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Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Sep. 30, 2018	Oct. 31, 2018
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Sep. 30, 2018
Document Fiscal Year Focus	2018
Document Fiscal Period Focus	Q3
Trading Symbol	XON
Entity Registrant Name	INTREXON CORP
Entity Central Index Key	0001356090
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Entity Emerging Growth Company	false
Entity Small Business	false
Entity Common Stock, Shares Outstanding		137,221,526

Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Current assets
Cash and cash equivalents	$ 82,417	$ 68,111
Restricted cash	6,987	6,987
Short-term investments	164,162	6,273
Equity securities	714	5,285
Receivables
Trade, net	18,161	19,775
Related parties, net	8,841	17,913
Other	3,305	2,153
Inventory	18,294	20,493
Prepaid expenses and other	7,589	7,057
Total current assets	310,470	154,047
Equity securities, noncurrent	3,983	9,815
Investments in preferred stock	158,421	161,225
Property, plant and equipment, net	122,707	112,674
Intangible assets, net	213,244	232,877
Goodwill	151,276	153,289
Investments in affiliates	17,944	18,870
Other assets	2,370	4,054
Total assets	980,415	846,851
Current liabilities
Accounts payable	8,522	8,701
Accrued compensation and benefits	23,885	6,474
Other accrued liabilities	20,998	21,080
Deferred revenue, including $16,967 and $29,155 from related parties as of September 30, 2018 and December 31, 2017, respectively	38,036	42,870
Lines of credit	200	233
Current portion of long-term debt	546	502
Related party payables	143	313
Total current liabilities	92,330	80,173
Long-term debt, net of current portion, including $30,060 and $0 to related parties as of September 30, 2018 and December 31, 2017, respectively	183,133	7,535
Deferred revenue, net of current portion, including $115,885 and $157,628 from related parties as of September 30, 2018 and December 31, 2017, respectively	136,942	193,527
Deferred tax liabilities, net	9,363	15,620
Other long-term liabilities	3,204	3,451
Total liabilities	424,972	300,306
Commitments and contingencies (Note 16)
Total equity
Common stock, no par value, 200,000,000 shares authorized as of September 30, 2018 and December 31, 2017; 137,144,902 and 122,087,040 shares issued and outstanding as of September 30, 2018 and December 31, 2017, respectively	0	0
Additional paid-in capital	1,552,379	1,397,005
Accumulated deficit	(990,080)	(847,820)
Accumulated other comprehensive loss	(22,900)	(15,554)
Total Intrexon shareholders' equity	539,399	533,631
Noncontrolling interests	16,044	12,914
Total equity	555,443	546,545
Total liabilities and total equity	$ 980,415	$ 846,851

Consolidated Balance Sheets (Parenthetical) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Related Party Transaction [Line Items]
Current portion of deferred revenue	$ 38,036	$ 42,870
Long-term portion of deferred revenue	136,942	193,527
Long-term debt, net of current portion	$ 183,133	$ 7,535
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	137,144,902	122,087,040
Common stock, shares outstanding	137,144,902	122,087,040
Related Parties, Aggregated
Related Party Transaction [Line Items]
Current portion of deferred revenue	$ 16,967	$ 29,155
Long-term portion of deferred revenue	115,885	157,628
Long-term debt, net of current portion	$ 30,060	$ 0

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Revenues
Revenues	$ 32,448	$ 46,016	$ 117,389	$ 153,953
Operating Expenses
Research and development	44,885	36,472	124,072	104,663
Selling, general and administrative	38,708	39,277	112,872	113,258
Total operating expenses	98,919	90,763	286,117	265,351
Operating loss	(66,471)	(44,747)	(168,728)	(111,398)
Other Income (Expense), Net
Unrealized and realized appreciation (depreciation) in fair value of equity securities and preferred stock, net	(7,287)	2,175	(27,565)	9,240
Interest expense	(3,999)	(138)	(4,240)	(498)
Interest and dividend income	6,107	5,070	17,323	14,437
Other income (expense), net	1,452	(1,021)	571	4,453
Total other income (expense), net	(3,727)	6,086	(13,911)	27,632
Equity in net loss of affiliates	(2,870)	(2,993)	(9,880)	(11,273)
Loss before income taxes	(73,068)	(41,654)	(192,519)	(95,039)
Income tax benefit	14,322	818	19,535	2,164
Net loss	(58,746)	(40,836)	(172,984)	(92,875)
Net loss attributable to the noncontrolling interests	1,422	1,147	4,113	3,123
Net loss attributable to Intrexon	$ (57,324)	$ (39,689)	$ (168,871)	$ (89,752)
Net loss attributable to Intrexon per share, basic and diluted (in usd per share)	$ (0.44)	$ (0.33)	$ (1.31)	$ (0.75)
Weighted average shares outstanding, basic and diluted (in shares)	129,518,989	120,518,885	128,843,991	119,741,291
Collaboration and licensing agreements
Revenues
Revenues	$ 14,324	$ 28,155	$ 51,622	$ 89,384
Products
Revenues
Revenues	6,829	7,670	23,549	25,780
Operating Expenses
Cost of products and services	8,877	8,001	28,046	25,625
Services
Revenues
Revenues	10,414	9,975	40,379	37,890
Operating Expenses
Cost of products and services	6,449	7,013	21,127	21,805
Other
Revenues
Revenues	$ 881	$ 216	$ 1,839	$ 899

Consolidated Statements of Operations (Parenthetical) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Related Party Transaction [Line Items]
Revenues	$ 32,448	$ 46,016	$ 117,389	$ 153,953
Collaboration and licensing agreements
Related Party Transaction [Line Items]
Revenues	14,324	28,155	51,622	89,384
Collaboration and licensing agreements \| Related Parties, Aggregated
Related Party Transaction [Line Items]
Revenues	$ 11,952	$ 24,492	$ 41,740	$ 77,937

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Statement of Comprehensive Income [Abstract]
Net loss	$ (58,746)	$ (40,836)	$ (172,984)	$ (92,875)
Other comprehensive income (loss):
Unrealized gain (loss) on investments	(96)	79	(94)	74
Gain (loss) on foreign currency translation adjustments	(914)	7,410	(7,207)	19,405
Comprehensive loss	(59,756)	(33,347)	(180,285)	(73,396)
Comprehensive loss attributable to the noncontrolling interests	1,380	1,129	4,172	3,096
Comprehensive loss attributable to Intrexon	$ (58,376)	$ (32,218)	$ (176,113)	$ (70,300)

- Definition

The consolidated profit or loss for the period, net of income taxes, including the portion attributable to the noncontrolling interest.

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+ Details

Consolidated Statements of Shareholders' and Total Equity - 9 months ended Sep. 30, 2018 - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Loss	Accumulated Deficit	Total Intrexon Shareholders' Equity	Noncontrolling Interests
Balances (in shares) at Dec. 31, 2017	122,087,040	122,087,040
Balances at Dec. 31, 2017	$ 546,545	$ 0	$ 1,397,005	$ (15,554)	$ (847,820)	$ 533,631	$ 12,914
Increase (Decrease) in Stockholders' Equity
Cumulative effect of adoption of ASC 606	26,507		0	(104)	26,611	26,507	0
Stock-based compensation expense	28,340		28,251			28,251	89
Shares issued upon vesting of restricted stock units and for exercises of stock options and warrants (in shares)		66,314
Shares issued upon vesting of restricted stock units and for exercises of stock options and warrants	1,074		262			262	812
Shares issued as payment for services (in shares)		612,117
Shares issued as payment for services	8,404		8,404			8,404	0
Shares and warrants issued in public offerings, net of issuance costs (in shares)		6,900,000
Shares and warrants issued in public offerings, net of issuance costs	87,990		82,374			82,374	5,616
Equity component of convertible debt, net of issuance costs and deferred taxes	36,868		36,868			36,868	0
Shares issued pursuant to share lending agreement (in shares)		7,479,431
Shares issued pursuant to share lending agreement	0		0			0	0
Adjustments for noncontrolling interests	0		(785)			(785)	785
Net loss	(172,984)				(168,871)	(168,871)	(4,113)
Other comprehensive loss	$ (7,301)			(7,242)		(7,242)	(59)
Balances (in shares) at Sep. 30, 2018	137,144,902	137,144,902
Balances at Sep. 30, 2018	$ 555,443	$ 0	$ 1,552,379	$ (22,900)	$ (990,080)	$ 539,399	$ 16,044

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017
Cash flows from operating activities
Net loss	$ (172,984)	$ (92,875)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	25,184	22,881
Loss on disposal of assets, net	4,110	1,311
Write-off of in-process research and development acquired in asset acquisition	8,721	0
Unrealized and realized (appreciation) depreciation on equity securities and preferred stock, net	27,565	(9,240)
Noncash dividend income	(14,575)	(12,303)
Amortization of premiums (discounts) on investments, net	(275)	411
Equity in net loss of affiliates	9,880	11,273
Stock-based compensation expense	28,340	31,949
Shares issued as payment for services	8,404	8,440
Provision for bad debts	1,597	1,093
Accretion of debt discount and amortization of deferred financing costs	2,116	0
Deferred income taxes	(19,335)	(2,294)
Other noncash items	635	(1,848)
Receivables:
Trade	399	2,491
Related parties	6,085	(1,073)
Other	(909)	537
Inventory	2,577	3,418
Prepaid expenses and other	(511)	(516)
Other assets	584	(617)
Accounts payable	(731)	(3,756)
Accrued compensation and benefits	17,561	3,291
Other accrued liabilities	1,591	1,554
Deferred revenue	(22,993)	(35,281)
Deferred consideration	0	(313)
Related party payables	(167)	356
Other long-term liabilities	253	1,271
Net cash used in operating activities	(86,878)	(69,840)
Cash flows from investing activities
Purchases of investments	(178,681)	0
Maturities of investments	20,975	136,300
Purchases of preferred stock and warrants	0	(1,161)
Proceeds from sales of equity securities	217	235
Cash acquired in business combination	0	2,054
Investments in affiliates	(14,139)	(10,639)
Return of investment in affiliate	2,598	0
Cash received (paid) in asset acquisition	15,500	(14,219)
Purchases of property, plant and equipment	(30,354)	(32,675)
Proceeds from sale of assets	1,930	1,423
Issuances of notes receivable	0	(2,400)
Proceeds from repayment of notes receivable	0	1,500
Net cash provided by (used in) investing activities	(181,954)	80,418
Cash flows from financing activities
Proceeds from issuance of shares and warrants in public offerings, net of issuance costs	87,990	0
Acquisitions of noncontrolling interests	0	(913)
Advances from lines of credit	3,231	4,563
Repayments of advances from lines of credit	(3,264)	(5,149)
Proceeds from long-term debt, net of issuance costs	194,000	285
Payments of long-term debt	(485)	(385)
Payments of deferred consideration for acquisition	0	(8,678)
Proceeds from stock option and warrant exercises	1,074	867
Payment of issuance costs	0	(10)
Net cash provided by (used in) financing activities	282,546	(9,420)
Effect of exchange rate changes on cash, cash equivalents, and restricted cash	578	892
Net increase in cash, cash equivalents, and restricted cash	14,292	2,050
Cash, cash equivalents, and restricted cash
Beginning of period	75,545	69,594
End of period	89,837	71,644
Supplemental disclosure of cash flow information
Cash paid during the period for interest	360	534
Cash paid during the period for income taxes	193	497
Significant noncash financing and investing activities
Stock and warrants issued in business combination	0	16,997
Stock issued to acquire noncontrolling interests	0	5,082
Long-term debt issued to a related party in an asset acquisition	30,000	0
Noncash dividend to shareholders	0	22,385
Purchases of property and equipment included in accounts payable and other accrued liabilities	2,088	2,137
Purchases of equipment financed through debt	$ 193	$ 0

Consolidated Statements of Cash Flows (Reconciliation of Cash) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Statement of Cash Flows [Abstract]
Cash and cash equivalents	$ 82,417	$ 68,111
Restricted cash	6,987	6,987
Restricted cash included in other assets	433	447
Cash, cash equivalents, and restricted cash	$ 89,837	$ 75,545

Organization	9 Months Ended
Organization	Sep. 30, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Organization	Organization Intrexon Corporation ("Intrexon"), a Virginia corporation, including through its wholly owned subsidiaries Precigen, Inc. ("Precigen") and ActoBio Therapeutics, Inc. ("ActoBio"), uses synthetic biology to focus on programming biological systems to alleviate disease, remediate environmental challenges, and provide sustainable food and industrial chemicals, which may be accomplished through collaborations and joint ventures. Intrexon's primary domestic operations are in California, Florida, Maryland, and Virginia, and its primary international operations are in Belgium and Hungary. There have been no commercialized products derived from Intrexon's collaborations to date. Trans Ova Genetics, L.C. ("Trans Ova"), and Progentus, L.C. ("Progentus"), providers of advanced reproductive technologies, including services and products sold to cattle breeders and other producers, are wholly owned subsidiaries with primary operations in Iowa, Maryland, Missouri, New York, Oklahoma, and Texas. Oxitec Limited ("Oxitec"), a pioneering company in biological insect control solutions, is a wholly owned subsidiary of Intrexon with primary operations in England and Brazil. Intrexon Produce Holdings, Inc. ("IPHI") is a wholly owned subsidiary of Intrexon. Okanagan Specialty Fruits, Inc. ("Okanagan"), a company that developed and received regulatory approval for the world's first non-browning apple without the use of any artificial additives, is a wholly owned subsidiary of IPHI with primary operations in Canada. Fruit Orchard Holdings, Inc. ("FOHI") is a wholly owned subsidiary of IPHI with primary operations in Washington. ViaGen, L.C. ("ViaGen"), a provider of genetic preservation and cloning technologies, and Exemplar Genetics, LLC ("Exemplar"), a provider of genetically engineered swine for medical and genetic research, are wholly owned subsidiaries with primary operations in Iowa. In January 2018, AquaBounty Technologies, Inc. ("AquaBounty"), a company focused on improving productivity in commercial aquaculture, completed an underwritten public offering that resulted in net proceeds of $10,616 after deducting discounts, fees and expenses. As part of this offering, Intrexon purchased $5,000 of additional AquaBounty common stock, reducing its ownership stake from approximately 58% to approximately 53%. As of September 30, 2018, Intrexon owned approximately 52% of AquaBounty. Intrexon and its consolidated subsidiaries are hereinafter referred to as the "Company."

Summary of Significant Accounting Policies

9 Months Ended

Sep. 30, 2018

Accounting Policies [Abstract]

Summary of Significant Accounting Policies

Basis of Presentation

The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with accounting principles generally accepted in the United States of America ("U.S. GAAP"). Certain information and footnote disclosures normally included in the Company's annual financial statements have been condensed or omitted. These interim consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for fair statement of the Company's financial position as of September 30, 2018 and results of operations and cash flows for the interim periods ended September 30, 2018 and 2017. The year-end consolidated balance sheet data was derived from the Company's audited financial statements but does not include all disclosures required by U.S. GAAP. These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2018, or for any other future annual or interim period. The accompanying interim unaudited consolidated financial statements should be read in conjunction with the audited consolidated financial statements and related notes thereto included in the Company's Annual Report on Form 10-K for the year ended December 31, 2017 ("Annual Report").

The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated.

Revenue Recognition

Effective January 1, 2018, the Company applies Accounting Standards Codification ("ASC") Topic 606, Revenue from Contracts with Customers ("ASC 606"). Under ASC 606, the Company recognizes revenue when its customer obtains control of the promised goods or services, in an amount that reflects the consideration that the Company expects to receive in exchange for those goods or services. To determine revenue recognition for arrangements that are within the scope of ASC 606, the Company performs the following five steps: (i) identify the contract(s) with a customer, (ii) identify the promises and distinct performance obligations in the contract, (iii) determine the transaction price, (iv) allocate the transaction price to the performance obligations in the contract, and (v) recognize revenue when (or as) the Company satisfies the performance obligations.

The Company's revenue recognition accounting policies for periods prior to January 1, 2018 can be found in the audited consolidated financial statements and related notes thereto included in the Company's Annual Report.

Collaboration and licensing revenues

The Company generates collaboration and licensing revenues through the execution of agreements with collaborators (known as exclusive channel collaborations, "ECC" or "ECCs") and licensing agreements whereby the collaborators or the licensee obtain exclusive access to the Company's proprietary technologies for use in the research, development and commercialization of products and/or treatments in a contractually specified field of use. Generally, the terms of these agreements provide that the Company receives some or all of the following: (i) upfront payments upon consummation of the agreement; (ii) reimbursements for costs incurred by the Company for research and development and/or manufacturing efforts related to specific applications provided for in the agreement; (iii) milestone payments upon the achievement of specified development, regulatory and commercial activities; and (iv) royalties on sales of products arising from the collaboration or licensing agreement. The agreement typically continues in perpetuity unless terminated and each of the Company's collaborators retain a right to terminate the agreement upon providing the Company written notice a certain period of time prior to such termination, generally 90 days.

The Company's collaboration and licensing agreements typically contain multiple promises, including technology licenses, research and development services, and in certain cases manufacturing services. The Company determines whether each of the promises is a distinct performance obligation. As the nature of the promises in the Company's collaboration and licensing agreements are highly integrated and interrelated, the Company typically combines most of its promises into a single performance obligation. Because the Company is performing research and development services during early-stage development, the services are integral to the utilization of the technology license. Therefore, the Company has determined that the technology license and research and development services are typically inseparable from each other during the performance period of its collaboration and licensing agreements. Contingent manufacturing services that may be provided under certain of the Company's agreements are considered to be a separate future contract and not part of the current collaboration or licensing agreement.

At contract inception, the Company determines the transaction price, including fixed consideration and any estimated amounts of variable consideration. The upfront payment received upon consummation of the agreement is fixed and nonrefundable. Variable consideration is subject to a constraint and amounts are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Variable consideration may include reimbursements for costs incurred by the Company for research and development efforts, milestone payments upon the achievement of certain development, regulatory and commercial activities, and royalties on sales of products arising from the collaboration or licensing agreement. The Company determines the initial transaction price and excludes variable consideration that is otherwise constrained pursuant to the guidance in ASC 606.

The transaction price is allocated to the performance obligations in the agreement based on the standalone selling price of each performance obligation. The Company typically groups the promises in its collaboration and licensing agreements into one performance obligation so the entire transaction price relates to this single performance obligation. The technology license included in the single performance obligation is considered a functional license. However, it is typically combined into a single performance obligation as the Company provides interrelated research and development services along with other obligations over an estimated period of performance. The Company utilizes judgment to determine the most appropriate method to measure its progress of performance under the agreement, primarily based on inputs necessary to fulfill the performance obligation. The Company evaluates its measure of progress to recognize revenue each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. The Company's measure of performance and revenue recognition involves significant judgment and assumptions, including, but not limited to, estimated costs and timelines to complete its performance obligations. The Company evaluates modifications and amendments to its contracts to determine whether any changes should be accounted for prospectively or on a cumulative catch-up basis.

Payments received for cost reimbursements for research and development efforts are recognized as revenue as the services are performed, in connection with the single performance obligation discussed above. The reimbursements relate specifically to the Company's efforts to provide services and the reimbursements are consistent with what the Company would typically charge other collaborators for similar services.

Milestone payments are evaluated at the inception of the agreement to determine whether the milestones are considered probable of being achieved. The Company typically determines that the milestones are not probable at inception of the agreement due to the uncertainty of when and if the milestone will be achieved.

Royalties, including sales-based milestones, received under the agreements will be recognized as revenue when sales have occurred because the Company applies the sales- or usage-based royalties recognition exception provided for under ASC 606. The Company determined the application of this exception is appropriate because at the time the royalties are generated, the technology license granted in the agreement is the predominant item to which the royalties relate.

As the Company receives upfront payments in its collaboration and licensing agreements, it evaluates whether any significant financing components exist in its collaboration and licensing agreements. Based on the nature of its collaboration and licensing agreements, there are no significant financing components as the purpose of the upfront payment is not to provide financing. The purpose is to provide the collaborator with assurance that the Company will complete its obligations under the contract or to secure the right to a specific product or service at the collaborator's discretion. In addition, the variable payments generally align with the timing of performance or the timing of the consideration varies on the basis of the occurrence or nonoccurrence of a future event that is not substantially within the control of the collaborator or the Company.

From time to time, the Company and certain collaborators may cancel their agreements, relieving the Company of any further performance obligations under the agreement. Upon such cancellation or when the Company has determined no further performance obligations are required of the Company under an agreement, the Company recognizes any remaining deferred revenue.

Product and service revenues

The Company generates product and service revenues primarily through sales of products and services that are created from technologies developed or owned by the Company. The Company's current offerings include sales of advanced reproductive technologies, including the Company's bovine embryo transfer and in vitro fertilization processes and from genetic preservation and sexed semen processes and applications of such processes to other livestock, as well as sales of livestock and embryos produced using these processes and used in production. As each promised product or service is distinct, the Company recognizes the transaction price as revenue when the customer takes ownership of the promised product or when the promised service is rendered. Payment terms are typically due within 30 days.

Equity Method Investments

The Company accounts for its investments in each of its joint ventures and for its investments in start-up entities backed by the Harvest Intrexon Enterprise Fund I, LP ("Harvest"), a related party, (Note 17) using the equity method of accounting based upon relative ownership interest. The Company's investments in these entities are included in investments in affiliates in the accompanying consolidated balance sheets. See additional discussion related to certain of the Harvest start-up entities in Note 3.

The Company accounts for its investment in Oragenics, Inc. ("Oragenics"), one of its collaborators and a related party, using the fair value option. The fair value of the Company's investment in Oragenics was $1,538 and $3,085 as of September 30, 2018 and December 31, 2017, respectively, and is included as equity securities, noncurrent, in the accompanying consolidated balance sheets. The Company's ownership of Oragenics was 7.9% and 29.4% as of September 30, 2018 and December 31, 2017, respectively. Unrealized appreciation (depreciation) in the fair value of these securities was $(387) and $827 for the three months ended September 30, 2018 and 2017, respectively, and $(1,547) and $(1,610) for the nine months ended September 30, 2018 and 2017, respectively. As of September 30, 2018, Oragenics was no longer considered an equity method investment as the Company's ownership level has significantly decreased during the three months ended September 30, 2018. See Note 7 for additional discussion regarding Oragenics.

Summarized financial data as of September 30, 2018 and December 31, 2017 and for the three and nine months ended September 30, 2018 and 2017, for the Company's equity method investments are shown in the following tables.



	September 30, 2018		December 31, 2017
Current assets	$	21,044	$	61,086
Noncurrent assets	27,827		13,598
Total assets	48,871		74,684
Current liabilities	5,324		6,213
Net assets	$	43,547	$	68,471



	Three Months Ended September 30,						Nine Months Ended September 30,
	2018			2017			2018			2017
Revenues	$	113		$	58		$	353		$	175
Operating expenses	11,621			9,693			30,762			33,128
Operating loss	(11,508		)	(9,635		)	(30,409		)	(32,953		)
Other, net	12			(145		)	33			37
Net loss	$	(11,496	)	$	(9,780	)	$	(30,376	)	$	(32,916	)

Variable Interest Entities

As of September 30, 2018 and December 31, 2017, the Company determined that certain of its collaborators and joint ventures as well as Harvest were variable interest entities ("VIE" or "VIEs"). The Company was not the primary beneficiary for these entities since it did not have the power to direct the activities that most significantly impact the economic performance of the VIEs. The Company's aggregate investment balances of these VIEs as of September 30, 2018 and December 31, 2017 were $179,433 and $185,261, respectively, which represents the Company's maximum risk of loss related to the identified VIEs.

Convertible Notes

The Company allocated the proceeds received in July 2018 from the issuance of Intrexon's 3.50% convertible senior notes due 2023 (the "Convertible Notes") between long-term debt (liability component) and additional paid-in capital (equity component) within the consolidated balance sheet. The original value assigned to long-term debt is the estimated fair value as of the issuance date of a similar debt instrument without a conversion option. The original value assigned to additional paid-in capital represents the value of the conversion option and is calculated by deducting the fair value of the long-term debt from the principal amount of the Convertible Notes and is not remeasured as long as it continues to meet the requirements for equity classification. The original value of the conversion option will accrete to the carrying value of the long-term debt and result in additional non-cash interest expense over the expected life of the Convertible Notes using the effective interest method.

Debt issuance costs related to the Convertible Notes are also allocated between long-term debt and additional paid-in capital based on the original value assigned to each. Debt issuance costs allocated to long-term debt reduced the original carrying value and will accrete to the carrying value of the long-term debt and result in additional non-cash interest expense over the expected life of the Convertible Notes using the effective interest method. Debt issuance costs allocated to additional paid-in capital are recorded as reduction of the original value assigned to the conversion option.

See Note 12 for the further discussion of the Convertible Notes.

Income Taxes

Income taxes are accounted for under the asset and liability method. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to both differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases as well as operating loss and tax credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period that includes the enactment date of the change. Valuation allowances are established when necessary to reduce deferred tax assets to the amount expected to be realized.

The Company identifies any uncertain income tax positions and recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than 50% likely of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. The Company records interest, if any, related to unrecognized tax benefits as a component of interest expense. Penalties, if any, are recorded in selling, general and administrative expenses.

On December 22, 2017, the Tax Cuts and Jobs Act of 2017 (the "Tax Act") was signed into law and significantly revised U.S. corporate income tax law by, among other things, reducing the corporate income tax rate to 21% effective January 1, 2018, eliminating the corporate alternative minimum tax and implementing a modified territorial tax system that includes a one-time transition tax on deemed repatriated earnings from foreign subsidiaries. The U.S. Securities and Exchange Commission ("SEC") Staff issued Staff Accounting Bulletin No. 118 ("SAB 118") to address the application of U.S. GAAP in situations when a registrant does not have the necessary information available, prepared, or analyzed, including computations, in reasonable detail to complete the accounting for certain income tax effects of the Tax Act. The Company recognized provisional tax impacts related to revaluation of most of the Company's domestic deferred tax assets, the impact of revaluation of those deferred tax assets on the Company's valuation allowance and elimination of the corporate alternative minimum tax, and included those amounts in the consolidated financial statements for the year ended December 31, 2017. The actual impact of the Tax Act may differ from the Company's estimates due to, among other things, changes in interpretations and assumptions made, and guidance that may be issued as a result of the Tax Act.

In addition, the Tax Act implemented a new minimum tax on global intangible low-taxed income ("GILTI"). A company can elect an accounting policy to account for GILTI in either of the following ways:


•	As a period charge in the future period in which the tax arises; or


•	As part of deferred taxes related to the investment or subsidiary.

The Company has not made a policy decision regarding whether to record deferred taxes under the GILTI regime, and there was no impact to the accompanying consolidated financial statements as of and for the periods ended September 30, 2018.

The accounting is expected to be completed within the one-year measurement period as allowed by SAB 118 for items impacted or introduced by the Tax Act. See Note 13 for discussion of adjustments made to these provisional amounts in the nine months ended September 30, 2018.

Segment Information

While the Company generates revenues from multiple sources, including collaboration agreements, licensing, and products and services primarily associated with bovine reproduction, management is organized around a singular research and development focus to further the development of the Company's underlying synthetic biology technologies. Accordingly, the Company has determined that it operates in one segment. As of September 30, 2018 and December 31, 2017, the Company had $16,984 and $21,837, respectively, of long-lived assets in foreign countries. The Company recognized revenues derived in foreign countries totaling $2,235 and $4,448 for the three months ended September 30, 2018 and 2017, respectively, and $10,389 and $11,773 for the nine months ended September 30, 2018 and 2017, respectively.

Use of Estimates

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, 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 periods. Actual results could differ from those estimates.

Recently Adopted Accounting Pronouncements

The Company adopted ASC 606 for open contracts on January 1, 2018 using the modified retrospective approach. As a result of the adoption of ASC 606, including guidance on contract modifications, the Company recognized a cumulative catch-up adjustment to decrease deferred revenue in the net amount of $26,507 and accumulated deficit in the net amount of $26,611 and to increase accumulated other comprehensive loss in the net amount of $104.

In accordance with ASC 606, the disclosure of the impacted line items upon adoption of ASC 606 on the Company's consolidated statements of operations for the three and nine months ended September 30, 2018 and consolidated balance sheet as of September 30, 2018 was as follows:



	Three Months Ended September 30, 2018									Nine Months Ended September 30, 2018
	As Reported			Balances Without Adoption of ASC 606			Effect of Change			As Reported			Balances Without Adoption of ASC 606			Effect of Change
Consolidated Statements of Operations
Collaboration and licensing revenues	$	14,324		$	16,210		$	(1,886	)	$	51,622		$	58,305		$	(6,683	)
Net loss	(58,746		)	(56,860		)	(1,886		)	(172,984		)	(166,301		)	(6,683		)
Net loss attributable to Intrexon	(57,324		)	(55,438		)	(1,886		)	(168,871		)	(162,188		)	(6,683		)



	September 30, 2018
	As Reported			Balances Without Adoption of ASC 606			Effect of Change
Consolidated Balance Sheet
Liabilities
Deferred revenue, current	$	38,036		$	39,594		$	(1,558	)
Deferred revenue, net of current portion	136,942			156,803			(19,861		)
Total equity
Accumulated deficit	(990,080		)	(1,010,007		)	19,927
Accumulated other comprehensive loss	(22,900		)	(22,860		)	(40		)

In May 2017, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2017-09, Compensation-Stock Compensation (Topic 718) – Scope of Modification Accounting ("ASU 2017-09"). The provisions of ASU 2017-09 provide guidance about which changes to the terms or conditions of a share-based payment award require an entity to apply modification accounting in ASC Topic 718 ("ASC 718"). An entity should account for the effects of a modification unless (a) the fair value of the modified award is the same as the fair value of the original award, (b) the vesting conditions of the modified award are the same as the vesting conditions of the original award and (c) the classification of the modified award as an equity instrument or a liability instrument is the same as the classification of the original award immediately before the original award is modified. The Company adopted this standard effective January 1, 2018, and will apply this guidance to future modifications.

In November 2016, the FASB issued ASU 2016-18, Statement of Cash Flows (Topic 230) - Restricted Cash (A Consensus of the FASB Emerging Issues Task Force) ("ASU 2016-18"). The provisions of ASU 2016-18 require amounts generally described as restricted cash and restricted cash equivalents to be included with cash and cash equivalents when reconciling the total beginning and ending balances for the periods presented on the statement of cash flows. The Company adopted this standard effective January 1, 2018. In accordance with the provisions of ASU 2016-18, the "Cash, cash equivalents, and restricted cash" beginning period balance increased by $7,434 for the nine months ended September 30, 2018 in the accompanying consolidated statement of cash flows. The beginning and ending period balances increased by $6,987 and $7,428, respectively, in the accompanying consolidated statement of cash flows for the nine months ended September 30, 2017 from what was previously reported in the Company's Quarterly Report on Form 10-Q for the period ended September 30, 2017.

In October 2016, the FASB issued ASU 2016-16, Income Taxes (Topic 740) - Intra-Entity Transfers of Assets Other Than Inventory ("ASU 2016-16"). The provisions of ASU 2016-16 remove the prohibition in ASC Topic 740 against the immediate recognition of the current and deferred income tax effects of intra-entity transfers of assets other than inventory. The Company adopted this standard effective January 1, 2018, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements.

In August 2016, the FASB issued ASU 2016-15, Statement of Cash Flows (Topic 230) - Classification of Certain Cash Receipts and Cash Payments ("ASU 2016-15"). The provisions of ASU 2016-15 address eight specific cash flow issues and how those certain cash receipts and cash payments are presented and classified in the statement of cash flows under ASC Topic 230 and other Topics. The Company adopted this standard effective January 1, 2018, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements.

In January 2016, the FASB issued ASU 2016-01, Financial Instruments - Overall (Subtopic 825-10) - Recognition and Measurement of Financial Assets and Financial Liabilities ("ASU 2016-01"). The provisions of ASU 2016-01 make targeted improvements to enhance the reporting model for financial instruments to provide users of financial statements with more decision-useful information, including certain aspects of recognition, measurement, presentation, and disclosure of financial instruments. In February 2018, the FASB issued ASU 2018-03, Technical Corrections and Improvements to Financial Instruments-Overall (Subtopic 825-10): Recognition and Measurement of Financial Assets and Financial Liabilities, to clarify certain aspects of the guidance issued in ASU 2016-01. The Company adopted this standard effective January 1, 2018, and the implementation of this standard did not have a material impact on the Company's consolidated financial statements.

Recently Issued Accounting Pronouncements

In October 2018, the FASB issued ASU 2018-18, Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606 ("ASU 2018-17"). The provisions of ASU 2018-18 clarify when certain transactions between collaborative arrangement participants should be accounted for under ASC 606 and incorporates unit-of-account guidance consistent with ASC 606 to aid in this determination. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2019, with early adoption permitted, and is effective for the Company for the year ending December 31, 2020. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements.

In October 2018, the FASB issued ASU 2018-17, Consolidation (Topic 810): Targeted Improvements to Related Party Guidance for Variable Interest Entities ("ASU 2018-17"). The provisions of ASU 2018-17 modify the guidance under ASC Topic 810 related to the evaluation of indirect interests held through related parties under common control when determining whether fees paid to decision makers and service providers are variable interests. Indirect interests held through related parties that are under common control are no longer considered to be the equivalent of direct interests in their entirety and instead should be considered on a proportional basis. This guidance more closely aligns with accounting of how indirect interests held through related parties under common control are considered for determining whether a reporting entity must consolidate a VIE. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2019, with early adoption permitted, and is effective for the Company for the year ending December 31, 2020. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements.

In August 2018, the SEC adopted final rules under SEC Release No. 33-10532, Disclosure Update and Simplification, to amend certain disclosure requirements that were redundant, duplicative, overlapping, outdated or superseded in light of other SEC disclosure requirements, U.S. GAAP or changes in the information environment. In addition, the amendments added a requirement for interim financial statements to disclose an analysis of changes in each caption of shareholders' equity presented in the balance sheet. Previously, this disclosure was only required in annual financial statements. Under the amendments, the analysis must be provided in a note or separate statement and should be accompanied by a reconciliation of the beginning balance to the ending balance of each period for which a statement of comprehensive income is required to be filed. This final rule was effective on November 5, 2018, except that companies may delay adoption of the rule relating to changes in shareholders' equity until the Form 10-Q for the quarter that begins after November 5, 2018. The Company will apply the amendments relating to changes in shareholders' equity in the Quarterly Report for the period ending March 31, 2019.

In August 2018, the FASB issued ASU 2018-15, Intangibles-Goodwill and Other-Internal-Use Software (Subtopic 350-40): Customer's Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract ("ASU 2018-15"). The provisions of ASU 2018-15 clarify the accounting for implementation costs of a hosting arrangement that is a service contract. The new standard requires an entity (customer) in a hosting arrangement that is a service contract to follow existing internal-use software guidance to determine which implementation costs to capitalize as an asset related to the service contract and which costs to expense. Capitalized implementation costs of a hosting arrangement that is a service contract should be amortized over the term of the hosting arrangement, which might extend beyond the noncancelable period if there are options to extend or terminate. ASU 2018-15 also specifies the financial statement presentation of capitalized implementation costs and related amortization, in addition to required disclosures for material capitalized implementation costs related to hosting arrangements that are service contracts. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2019, with early adoption permitted, and is effective for the Company for the year ending December 31, 2020. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements.

In August 2018, the FASB issued ASU 2018-13, Fair Value Measurements (Topic 820): Disclosure Framework-Changes to the Disclosure Requirements for Fair Value Measurements ("ASU 2018-13"). The provisions of ASU 2018-13 modify the disclosures related to recurring and nonrecurring fair value measurements. Disclosures related to the transfer of assets between Level 1 and Level 2 hierarchies have been eliminated and various additional disclosures related to Level 3 fair value measurements have been added, modified or removed. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2019, but entities are permitted to early adopt either the entire standard or only the provisions that eliminate or modify the requirements. This standard is effective for the Company for the year ending December 31, 2020. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements.

In June 2018, the FASB issued ASU 2018-07, Compensation-Stock Compensation (Topic 718): Improvements to Nonemployee Share-Based Payment Accounting ("ASU 2018-07"). The provisions of ASU 2018-07 expand the scope of ASC 718 to include share-based payment transactions for acquiring goods and services from nonemployees. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, with early adoption permitted no earlier than an entity's adoption date of ASC 606, and is effective for the Company for the year ending December 31, 2019. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements.

In February 2018, the FASB issued ASU 2018-02, Income Statement-Reporting Comprehensive Income (Topic 220): Reclassification of Certain Tax Effects from Accumulated Other Comprehensive Income ("ASU 2018-02"). The provisions of ASU 2018-02 allow a reclassification from accumulated other comprehensive income to retained earnings for stranded tax effects resulting from the Tax Act. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, with early adoption permitted, and is effective for the Company for the year ending December 31, 2019. The amendments in ASU 2018-02 may be applied either in the period of adoption or retrospectively to each period (or periods) in which the effect of the change in the U.S. federal corporate income tax rate in the Tax Act is recognized. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements.

In July 2017, the FASB issued ASU 2017-11, Earnings Per Share (Topic 260), Distinguishing Liabilities from Equity (Topic 480) and Derivatives and Hedging (Topic 815): I. Accounting for Certain Financial Instruments with Down Round Features; II. Replacement of the Indefinite Deferral for Mandatorily Redeemable Financial Instruments of Certain Nonpublic Entities and Certain Mandatorily Redeemable Noncontrolling Interests with a Scope Exception ("ASU 2017-11"). The amendments in Part I of ASU 2017-11 change the classification analysis of certain equity-linked financial instruments (or embedded features) with down round features. When determining whether certain financial instruments should be classified as liabilities or equity instruments, a down round feature no longer precludes equity classification when assessing whether the instrument is indexed to an entity's own stock. The amendments also clarify existing disclosure requirements for equity-classified instruments. As a result, a freestanding equity-linked financial instrument (or embedded conversion option) no longer would be accounted for as a derivative liability at fair value as a result of the existence of a down round feature. For freestanding equity-classified financial instruments, the amendments require entities that present earnings per share ("EPS") in accordance with ASC Topic 260 ("ASC 260") to recognize the effect of the down round feature when it is triggered. That effect is treated as a dividend and as a reduction of income available to common shareholders in basic EPS. Convertible instruments with embedded conversion options that have down round features are now subject to the specialized guidance for contingent beneficial conversion features (in Subtopic 470-20, Debt-Debt with Conversion and Other Options), including related EPS guidance (in ASC 260). The amendments in Part II of ASU 2017-11 re-characterize the indefinite deferral of certain provisions of ASC Topic 480 that now are presented as pending content in the FASB codification, to a scope exception. Those amendments do not have an accounting effect. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, with early adoption permitted, and is effective for the Company for the year ending December 31, 2019. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements.

In June 2016, the FASB issued ASU 2016-13, Financial Instruments-Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments ("ASU 2016-13"). The provisions of ASU 2016-13 modify the impairment model to utilize an expected loss methodology in place of the currently used incurred loss methodology, and requires a consideration of a broader range of reasonable and supportable information to inform credit loss estimates. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2019, with early adoption permitted, and is effective for the Company for the year ending December 31, 2020. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements.

In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842) ("ASU 2016-02"). The provisions of ASU 2016-02 set out the principles for the recognition, measurement, presentation and disclosure of leases for both parties to a contract (i.e. lessees and lessors). The new standard requires lessees to apply a dual approach, classifying leases as either finance or operating leases based on the principle of whether or not the lease is effectively a financed purchase by the lessee. This classification will determine whether lease expense is recognized based on an effective interest method or on a straight-line basis over the term of the lease, respectively. A lessee is also required to record a right-of-use asset and a lease liability for all leases with a term of greater than 12 months regardless of their classification. Leases with a term of 12 months or less will be accounted for in a similar manner as under existing guidance for operating leases today. ASU 2016-02 supersedes the previous lease standard, ASC Topic 840 ("ASC 840"), Leases. In July 2018, the FASB issued ASU 2018-10, Codification Improvements to Topic 842 (Leases), and ASU 2018-11, Leases (Topic 842), Targeted Improvements ("ASU 2018-11"), which provide (i) narrow amendments to clarify how to apply certain aspects of the new lease standard, (ii) entities with an additional transition method to adopt the new standard, and (ii) lessors with a practical expedient for separating components of a contract. ASU 2018-11 specifically permits an entity to elect an additional transition method to the existing modified retrospective transition requirements. Under the new transition method, an entity could adopt the provisions of ASU No. 2016-02 by recognizing a cumulative-effect adjustment to the opening balance of retained earnings in the period of adoption without adjustment to the financial statements for periods prior to adoption. Consequently, an entity's reporting for the comparative periods presented in the financial statements in which it adopts the new leases standard will continue to be in accordance with the previous lease guidance in ASC 840. ASU No. 2018-11 also allows a practical expedient that permits lessors to not separate non-lease components from the associated lease component if certain conditions are present. All of these ASUs related to ASC Topic 842 are effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, and is effective for the Company for the year ending December 31, 2019. The Company is currently evaluating its lease agreements to determine the impact that the implementation of this standard will have on the Company's consolidated financial statements as it relates to the classification of leases under the dual approach and the recognition of a right-of-use asset and a lease liability as well as assessing the adoption method.

Mergers and Acquisitions

9 Months Ended

Sep. 30, 2018

Mergers and Acquisitions [Abstract]

Mergers and Acquisitions

Asset Acquisition of Certain Harvest Entities

In September 2018, the Company, through its wholly owned subsidiary ActoBio, issued $30,000 of convertible promissory notes to Harvest, a related party, to acquire Harvest's ownership in CRS Bio, Inc., Genten Therapeutics, Inc., and Relieve Genetics, Inc. (collectively the "Harvest entities") (Note 17). The Company also received $15,500 cash in the transaction from the acquisition of the Harvest entities. Prior to the transaction, the Company held a noncontrolling interest in the Harvest entities, with a combined carrying value for all entities of $4,303, and accounted for its ownership using the equity method of accounting. Following the transaction, the Company owns 100% of the equity interests of the Harvest entities including the rights that had been previously licensed to the Harvest entities by the Company. The Harvest entities did not meet the definition of a business and accordingly, the transaction was accounted for as an asset acquisition.

By reacquiring the rights previously licensed to the Harvest entities, the Company is relieved from its obligations under the original ECCs and therefore wrote off deferred revenue of $10,078 as part of the transaction. The remaining value acquired of $8,721 was considered in-process research and development related to the reacquired rights under the ECCs and expensed immediately. No revenues were recognized under the ECCs with these entities during the three months ended September 30, 2018.

See additional discussion of the convertible promissory notes at Note 12.

GenVec Acquisition

In June 2017, pursuant to an Agreement and Plan of Merger (the "GenVec Merger Agreement"), the Company acquired 100% of the outstanding shares of GenVec, Inc. ("GenVec"), a clinical-stage company and pioneer in the development of AdenoVerse gene delivery technology. Pursuant to the GenVec Merger Agreement, the former shareholders of GenVec received an aggregate of 684,240 shares of the Company's common stock and have the right to receive contingent consideration equal to 50% of any milestone or royalty payments received under one of GenVec's collaboration agreements, provided such payments are received within three years after the closing of the transaction. The Company also assumed warrants held by certain former shareholders of GenVec. The results of GenVec's operations subsequent to the acquisition date have been included in the consolidated financial statements.

The fair value of the total consideration transferred was $17,582. The acquisition date fair value of each class of consideration transferred is presented below:



Common shares	$	15,616
Warrants	1,381
Contingent consideration	585
	$	17,582

The fair value of the shares of the Company's common stock issued was based on the quoted closing price of the Company's common stock immediately prior to the closing of the acquisition. The fair value of the warrants assumed was estimated using the Black-Scholes option-pricing model. The fair value of the contingent consideration was determined using a probability weighted discounted cash flows model and is considered a freestanding financial instrument and recorded at fair value each reporting period. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below:



Cash and cash equivalents	$	2,054
Short-term investments	542
Trade receivables	75
Other receivables	97
Prepaid expenses and other	227
Property and equipment	250
Intangible assets	14,000
Other noncurrent assets	58
Total assets acquired	17,303
Accounts payable	2,158
Accrued compensation and benefits	1,226
Other accrued expenses	856
Other long-term liabilities	92
Deferred tax liabilities	239
Total liabilities assumed	4,571
Net assets acquired	12,732
Goodwill	4,850
Total consideration	$	17,582

The acquired intangible assets include developed technology, the fair value of which was determined using the multi-period excess earning method, which is a variation of the income approach that converts future cash flows to single discounted present value amounts. The intangible assets are being amortized over a useful life of eleven years. Goodwill, which is not deductible for tax purposes, represents the assembled workforce and the anticipated buyer-specific synergies arising from the combination of the Company's and GenVec's technology.

Acquisition-related costs totaling $9 and $507 are included in selling, general and administrative expenses in the accompanying consolidated statements of operations for the three and nine months ended September 30, 2017, respectively.

Condensed Pro Forma Financial Information

GenVec's results of operations subsequent to the acquisition are included in the consolidated statements of operations. The following condensed pro forma financial information for the nine months ended September 30, 2017 is presented as if the acquisition had been consummated on January 1, 2016:



	Nine Months Ended September 30,
	2017
	Pro forma
Revenues	$	154,185
Loss before income taxes	(102,305		)
Net loss	(100,330		)
Net loss attributable to the noncontrolling interests	3,123
Net loss attributable to Intrexon	(97,207		)

Investments in Joint Ventures	9 Months Ended
Investments in Joint Ventures	Sep. 30, 2018
Equity Method Investments and Joint Ventures [Abstract]
Investments in Joint Ventures	Investments in Joint Ventures S & I Ophthalmic In September 2013, the Company entered into a Limited Liability Company Agreement ("Sun LLC Agreement") with Sun Pharmaceutical Industries, Inc. ("Sun Pharmaceutical Subsidiary"), an indirect subsidiary of Sun Pharmaceutical Industries Ltd. ("Sun Pharmaceutical"), an international specialty pharmaceutical company focused on chronic diseases, to form S & I Ophthalmic, LLC ("S & I Ophthalmic"). The Sun LLC Agreement governed the affairs and the conduct of business of S & I Ophthalmic. S & I Ophthalmic leveraged experience and technology from both the Company and Sun Pharmaceutical. Both the Company and Sun Pharmaceutical Subsidiary made an initial capital contribution of $5,000 in October 2013 for a 50% membership interest in S & I Ophthalmic. S & I Ophthalmic was governed by a board of managers, which had four members, two each from the Company and Sun Pharmaceutical Subsidiary. In 2015, both the Company and Sun Pharmaceutical Subsidiary made subsequent capital contributions of $5,000. In December 2017, both the Company and Sun Pharmaceutical Subsidiary agreed to dissolve S & I Ophthalmic and terminate the related ECC agreement. In January 2018, the Company received $2,598 upon the dissolution of S & I Ophthalmic, which represented the Company's portion of S & I Ophthalmic's remaining cash after all liabilities were settled. OvaXon In December 2013, the Company and OvaScience, Inc. ("OvaScience"), a life sciences company focused on the discovery, development, and commercialization of new treatments for infertility, entered into a Limited Liability Company Agreement ("OvaXon LLC Agreement") to form OvaXon, LLC ("OvaXon"), a joint venture to create new applications for improving human and animal health. Both the Company and OvaScience made an initial capital contribution of $1,500 in January 2014 for a 50% membership interest in OvaXon. OvaXon is governed by the OvaXon board of managers ("OvaXon Board"), which has four members, two each from the Company and OvaScience. In cases in which the OvaXon Board determines that additional capital contributions are necessary in order for OvaXon to conduct business and comply with its obligations, each of the Company and OvaScience has the right, but not the obligation, to make additional capital contributions to OvaXon subject to the OvaXon LLC Agreement. Through September 30, 2018, both the Company and OvaScience have made subsequent capital contributions of $4,350. In March 2018, the Company and OvaScience agreed to terminate the ECC agreement with OvaScience. The Company and OvaScience are in discussions regarding the future of the OvaXon joint venture and the related ECC agreement. The Company's investment in OvaXon was $140 and $146 as of September 30, 2018 and December 31, 2017, respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets. Intrexon Energy Partners In March 2014, the Company and certain investors (the "IEP Investors"), including an affiliate of Third Security, LLC ("Third Security"), a related party, entered into a Limited Liability Company Agreement that governs the affairs and conduct of business of Intrexon Energy Partners, LLC ("Intrexon Energy Partners"), a joint venture formed to optimize and scale-up the Company's methane bioconversion platform ("MBP") technology for the production of certain fuels and lubricants. The Company also entered into an ECC with Intrexon Energy Partners providing exclusive rights to the Company's technology for the use in bioconversion, as a result of which the Company received a technology access fee of $25,000 while retaining a 50% membership interest in Intrexon Energy Partners. The IEP Investors made initial capital contributions, totaling $25,000 in the aggregate, in exchange for pro rata membership interests in Intrexon Energy Partners totaling 50%. In addition, Intrexon has committed to make capital contributions of up to $25,000, and the IEP Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon Energy Partners, have committed to make additional capital contributions of up to $25,000, at the request of Intrexon Energy Partners' board of managers (the "Intrexon Energy Partners Board") and subject to certain limitations. As of September 30, 2018, the Company's remaining commitment was $5,132. Intrexon Energy Partners is governed by the Intrexon Energy Partners Board, which has five members. Two members of the Intrexon Energy Partners Board are designated by the Company and three members are designated by a majority of the IEP Investors. The Company and the IEP Investors have the right, but not the obligation, to make additional capital contributions above the initial limits when and if solicited by the Intrexon Energy Partners Board. The Company's investment in Intrexon Energy Partners was $(506) and $(444) as of September 30, 2018 and December 31, 2017, respectively, and is included in other accrued liabilities in the accompanying consolidated balance sheets. Intrexon Energy Partners II In December 2015, the Company and certain investors (the "IEPII Investors"), including Harvest, entered into a Limited Liability Company Agreement that governs the affairs and conduct of business of Intrexon Energy Partners II, LLC ("Intrexon Energy Partners II"), a joint venture formed to utilize the Company's MBP technology for the production of 1,4-butanediol, an industrial chemical used to manufacture spandex, polyurethane, plastics, and polyester. The Company also entered into an ECC with Intrexon Energy Partners II that provides exclusive rights to the Company's technology for use in the field, as a result of which the Company received a technology access fee of $18,000 while retaining a 50% membership interest in Intrexon Energy Partners II. The IEPII Investors made initial capital contributions, totaling $18,000 in the aggregate, in exchange for pro rata membership interests in Intrexon Energy Partners II totaling 50%. In December 2015, the owners of Intrexon Energy Partners II made a capital contribution of $4,000, half of which was paid by the Company. Intrexon has committed to make additional capital contributions of up to $10,000, and the IEPII Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon Energy Partners II, have committed to make additional capital contributions of up to $10,000, at the request of Intrexon Energy Partners II's board of managers (the "Intrexon Energy Partners II Board") and subject to certain limitations. Intrexon Energy Partners II is governed by the Intrexon Energy Partners II Board, which has five members. One member of the Intrexon Energy Partners II Board is designated by the Company and four members are designated by a majority of the IEPII Investors. The Company and the IEPII Investors have the right, but not the obligation, to make additional capital contributions above the initial limits when and if solicited by the Intrexon Energy Partners II Board. The Company's investment in Intrexon Energy Partners II was $184 and $572 as of September 30, 2018 and December 31, 2017, respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets. EnviroFlight In February 2016, the Company entered into a series of transactions involving EnviroFlight, LLC ("Old EnviroFlight"), Darling Ingredients Inc. ("Darling") and a newly formed venture between the Company and Darling ("New EnviroFlight"). New EnviroFlight was formed to generate high-nutrition, low environmental impact animal and fish feed, as well as fertilizer products, from black soldier fly larvae. Through September 30, 2018, both the Company and Darling have made subsequent capital contributions of $14,750. The Company's investment in New EnviroFlight was $15,286 and $7,092 as of September 30, 2018 and December 31, 2017, respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets. Intrexon T1D Partners In March 2016, the Company and certain investors (the "T1D Investors"), including affiliates of Third Security, entered into a Limited Liability Company Agreement that governs the affairs and conduct of business of Intrexon T1D Partners, LLC ("Intrexon T1D Partners"), a joint venture formed to utilize the Company's proprietary ActoBiotics platform to develop and commercialize products to treat type 1 diabetes. The Company also entered into an ECC with Intrexon T1D Partners that provides the exclusive rights to the Company's technology for use in the field, as a result of which the Company received a technology access fee of $10,000 while retaining a 50% membership interest in Intrexon T1D Partners. The T1D Investors made initial capital contributions, totaling $10,000 in the aggregate, in exchange for pro rata membership interests in Intrexon T1D Partners totaling 50%. Intrexon committed to make capital contributions of up to $5,000, and the T1D Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon T1D Partners, committed to make additional capital contributions of up to $5,000, at the request of Intrexon T1D Partners' board of managers (the "Intrexon T1D Partners Board") and subject to certain limitations. As of September 30, 2018, the Company has satisfied its commitment. Intrexon T1D Partners is governed by the Intrexon T1D Partners Board, which has five members. Two members of the Intrexon T1D Partners Board are designated by the Company and three members are designated by a majority of the T1D Investors. The Company and the T1D Investors have the right, but not the obligation, to make additional capital contributions above these limits when and if solicited by the Intrexon T1D Partners Board. The Company's investment in Intrexon T1D Partners was $0 and $(943) as of September 30, 2018 and December 31, 2017, respectively, and is included in other accrued liabilities in the accompanying consolidated balance sheets.

Collaboration and Licensing Revenue

9 Months Ended

Sep. 30, 2018

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Collaboration and Licensing Revenue

The Company's collaborations and licensing agreements provide for multiple promises to be satisfied by the Company and typically include a license to the Company's technology platforms, participation in collaboration committees, and performance of certain research and development services. Based on the nature of the promises in the Company's collaboration and licensing agreements, the Company typically combines most of its promises into a single performance obligation because the promises are highly interrelated and not individually distinct. At contract inception, the transaction price is typically the upfront payment received and is allocated to the single performance obligation. The Company has determined the transaction price should be recognized as revenue based on its measure of progress under the agreement primarily based on inputs necessary to fulfill the performance obligation.

The Company recognizes the reimbursement payments received for research and development services in the period when the services are performed. At inception of each collaboration, the Company determines whether any milestone payments are probable and can be included in the transaction price. The milestone payments are typically not considered probable at inception and are therefore constrained under ASC 606. Royalties related to product sales will be recognized when sales have occurred since the royalties relate directly to the technology license granted in the agreement.

See Note 2 for additional discussion of the Company's revenue recognition policy related to collaboration and licensing payments.

The Company determines whether collaborations and licensing agreements are individually significant for disclosure based on a number of factors, including total revenue recorded by the Company pursuant to collaboration and licensing agreements, collaborators or licensees with either majority-owned subsidiaries or equity method investments, or other qualitative factors. Collaboration and licensing revenues generated from consolidated subsidiaries are eliminated in consolidation. Amounts for periods subsequent to January 1, 2018 reflect revenue recognition under ASC 606.

The following tables summarize the amounts recorded as revenue in the consolidated statements of operations for each significant counterparty to a collaboration or licensing agreement for the three and nine months ended September 30, 2018 and 2017.



	Three Months Ended September 30,				Nine Months Ended September 30,
	2018		2017		2018		2017
ZIOPHARM Oncology, Inc.	$	4,826	$	10,373	$	13,626	$	31,322
Oragenics, Inc.	705		475		867		1,519
Fibrocell Science, Inc.	391		1,683		1,015		5,375
Genopaver, LLC	689		1,422		3,076		4,615
S & I Ophthalmic, LLC	—		376		—		751
OvaXon, LLC	—		262		—		1,966
Intrexon Energy Partners, LLC	1,329		1,903		3,345		8,909
Persea Bio, LLC	199		266		714		821
Ares Trading S.A.	1,576		2,356		7,525		8,474
Intrexon Energy Partners II, LLC	754		816		1,685		2,921
Intrexon T1D Partners, LLC	368		1,462		2,399		3,882
Harvest start-up entities (1)	2,691		4,020		11,792		11,835
Other	796		2,741		5,578		6,994
Total	$	14,324	$	28,155	$	51,622	$	89,384

(1)

For the three and nine months ended September 30, 2018 and 2017, revenues recognized from collaborations with Harvest start-up entities include: Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; and AD Skincare, Inc. For the nine months ended September 30, 2018 and the three and nine months ended September 30, 2017, revenues recognized from collaborations with Harvest start-up entities also include Genten Therapeutics, Inc. and CRS Bio, Inc. For the three and nine months ended September 30, 2017, revenues recognized from collaborations with Harvest start-up entities also include Relieve Genetics, Inc.

Other than the termination of the OvaScience ECC in March 2018 (Note 4) and the asset acquisition regarding certain of the Harvest entities in September 2018 (Note 3), there have been no significant changes to the agreements with our collaborators and licensees in the nine months ended September 30, 2018. See also Note 19 for discussion of the Company's collaboration with ZIOPHARM Oncology, Inc. ("ZIOPHARM"). See Note 5 in the Company's Annual Report for additional details of the Company's existing collaboration and licensing agreements.

Deferred Revenue

Deferred revenue primarily consists of consideration received for the Company's collaborations and licensing agreements and prepayments for product and service revenues. Deferred revenue consists of the following:



	September 30, 2018		December 31, 2017
Collaboration and licensing agreements	$	170,356	$	231,583
Prepaid product and service revenues	3,119		4,681
Other	1,503		133
Total	$	174,978	$	236,397
Current portion of deferred revenue	$	38,036	$	42,870
Long-term portion of deferred revenue	136,942		193,527
Total	$	174,978	$	236,397

The following table summarizes the remaining balance of deferred revenue associated with upfront and milestone payments for each significant counterparty to a collaboration or licensing agreement as of September 30, 2018 and December 31, 2017, including the estimated remaining performance period as of September 30, 2018.



	Average Remaining Performance Period (Years)	September 30, 2018		December 31, 2017
ZIOPHARM Oncology, Inc.	5.3	$	51,084	$	90,496
Oragenics, Inc.	5.7	6,240		6,719
Fibrocell Science, Inc.	6.1	17,846		16,607
Genopaver, LLC	5.5	1,346		1,704
Intrexon Energy Partners, LLC	5.5	13,164		15,625
Persea Bio, LLC	6.3	2,802		3,500
Ares Trading S.A.	5.6	34,608		40,789
Intrexon Energy Partners II, LLC	6.2	14,910		13,833
Intrexon T1D Partners, LLC	6.5	8,760		8,435
Harvest start-up entities (1)	6.4	8,007		18,400
Other	4.5	10,721		14,423
Total		$	169,488	$	230,531

(1)

As of September 30, 2018 and December 31, 2017, the balance of deferred revenue for collaborations with Harvest start-up entities includes: Thrive Agrobiotics, Inc.; Exotech Bio, Inc.; and AD Skincare, Inc. As of December 31, 2017, the balance of deferred revenue for collaborations with Harvest start-up entities also includes: Relieve Genetics, Inc.; Genten Therapeutics, Inc.; and CRS Bio, Inc. See Note 3 for further discussion of the asset acquisition of certain Harvest entities.

Short-term Investments

9 Months Ended

Sep. 30, 2018

Investments, Debt and Equity Securities [Abstract]

Short-term Investments

The Company's investments are classified as available-for-sale. The following table summarizes the amortized cost, gross unrealized gains and losses, and fair value of available-for-sale investments as of September 30, 2018:



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Aggregate Fair Value
U.S. government debt securities	$	163,905	$	—	$	(96	)	$	163,809
Certificates of deposit	353		—		—			353
Total	$	164,258	$	—	$	(96	)	$	164,162

The following table summarizes the amortized cost, gross unrealized gains and losses, and fair value of available-for-sale investments as of December 31, 2017:



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Aggregate Fair Value
U.S. government debt securities	$	6,000	$	—	$	(2	)	$	5,998
Certificates of deposit	275		—		—			275
Total	$	6,275	$	—	$	(2	)	$	6,273

For more information on the Company's method for determining the fair value of its assets, see Note 2 – "Fair Value of Financial Instruments" in the Company's Annual Report.

As of September 30, 2018, all of the available-for-sale investments were due within one year based on their contractual maturities.

Changes in market interest rates and bond yields cause certain investments to fall below their cost basis, resulting in unrealized losses on investments. The unrealized losses of the Company's investments were primarily a result of unfavorable changes in interest rates subsequent to the initial purchase of these investments and were not significant as of September 30, 2018.

As of September 30, 2018 and December 31, 2017, the Company did not consider any of its investments to be other-than-temporarily impaired. When evaluating its investments for other-than-temporary impairment, the Company reviews factors such as the length of time and extent to which fair value has been below its cost basis, the financial condition of the issuer, the Company's ability and intent to hold the security and whether it is more likely than not that it will be required to sell the investment before recovery of its cost basis.

Investments in Preferred Stock

9 Months Ended

Sep. 30, 2018

Investment in Preferred Stock [Abstract]

Investments In Preferred Stock

Investments in Preferred Stock

Investment in ZIOPHARM Preferred Stock

In June 2016, the Company received 100,000 shares of Series 1 Preferred Stock (the "Preferred Shares") of ZIOPHARM, with a per share stated value of $1,200, as consideration for amending their two previously existing ECC agreements. The Company received a monthly dividend, paid in additional Preferred Shares, equal to $12.00 per Preferred Share held per month divided by the stated value of the Preferred Shares. In conjunction with the license agreement with ZIOPHARM in October 2018 (Note 19), the Company returned to ZIOPHARM all of the Preferred Shares owned or accrued by the Company as of the effective date of the agreement.

The investment in ZIOPHARM preferred stock is categorized as Level 3 as there are significant unobservable inputs and the Preferred Shares are not traded on a public exchange. The fair value of the investment in ZIOPHARM preferred stock is estimated using a probability-weighted expected return ("PWERM") model. The key inputs used in the PWERM model are (i) estimating the future returns for conversion of the Preferred Shares for both product approval and a change in control of ZIOPHARM (the "conversion events") using market data of the change in value for guideline companies as a result of these conversion events; (ii) estimating the expected date and likelihood of each conversion event; and (iii) discounting these estimated future returns using a discount rate for the Preferred Shares considering industry debt issuances originated by public funds and venture capital rates of return. A significant change in unobservable inputs discussed above could result in a significant impact on the fair value of the Company's investment in ZIOPHARM preferred stock. The fair value of the Company's investment in ZIOPHARM preferred stock, including additional Preferred Shares received as dividends, was $158,122 and $160,832 as of September 30, 2018 and December 31, 2017, respectively. During the three months ended September 30, 2018 and 2017, the Company received an additional 3,847 and 3,414 Preferred Shares and recognized $4,649 and $4,311 of dividend income in the accompanying consolidated statements of operations, respectively. During the nine months ended September 30, 2018 and 2017, the Company received an additional 11,205 and 9,943 Preferred Shares and recognized $14,539 and $12,276 of dividend income in the accompanying consolidated statements of operations, respectively.

Investment in Fibrocell Preferred Stock

In March 2017, Fibrocell Science, Inc. ("Fibrocell"), one of the Company's collaborators and a related party, sold Series A Convertible Preferred Stock (the "Convertible Preferred Shares"), convertible into shares of Fibrocell common stock, and warrants to purchase shares of Fibrocell common stock to certain institutional and accredited investors, including the Company and affiliates of Third Security. The Company paid $1,161 in exchange for 1,161 Convertible Preferred Shares and warrants to acquire 99,769 shares of Fibrocell common stock. The share data reflect a 1-for-5 reverse stock split of Fibrocell's common stock effective May 25, 2018. The Convertible Preferred Shares are convertible at any time at the election of the Company and accrue dividends at 4% per annum, compounded quarterly, increasing the stated value of the shares. The investment in Fibrocell preferred stock is categorized as Level 3 as there are significant unobservable inputs and the Convertible Preferred Shares are not traded on a public exchange. The fair value of the investment in Fibrocell preferred stock is estimated using a conversion plus dividend approach utilizing the trading value of the underlying common stock and an estimated premium for the preferred stock dividend and other preferences. Market price volatility of Fibrocell's common stock and a significant change in the estimated preferred stock premium could result in a significant impact to the fair value of the investment in Fibrocell preferred stock. As of September 30, 2018 and December 31, 2017, the fair value of the Company's investment in Fibrocell preferred stock totaled $299 and $393, respectively. See Note 17 for additional discussion of the warrants.

Investment in Oragenics Preferred Stock

In November 2017, concurrent with Oragenics closing a preferred stock private placement, the Company exchanged a promissory note, including accrued interest, purchased from Oragenics in May 2017 and receivables due from Oragenics totaling $3,385 for Oragenics Series C preferred stock ("Series C Preferred Stock"). The Series C Preferred Stock is non-voting and non-convertible and is redeemable in whole or part at any time by Oragenics in cash. The Series C Preferred Stock accrues an annual 12% dividend payable in additional Series C Preferred Stock through May 10, 2019, and after such date, the annual dividend increases to 20%. Additionally, the Company and Oragenics amended certain future payment terms under its ECCs, as discussed in Note 5 of the Company's Annual Report. As of September 30, 2018 and December 31, 2017, based on the most recent financial information available on Oragenics, the Company concluded that there was no value to its investment in Oragenics preferred stock.

Changes in the Fair Value of Investments in Preferred Stock

The following table summarizes the changes in the Level 3 investments in preferred stock during the nine months ended September 30, 2018.



	Nine Months Ended September 30, 2018
Beginning balance	$	161,225
Dividend income from investments in preferred stock	14,575
Net unrealized depreciation in the fair value of the investments in preferred stock	(17,379		)
Ending balance	$	158,421

Fair Value Measurements

9 Months Ended

Sep. 30, 2018

Fair Value Disclosures [Abstract]

Fair Value Measurements

The carrying amount of cash and cash equivalents, restricted cash, receivables, prepaid expenses and other current assets, accounts payable, accrued compensation and benefits, other accrued liabilities, and related party payables approximate fair value due to the short maturity of these instruments.

Assets

The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at September 30, 2018:



	Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		September 30, 2018
Assets
U.S. government debt securities	$	—	$	163,809	$	—	$	163,809
Equity securities	3,591		1,106		—		4,697
Preferred stock	—		—		158,421		158,421
Other	—		653		—		653
Total	$	3,591	$	165,568	$	158,421	$	327,580



	Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		December 31, 2017
Assets
U.S. government debt securities	$	—	$	5,998	$	—	$	5,998
Equity securities	10,537		4,563		—		15,100
Preferred stock	—		—		161,225		161,225
Other	—		850		—		850
Total	$	10,537	$	11,411	$	161,225	$	183,173

The method used to estimate the fair value of the Level 1 assets in the tables above is based on observable market data as these equity securities are publicly-traded. The method used to estimate the fair value of the Level 2 short-term investments in the tables above is based on professional pricing sources for identical or comparable instruments, rather than direct observations of quoted prices in active markets. The method used to estimate the fair value of the Level 2 equity securities in the tables above is based on the quoted market price of the publicly-traded security, adjusted for a discount for lack of marketability. The methods used to estimate the fair value of the Level 3 assets are discussed in Note 7.

There were no transfers between levels of the fair value hierarchy during the nine months ended September 30, 2018.

Liabilities

The carrying values of the Company's long-term debt, excluding the Convertible Notes as discussed below, approximates fair value due to the length of time to maturity and/or the existence of interest rates that approximate prevailing market rates.

The calculated fair value of the Convertible Notes (Note 12) is approximately $237,000 as of September 30, 2018 and is based on the most recent third party trade of the instrument as of the balance sheet date. The fair value of the Convertible Notes are classified as Level 2 within the fair value hierarchy as there is not an active market for the Convertible Notes, however, third party trades of the instrument are considered observable inputs. The Convertible Notes are reflected at amortized cost on the accompanying consolidated balance sheet which was $145,839 as of September 30, 2018.

The Company's contingent consideration liabilities from previous acquisitions are measured on a recurring basis and were $585 at September 30, 2018 and December 31, 2017. These fair value measurements were based on significant inputs not observable in the market and thus represented a Level 3 measurement. A significant change in unobservable inputs could result in a significant impact on the fair value of the Company's contingent consideration liabilities. The contingent consideration liabilities are remeasured to fair value at each reporting date until the contingencies are resolved, and those changes in fair value are recognized in earnings. There were no changes in the fair value of the Level 3 liabilities during the nine months ended September 30, 2018.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Inventory

9 Months Ended

Sep. 30, 2018

Inventory Disclosure [Abstract]

Inventory

Inventory consists of the following:



	September 30, 2018		December 31, 2017
Supplies, embryos and other production materials	$	3,368	$	2,673
Work in process	4,578		4,767
Livestock	8,453		11,040
Feed	1,895		2,013
Total inventory	$	18,294	$	20,493

Property, Plant and Equipment, Net

9 Months Ended

Sep. 30, 2018

Property, Plant and Equipment [Abstract]

Property, Plant and Equipment, Net

Property, plant and equipment consist of the following:



	September 30, 2018			December 31, 2017
Land and land improvements	$	12,373		$	11,767
Buildings and building improvements	18,533			18,183
Furniture and fixtures	1,716			2,515
Equipment	72,126			65,863
Leasehold improvements	25,281			25,277
Breeding stock	4,827			3,832
Computer hardware and software	11,490			10,128
Trees	10,635			6,642
Construction and other assets in progress	18,658			14,113
	175,639			158,320
Less: Accumulated depreciation and amortization	(52,932		)	(45,646		)
Property, plant and equipment, net	$	122,707		$	112,674

During the three and nine months ended September 30, 2018, the Company recorded losses of $85 and $5,057, respectively, on disposal of certain leasehold improvements, equipment, and other fixed assets in conjunction with the closing of one of its research and development facilities in Brazil.

Depreciation expense was $3,614 and $2,989 for the three months ended September 30, 2018 and 2017, respectively, and $10,712 and $8,623 for the nine months ended September 30, 2018 and 2017, respectively.

Goodwill and Intangible Assets, Net

9 Months Ended

Sep. 30, 2018

Goodwill and Intangible Assets Disclosure [Abstract]

Goodwill and Intangible Assets, Net

The changes in the carrying amount of goodwill for the nine months ended September 30, 2018 are as follows:



Balance at December 31, 2017	$	153,289
Foreign currency translation adjustments	(2,013		)
Balance at September 30, 2018	$	151,276

The Company had $13,823 of accumulated impairment losses as of September 30, 2018 and December 31, 2017.

Intangible assets consist of the following as of September 30, 2018:



	Gross Carrying Amount		Accumulated Amortization			Net
Patents, developed technologies and know-how	$	257,318	$	(56,551	)	$	200,767
Customer relationships	10,700		(7,346		)	3,354
Trademarks	6,800		(3,148		)	3,652
In-process research and development	5,471		—			5,471
Total	$	280,289	$	(67,045	)	$	213,244

Intangible assets consist of the following as of December 31, 2017:



	Gross Carrying Amount		Accumulated Amortization			Net
Patents, developed technologies and know-how	$	263,615	$	(44,954	)	$	218,661
Customer relationships	10,700		(6,383		)	4,317
Trademarks	6,800		(2,567		)	4,233
In-process research and development	5,666		—			5,666
Total	$	286,781	$	(53,904	)	$	232,877

The balance of in-process research and development includes certain in-process research and development technology acquired

in the Company's acquisition of Oxitec in September 2015, and amortization will begin once certain regulatory approvals have

been obtained for the in-process programs.

Amortization expense was $4,689 and $5,001 for the three months ended September 30, 2018 and 2017, respectively, and $14,472 and $14,258 for the nine months ended September 30, 2018 and 2017, respectively.

Lines of Credit and Long-Term Debt

9 Months Ended

Sep. 30, 2018

Debt Disclosure [Abstract]

Lines of Credit and Long-Term Debt

Lines of Credit

Trans Ova has a $5,000 revolving line of credit with First National Bank of Omaha, which matures on May 1, 2019. The line of credit bears interest at the greater of 2.95% above the London Interbank Offered Rate or 3.00%, and the actual rate was 5.06% as of September 30, 2018. As of September 30, 2018, there was no outstanding balance. The amount available under the line of credit is based on eligible accounts receivable and inventory up to the maximum principal amount. The line of credit is collateralized by certain of Trans Ova's assets and contains certain restricted covenants that include maintaining minimum tangible net worth and working capital and maximum allowable annual capital expenditures. Trans Ova was in compliance with these covenants as of September 30, 2018.

Exemplar has a $700 revolving line of credit with American State Bank, which matures on October 30, 2019. As of September 30, 2018, the line of credit bore interest at 5.25% per annum. As of September 30, 2018, there was an outstanding balance of $200.

Long-Term Debt

Long-term debt consists of the following:



	September 30, 2018		December 31, 2017
Convertible debt	$	175,899	$	—
Notes payable	4,667		5,010
Royalty-based financing	2,147		2,132
Other	966		895
Long-term debt	183,679		8,037
Less current portion	546		502
Long-term debt, less current portion	$	183,133	$	7,535

Convertible Debt

Intrexon Convertible Notes

In July 2018, Intrexon completed a registered underwritten public offering of $200,000 aggregate principal amount of Convertible Notes and issued the Convertible Notes under an indenture (the "Base Indenture") between Intrexon and The Bank of New York Mellon Trust Company, N.A., as trustee, as supplemented by the First Supplemental Indenture (together with the Base Indenture, the "Indenture"). Intrexon received net proceeds of $193,958 after deducting underwriting discounts and offering expenses of $6,042.

The Convertible Notes are senior unsecured obligations of Intrexon and bear interest at a rate of 3.50% per year, payable semiannually in arrears on January 1 and July 1 of each year beginning on January 1, 2019. The Convertible Notes mature on July 1, 2023, unless earlier repurchased or converted. The Convertible Notes are convertible into cash, shares of Intrexon's common stock or a combination of cash and shares, at Intrexon's election. The initial conversion rate of the Convertible Notes is 58.6622 shares of Intrexon common stock per $1,000 principal amount of Convertible Notes (equivalent to an initial conversion price of approximately $17.05 per share of common stock). The conversion rate is subject to adjustment upon the occurrence of certain events, but will not be adjusted for any accrued and unpaid interest. In addition, following certain corporate events that occur prior to the maturity date as defined in the Indenture, Intrexon will increase the conversion rate for a holder who elects to convert its Convertible Notes in connection with such a corporate event in certain circumstances. Prior to April 1, 2023, the holders may convert the Convertible Notes at their option only upon the satisfaction of the following circumstances:


•	During any calendar quarter commencing after the calendar quarter ending on September 30, 2018, if the last reported sales price of Intrexon's common stock for at least 20 trading days (whether or not consecutive) during the last 30 consecutive trading days of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day;


•	During the five business day period after any five consecutive trading day period in which the trading price, as defined in the Indenture, for the Convertible Notes is less than 98% of the product of the last reported sales price of Intrexon's common stock and the conversion rate for the Convertible Notes on each such trading day; or


•	Upon the occurrence of specified corporate events as defined in the Indenture.

None of the above events allowing for conversion prior to April 1, 2023 occurred during the three months ended September 30, 2018. On or after April 1, 2023 until June 30, 2023, holders may convert their Convertible Notes at any time. Intrexon may not redeem the Notes prior to the maturity date.

If Intrexon undergoes a fundamental change, as defined in the Indenture, holders of the Convertible Notes may require Intrexon to repurchase for cash all or any portion of their Convertible Notes at a fundamental change repurchase price equal to 100% of the principal amount of the Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date. The Indenture contains customary events of default, as defined in the agreement, and, if any of the events occur, could require repayment of a portion or all of the Convertible Notes, including accrued and unpaid interest. Additionally, the Indenture provides that Intrexon shall not consolidate with or merge with or into, or sell, convey, transfer or lease all or substantially all of its properties and assets to, another entity, unless (i) the surviving entity is organized under the laws of the United States and such entity expressly assumes all of Intrexon's obligations under the Convertible Notes and the Indenture; and (ii) immediately after such transaction, no default or event of default has occurred and is continuing under the Indenture.

The net proceeds received from the issuance of the Convertible Notes were initially allocated between long-term debt, the liability component, at $143,723 and additional paid-in capital, the equity component, at $50,235. Additional paid-in capital was further reduced by $13,367 of deferred taxes resulting from the difference between the carrying amount and the tax basis of the Convertible Notes that is created by the equity component (Note 13). As of September 30, 2018, the outstanding principal balance on the Convertible Notes was $200,000 and the carrying value of long-term debt was $145,839. The effective interest rate on the Convertible Notes, including amortization of the long-term debt discount and debt issuance costs, is 11.02%. As of September 30, 2018, the unamortized long-term debt discount and debt issuance costs totaled $54,161.

Total interest expense related to the Convertible Notes was $3,847 for the three and nine months ended September 30, 2018, which consists of $1,731 interest expense to be paid in cash and $2,116 of non-cash interest expense. Accrued cash interest of $1,731 is included in other accrued liabilities on the accompanying consolidated balance sheet as of September 30, 2018.

ActoBio Convertible Notes

In September 2018, ActoBio issued $30,000 of convertible promissory notes (the "ActoBio Notes") to a related party in conjunction with an asset acquisition with Harvest (Note 3). The ActoBio Notes have a maturity date of September 6, 2020, accrue interest at 3.0% compounded annually, are convertible into shares of ActoBio common stock at any time by the holder, and are automatically convertible in shares of ActoBio common stock upon the closing of certain financing events as defined in the ActoBio Notes. If the ActoBio Notes have not been converted to ActoBio common stock by the maturity date, ActoBio can pay the principal and accrued interest in cash or with shares of Intrexon common stock at its election. There are no embedded features that are required to be separated from the debt host and accounted for separately, so the ActoBio Notes are recorded at $30,000. Interest expense for the three and nine months ended September 30, 2018 was $60. As of September 30, 2018, the carrying value of the ActoBio Notes, including accrued interest, was $30,060.

Notes Payable

Trans Ova has a note payable to American State Bank, which matures in April 2033 and has an outstanding principal balance of $4,581 as of September 30, 2018. Trans Ova pays monthly installments of $39, which includes interest at 3.95%. The note payable is collateralized by certain of Trans Ova's real estate and non-real estate assets.

Royalty-based Financing

AquaBounty has a royalty-based financing grant from the Atlantic Canada Opportunities Agency, a Canadian government agency, to provide funding of a research and development project. The total amount available under the award was $2,225, which AquaBounty claimed over a five year period. All amounts claimed by AquaBounty must be repaid in the form of a 10% royalty on any products commercialized out of this research and development project until fully paid. Because the timing of commercialization is subject to additional regulatory considerations, the timing of repayment is uncertain. As of the date of the acquisition by Intrexon in March 2013, AquaBounty had claimed $1,952 of the available funds and this amount was recorded at its acquisition date fair value of $1,107. The Company accretes the difference of $845 between the face value of amounts drawn and the acquisition date fair value over the expected period of repayment. Subsequent to the acquisition date, AquaBounty claimed the remaining balance available under the grant, resulting in total long-term debt of $2,147 as of September 30, 2018.

Future Maturities

Future maturities of long-term debt are as follows:



2018	$	210
2019	449
2020	30,463
2021	832
2022	375
2023	200,389
Thereafter	2,974
Total	$	235,692

The AquaBounty royalty-based financing grant is not included in the table above due to the uncertainty of the timing of repayment.

Income Taxes	9 Months Ended
Income Taxes	Sep. 30, 2018
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes Tax provisions for interim periods are calculated using an estimate of actual taxable income or loss for the respective period, rather than estimating the Company's annual effective income tax rate, as the Company is currently unable to reliably estimate its income for the full year. For the three and nine months ended September 30, 2018, the Company had U.S. taxable loss of approximately $39,100 and $104,400, respectively, and recorded $31 of current domestic income tax benefit and $82 of current domestic income tax expense, respectively. For the three and nine months ended September 30, 2018, the Company recognized $45 and $282, respectively, of current foreign income tax benefit. For the three and nine months ended September 30, 2017, the Company had U.S. taxable income of approximately $3,930 and $23,680, respectively, and recorded $78 and $473, respectively, of current domestic income tax expense. For the three and nine months ended September 30, 2017, the Company recognized $121 and $343, respectively, of current foreign income tax benefit. For the three and nine months ended September 30, 2018, the Company recorded deferred tax benefit of $14,246 and $19,335, respectively. Of these amounts, $13,367 relates to deferred tax benefits recognized from the reversal of valuation allowances on current year domestic operating losses in the same amount as the deferred taxes recorded as a direct reduction of additional paid-in capital related to the issuance of the Convertible Notes (Note 12). The Company considered amounts recorded directly to shareholders' equity in evaluating the need for a valuation allowance on deferred tax assets related to continuing operations. For the three and nine months ended September 30, 2017, the Company recorded deferred tax benefit of $775 and $2,294, respectively. The Company's net deferred tax assets, excluding certain deferred tax liabilities totaling $9,363, are offset by a valuation allowance due to the Company's history of net losses combined with an inability to confirm recovery of the tax benefits of the Company's losses and other net deferred tax assets. In assessing the realizability of deferred tax assets, management considers whether it is more likely than not that some portion or all of the deferred tax assets will not be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during the periods in which those temporary differences become deductible. Management considers the scheduled reversal of deferred tax liabilities, projected future taxable income and tax planning strategies in making this assessment. As of September 30, 2018, the Company has loss carryforwards for U.S. federal income tax purposes of approximately $357,000 available to offset future taxable income, and federal and state research and development tax credits of approximately $7,900, prior to consideration of annual limitations that may be imposed under Section 382 of the Internal Revenue Code of 1986, as amended. These carryforwards will begin to expire in 2022. As of September 30, 2018, the Company's direct foreign subsidiaries have foreign loss carryforwards of approximately $159,700, most of which do not expire. In 2017, the Company recorded a net provisional income tax benefit of $2,185 upon enactment of the Tax Act, which is comprised of several items. Amounts related to the remeasurement of most of the Company's domestic deferred tax assets as a result of the U.S. corporate rate change to 21% as part of the Tax Act were $87,473, which was fully offset by a reduction in the Company's valuation allowance. The Company's net U.S. deferred tax liability that is not offset by a valuation allowance was similarly written down, and the Company recorded a provisional deferred tax benefit of $1,730. The Company also recorded a provisional current tax benefit of $455, subsequently reduced to $13 in the three and nine months ended September 30, 2018, related to the expected refundability of accumulated corporate minimum tax credits. The Company has provisionally estimated its transition tax exposure to be zero, as any accumulated earnings in foreign subsidiaries are offset by accumulated deficits in other foreign subsidiaries. The provisional amounts recorded are subject to further refinement within the measurement period prescribed by SAB 118. As a result, the recorded amounts are subject to change, possibly materially, due to, among other things, changes in interpretations of the Tax Act, any legislative action to address questions that arise because of the Tax Act, any changes in accounting standards for income taxes or related interpretations in response to the Tax Act, or any updates or changes to estimates the Company utilized to provisionally compute the transition impact. No other adjustments to these provisional amounts were recorded during the nine months ended September 30, 2018.

Shareholders' Equity

9 Months Ended

Sep. 30, 2018

Equity [Abstract]

Shareholders' Equity

Issuances of Common Stock

In January 2018, Intrexon closed a public offering of 6,900,000 shares of its common stock, including 1,000,000 shares of common stock purchased by affiliates of Third Security. The net proceeds of the offering were $82,374, after deducting underwriting discounts of $3,688 and offering expenses of $188, all of which were capitalized.

Share Lending Agreement

Concurrently with the offering of the Convertible Notes (Note 12), Intrexon entered into a share lending agreement (the "Share Lending Agreement") with J.P. Morgan Securities LLC (the "Share Borrower") pursuant to which Intrexon loaned and delivered 7,479,431 shares of its common stock (the "Borrowed Shares") to the Share Borrower. The Share Lending Agreement will terminate, and the Borrowed Shares will be returned to Intrexon within five business days of such termination, upon (a) termination by the Share Borrower or (b) the earliest to occur of (i) October 1, 2023 and (ii) the date, if any, on which the Share Lending Agreement is either mutually terminated or terminated by one party upon a default by the other party. The Borrowed Shares were offered and sold to the public at a price of $13.37 per share under a registered offering (the "Borrowed Shares Offering"). Intrexon did not receive any proceeds from the sale of the Borrowed Shares to the public. The Share Borrower or its affiliates received all the proceeds from the sale of the Borrowed Shares to the public. Affiliates of Third Security purchased all of the shares of common stock in the Borrowed Shares Offering.

The Share Lending Agreement was entered into at fair value and met the requirements for equity classification. Therefore, the value is netted against the issuance of the Borrowed Shares in additional paid-in capital. Additionally, the Borrowed Shares are not included in the denominator for loss per share attributable to Intrexon shareholders unless the Share Borrower defaults on the Share Lending Agreement.

Components of Accumulated Other Comprehensive Loss

The components of accumulated other comprehensive loss are as follows:



	September 30, 2018			December 31, 2017
Unrealized loss on investments	$	(96	)	$	(2	)
Loss on foreign currency translation adjustments	(22,804		)	(15,552		)
Total accumulated other comprehensive loss	$	(22,900	)	$	(15,554	)

Share-Based Payments

9 Months Ended

Sep. 30, 2018

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Share-Based Payments

The Company records the fair value of stock options and restricted stock units ("RSUs") issued to employees and nonemployees as of the grant date as stock-based compensation expense. Stock-based compensation expense for employees and nonemployees is recognized over the requisite service period, which is typically the vesting period. Stock-based compensation costs included in the consolidated statements of operations are presented below:



	Three Months Ended September 30,				Nine Months Ended September 30,
	2018		2017		2018		2017
Cost of products	$	14	$	30	$	64	$	86
Cost of services	51		82		207		242
Research and development	1,681		2,383		7,315		7,018
Selling, general and administrative	6,386		9,562		20,754		24,603
Total	$	8,132	$	12,057	$	28,340	$	31,949

Intrexon Stock Option Plans

In April 2008, Intrexon adopted the 2008 Equity Incentive Plan (the "2008 Plan") for employees and nonemployees pursuant to which Intrexon's board of directors granted share based awards, including stock options, to officers, key employees and nonemployees. Upon the effectiveness of the 2013 Omnibus Incentive Plan (the "2013 Plan"), no new awards may be granted under the 2008 Plan. As of September 30, 2018, there were 414,754 stock options outstanding under the 2008 Plan.

Intrexon adopted the 2013 Plan for employees and nonemployees pursuant to which Intrexon's board of directors may grant share based awards, including stock options and shares of common stock, to employees, officers, consultants, advisors, and nonemployee directors. The 2013 Plan became effective upon the closing of the Company's initial public offering in August 2013, and as of September 30, 2018, there were 20,000,000 shares authorized for issuance under the 2013 Plan, of which 10,745,770 stock options and 980,758 RSUs were outstanding and 5,310,530 shares were available for grant.

Stock option activity was as follows:



	Number of Shares		Weighted Average Exercise Price			Weighted Average Remaining Contractual Term (Years)
Balances at December 31, 2017	11,382,747		$	28.99		7.32
Granted	1,174,839		15.04
Exercised	(41,314	)	(6.33		)
Forfeited	(808,086	)	(21.41		)
Expired	(547,662	)	(27.40		)
Balances at September 30, 2018	11,160,524		28.23			6.79
Exercisable at September 30, 2018	7,177,315		30.15			6.02

During the nine months ended September 30, 2018, Intrexon granted 1,069,126 RSUs with a weighted average grant date fair value of $13.84 per share, of which 25,000 have vested and 980,758 remain outstanding and unvested as of September 30, 2018.

Intrexon currently uses authorized and unissued shares to satisfy share award exercises.

In October 2015, the compensation committee and the independent members of Intrexon's board of directors approved a compensation arrangement whereby the Company's Chief Executive Officer ("CEO") would receive a monthly salary. Previously, the CEO did not receive compensation for his services as an employee of the Company other than through his participation in the Company's Annual Executive Incentive Plan, which became effective January 1, 2015. Pursuant to the compensation agreement, the CEO receives a base salary of $200 per month payable in fully vested shares of Intrexon common stock with such shares subject to a three-year lock-up on resale. The monthly number of shares of common stock is calculated based on the closing price on the last trading day of each month and the shares are issued pursuant to the terms of a Restricted Stock Unit Agreement ("RSU Agreement") that was executed between Intrexon and the CEO pursuant to the terms of the 2013 Plan. The RSU Agreement became effective in November 2015, and had an initial term of twelve months. The independent members of Intrexon's board of directors, with the recommendation of the compensation committee of the board of directors, subsequently approved extensions of the RSU Agreement through March 31, 2019, all of which are on the same terms as the original RSU Agreement. The fair value of the shares issued as compensation for services is included in selling, general and administrative expenses in the Company's consolidated statements of operations and totaled $499 and $480 for the three months ended September 30, 2018 and 2017, respectively, and $1,468 and $1,428 for the nine months ended September 30, 2018 and 2017, respectively.

AquaBounty Stock Option Plans

In March 2016, AquaBounty's board of directors adopted the AquaBounty 2016 Equity Incentive Plan ("AquaBounty 2016 Plan") to replace the AquaBounty 2006 Equity Incentive Plan ("AquaBounty 2006 Plan"). The AquaBounty 2016 Plan provides for the issuance of incentive stock options, non-qualified stock options and awards of restricted and direct stock purchases to directors, officers, employees, and consultants of AquaBounty. The AquaBounty 2016 Plan was approved by AquaBounty's shareholders at its annual meeting in April 2016. Upon the effectiveness of the AquaBounty 2016 Plan, no new awards may be granted under the AquaBounty 2006 Plan.

As of September 30, 2018, there were 339,964 options outstanding under both AquaBounty plans, of which 271,467 were exercisable, at a weighted average exercise price of $7.09 per share.

Commitments and Contingencies

9 Months Ended

Sep. 30, 2018

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Operating Leases

The Company leases certain facilities and equipment under noncancelable operating leases. The equipment leases are renewable at the option of the Company. At September 30, 2018, future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows:



2018	$	1,508
2019	9,417
2020	9,577
2021	8,904
2022	8,072
2023	7,009
Thereafter	31,330
Total	$	75,817

Rent expense, including other facility expenses, was $3,286 and $3,165 for the three months ended September 30, 2018 and 2017, respectively, and $9,874 and $7,772 for the nine months ended September 30, 2018 and 2017, respectively.

Purchase Commitments

As of September 30, 2018, the Company had outstanding contractual purchase commitments of $8,826, which primarily relate to amounts that will be paid in 2018, 2019, and 2020 upon delivery of commercial non-browning apple trees.

Contingencies

In March 2012, Trans Ova was named as a defendant in a licensing and patent infringement suit brought by XY, LLC ("XY") alleging that certain of Trans Ova's activities breached a 2004 licensing agreement and infringed on patents that XY allegedly owned. Trans Ova filed a number of counterclaims in the case. In Colorado District Court, the matter proceeded to a jury trial in January 2016. The jury determined that XY and Trans Ova had each breached the licensing agreement and that Trans Ova had infringed XY's patents. In April 2016, the court issued its post-trial order, awarding $528 in damages to Trans Ova and $6,066 in damages to XY. The order also provided Trans Ova with a compulsory license to XY's technology, subject to an ongoing royalty obligation. Both parties appealed the district court's order, which appeal was decided in May 2018 by the Court of Appeals for the Federal Circuit. The Court denied Trans Ova's appeal of its claims for antitrust, breach of contract and patent invalidity (except as to one patent, for which the Court affirmed invalidity in a separate, same-day ruling in a third-party case). The Court considered the issue of willfulness to be moot since the district court did not award damages for the willfulness finding. Finally, the Court remanded the district court's calculation of the ongoing royalty and instructed the district court to re-calculate the ongoing royalty in light of post-verdict economic factors.

Since the inception of the 2004 agreement, Trans Ova has remitted payments to XY pursuant to the terms of that agreement, or pursuant to the terms of the April 2016 court order, and has recorded these payments in cost of services in the consolidated statements of operations for the respective periods. For the period from inception of the 2004 agreement through the court's April 2016 order, aggregate royalty and license payments were $3,170, of which $2,759 had not yet been deposited by XY. In 2016, the Company recorded expense of $4,228 representing the excess of the net damages awarded to XY, including prejudgment interest, over the liability previously recorded by Trans Ova for uncashed checks previously remitted to XY. In August 2016, Trans Ova deposited the net damages amount, including prejudgment interest, into the court's treasury, to be held until the appeals process is complete and final judgment amounts are determined. As of September 30, 2018, this amount is included in restricted cash on the accompanying consolidated balance sheet. In December 2016, Trans Ova elected to void the outstanding checks discussed above, and these amounts have been reclassified to other accrued liabilities on the accompanying consolidated balance sheets as of September 30, 2018 and December 31, 2017.

In December 2016, XY filed a complaint for patent infringement and trade secret misappropriation against Trans Ova in the District Court of Waco, Texas. Since the claims in this 2016 complaint directly relate to the 2012 licensing dispute and patent issues, Trans Ova filed and was granted a motion for change of venue to Colorado District Court. Trans Ova also filed a motion to dismiss, from which the Court recently dismissed nine of the twelve counts of the complaint. Presently, three counts for patent infringement remain pending. Trans Ova and the Company could elect to enter into a settlement agreement in order to avoid the further costs and uncertainties of litigation.

In January 2017, the Division of Enforcement of the SEC informed the Company of an investigation that the Company believes concerned certain issues raised by a previously disclosed consolidated putative shareholder class action lawsuit that was dismissed on November 1, 2017, and a previously disclosed shareholder derivative action that was dismissed on January 25, 2018. In September 2018, the Division of Enforcement informed the Company that it had concluded its investigation of these matters and that the Division of Enforcement does not intend to recommend enforcement action against the Company based on the investigation.

The Company may become subject to other claims, assessments and governmental investigations from time to time in the ordinary course of business. Such matters are subject to many uncertainties and outcomes are not predictable with assurance. The Company accrues liabilities for such matters when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. As of September 30, 2018 and December 31, 2017, the Company does not believe that any such matters, individually or in the aggregate, will have a material adverse effect on the Company's business, financial condition, results of operations, or cash flows.

Related Party Transactions	9 Months Ended
Related Party Transactions	Sep. 30, 2018
Related Party Transactions [Abstract]
Related Party Transactions	Related Party Transactions Third Security and Affiliates The Company's CEO and Chairman of the board of directors is also the Senior Managing Director and CEO of Third Security and owns 100% of the equity interests of Third Security. In November 2015, the independent members of Intrexon's board of directors, with the recommendation of the audit committee of the board of directors, approved the execution of a Services Agreement ("Services Agreement") with Third Security pursuant to which Third Security provides the Company with certain professional, legal, financial, administrative, and other support services necessary to support the Company and its CEO. As consideration for providing these services, Third Security is entitled to a fee of $800 per month to be paid in the form of fully-vested shares of the Company's common stock. The number of shares of common stock is calculated based on the closing price of the Company's common stock on the 15th day of each month. The payments made by the Company under the Services Agreement constitute, in the aggregate, an award under the 2013 Plan and are subject to the terms of the 2013 Plan (Note 15). The Services Agreement had a term of one year, can be terminated by the Company at any time, and may be extended only by agreement of the parties, including approval of a majority of the independent members of Intrexon's board of directors. The independent members of Intrexon's board of directors, with the recommendation of the audit committee of the board of directors, subsequently approved extensions of the Services Agreement through January 1, 2019. For the three months ended September 30, 2018 and 2017, the Company issued 166,143 shares and 118,828 shares, respectively, with values of $2,417 and $2,251, respectively, to Third Security as payment for services pursuant to the Services Agreement. For the nine months ended September 30, 2018 and 2017, the Company issued 466,460 shares and 329,649 shares, respectively, with values of $6,522 and $6,506, respectively, to Third Security as payment for services pursuant to the Services Agreement. In addition to the foregoing Services Agreement, the Company reimburses Third Security for certain out-of-pocket expenses incurred on the Company's behalf, and the total expenses incurred by the Company under this arrangement were $16 and $4 for the three months ended September 30, 2018 and 2017, respectively, and $33 and $428 for the nine months ended September 30, 2018 and 2017, respectively. See also Note 15 regarding compensation arrangements between the Company and its CEO. In October 2017, the Company entered into a Preferred Stock Equity Facility ("Preferred Stock Facility") with an affiliate of Third Security ("Third Security Affiliate"). Under the Preferred Stock Facility, the Company could, from time to time at its sole and exclusive option, issue and sell to the Third Security Affiliate, up to $100,000 of newly issued Series A Redeemable Preferred Stock ("Series A Preferred Stock"). In conjunction with the Company's July 2018 registered underwritten public offering of Convertible Notes (Note 14), the Preferred Stock Facility was terminated. No shares of Series A Preferred Stock had been issued under the Preferred Stock Facility. The Company also subleases certain administrative offices to Third Security. The significant terms of the lease mirror the terms of the Company's lease with the landlord, and the Company recorded sublease income of $22 and $10 for the three months ended September 30, 2018 and 2017, respectively, and $66 and $32 for the nine months ended September 30, 2018 and 2017, respectively. Transactions with ECC Parties In addition to entities controlled by Third Security, any entity in which the Company holds equity securities, including securities received as upfront or milestone consideration, and which also are party to a collaboration with the Company are considered to be related parties. The Company holds a promissory note convertible into shares of Fibrocell common stock ("convertible note") and warrants to purchase shares of Fibrocell common stock. As of September 30, 2018 and December 31, 2017, the value of the convertible note and warrants totaled $300 and $575, respectively, and is included in other assets on the accompanying consolidated balance sheets. See Note 7 for additional discussion of the Company's investments in Fibrocell. Other Related Parties In June 2015, the Company entered into an agreement with Harvest, an investment fund sponsored by Harvest Capital Strategies, LLC, and a related party based on ownership in the fund by affiliates of Third Security. Harvest was established to invest in life science research and development start-up opportunities that the Company offered to Harvest with exclusive rights of first-look and first negotiation. Based on this agreement, Harvest established six new collaboration entities, each of which entered into an ECC with the Company in a designated field. The terms of such ECCs were negotiated between the Company and Harvest. As consideration for providing exclusive rights of first-look and first negotiation for start-up opportunities, the Company received a portion of the management fee collected by the fund sponsor of Harvest. These fees are included in other income in the accompanying consolidated statements of operations and totaled $613 and $1,839 for the three and nine months ended September 30, 2017, respectively. In September 2017, the commitment period for Harvest was terminated and, as a result, the agreement with Harvest terminated. The termination of the agreement had no effect on the existing collaborations with Harvest-controlled entities. See Note 3 for further discussion of the asset acquisition of certain Harvest entities.

Net Loss per Share

9 Months Ended

Sep. 30, 2018

Earnings Per Share [Abstract]

Net Loss per Share

The following table presents the computation of basic and diluted net loss per share:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2018			2017			2018			2017
Historical net loss per share:
Numerator:
Net loss attributable to Intrexon	$	(57,324	)	$	(39,689	)	$	(168,871	)	$	(89,752	)
Denominator:
Weighted average shares outstanding, basic and diluted	129,518,989			120,518,885			128,843,991			119,741,291
Net loss attributable to Intrexon per share, basic and diluted	$	(0.44	)	$	(0.33	)	$	(1.31	)	$	(0.75	)

The following potentially dilutive securities as of September 30, 2018 and 2017, have been excluded from the above computations of diluted weighted average shares outstanding for the three and nine months then ended as they would have been anti-dilutive:



	September 30,
	2018	2017
Convertible debt	13,507,746	—
Options	11,160,524	12,641,770
Restricted stock units	980,758	—
Warrants	133,264	133,264
Total	25,782,292	12,775,034

Subsequent Events	9 Months Ended
Subsequent Events	Sep. 30, 2018
Subsequent Events [Abstract]
Subsequent Events	Subsequent Events In October 2018, the Company, through its wholly owned subsidiary Precigen, entered into a license agreement (the "License Agreement") with ZIOPHARM, which terminated and replaced the terms of the original ZIOPHARM ECC, including amendments. Pursuant to the terms of the License Agreement, the Company granted ZIOPHARM an exclusive, worldwide, royalty-bearing, sub-licensable license to research, develop and commercialize (i) products utilizing the Company's RheoSwitch gene switch ("RTS") to express IL-12 (the "IL-12 Products") for the treatment of cancer, (ii) chimeric antigen receptor ("CAR") products directed to (a) CD19 for the treatment of cancer (the "CD19 Products"), and (b) a second target, subject to the rights of Ares Trading S.A. ("Ares Trading") to pursue such target under the License and Collaboration Agreement entered into between the Company and Ares Trading (the "Merck Agreement"), and (iii) T-cell receptor ("TCR") products (the "TCR Products") designed for neoantigens for the treatment of cancer or the treatment and prevention of human papilloma virus ("HPV") to the extent that the primary reason for such treatment or prevention is to prevent cancer, which is referred to as the HPV Field. The Company has also granted ZIOPHARM an exclusive, worldwide, royalty-bearing, sub-licensable license for certain patents relating to the Company's Sleeping Beauty technology to research, develop and commercialize TCR Products for both neoantigens and shared antigens for the treatment of cancer and in the HPV Field. ZIOPHARM will be solely responsible for all aspects of the research, development and commercialization of the exclusively licensed products for the treatment of cancer. ZIOPHARM is required to use commercially reasonable efforts to develop and commercialize IL-12 Products and CD19 Products, and after a two-year period, the TCR Products. The Company also granted ZIOPHARM an exclusive, worldwide, royalty-bearing, sub-licensable license to research, develop and commercialize products utilizing an additional construct that expresses RTS IL-12 (the "Gorilla IL-12 Products") for the treatment of cancer and in the HPV Field. ZIOPHARM is responsible for all development costs associated with each of the licensed products, other than Gorilla IL-12 Products. ZIOPHARM and the Company will share the development costs and operating profits for Gorilla IL-12 Products, with ZIOPHARM responsible for 80% of the development costs and receiving 80% of the operating profits, and the Company responsible for the remaining 20% of the development costs and receiving 20% of the operating profits, except that ZIOPHARM will bear all development costs and the Company will share equally in operating profits for Gorilla IL-12 Products in the HPV Field. In consideration of the licenses and other rights granted by the Company, ZIOPHARM will pay the Company an annual license fee of $100 and has agreed to reimburse the Company up to $1,000, payable in four quarterly installments, with respect to historical Gorilla IL-12 Products. ZIOPHARM will make milestone payments, payable upon the initiation of later stage clinical trials and upon the approval of exclusively licensed products in various jurisdictions, totaling up to an additional $52,500 for each of four exclusively licensed products, up to an aggregate of $210,000. In addition, ZIOPHARM will pay the Company tiered royalties ranging from low-single digits to high-single digits on the net sales derived from the sales of any approved IL-12 Products and CAR products. ZIOPHARM will also pay the Company royalties ranging from low-single digits to mid-single digits on the net sales derived from the sales of any approved TCR Products, up to maximum royalty amount of $100,000 in the aggregate. ZIOPHARM will also pay the Company 20% of any sublicensing income received by ZIOPHARM relating to the licensed products. The Company will retain rights to research, develop and commercialize CAR products for all other targets, subject to the rights of Ares Trading to pursue such target under the Merck Agreement. In addition, the Company may research, develop and commercialize products for the treatment of cancer, outside of the products exclusively licensed to ZIOPHARM. The Company will pay ZIOPHARM royalties ranging from low-single digits to mid-single digits on the net sales derived from the sale of the Company's CAR products, up to $100,000. The Company will also be entitled to receive from ZIOPHARM reimbursement of costs incurred to transition the necessary knowledge and materials for ZIOPHARM programs for a period of up to one year from the effective date. The Company has agreed that, during the term of the License Agreement, it will not use the licensed intellectual property to research, develop or commercialize any exclusive product for the treatment of cancer. In addition, for a three year period following the effective date of the License Agreement, the Company will not research or develop products utilizing regulatable switches that control expression of IL-12 or TCR products designed for neoantigens, in each case for the treatment or prevention of cancer. The Company has agreed to amend the research and development agreement between the Company, ZIOPHARM, and the University of Texas MD Anderson Cancer Center or otherwise make arrangements in order to ensure that all of its benefits and rights therewith vest in ZIOPHARM from the Effective Date of the License Agreement. As between the parties, the Company has agreed to perform all of the obligations of ZIOPHARM under the Merck Agreement, other than an obligation of exclusivity thereunder and ZIOPHARM will remain responsible for all payments owed to Ares Trading with respect to CD19 and the other target under the Merck Agreement as a result of ZIOPHARM's, its affiliates' or its sublicensees' exploitation of CAR products. Further, the Company is entitled to receive all rights and financial considerations with respect to all other CAR products, subject to the CAR royalties due to ZIOPHARM for such products. The License Agreement will terminate on a product-by-product and/or country-by-country basis upon the expiration of the later to occur of (i) the expiration of the last to expire patent claim for a licensed product, or (ii) 12 years after the first commercial sale of a licensed product in such country. In addition, ZIOPHARM may terminate the License Agreement on a country-by-country or program-by-program basis following written notice to the Company, and either party may terminate the License Agreement following notice of a material breach. Pursuant to the License Agreement, the 2016 Securities Issuance Agreement between the Company and ZIOPHARM was terminated as of the effective date of the License Agreement, all of the benefits, rights, obligations and liabilities thereunder immediately ceased and terminated and the Company returned to ZIOPHARM all of the Preferred Shares owned by the Company as of the Effective Date. The Company's investment in ZIOPHARM preferred stock was valued at $158,122 as of September 30, 2018. The Company will record the effects of the transaction during the fourth quarter of 2018. The Company is still evaluating the accounting impact but anticipates an impact to earnings resulting from the difference between the fair value of the Preferred Shares returned to ZIOPHARM and the reduction in deferred revenue expected to arise from the curtailment of the Company's obligation to perform services for ZIOPHARM.

Summary of Significant Accounting Policies (Policies)

9 Months Ended

Sep. 30, 2018

Accounting Policies [Abstract]

Basis of Presentation

Consolidation

The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated.

Revenue Recognition

Collaboration and licensing revenues

Product and service revenues

Equity Method Investments

Recently Issued and Adopted Accounting Pronouncements

Recently Adopted Accounting Pronouncements



	Three Months Ended September 30, 2018									Nine Months Ended September 30, 2018
	As Reported			Balances Without Adoption of ASC 606			Effect of Change			As Reported			Balances Without Adoption of ASC 606			Effect of Change
Consolidated Statements of Operations
Collaboration and licensing revenues	$	14,324		$	16,210		$	(1,886	)	$	51,622		$	58,305		$	(6,683	)
Net loss	(58,746		)	(56,860		)	(1,886		)	(172,984		)	(166,301		)	(6,683		)
Net loss attributable to Intrexon	(57,324		)	(55,438		)	(1,886		)	(168,871		)	(162,188		)	(6,683		)



	September 30, 2018
	As Reported			Balances Without Adoption of ASC 606			Effect of Change
Consolidated Balance Sheet
Liabilities
Deferred revenue, current	$	38,036		$	39,594		$	(1,558	)
Deferred revenue, net of current portion	136,942			156,803			(19,861		)
Total equity
Accumulated deficit	(990,080		)	(1,010,007		)	19,927
Accumulated other comprehensive loss	(22,900		)	(22,860		)	(40		)

Recently Issued Accounting Pronouncements

Summary of Significant Accounting Policies (Tables)

9 Months Ended

Sep. 30, 2018

New Accounting Pronouncements or Change in Accounting Principle [Line Items]

Summarized Financial Information for the Equity Method Investments



	September 30, 2018		December 31, 2017
Current assets	$	21,044	$	61,086
Noncurrent assets	27,827		13,598
Total assets	48,871		74,684
Current liabilities	5,324		6,213
Net assets	$	43,547	$	68,471



	Three Months Ended September 30,						Nine Months Ended September 30,
	2018			2017			2018			2017
Revenues	$	113		$	58		$	353		$	175
Operating expenses	11,621			9,693			30,762			33,128
Operating loss	(11,508		)	(9,635		)	(30,409		)	(32,953		)
Other, net	12			(145		)	33			37
Net loss	$	(11,496	)	$	(9,780	)	$	(30,376	)	$	(32,916	)

Accounting Standards Update 2014-09

New Accounting Pronouncements or Change in Accounting Principle [Line Items]

Schedule of New Accounting Pronouncements and Changes in Accounting Principles



	Three Months Ended September 30, 2018									Nine Months Ended September 30, 2018
	As Reported			Balances Without Adoption of ASC 606			Effect of Change			As Reported			Balances Without Adoption of ASC 606			Effect of Change
Consolidated Statements of Operations
Collaboration and licensing revenues	$	14,324		$	16,210		$	(1,886	)	$	51,622		$	58,305		$	(6,683	)
Net loss	(58,746		)	(56,860		)	(1,886		)	(172,984		)	(166,301		)	(6,683		)
Net loss attributable to Intrexon	(57,324		)	(55,438		)	(1,886		)	(168,871		)	(162,188		)	(6,683		)



	September 30, 2018
	As Reported			Balances Without Adoption of ASC 606			Effect of Change
Consolidated Balance Sheet
Liabilities
Deferred revenue, current	$	38,036		$	39,594		$	(1,558	)
Deferred revenue, net of current portion	136,942			156,803			(19,861		)
Total equity
Accumulated deficit	(990,080		)	(1,010,007		)	19,927
Accumulated other comprehensive loss	(22,900		)	(22,860		)	(40		)

Mergers and Acquisitions (Tables)

9 Months Ended

Sep. 30, 2018

Business Acquisition [Line Items]

Condensed Pro forma Financial Information

The following condensed pro forma financial information for the nine months ended September 30, 2017 is presented as if the acquisition had been consummated on January 1, 2016:



	Nine Months Ended September 30,
	2017
	Pro forma
Revenues	$	154,185
Loss before income taxes	(102,305		)
Net loss	(100,330		)
Net loss attributable to the noncontrolling interests	3,123
Net loss attributable to Intrexon	(97,207		)

GenVec, Inc.

Business Acquisition [Line Items]

Fair Value of Consideration Transferred

The fair value of the total consideration transferred was $17,582. The acquisition date fair value of each class of consideration transferred is presented below:



Common shares	$	15,616
Warrants	1,381
Contingent consideration	585
	$	17,582

Fair Value of Assets Acquired and Liabilities Assumed

The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below:



Cash and cash equivalents	$	2,054
Short-term investments	542
Trade receivables	75
Other receivables	97
Prepaid expenses and other	227
Property and equipment	250
Intangible assets	14,000
Other noncurrent assets	58
Total assets acquired	17,303
Accounts payable	2,158
Accrued compensation and benefits	1,226
Other accrued expenses	856
Other long-term liabilities	92
Deferred tax liabilities	239
Total liabilities assumed	4,571
Net assets acquired	12,732
Goodwill	4,850
Total consideration	$	17,582

Collaboration and Licensing Revenue (Tables)

9 Months Ended

Sep. 30, 2018

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Summarized Collaboration and Licensing Revenues



	Three Months Ended September 30,				Nine Months Ended September 30,
	2018		2017		2018		2017
ZIOPHARM Oncology, Inc.	$	4,826	$	10,373	$	13,626	$	31,322
Oragenics, Inc.	705		475		867		1,519
Fibrocell Science, Inc.	391		1,683		1,015		5,375
Genopaver, LLC	689		1,422		3,076		4,615
S & I Ophthalmic, LLC	—		376		—		751
OvaXon, LLC	—		262		—		1,966
Intrexon Energy Partners, LLC	1,329		1,903		3,345		8,909
Persea Bio, LLC	199		266		714		821
Ares Trading S.A.	1,576		2,356		7,525		8,474
Intrexon Energy Partners II, LLC	754		816		1,685		2,921
Intrexon T1D Partners, LLC	368		1,462		2,399		3,882
Harvest start-up entities (1)	2,691		4,020		11,792		11,835
Other	796		2,741		5,578		6,994
Total	$	14,324	$	28,155	$	51,622	$	89,384

(1)

Summary of Deferred Revenue

Deferred revenue consists of the following:



	September 30, 2018		December 31, 2017
Collaboration and licensing agreements	$	170,356	$	231,583
Prepaid product and service revenues	3,119		4,681
Other	1,503		133
Total	$	174,978	$	236,397
Current portion of deferred revenue	$	38,036	$	42,870
Long-term portion of deferred revenue	136,942		193,527
Total	$	174,978	$	236,397

Summary of Deferred Revenue by Collaborator



	Average Remaining Performance Period (Years)	September 30, 2018		December 31, 2017
ZIOPHARM Oncology, Inc.	5.3	$	51,084	$	90,496
Oragenics, Inc.	5.7	6,240		6,719
Fibrocell Science, Inc.	6.1	17,846		16,607
Genopaver, LLC	5.5	1,346		1,704
Intrexon Energy Partners, LLC	5.5	13,164		15,625
Persea Bio, LLC	6.3	2,802		3,500
Ares Trading S.A.	5.6	34,608		40,789
Intrexon Energy Partners II, LLC	6.2	14,910		13,833
Intrexon T1D Partners, LLC	6.5	8,760		8,435
Harvest start-up entities (1)	6.4	8,007		18,400
Other	4.5	10,721		14,423
Total		$	169,488	$	230,531

(1)

Short-term Investments (Tables)

9 Months Ended

Sep. 30, 2018

Investments, Debt and Equity Securities [Abstract]

Summary of Amortized Cost, Gross Unrealized Gains and Losses, and Fair Value of Short-term Investments

The following table summarizes the amortized cost, gross unrealized gains and losses, and fair value of available-for-sale investments as of September 30, 2018:



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Aggregate Fair Value
U.S. government debt securities	$	163,905	$	—	$	(96	)	$	163,809
Certificates of deposit	353		—		—			353
Total	$	164,258	$	—	$	(96	)	$	164,162

The following table summarizes the amortized cost, gross unrealized gains and losses, and fair value of available-for-sale investments as of December 31, 2017:



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Aggregate Fair Value
U.S. government debt securities	$	6,000	$	—	$	(2	)	$	5,998
Certificates of deposit	275		—		—			275
Total	$	6,275	$	—	$	(2	)	$	6,273

Investments in Preferred Stock (Tables)

9 Months Ended

Sep. 30, 2018

Investment in Preferred Stock [Abstract]

Schedule of Changes in Level 3 Investments

The following table summarizes the changes in the Level 3 investments in preferred stock during the nine months ended September 30, 2018.



	Nine Months Ended September 30, 2018
Beginning balance	$	161,225
Dividend income from investments in preferred stock	14,575
Net unrealized depreciation in the fair value of the investments in preferred stock	(17,379		)
Ending balance	$	158,421

Fair Value Measurements (Tables)

9 Months Ended

Sep. 30, 2018

Fair Value Disclosures [Abstract]

Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis



	Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		September 30, 2018
Assets
U.S. government debt securities	$	—	$	163,809	$	—	$	163,809
Equity securities	3,591		1,106		—		4,697
Preferred stock	—		—		158,421		158,421
Other	—		653		—		653
Total	$	3,591	$	165,568	$	158,421	$	327,580



	Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)		Significant Unobservable Inputs (Level 3)		December 31, 2017
Assets
U.S. government debt securities	$	—	$	5,998	$	—	$	5,998
Equity securities	10,537		4,563		—		15,100
Preferred stock	—		—		161,225		161,225
Other	—		850		—		850
Total	$	10,537	$	11,411	$	161,225	$	183,173

Inventory (Tables)

9 Months Ended

Sep. 30, 2018

Inventory Disclosure [Abstract]

Schedule of Inventory

Inventory consists of the following:



	September 30, 2018		December 31, 2017
Supplies, embryos and other production materials	$	3,368	$	2,673
Work in process	4,578		4,767
Livestock	8,453		11,040
Feed	1,895		2,013
Total inventory	$	18,294	$	20,493

Property, Plant and Equipment, Net (Tables)

9 Months Ended

Sep. 30, 2018

Property, Plant and Equipment [Abstract]

Schedule of Property, Plant and Equipment

Property, plant and equipment consist of the following:



	September 30, 2018			December 31, 2017
Land and land improvements	$	12,373		$	11,767
Buildings and building improvements	18,533			18,183
Furniture and fixtures	1,716			2,515
Equipment	72,126			65,863
Leasehold improvements	25,281			25,277
Breeding stock	4,827			3,832
Computer hardware and software	11,490			10,128
Trees	10,635			6,642
Construction and other assets in progress	18,658			14,113
	175,639			158,320
Less: Accumulated depreciation and amortization	(52,932		)	(45,646		)
Property, plant and equipment, net	$	122,707		$	112,674

Goodwill and Intangible Assets, Net (Tables)

9 Months Ended

Sep. 30, 2018

Goodwill and Intangible Assets Disclosure [Abstract]

Schedule of Changes in Carrying Amount of Goodwill

The changes in the carrying amount of goodwill for the nine months ended September 30, 2018 are as follows:



Balance at December 31, 2017	$	153,289
Foreign currency translation adjustments	(2,013		)
Balance at September 30, 2018	$	151,276

Schedule of Intangible Assets

Intangible assets consist of the following as of September 30, 2018:



	Gross Carrying Amount		Accumulated Amortization			Net
Patents, developed technologies and know-how	$	257,318	$	(56,551	)	$	200,767
Customer relationships	10,700		(7,346		)	3,354
Trademarks	6,800		(3,148		)	3,652
In-process research and development	5,471		—			5,471
Total	$	280,289	$	(67,045	)	$	213,244

Intangible assets consist of the following as of December 31, 2017:



	Gross Carrying Amount		Accumulated Amortization			Net
Patents, developed technologies and know-how	$	263,615	$	(44,954	)	$	218,661
Customer relationships	10,700		(6,383		)	4,317
Trademarks	6,800		(2,567		)	4,233
In-process research and development	5,666		—			5,666
Total	$	286,781	$	(53,904	)	$	232,877

Lines of Credit and Long-Term Debt (Tables)

9 Months Ended

Sep. 30, 2018

Debt Disclosure [Abstract]

Schedule of Long-Term Debt Instruments

Long-term debt consists of the following:



	September 30, 2018		December 31, 2017
Convertible debt	$	175,899	$	—
Notes payable	4,667		5,010
Royalty-based financing	2,147		2,132
Other	966		895
Long-term debt	183,679		8,037
Less current portion	546		502
Long-term debt, less current portion	$	183,133	$	7,535

Schedule of Future Maturities of Long-Term Debt

Future maturities of long-term debt are as follows:



2018	$	210
2019	449
2020	30,463
2021	832
2022	375
2023	200,389
Thereafter	2,974
Total	$	235,692

- Definition

Tabular disclosure of long-debt instruments or arrangements, including identification, terms, features, collateral requirements and other information necessary to a fair presentation. These are debt arrangements that originally required repayment more than twelve months after issuance or greater than the normal operating cycle of the entity, if longer.

+ References

Reference 1: http://fasb.org/us-gaap/role/ref/legacyRef
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+ Details

Shareholders' Equity (Tables)

9 Months Ended

Sep. 30, 2018

Equity [Abstract]

Components of Accumulated Other Comprehensive Loss

The components of accumulated other comprehensive loss are as follows:



	September 30, 2018			December 31, 2017
Unrealized loss on investments	$	(96	)	$	(2	)
Loss on foreign currency translation adjustments	(22,804		)	(15,552		)
Total accumulated other comprehensive loss	$	(22,900	)	$	(15,554	)

Share-Based Payments (Tables)

9 Months Ended

Sep. 30, 2018

Disclosure of Compensation Related Costs, Share-based Payments [Abstract]

Schedule of Stock-Based Compensation Costs

Stock-based compensation costs included in the consolidated statements of operations are presented below:



	Three Months Ended September 30,				Nine Months Ended September 30,
	2018		2017		2018		2017
Cost of products	$	14	$	30	$	64	$	86
Cost of services	51		82		207		242
Research and development	1,681		2,383		7,315		7,018
Selling, general and administrative	6,386		9,562		20,754		24,603
Total	$	8,132	$	12,057	$	28,340	$	31,949

Schedule of Stock Option Activity

Stock option activity was as follows:



	Number of Shares		Weighted Average Exercise Price			Weighted Average Remaining Contractual Term (Years)
Balances at December 31, 2017	11,382,747		$	28.99		7.32
Granted	1,174,839		15.04
Exercised	(41,314	)	(6.33		)
Forfeited	(808,086	)	(21.41		)
Expired	(547,662	)	(27.40		)
Balances at September 30, 2018	11,160,524		28.23			6.79
Exercisable at September 30, 2018	7,177,315		30.15			6.02

Commitments and Contingencies (Tables)

9 Months Ended

Sep. 30, 2018

Commitments and Contingencies Disclosure [Abstract]

Future Minimum Lease Payments Under Noncancelable Operating Leases

At September 30, 2018, future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows:



2018	$	1,508
2019	9,417
2020	9,577
2021	8,904
2022	8,072
2023	7,009
Thereafter	31,330
Total	$	75,817

Net Loss per Share (Tables)

9 Months Ended

Sep. 30, 2018

Earnings Per Share [Abstract]

Computation of Basic and Diluted Net Loss per Share

The following table presents the computation of basic and diluted net loss per share:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2018			2017			2018			2017
Historical net loss per share:
Numerator:
Net loss attributable to Intrexon	$	(57,324	)	$	(39,689	)	$	(168,871	)	$	(89,752	)
Denominator:
Weighted average shares outstanding, basic and diluted	129,518,989			120,518,885			128,843,991			119,741,291
Net loss attributable to Intrexon per share, basic and diluted	$	(0.44	)	$	(0.33	)	$	(1.31	)	$	(0.75	)

Schedule of Antidilutive Securities Excluded from Computation of Net Loss per Share



	September 30,
	2018	2017
Convertible debt	13,507,746	—
Options	11,160,524	12,641,770
Restricted stock units	980,758	—
Warrants	133,264	133,264
Total	25,782,292	12,775,034

Organization (Details) - USD ($) $ in Thousands	1 Months Ended
Organization (Details) - USD ($) $ in Thousands	Jan. 31, 2018	Sep. 30, 2018	Dec. 31, 2017
Noncontrolling Interest [Line Items]
Net proceeds from public financing	$ 82,374
AquaBounty Technologies, Inc.
Noncontrolling Interest [Line Items]
Net proceeds from public financing	10,616
AquaBounty Technologies, Inc.
Noncontrolling Interest [Line Items]
Purchase of additional equity of majority-owned subsidiary	$ 5,000
Parent ownership interest	53.00%	52.00%	58.00%

Summary of Significant Accounting Policies - Revenue Recognition - Additional Information (Details)	9 Months Ended
	Sep. 30, 2018
Collaboration and licensing agreements
Disaggregation of Revenue [Line Items]
Typical required notice period for voluntary termination of collaboration agreement	90 days
Products and Services Revenues
Disaggregation of Revenue [Line Items]
Typical payment terms	30 days

Summary of Significant Accounting Policies - Equity Method Investments - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Dec. 31, 2017
Schedule of Equity Method Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 327,580		$ 327,580		$ 183,173
Oragenics, Inc.
Schedule of Equity Method Investments [Line Items]
Company's ownership percentage	7.90%		7.90%		29.40%
Equity securities \| Oragenics, Inc.
Schedule of Equity Method Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 1,538		$ 1,538		$ 3,085
Unrealized appreciation (depreciation) in fair value of equity securities	$ (387)	$ 827	$ (1,547)	$ (1,610)

Summary of Significant Accounting Policies - Summarized Unaudited Financial Information for the Equity Method Investments (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Dec. 31, 2017
Schedule of Equity Method Investments [Line Items]
Operating expenses	$ 98,919	$ 90,763	$ 286,117	$ 265,351
Operating loss	(66,471)	(44,747)	(168,728)	(111,398)
Other, net	(3,727)	6,086	(13,911)	27,632
Equity Method Investments
Schedule of Equity Method Investments [Line Items]
Current assets	21,044		21,044		$ 61,086
Noncurrent assets	27,827		27,827		13,598
Total assets	48,871		48,871		74,684
Current liabilities	5,324		5,324		6,213
Net assets	43,547		43,547		$ 68,471
Revenues	113	58	353	175
Operating expenses	11,621	9,693	30,762	33,128
Operating loss	(11,508)	(9,635)	(30,409)	(32,953)
Other, net	12	(145)	33	37
Net loss	$ (11,496)	$ (9,780)	$ (30,376)	$ (32,916)

Summary of Significant Accounting Policies - Variable Interest Entities - Additional Information (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Accounting Policies [Abstract]
Maximum risk of loss related to the identified VIEs	$ 179,433	$ 185,261

Summary of Significant Accounting Policies - Convertible Notes - Additional Information (Details)	Jul. 31, 2018
3.5% Convertible Notes Due 2023
Debt Instrument [Line Items]
Debt instrument, interest rate, stated percentage	3.50%

Summary of Significant Accounting Policies - Segment Information - Additional Information (Details) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018 USD ($)	Sep. 30, 2017 USD ($)	Sep. 30, 2018 USD ($) segment	Sep. 30, 2017 USD ($)	Dec. 31, 2017 USD ($)
Segment Reporting Information [Line Items]
Number of segments \| segment			1
Property, plant and equipment, net	$ 122,707		$ 122,707		$ 112,674
Foreign Countries
Segment Reporting Information [Line Items]
Property, plant and equipment, net	16,984		16,984		$ 21,837
Revenues	$ 2,235	$ 4,448	$ 10,389	$ 11,773

Summary of Significant Accounting Policies - Recently Issued and Adopted Accounting Pronouncements (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Jan. 01, 2018	Dec. 31, 2017	Dec. 31, 2016
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenues	$ 32,448	$ 46,016	$ 117,389	$ 153,953
Cumulative effect of adoption of ASC 606 (negated)					$ (26,507)
Net loss	(58,746)	(40,836)	(172,984)	(92,875)
Net loss attributable to Intrexon	(57,324)	(39,689)	(168,871)	(89,752)
Current portion of deferred revenue	38,036		38,036			$ 42,870
Long-term portion of deferred revenue	136,942		136,942			193,527
Accumulated deficit	(990,080)		(990,080)			(847,820)
Accumulated other comprehensive loss	(22,900)		(22,900)			(15,554)
Cash, cash equivalents, and restricted cash	89,837	71,644	89,837	71,644		75,545	$ 69,594
Calculated under Revenue Guidance in Effect before Topic 606 \| Accounting Standards Update 2014-09
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Net loss	(56,860)		(166,301)
Net loss attributable to Intrexon	(55,438)		(162,188)
Current portion of deferred revenue	39,594		39,594
Long-term portion of deferred revenue	156,803		156,803
Accumulated deficit	(1,010,007)		(1,010,007)
Accumulated other comprehensive loss	(22,860)		(22,860)
Difference between Revenue Guidance in Effect before and after Topic 606 \| Accounting Standards Update 2014-09
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Net loss	(1,886)		(6,683)
Net loss attributable to Intrexon	(1,886)		(6,683)
Current portion of deferred revenue	(1,558)		(1,558)
Long-term portion of deferred revenue	(19,861)		(19,861)
Accumulated deficit	19,927		19,927
Accumulated other comprehensive loss	(40)		(40)
Accounting Standards Update 2016-18
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Cash, cash equivalents, and restricted cash		7,428		7,428		$ 7,434	$ 6,987
Accumulated Deficit
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Cumulative effect of adoption of ASC 606 (negated)					(26,611)
Net loss			(168,871)
Accumulated Other Comprehensive Loss
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Cumulative effect of adoption of ASC 606 (negated)					$ 104
Collaboration and licensing agreements
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenues	14,324	$ 28,155	51,622	$ 89,384
Collaboration and licensing agreements \| Calculated under Revenue Guidance in Effect before Topic 606 \| Accounting Standards Update 2014-09
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenues	16,210		58,305
Collaboration and licensing agreements \| Difference between Revenue Guidance in Effect before and after Topic 606 \| Accounting Standards Update 2014-09
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenues	$ (1,886)		$ (6,683)

Mergers and Acquisitions - Asset Acquisition of Certain Harvest Entities (Details) - USD ($) $ in Thousands	1 Months Ended	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2018	Sep. 30, 2017	Aug. 31, 2018	Dec. 31, 2017
Business Acquisition [Line Items]
Long-term debt issued to a related party in an asset acquisition		$ 30,000	$ 0
Cash received in asset acquisition		15,500	(14,219)
Investments in affiliates	$ 17,944	17,944			$ 18,870
Deferred revenue	174,978	174,978			$ 236,397
Write-off of in-process research and development acquired in asset acquisition		$ 8,721	$ 0
Harvest Intrexon Enterprise Fund I, LP
Business Acquisition [Line Items]
Cash received in asset acquisition	15,500
Harvest Intrexon Enterprise Fund I, LP \| ActoBio Therapeutics Inc.
Business Acquisition [Line Items]
Long-term debt issued to a related party in an asset acquisition	$ 30,000
CRS Bio, Inc.; Genten Therapeutics, Inc.; and Relive Genetics, Inc.
Business Acquisition [Line Items]
Investments in affiliates				$ 4,303
Ownership interest	100.00%	100.00%
Deferred revenue	$ 10,078	$ 10,078
Write-off of in-process research and development acquired in asset acquisition	$ 8,721

Mergers and Acquisitions - GenVec - Additional Information (Details) - GenVec, Inc. - USD ($) $ in Thousands	1 Months Ended	3 Months Ended	9 Months Ended
	Jun. 30, 2017	Sep. 30, 2017	Sep. 30, 2017
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired	100.00%
Business combination, consideration paid, shares issued	684,240
Percent of collaboration payments	50.00%
Period subsequent to acquisition during which a portion of collaboration payments received will be paid to former stockholders of acquired entity	3 years
Expected useful life of intangible asset	11 years
Selling, general and administrative
Business Acquisition [Line Items]
Business combination, acquisition related costs		$ 9	$ 507

Mergers and Acquisitions - GenVec - Fair Value of Consideration Transferred (Details) - GenVec, Inc. $ in Thousands	1 Months Ended
	Jun. 30, 2017 USD ($)
Business Acquisition [Line Items]
Common shares	$ 15,616
Warrants	1,381
Contingent consideration	585
Total consideration transferred	$ 17,582

Mergers and Acquisitions - GenVec - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017	Jun. 30, 2017
Business Acquisition [Line Items]
Goodwill	$ 151,276	$ 153,289
GenVec, Inc.
Business Acquisition [Line Items]
Cash and cash equivalents			$ 2,054
Short-term investments			542
Trade receivables			75
Other receivables			97
Prepaid expenses and other			227
Property and equipment			250
Intangible assets			14,000
Other noncurrent assets			58
Total assets acquired			17,303
Accounts payable			2,158
Accrued compensation and benefits			1,226
Other accrued expenses			856
Other long-term liabilities			92
Deferred tax liabilities			239
Total liabilities assumed			4,571
Net assets acquired			12,732
Goodwill			4,850
Total consideration			$ 17,582

Mergers and Acquisitions - Condensed Pro forma Financial Information (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2017 USD ($)
Business Combinations [Abstract]
Revenues	$ 154,185
Loss before income taxes	(102,305)
Net loss	(100,330)
Net loss attributable to the noncontrolling interests	3,123
Net loss attributable to Intrexon	$ (97,207)

Investments in Joint Ventures - S & I Ophthalmic - Additional Information (Details) $ in Thousands	1 Months Ended		9 Months Ended		12 Months Ended
	Jan. 31, 2018 USD ($)	Oct. 31, 2013 USD ($)	Sep. 30, 2018 USD ($) board_seat	Sep. 30, 2017 USD ($)	Dec. 31, 2015 USD ($)
Schedule of Equity Method Investments [Line Items]
Return of investment upon dissolution of affiliate			$ 2,598	$ 0
S & I Ophthalmic, LLC
Schedule of Equity Method Investments [Line Items]
Capital contributions		$ 5,000			$ 5,000
Membership interest		50.00%
Total number of seats on the joint venture's governing board \| board_seat			4
Total number of seats on the joint venture's governing board, internally selected \| board_seat			2
Total number of seats on the joint venture's governing board, externally selected \| board_seat			2
Return of investment upon dissolution of affiliate	$ 2,598
S & I Ophthalmic, LLC \| Investors
Schedule of Equity Method Investments [Line Items]
Capital contributions		$ 5,000			$ 5,000
Membership interest		50.00%

Investments in Joint Ventures - OvaXon - Additional Information (Details) $ in Thousands	1 Months Ended	56 Months Ended
	Jan. 31, 2014 USD ($)	Sep. 30, 2018 USD ($) board_seat	Dec. 31, 2017 USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 17,944	$ 18,870
OvaXon, LLC
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 1,500	$ 4,350
Membership interest	50.00%
Total number of seats on the joint venture's governing board \| board_seat		4
Total number of seats on the joint venture's governing board, internally selected \| board_seat		2
Total number of seats on the joint venture's governing board, externally selected \| board_seat		2
OvaXon, LLC \| Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment		$ 140	$ 146
Investors \| OvaXon, LLC
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 1,500	$ 4,350
Membership interest	50.00%

Investments in Joint Ventures - Intrexon Energy Partners - Additional Information (Details)	1 Months Ended
	Mar. 31, 2014 USD ($)	Sep. 30, 2018 USD ($) board_seat	Dec. 31, 2017 USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 17,944,000	$ 18,870,000
Intrexon Energy Partners, LLC
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 25,000,000
Additional capital contributions committed, remaining commitment		$ 5,132,000
Total number of seats on the joint venture's governing board \| board_seat		5
Total number of seats on the joint venture's governing board, internally selected \| board_seat		2
Total number of seats on the joint venture's governing board, externally selected \| board_seat		3
Intrexon Energy Partners, LLC \| Other Accrued Liabilities
Schedule of Equity Method Investments [Line Items]
Investment		$ (506,000)	$ (444,000)
Intrexon Energy Partners, LLC \| Investors
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Capital contributions	$ 25,000,000
Maximum additional capital contribution committed	25,000,000
Upfront and Milestone Payments \| Intrexon Energy Partners, LLC \| Upfront
Schedule of Equity Method Investments [Line Items]
Collaborative arrangement consideration received, value	$ 25,000,000

Investments in Joint Ventures - Intrexon Energy Partners II - Additional Information (Details)	1 Months Ended
	Dec. 31, 2015 USD ($)	Sep. 30, 2018 USD ($) board_seat	Dec. 31, 2017 USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 17,944,000	$ 18,870,000
Intrexon Energy Partners II, LLC
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 10,000,000
Total number of seats on the joint venture's governing board \| board_seat		5
Total number of seats on the joint venture's governing board, internally selected \| board_seat		1
Total number of seats on the joint venture's governing board, externally selected \| board_seat		4
Intrexon Energy Partners II, LLC \| Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment		$ 184,000	$ 572,000
Intrexon Energy Partners II, LLC \| Investors
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Capital contributions	$ 18,000,000
Maximum additional capital contribution committed	10,000,000
Intrexon Energy Partners II, LLC \| All Investors
Schedule of Equity Method Investments [Line Items]
Capital contributions	4,000,000
Intrexon Energy Partners II, LLC \| Upfront and Milestone Payments \| Upfront
Schedule of Equity Method Investments [Line Items]
Collaborative arrangement consideration received, value	$ 18,000,000

Investments in Joint Ventures - EnviroFlight - Additional Information (Details) - USD ($) $ in Thousands	31 Months Ended
	Sep. 30, 2018	Dec. 31, 2017
Schedule of Equity Method Investments [Line Items]
Investment	$ 17,944	$ 18,870
EnviroFlight, LLC
Schedule of Equity Method Investments [Line Items]
Capital contributions	14,750
EnviroFlight, LLC \| Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment	15,286	$ 7,092
EnviroFlight, LLC \| Investors
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 14,750

Investments in Joint Ventures - Intrexon T1D Partners - Additional Information (Details)	1 Months Ended
	Mar. 31, 2016 USD ($)	Sep. 30, 2018 USD ($) board_seat	Dec. 31, 2017 USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 17,944,000	$ 18,870,000
Intrexon T1D Partners, LLC
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 5,000,000
Total number of seats on the joint venture's governing board \| board_seat		5
Total number of seats on the joint venture's governing board, internally selected \| board_seat		2
Total number of seats on the joint venture's governing board, externally selected \| board_seat		3
Intrexon T1D Partners, LLC \| Investors
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Capital contributions	$ 10,000,000
Maximum additional capital contribution committed	5,000,000
Intrexon T1D Partners, LLC \| Upfront \| Upfront and Milestone Payments
Schedule of Equity Method Investments [Line Items]
Collaborative arrangement consideration received, value	$ 10,000,000
Intrexon T1D Partners, LLC \| Other Accrued Liabilities
Schedule of Equity Method Investments [Line Items]
Investment		$ 0	$ (943,000)

Collaboration and Licensing Revenue - Summarized Collaboration and Licensing Revenues (Details) - USD ($)
$ in Thousands

3 Months Ended

9 Months Ended

Sep. 30, 2018

Sep. 30, 2017

Sep. 30, 2018

Sep. 30, 2017

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

$ 32,448

$ 46,016

$ 117,389

$ 153,953

Collaboration and licensing agreements

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

14,324

28,155

51,622

89,384

Collaboration and licensing agreements | ZIOPHARM Oncology, Inc.

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

4,826

10,373

13,626

31,322

Collaboration and licensing agreements | Oragenics, Inc.

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

705

475

867

1,519

Collaboration and licensing agreements | Fibrocell Science, Inc.

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

391

1,683

1,015

5,375

Collaboration and licensing agreements | Genopaver, LLC

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

689

1,422

3,076

4,615

Collaboration and licensing agreements | S & I Ophthalmic, LLC

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

376

751

Collaboration and licensing agreements | OvaXon, LLC

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

262

1,966

Collaboration and licensing agreements | Intrexon Energy Partners, LLC

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

1,329

1,903

3,345

8,909

Collaboration and licensing agreements | Persea Bio, LLC

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

199

266

714

821

Collaboration and licensing agreements | Ares Trading S.A.

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

1,576

2,356

7,525

8,474

Collaboration and licensing agreements | Intrexon Energy Partners II, LLC

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

754

816

1,685

2,921

Collaboration and licensing agreements | Intrexon T1D Partners, LLC

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

368

1,462

2,399

3,882

Collaboration and licensing agreements | Harvest start-up entities

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

^[1]

2,691

4,020

11,792

11,835

Collaboration and licensing agreements | Other

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Revenues

$ 796

$ 2,741

$ 5,578

$ 6,994

[1]

Collaboration and Licensing Revenue - Summary of Deferred Revenue (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Contract With Customer, Asset And Liability [Line Items]
Deferred revenue	$ 174,978	$ 236,397
Current portion of deferred revenue	38,036	42,870
Long-term portion of deferred revenue	136,942	193,527
Collaboration and licensing agreements
Contract With Customer, Asset And Liability [Line Items]
Deferred revenue	170,356	231,583
Prepaid product and service revenues
Contract With Customer, Asset And Liability [Line Items]
Deferred revenue	3,119	4,681
Other
Contract With Customer, Asset And Liability [Line Items]
Deferred revenue	$ 1,503	$ 133

Short-term Investments - Summary of Amortized Cost, Gross Unrealized Gains and Losses, and Fair Value of Short-term Investments (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Debt Securities, Available-for-sale [Line Items]
Aggregate Fair Value	$ 164,162	$ 6,273
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(96)	(2)
Amortized Cost	164,258	6,275
US Government Debt Securities [Member]
Debt Securities, Available-for-sale [Line Items]
Aggregate Fair Value	163,809	5,998
Gross Unrealized Gains	0	0
Gross Unrealized Losses	(96)	(2)
Amortized Cost	163,905	6,000
Certificates of Deposit [Member]
Debt Securities, Available-for-sale [Line Items]
Aggregate Fair Value	353	275
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Amortized Cost	$ 353	$ 275

Investments in Preferred Stock - Additional Information (Details)		1 Months Ended			3 Months Ended		9 Months Ended
	May 25, 2018	Nov. 30, 2017 USD ($)	Mar. 31, 2017 USD ($) shares	Jun. 30, 2016 $ / shares shares	Sep. 30, 2018 USD ($) shares	Sep. 30, 2017 USD ($) shares	Sep. 30, 2018 USD ($) $ / shares shares	Sep. 30, 2017 USD ($) shares	Dec. 31, 2017 USD ($)
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis					$ 327,580,000		$ 327,580,000		$ 183,173,000
Noncash dividend income							14,575,000	$ 12,303,000
Purchases of preferred stock and warrants							$ 0	$ 1,161,000
Fibrocell Science, Inc.
Schedule of Investments [Line Items]
Convertible preferred shares issued (in shares) \| shares			1,161
Number of common shares into which warrants are convertible (in shares) \| shares			99,769
Reverse stock split ratio	1-for-5
Reverse stock split (percentage)	0.2
Convertible preferred shares, dividend rate							4.00%
ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Preferred shares, stated value (in usd per share) \| $ / shares				$ 1,200
Preferred shares, dividend rate (in usd per share) \| $ / shares							$ 12.00
Other Contractual Payments \| Upfront and Milestone Payments \| ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Collaborative arrangement consideration received, number of preferred shares (in shares) \| shares				100,000
ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Dividend income, number of preferred shares received (in shares) \| shares					3,847	3,414	11,205	9,943
Noncash dividend income					$ 4,649,000	$ 4,311,000	$ 14,539,000	$ 12,276,000
ZIOPHARM Oncology, Inc. \| Preferred stock
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis					158,122,000		158,122,000		160,832,000
Fibrocell Science, Inc.
Schedule of Investments [Line Items]
Purchases of preferred stock and warrants			$ 1,161,000
Fibrocell Science, Inc. \| Preferred stock
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis					299,000		299,000		393,000
Oragenics, Inc. \| Preferred stock
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis					$ 0		$ 0		$ 0
Receivables converted to preferred stock		$ 3,385,000
Preferred shares, initial dividend rate							12.00%
Preferred shares, subsequent dividend rate							20.00%

Investments in Preferred Stock - Schedule of Changes in Level 3 Investments (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Dividend income from investments in preferred stock	$ 14,575	$ 12,303
Significant Unobservable Inputs (Level 3)
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Beginning balance	161,225
Dividend income from investments in preferred stock	14,575
Net unrealized depreciation in the fair value of the investments in preferred stock	(17,379)
Ending balance	$ 158,421

Fair Value Measurements - Additional Information (Details) - USD ($)	9 Months Ended
	Sep. 30, 2018	Jul. 31, 2018	Dec. 31, 2017
Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of financial liabilities measured at fair value on a recurring basis	$ 585,000		$ 585,000
Changes in fair value of Level 3 liabilities	0
Convertible Notes
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of convertible debt	237,000,000
3.5% Convertible Notes Due 2023
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Carrying value of convertible debt	$ 145,839,000	$ 143,723,000

Inventory (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Inventory [Line Items]
Inventory	$ 18,294	$ 20,493
Supplies, embryos and other production materials
Inventory [Line Items]
Inventory	3,368	2,673
Work in process
Inventory [Line Items]
Inventory	4,578	4,767
Livestock
Inventory [Line Items]
Inventory	8,453	11,040
Feed
Inventory [Line Items]
Inventory	$ 1,895	$ 2,013

Property, Plant and Equipment, Net - Schedule of Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Property, Plant and Equipment [Abstract]
Land and land improvements	$ 12,373	$ 11,767
Buildings and building improvements	18,533	18,183
Furniture and fixtures	1,716	2,515
Equipment	72,126	65,863
Leasehold improvements	25,281	25,277
Breeding stock	4,827	3,832
Computer hardware and software	11,490	10,128
Trees	10,635	6,642
Construction and other assets in progress	18,658	14,113
Property, plant and equipment, gross	175,639	158,320
Less: Accumulated depreciation and amortization	(52,932)	(45,646)
Property, plant and equipment, net	$ 122,707	$ 112,674

Property, Plant and Equipment, Net - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Property, Plant and Equipment [Line Items]
Depreciation expense	$ 3,614	$ 2,989	$ 10,712	$ 8,623
Brazilian R&D facility closure
Property, Plant and Equipment [Line Items]
Loss on disposal of property, plant, and equipment	$ 85		$ 5,057

Goodwill and Intangible Assets, Net - Schedule of Changes in Carrying Amount of Goodwill (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2018 USD ($)
Goodwill
Beginning balance	$ 153,289
Foreign currency translation adjustments	(2,013)
Ending balance	$ 151,276

Goodwill and Intangible Assets, Net - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Dec. 31, 2017
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill accumulated impairment losses	$ 13,823		$ 13,823		$ 13,823
Amortization expense	$ 4,689	$ 5,001	$ 14,472	$ 14,258

Goodwill and Intangible Assets, Net - Schedule of Intangible Assets (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Finite-Lived Intangible Assets, Net [Abstract]
Accumulated Amortization	$ (67,045)	$ (53,904)
Intangible Assets
Gross Carrying Amount	280,289	286,781
Net	213,244	232,877
Patents, developed technologies and know-how
Finite-Lived Intangible Assets, Net [Abstract]
Gross Carrying Amount	257,318	263,615
Accumulated Amortization	(56,551)	(44,954)
Net	200,767	218,661
Customer relationships
Finite-Lived Intangible Assets, Net [Abstract]
Gross Carrying Amount	10,700	10,700
Accumulated Amortization	(7,346)	(6,383)
Net	3,354	4,317
Trademarks
Finite-Lived Intangible Assets, Net [Abstract]
Gross Carrying Amount	6,800	6,800
Accumulated Amortization	(3,148)	(2,567)
Net	3,652	4,233
In-process research and development
Finite-Lived Intangible Assets, Net [Abstract]
Indefinite-lived intangible assets	$ 5,471	$ 5,666

Lines of Credit and Long-Term Debt - Lines of Credit - Additional Information (Details) - Revolving Line of Credit	9 Months Ended
	Sep. 30, 2018 USD ($)
Trans Ova Genetics, LC \| First National Bank of Omaha
Line of Credit Facility [Line Items]
Line of credit facility, maximum borrowing capacity	$ 5,000,000
Line of credit facility, interest rate at period end	5.06%
Line of credit facility, outstanding balance	$ 0
Trans Ova Genetics, LC \| First National Bank of Omaha \| Minimum
Line of Credit Facility [Line Items]
Debt instrument, interest rate, stated percentage	3.00%
Trans Ova Genetics, LC \| First National Bank of Omaha \| London Interbank Offered Rate (LIBOR)
Line of Credit Facility [Line Items]
Line of credit facility, basis spread on variable rate	2.95%
Exemplar Genetics, LLC \| American State Bank
Line of Credit Facility [Line Items]
Line of credit facility, maximum borrowing capacity	$ 700,000
Debt instrument, interest rate, stated percentage	5.25%
Line of credit facility, outstanding balance	$ 200,000

Lines of Credit and Long-Term Debt - Schedule of Long-Term Debt Instruments (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Debt Instrument [Line Items]
Long-term debt	$ 183,679	$ 8,037
Less current portion	546	502
Long-term debt, net of current portion	183,133	7,535
Convertible debt
Debt Instrument [Line Items]
Long-term debt	175,899	0
Notes payable
Debt Instrument [Line Items]
Long-term debt	4,667	5,010
Royalty-based financing
Debt Instrument [Line Items]
Long-term debt	2,147	2,132
Other
Debt Instrument [Line Items]
Long-term debt	$ 966	$ 895

Lines of Credit and Long-Term Debt - Long-Term Debt - Additional Information (Details)	1 Months Ended		3 Months Ended		9 Months Ended
	Sep. 30, 2018 USD ($)	Jul. 31, 2018 USD ($) $ / shares	Sep. 30, 2018 USD ($)	Sep. 30, 2017 USD ($)	Sep. 30, 2018 USD ($)	Sep. 30, 2017 USD ($)	Dec. 31, 2017 USD ($)	Mar. 31, 2013 USD ($)
Debt Instrument [Line Items]
Proceeds from long-term debt, net of issuance costs					$ 194,000,000	$ 285,000
Equity component of convertible debt, net of issuance costs and deferred taxes					36,868,000
Deferred income taxes			$ 14,246,000	$ 775,000	19,335,000	2,294,000
Long-term debt issued to a related party in an asset acquisition					30,000,000	0
Interest expense			3,999,000	$ 138,000	4,240,000	$ 498,000
Long-term debt	$ 183,679,000		183,679,000		183,679,000		$ 8,037,000
Convertible debt
Debt Instrument [Line Items]
Long-term debt	175,899,000		175,899,000		175,899,000		0
Royalty-based financing
Debt Instrument [Line Items]
Long-term debt	$ 2,147,000		$ 2,147,000		$ 2,147,000		$ 2,132,000
ActoBio Therapeutics Inc. \| Convertible debt \| Harvest Intrexon Enterprise Fund I, LP
Debt Instrument [Line Items]
Debt instrument, interest rate, stated percentage	3.00%		3.00%		3.00%
Interest expense			$ 60,000		$ 60,000
Long-term debt	$ 30,060,000		$ 30,060,000		$ 30,060,000
Trans Ova Genetics, LC \| Notes payable to banks \| American State Bank
Debt Instrument [Line Items]
Debt instrument, interest rate, stated percentage	3.95%		3.95%		3.95%
Long-term debt	$ 4,581,000		$ 4,581,000		$ 4,581,000
Debt instrument, periodic payment					39,000
AquaBounty Technologies, Inc. \| Royalty-based financing \| Atlantic Canada Opportunities Agency
Debt Instrument [Line Items]
Long-term debt	2,147,000		2,147,000		2,147,000
Amount available under the grant for research and development	2,225,000		2,225,000		$ 2,225,000
Claims period					5 years
Royalty on products, percentage					10.00%
Amount claimed								$ 1,952,000
Long-term debt, fair value at date of business combination								1,107,000
Accreted difference between face value of amount drawn and acquisition date fair value								$ 845,000
Harvest Intrexon Enterprise Fund I, LP \| ActoBio Therapeutics Inc.
Debt Instrument [Line Items]
Long-term debt issued to a related party in an asset acquisition	30,000,000
3.5% Convertible Notes Due 2023
Debt Instrument [Line Items]
Aggregate principal amount	200,000,000	$ 200,000,000	200,000,000		$ 200,000,000
Proceeds from long-term debt, net of issuance costs		193,958,000
Debt issuance costs		$ 6,042,000
Debt instrument, interest rate, stated percentage		3.50%
Conversion rate		58.6622
Principal amount used in conversion		$ 1,000
Conversion price (in usd per share) \| $ / shares		$ 17.05
Debt instrument redemption price, percentage		100.00%
Carrying value of convertible debt	$ 145,839,000	$ 143,723,000	145,839,000		145,839,000
Equity component of convertible debt, net of issuance costs and deferred taxes		50,235,000
Deferred income taxes		$ 13,367,000	$ 13,367,000		$ 13,367,000
Effective interest rate on convertible notes	11.02%		11.02%		11.02%
Convertible notes, unamortized discount and issuance costs	$ 54,161,000		$ 54,161,000		$ 54,161,000
Total interest expense			3,847,000		3,847,000
Interest expense payable in cash			1,731,000		1,731,000
Noncash interest expense			2,116,000		2,116,000
3.5% Convertible Notes Due 2023 \| Other Accrued Liabilities
Debt Instrument [Line Items]
Accrued interest payable in cash	$ 1,731,000		$ 1,731,000		$ 1,731,000
3.5% Convertible Notes Due 2023 \| Minimum
Debt Instrument [Line Items]
Common stock price trading days		20
Common stock price consecutive trading days		30
Percentage of common share price over conversion price for conversion		130.00%
3.5% Convertible Notes Due 2023 \| Maximum
Debt Instrument [Line Items]
Common stock price trading days		5
Common stock price consecutive trading days		5
Debt instrument redemption price, percentage		98.00%

Lines of Credit and Long-Term Debt - Schedule of Future Maturities of Long-Term Debt (Details) $ in Thousands	Sep. 30, 2018 USD ($)
Debt Disclosure [Abstract]
2018	$ 210
2019	449
2020	30,463
2021	832
2022	375
2023	200,389
Thereafter	2,974
Total	$ 235,692

Income Taxes (Details) - USD ($)	1 Months Ended	3 Months Ended		9 Months Ended		12 Months Ended
Income Taxes (Details) - USD ($)	Jul. 31, 2018	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Dec. 31, 2017
Operating Loss Carryforwards [Line Items]
Deferred income tax benefit		$ 14,246,000	$ 775,000	$ 19,335,000	$ 2,294,000
Deferred tax liabilities		9,363,000		9,363,000
Estimated tax benefit upon enactment of Tax Act						$ 2,185,000
Change in deferred tax assets resulting from enactment of Tax Act						87,473,000
Estimated tax benefit due to changes in deferred tax liabilities upon enactment of Tax Act						1,730,000
Provisional current tax benefit related to the expected refundability of accumulated corporate alternative minimum tax credits		13,000		13,000		455,000
Provisional transition tax amount						$ 0
Domestic Tax Authority
Operating Loss Carryforwards [Line Items]
Taxable income (loss)		(39,100,000)	3,930,000	(104,400,000)	23,680,000
Current income tax expense (benefit)		(31,000)	78,000	82,000	473,000
Operating loss carryforwards		357,000,000		357,000,000
Estimated current tax benefit upon enactment of Tax Act		7,900,000		7,900,000
Foreign Tax Authority
Operating Loss Carryforwards [Line Items]
Current income tax expense (benefit)		(45,000)	$ (121,000)	(282,000)	$ (343,000)
Operating loss carryforwards		159,700,000		159,700,000
3.5% Convertible Notes Due 2023
Operating Loss Carryforwards [Line Items]
Deferred income tax benefit	$ 13,367,000	$ 13,367,000		$ 13,367,000

Shareholders' Equity - Issuances of Common Stock (Details) $ in Thousands	1 Months Ended
	Jan. 31, 2018 USD ($) shares
Class of Stock [Line Items]
Shares issued (in shares) \| shares	6,900,000
Net proceeds from public financing	$ 82,374
Underwriting discounts and commissions	3,688
Capitalized offering expenses	$ 188
Affiliate of Third Security, LLC
Class of Stock [Line Items]
Shares issued (in shares) \| shares	1,000,000

Shareholders' Equity - Share Lending Agreement (Details)	1 Months Ended
	Jul. 31, 2018 $ / shares shares
Equity [Abstract]
Borrowed shares, number issued (in shares) \| shares	7,479,431
Borrowed shares, public offering price per share (in usd per share) \| $ / shares	$ 13.37

Shareholders' Equity - Components of Accumulated Other Comprehensive Loss (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	$ 539,399	$ 533,631
Unrealized loss on investments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	(96)	(2)
Loss on foreign currency translation adjustments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	(22,804)	(15,552)
Total accumulated other comprehensive loss
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	$ (22,900)	$ (15,554)

Share-Based Payments - Schedule of Stock-Based Compensation Costs (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	$ 8,132	$ 12,057	$ 28,340	$ 31,949
Cost of products
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	14	30	64	86
Cost of services
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	51	82	207	242
Research and development
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	1,681	2,383	7,315	7,018
Selling, general and administrative
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	$ 6,386	$ 9,562	$ 20,754	$ 24,603

Share-Based Payments - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Nov. 30, 2015	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Dec. 31, 2017	Apr. 30, 2016	Aug. 31, 2013
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares issued as payment for services				$ 8,404	$ 8,440
Chief Executive Officer
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Monthly compensation, in the form of equity	$ 200
Lock-up period	3 years
Initial term of compensation arrangement	12 months
Chief Executive Officer \| Selling, general and administrative
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares issued as payment for services		$ 499	$ 480	$ 1,468	$ 1,428
Intrexon Stock Option Plan - 2008 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)								0
Options outstanding (in shares)		414,754		414,754
Intrexon Stock Option Plan - 2013 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)		5,310,530		5,310,530
Options outstanding (in shares)		10,745,770		10,745,770
Number of shares authorized for issuance (in shares)		20,000,000		20,000,000
RSUs outstanding (in shares)		980,758		980,758
RSUs granted (in shares)				1,069,126
Weighted average grant date fair value of RSUs granted (in usd per share)				$ 13.84
RSUs vested (in shares)				25,000
Intrexon Stock Option Plans
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)		11,160,524		11,160,524		11,382,747
Options exercisable (in shares)		7,177,315		7,177,315
Weighted average exercise price of option (in usd per share)		$ 28.23		$ 28.23		$ 28.99
AquaBounty Stock Option Plan - 2006 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)							0
Aqua Bounty Stock Option Plans
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)		339,964		339,964
Options exercisable (in shares)		271,467		271,467
Weighted average exercise price of option (in usd per share)		$ 7.09		$ 7.09

Share-Based Payments - Schedule of Stock Option Activity (Details) - Intrexon Stock Option Plans - $ / shares	9 Months Ended	12 Months Ended
	Sep. 30, 2018	Dec. 31, 2017
Number of Shares
Balances at beginning of period (in shares)	11,382,747
Granted (in shares)	1,174,839
Exercised (in shares)	(41,314)
Forfeited (in shares)	(808,086)
Expired (in shares)	(547,662)
Balances at end of period (in shares)	11,160,524	11,382,747
Exercisable at end of period (in shares)	7,177,315
Weighted Average Exercise Price
Balances at beginning of period (in usd per share)	$ 28.99
Granted (in usd per share)	15.04
Exercised (in usd per share)	(6.33)
Forfeited (in usd per share)	(21.41)
Expired (in usd per share)	(27.40)
Balances at period end (in usd per share)	28.23	$ 28.99
Exercisable, weighted average exercise price, at end of period (in usd per share)	$ 30.15
Weighted Average Remaining Contractual Term (Years)
Balances, weighted average remaining contractual period	6 years 9 months 15 days	7 years 3 months 24 days
Exercisable at period end, weighted average remaining contractual period	6 years 6 days

Commitments and Contingencies - Future Minimum Lease Payments Under Noncancelable Operating Leases (Details) $ in Thousands	Sep. 30, 2018 USD ($)
Commitments and Contingencies Disclosure [Abstract]
2018	$ 1,508
2019	9,417
2020	9,577
2021	8,904
2022	8,072
2023	7,009
Thereafter	31,330
Total	$ 75,817

Commitments and Contingencies - Operating Leases - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Commitments and Contingencies Disclosure [Abstract]
Rent expense	$ 3,286	$ 3,165	$ 9,874	$ 7,772

Commitments and Contingencies - Purchase Commitments - Additional Information (Details) $ in Thousands	Sep. 30, 2018 USD ($)
Commitments and Contingencies Disclosure [Abstract]
Outstanding contractual purchase commitments	$ 8,826

Commitments and Contingencies - Contingencies - Additional Information (Details) - Licensing and patent infringement suit $ in Thousands	1 Months Ended	9 Months Ended	12 Months Ended	50 Months Ended
	Apr. 30, 2016 USD ($)	Sep. 30, 2018 claim	Dec. 31, 2016 USD ($)	Apr. 30, 2016 USD ($)
Loss Contingencies [Line Items]
Damages awarded to Trans Ova	$ 528
Cumulative payments for royalties and licenses				$ 3,170
Royalty payments not yet deposited	2,759			$ 2,759
Litigation settlement expense			$ 4,228
XY, LLC
Loss Contingencies [Line Items]
Damages awarded against Trans Ova	$ 6,066
Claims dismissed (in claims) \| claim		9
Total claims \| claim		12
Claims pending resolution \| claim		3

Related Party Transactions (Details) - USD ($)	1 Months Ended		3 Months Ended		9 Months Ended		10 Months Ended
Related Party Transactions (Details) - USD ($)	Jan. 31, 2018	Nov. 30, 2015	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017	Jul. 31, 2018	Dec. 31, 2017	Oct. 31, 2017
Related Party Transaction [Line Items]
Shares issued as payment for services					$ 8,404,000
Shares issued (in shares)	6,900,000
Fair value of financial assets measured at fair value on a recurring basis			$ 327,580,000		327,580,000			$ 183,173,000
Other nonoperating income			1,452,000	$ (1,021,000)	571,000	$ 4,453,000
Series A preferred shares
Related Party Transaction [Line Items]
Shares issued (in shares)							0
Affiliate of Third Security, LLC
Related Party Transaction [Line Items]
Shares issued (in shares)	1,000,000
Affiliate of Third Security, LLC \| Series A preferred shares
Related Party Transaction [Line Items]
Value of convertible preferred shares authorized for issuance									$ 100,000,000
Third Security, LLC
Related Party Transaction [Line Items]
Expense for services			$ 16,000	$ 4,000	$ 33,000	$ 428,000
Initial term of services agreement		1 year
Shares issued as payment for services (in shares)			166,143	118,828	466,460	329,649
Shares issued as payment for services			$ 2,417,000	$ 2,251,000	$ 6,522,000	$ 6,506,000
Sublease rental income			22,000	10,000	66,000	32,000
Third Security, LLC \| Common Stock
Related Party Transaction [Line Items]
Expense for services		$ 800,000
Harvest Intrexon Enterprise Fund I, LP
Related Party Transaction [Line Items]
Other nonoperating income				$ 613,000		$ 1,839,000
Convertible Note and Warrants \| Other Assets \| Fibrocell Science, Inc.
Related Party Transaction [Line Items]
Fair value of financial assets measured at fair value on a recurring basis			$ 300,000		$ 300,000			$ 575,000
Third Security, LLC \| Chief Executive Officer
Related Party Transaction [Line Items]
Ownership interest			100.00%		100.00%

Net Loss per Share - Computation of Basic and Diluted Net Loss Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Numerator:
Net loss attributable to Intrexon	$ (57,324)	$ (39,689)	$ (168,871)	$ (89,752)
Denominator:
Weighted average shares outstanding, basic and diluted (in shares)	129,518,989	120,518,885	128,843,991	119,741,291
Net loss attributable to Intrexon per share, basic and diluted (in usd per share)	$ (0.44)	$ (0.33)	$ (1.31)	$ (0.75)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References + Details

Net Loss per Share - Schedule of Antidilutive Securities Excluded from Calculation of Net Loss per Share (Details) - shares	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	25,782,292	12,775,034	25,782,292	12,775,034
Convertible debt
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	13,507,746	0	13,507,746	0
Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	11,160,524	12,641,770	11,160,524	12,641,770
Restricted stock units
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	980,758	0	980,758	0
Warrants
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	133,264	133,264	133,264	133,264

Subsequent Events - Additional Information (Details) $ in Thousands	1 Months Ended
	Oct. 31, 2018 USD ($) quarterly_installment product	Sep. 30, 2018 USD ($)	Dec. 31, 2017 USD ($)
Subsequent Event [Line Items]
Fair value of financial assets measured at fair value on a recurring basis		$ 327,580	$ 183,173
Licensing Agreement Between ZIOPHARM and Intrexon 2018 \| Subsequent Event
Subsequent Event [Line Items]
Period after which reasonable efforts to be made to develop and commercialize additional products	2 years
Percentage of development costs	20.00%
Percentage of operating profits	20.00%
Annual licensing fee	$ 100
Milestone payments due, aggregated	210,000
Royalty due, aggregated	$ 100,000
Period during which research and development is restricted on certain products	3 years
Period following triggering event after which license agreement terminates	12 years
Percentage of sublicensing income	20.00%
Licensing Agreement Between ZIOPHARM and Intrexon 2018 \| ZIOPHARM Oncology, Inc. \| Subsequent Event
Subsequent Event [Line Items]
Percentage of development costs	80.00%
Percentage of operating profits	80.00%
Royalty due, aggregated	$ 100,000
Licensing Agreement Between ZIOPHARM and Intrexon 2018 \| Maximum \| Subsequent Event
Subsequent Event [Line Items]
Reimbursement of historical costs	$ 1,000
Number of quarterly installments for reimbursement of historical costs \| quarterly_installment	4
Milestone payments due per product	$ 52,500
Exclusively licensed products \| product	4
Transition period during which costs will be reimbursed	1 year
Preferred stock \| ZIOPHARM Oncology, Inc.
Subsequent Event [Line Items]
Fair value of financial assets measured at fair value on a recurring basis		$ 158,122	$ 160,832

Fair Value Measurements - Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis (Details) - USD ($) $ in Thousands	Sep. 30, 2018	Dec. 31, 2017
Assets
Fair value of financial assets measured at fair value on a recurring basis	$ 327,580	$ 183,173
Quoted Prices in Active Markets (Level 1)
Assets
Fair value of financial assets measured at fair value on a recurring basis	3,591	10,537
Significant Other Observable Inputs (Level 2)
Assets
Fair value of financial assets measured at fair value on a recurring basis	165,568	11,411
Significant Unobservable Inputs (Level 3)
Assets
Fair value of financial assets measured at fair value on a recurring basis	158,421	161,225
U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	163,809	5,998
U.S. government debt securities \| Quoted Prices in Active Markets (Level 1)
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
U.S. government debt securities \| Significant Other Observable Inputs (Level 2)
Assets
Fair value of financial assets measured at fair value on a recurring basis	163,809	5,998
U.S. government debt securities \| Significant Unobservable Inputs (Level 3)
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	4,697	15,100
Equity securities \| Quoted Prices in Active Markets (Level 1)
Assets
Fair value of financial assets measured at fair value on a recurring basis	3,591	10,537
Equity securities \| Significant Other Observable Inputs (Level 2)
Assets
Fair value of financial assets measured at fair value on a recurring basis	1,106	4,563
Equity securities \| Significant Unobservable Inputs (Level 3)
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Preferred stock
Assets
Fair value of financial assets measured at fair value on a recurring basis	158,421	161,225
Preferred stock \| Quoted Prices in Active Markets (Level 1)
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Preferred stock \| Significant Other Observable Inputs (Level 2)
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Preferred stock \| Significant Unobservable Inputs (Level 3)
Assets
Fair value of financial assets measured at fair value on a recurring basis	158,421	161,225
Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	653	850
Other \| Quoted Prices in Active Markets (Level 1)
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Other \| Significant Other Observable Inputs (Level 2)
Assets
Fair value of financial assets measured at fair value on a recurring basis	653	850
Other \| Significant Unobservable Inputs (Level 3)
Assets
Fair value of financial assets measured at fair value on a recurring basis	$ 0	$ 0