares
Number of Shares
Beginning Balance \| shares	1,586,388
Granted \| shares	0
Vested \| shares	(350,000)
Cancelled \| shares	0
Ending Balance \| shares	1,236,388
Weighted Average Grant Date Fair Value
Beginning Balance \| $ / shares	$ 9.00
Granted \| $ / shares	0
Vested \| $ / shares	9.35
Cancelled \| $ / shares	0
Ending Balance \| $ / shares	$ 9.00

Preferred Stock - Additional Information (Detail) - USD ($) $ / shares in Units, $ in Thousands		3 Months Ended	9 Months Ended
	Jun. 29, 2016	Sep. 30, 2016	Sep. 30, 2016	Jul. 01, 2016	Dec. 31, 2015
Preferred Stock [Line Items]
Preferred stock, shares authorized		30,000,000	30,000,000		30,000,000
Change in fair value of derivative liability		$ 21	$ 21
Series 1 Preferred Stock
Preferred Stock [Line Items]
Preferred stock, shares authorized		250,000	250,000		250,000
Preferred stock, shares issued		103,063	103,063		0
Preferred stock, stated value		$ 1,200	$ 1,200		$ 1,200
Maximum percentage of common stock issuable upon conversion of preferred stock			19.90%
Fair value of Series 1 preferred stock as a component of temporary equity		$ 121,812	$ 121,812
Temporary equity, fair value		3,600	3,600
Intrexon Corporation
Preferred Stock [Line Items]
Embedded conversion liability		$ 700	$ 700
Fair value of Series 1 preferred stock as a component of temporary equity				$ 118,400
Intrexon Corporation \| Series 1 Preferred Stock
Preferred Stock [Line Items]
Preferred stock, shares issued	100,000	3,063	3,063
Preferred stock, stated value	$ 1,200
Preferred stock, conversion rate			$ 1.00
Maximum percentage of common stock issuable upon conversion of preferred stock			19.90%
Preferred stock monthly dividend payable (per share)	$ 12.00
Intrexon Corporation \| Series 1 Preferred Stock \| Before Conversion Event Date
Preferred Stock [Line Items]
Preferred stock monthly dividend payable (per share)			$ 12.00
Intrexon Corporation \| Series 1 Preferred Stock \| Remaining Unconverted Shares
Preferred Stock [Line Items]
Preferred stock monthly dividend payable (per share)			$ 24.00

Fair Value Assumptions Used in Probability Weighted Approach and Monte Carlo Simulation Model (Detail) - Series 1 Preferred Stock	9 Months Ended
	Sep. 30, 2016 $ / shares
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Risk-free interest rate	1.04%
Expected dividend rate	0.00%
Expected volatility	70.50%
Preferred stock conversion limit - percentage of outstanding common stock	19.90%
Preferred conversion floor price	$ 1.00

Fair Values of Derivative Instruments to be classified as Derivative Liabilities on Balance Sheet (Detail) - USD ($) $ in Thousands	Sep. 30, 2016	Jul. 01, 2016
Derivatives, Fair Value [Line Items]
Derivative liabilities	$ 694	$ 694
Liabilities
Derivatives, Fair Value [Line Items]
Derivative liabilities	$ 694

Change in Derivative Liability (Detail) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2016
Derivatives, Fair Value [Line Items]
Balance, June 30, 2016	$ 694
Dividends	21
Mark-to-market	(21)	$ (21)
Balance, September 30, 2016	$ 694	$ 694