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Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Jun. 30, 2016	Aug. 01, 2016
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Jun. 30, 2016
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	Q3
Trading Symbol	ENTA
Entity Registrant Name	ENANTA PHARMACEUTICALS INC
Entity Central Index Key	0001177648
Current Fiscal Year End Date	--09-30
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		19,035,910

Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2016	Sep. 30, 2015
Current assets:
Cash and cash equivalents	$ 24,789	$ 21,726
Short-term marketable securities	193,676	123,479
Accounts receivable	13,978	15,289
Unbilled receivables		433
Deferred tax assets	1,147	1,447
Prepaid expenses and other current assets	8,200	8,267
Total current assets	241,790	170,641
Property and equipment, net	7,499	5,886
Long-term marketable securities	26,194	64,238
Deferred tax assets	5,843	4,640
Restricted cash	608	608
Total assets	281,934	246,013
Current liabilities:
Accounts payable	2,044	1,543
Accrued expenses and other current liabilities	4,583	3,962
Income taxes payable	2,942	1,199
Total current liabilities	9,569	6,704
Warrant liability	1,237	1,276
Other long-term liabilities	1,963	1,713
Total liabilities	12,927	9,856
Commitments and contingencies (Note 11)
Stockholders' equity:
Common stock; $0.01 par value, 100,000,000 shares authorized; 19,035,763 and 18,716,834 shares issued and outstanding at June 30, 2016 and September 30, 2015, respectively;	190	187
Additional paid-in capital	239,252	229,957
Accumulated other comprehensive income	117	33
Retained earnings	29,448	5,980
Total stockholders' equity	269,007	236,157
Total liabilities and stockholders' equity	281,934	246,013
Series 1 Nonconvertible Preferred Stock [Member]
Current liabilities:
Series 1 nonconvertible preferred stock	$ 158	$ 163

Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2016	Sep. 30, 2015
Statement of Financial Position [Abstract]
Common stock, par value	$ 0.01	$ 0.01
Common stock, shares authorized	100,000,000	100,000,000
Common stock, shares issued	19,035,763	18,716,834
Common stock, shares outstanding	19,035,763	18,716,834

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Revenue
Milestones			$ 30,000	$ 125,000
Royalties	$ 13,978	$ 11,390	44,851	19,743
Other		209	576	1,721
Total revenue	13,978	11,599	75,427	146,464
Operating expenses:
Research and development	10,785	6,253	28,961	16,140
General and administrative	4,282	3,643	12,526	9,850
Total operating expenses	15,067	9,896	41,487	25,990
Income (loss) from operations	(1,089)	1,703	33,940	120,474
Other income (expense):
Interest income	474	304	1,238	660
Interest expense	(11)	(2)	(34)	(6)
Change in fair value of warrant liability and Series 1 nonconvertible preferred stock	(16)	(15)	44	144
Total other income (expense), net	447	287	1,248	798
Income (loss) before income taxes	(642)	1,990	35,188	121,272
Income tax (expense) benefit	(434)	428	(11,720)	(48,092)
Net income (loss)	$ (1,076)	$ 2,418	$ 23,468	$ 73,180
Net income (loss) per share:
Basic	$ (0.06)	$ 0.13	$ 1.24	$ 3.92
Diluted	$ (0.06)	$ 0.13	$ 1.22	$ 3.80
Weighted average shares outstanding:
Basic	18,982,825	18,697,104	18,892,627	18,659,742
Diluted	18,982,825	19,277,966	19,223,359	19,276,767

Consolidated Statements of Comprehensive Income (Loss) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Statement of Comprehensive Income [Abstract]
Net income (loss)	$ (1,076)	$ 2,418	$ 23,468	$ 73,180
Other comprehensive income (loss):
Net unrealized gains (losses) on marketable securities, net of tax of $185, ($40), $50 and $18	(84)	(57)	84	26
Total other comprehensive income (loss)	(84)	(57)	84	26
Comprehensive income (loss)	$ (1,160)	$ 2,361	$ 23,552	$ 73,206

Consolidated Statements of Comprehensive Income (Loss) (Parenthetical) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Statement of Comprehensive Income [Abstract]
Net unrealized gains on marketable securities, tax	$ 185	$ (40)	$ 50	$ 18

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015
Cash flows from operating activities
Net income	$ 23,468	$ 73,180
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation and amortization expense	1,206	435
Non-cash interest expense		6
Change in fair value of warrant liability and Series 1 nonconvertible preferred stock	(44)	(144)
Stock-based compensation expense	6,844	4,041
Gain on sale of fixed assets		(21)
Premium on marketable securities	(130)	(2,063)
Gain on sale of marketable securities		(4)
Amortization of premium on marketable securities	1,304	1,651
Deferred income taxes	546	11,076
Income tax benefit from the exercise of stock options	(1,749)	(1,817)
Change in operating assets and liabilities:
Accounts receivable	1,311	(10,000)
Unbilled receivables	433	1,394
Prepaid expenses and other current assets	67	(1,108)
Accounts payable	677	(332)
Accrued expenses	1,946	391
Income taxes payable	1,754	2,229
Other long-term liabilities	302	134
Net cash provided by operating activities	37,935	79,048
Cash flows from investing activities
Purchase of property and equipment	(4,323)	(756)
Purchase of marketable securities	(150,490)	(155,583)
Sale of marketable securities		2,210
Maturities of marketable securities	117,297	62,017
Increase in restricted cash		(172)
Net cash used in investing activities	(37,516)	(92,284)
Cash flows from financing activities
Proceeds from exercise of stock options	945	564
Payments of capital lease obligations	(50)
Income tax benefit from the exercise of stock options	1,749	1,817
Net cash provided by financing activities	2,644	2,381
Net increase (decrease) in cash and cash equivalents	3,063	(10,855)
Cash and cash equivalents at beginning of period	21,726	30,699
Cash and cash equivalents at end of period	24,789	19,844
Supplemental disclosure of cash flow information:
Cash paid for income taxes	9,116	39,566
Series 1 Nonconvertible Preferred Stock [Member]
Adjustments to reconcile net income to net cash provided by operating activities:
Change in fair value of warrant liability and Series 1 nonconvertible preferred stock	$ (44)	$ (144)

Nature of the Business and Basis of Presentation

9 Months Ended

Jun. 30, 2016

Accounting Policies [Abstract]

Nature of the Business and Basis of Presentation

1.	Nature of the Business and Basis of Presentation

Enanta Pharmaceuticals, Inc. (the “Company”), incorporated in Delaware in 1995, is a research and development-focused biotechnology company that uses its robust chemistry-driven approach and drug discovery capabilities to create small molecule drugs primarily for the treatment of viral infections and liver diseases. The Company’s research and development is currently focused on four disease targets: hepatitis C virus (“HCV”); hepatitis B virus (“HBV”); non-alcoholic steatohepatitis (“NASH”); and respiratory syncytial virus (“RSV”).

The Company is subject to risks common to companies in the biotechnology industry including, but not limited to, the uncertainties of research and development, competition from technological innovations of others, dependence on collaborative arrangements, protection of proprietary technology, dependence on key personnel, compliance with government regulations and the need to obtain additional financing. Product candidates currently under development will require significant additional research and development efforts, including extensive preclinical and clinical testing and regulatory approval, prior to commercialization. These efforts require significant amounts of additional capital, adequate personnel infrastructure, and extensive compliance reporting capabilities.

Unaudited Interim Financial Information

The consolidated balance sheet at September 30, 2015 was derived from audited financial statements, but does not include all disclosures required by accounting principles generally accepted in the United States of America (“GAAP”). The accompanying unaudited consolidated financial statements as of June 30, 2016 and for the three and nine months ended June 30, 2016 and 2015 have been prepared by the Company, pursuant to the rules and regulations of the Securities and Exchange Commission (“SEC”) for interim financial statements. Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted pursuant to such rules and regulations. These financial statements should be read in conjunction with the Company’s audited financial statements and the notes thereto included in the Company’s Annual Report on Form 10-K for the year ended September 30, 2015.

In the opinion of management, all adjustments, consisting only of normal recurring adjustments necessary for a fair statement of the Company’s financial position as of June 30, 2016 and results of operations for the three and nine months ended June 30, 2016 and 2015 and cash flows for the nine months ended June 30, 2016 and 2015 have been made. The results of operations for the three and nine months ended June 30, 2016 are not necessarily indicative of the results of operations that may be expected for subsequent quarters or the year ending September 30, 2016.

The accompanying consolidated financial statements have been prepared in conformity with GAAP. All dollar amounts in the consolidated financial statements and in the notes to the consolidated financial statements, except share and per share amounts, are in thousands unless otherwise indicated.

Summary of Significant Accounting Policies

9 Months Ended

Jun. 30, 2016

Accounting Policies [Abstract]

Summary of Significant Accounting Policies

2.	Summary of Significant Accounting Policies

For the Company’s Significant Accounting Policies refer to its Annual Report on Form 10-K for the fiscal year ended September 30, 2015.

Use of Estimates

The preparation of consolidated financial statements in conformity with 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 consolidated financial statements, and the reported amounts of revenues and expenses during the reporting period. Significant estimates and assumptions reflected in these consolidated financial statements include, but are not limited to, management’s judgments of separate units of accounting and best estimate of selling price of those units of accounting within its revenue arrangements; valuation of stock-based awards; the useful lives of property and equipment; and the accounting for income taxes, including uncertain tax positions and the valuation of net deferred tax assets. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Actual results could differ from the Company’s estimates.

Recently Issued Accounting Pronouncements

In May 2014, the Financial Accounting Standards Board (the “FASB”) issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606), which supersedes all existing revenue recognition requirements, including most industry-specific guidance. The new standard requires a company to recognize revenue when it transfers goods or services to customers in an amount that reflects the consideration that the company expects to receive for those goods or services. In March 2016, the FASB issued ASU No. 2016-08, Revenue from Contracts with Customers: Principal versus Agent Considerations. The amendment includes indicators to assist an entity in determining whether it controls a specified good or service before it is transferred to the customers. In April 2016, the FASB issued ASU No. 2016-10, Revenue from Contracts with Customers: Identifying Performance Obligations and Licensing in April 2016 to clarify guidance from ASU 2014-09. Specifically, this amendment addresses an entity’s identification of its performance obligations in a contract, as well as an entity’s evaluation of the nature of its promise to grant a license of intellectual property and whether or not that revenue is recognized over time or at a point in time. The FASB also issued ASU No. 2016-12 Revenue from Contracts with Customers: Narrow-Scope Improvements and Practical Expedients, in May 2016. This amendment addresses collectability, non-cash consideration, presentation of sales tax and transitioning to the new standard. These new standards will be effective for the Company on October 1, 2018. The Company is currently evaluating the potential impact that Topic 606 may have on its financial position and results of operations.

In November 2015, the FASB issued ASU No. 2015-17, Balance Sheet Classification of Deferred Taxes (“ASU 2015-17”), which simplifies the presentation of deferred income taxes by eliminating the need for entities to separate deferred income tax liabilities and assets into current and noncurrent amounts in a classified statement of financial position. This amendment is effective for the Company in the fiscal year beginning October 1, 2017, but early adoption is permissible. The Company is currently evaluating the potential impact that ASU 2015-17 may have on its financial position.

In February 2016, the FASB issued ASU No. 2016-02, Leases (“ASU 2016-02”), which will replace the existing guidance in ASC 840, “Leases.” The updated standard aims to increase transparency and comparability among organizations by requiring lessees to recognize lease assets and lease liabilities on the balance sheet and requiring disclosure of key information about leasing arrangements. This amendment is effective for the Company in the fiscal year beginning October 1, 2019, but early adoption is permissible. The Company is currently evaluating the potential impact that ASU 2016-02 may have on its financial position and results of operations.

In March 2016, the FASB issued ASU No. 2016-09, Improvements to Employee Share-Based Payment Accounting (“ASU 2016-09”), which intends to simplify several aspects of accounting for share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, an option to recognize gross stock compensation expense with actual forfeitures recognized as they occur, as well as certain classifications on the statement of cash flows. This amendment is effective for the Company in the fiscal year beginning October 1, 2017, but early adoption is permissible. The Company is currently evaluating the potential impact that ASU 2016-09 may have on its financial position and results of operations.

Other accounting standards that have been issued or proposed by the FASB or other standards-setting bodies that do not require adoption until a future date are not expected to have a material impact on the Company’s financial statements upon adoption.

Fair Value of Financial Assets and Liabilities

9 Months Ended

Jun. 30, 2016

Fair Value Disclosures [Abstract]

Fair Value of Financial Assets and Liabilities

3.	Fair Value of Financial Assets and Liabilities

The following tables present information about the Company’s financial assets and liabilities that were subject to fair value measurement on a recurring basis as of June 30, 2016 and September 30, 2015 and indicate the fair value hierarchy of the valuation inputs utilized to determine such fair value:


	Fair Value Measurements at June 30, 2016 Using:
	Level 1		Level 2		Level 3		Total
Assets:
U.S. Treasury notes	$	62,658	$	—	$	—	$	62,658
Cash equivalents		20,534		—		—		20,534
Corporate bonds		—		79,326		—		79,326
Commercial paper		—		46,819		—		46,819
U.S. Agency bonds		—		31,067		—		31,067

	$	83,192	$	157,212	$	—	$	240,404

Liabilities:
Warrant liability	$	—	$	—	$	1,237	$	1,237
Series 1 nonconvertible preferred stock		—		—		158		158

	$	—	$	—	$	1,395	$	1,395


	Fair Value Measurements at September 30, 2015 Using:
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents	$	21,327	$	—	$	—	$	21,327
Corporate bonds		—		151,020		—		151,020
U.S. Agency bonds		—		36,697		—		36,697

	$	21,327	$	187,717	$	—	$	209,044

Liabilities:
Warrant liability	$	—	$	—	$	1,276	$	1,276
Series 1 nonconvertible preferred stock		—		—		163		163

	$	—	$	—	$	1,439	$	1,439

During the three and nine months ended June 30, 2016 and 2015, there were no transfers between Level 1, Level 2 and Level 3.

As of June 30, 2016 and September 30, 2015, respectively, the warrant liability was comprised of the value of warrants for the purchase of Series 1 nonconvertible preferred stock measured at fair value. The outstanding Series 1 nonconvertible preferred stock was also measured at fair value. The fair value of both of these instruments was based on significant inputs not observable in the market, which represented a Level 3 measurement within the fair value hierarchy. The Company utilized a probability-weighted valuation model which takes into consideration various outcomes that may require the Company to transfer assets upon exercise. Changes in the fair value of the warrant liability and Series 1 nonconvertible preferred stock are recognized in the consolidated statements of operations.

As of June 30, 2016 and September 30, 2015, the recurring Level 3 fair value measurements of the Company’s warrant liability and Series 1 nonconvertible preferred stock using probability-weighted discounted cash flow include the following significant unobservable inputs:


	Unobservable Input	June 30, 2016 Range (Weighted Average)
Warrant liability and Series 1 nonconvertible preferred stock	Probabilities of payout	0% - 60%
	Periods in which payout is expected to occur	2016 – 2017
	Discount rate	4.50%
	Unobservable Input	September 30, 2015 Range (Weighted Average)
Warrant liability and Series 1 nonconvertible preferred stock	Probabilities of payout	5% - 60%
	Periods in which payout is expected to occur	2016 – 2017
	Discount rate	4.25%

The following table provides a rollforward of the aggregate fair values of the Company’s warrants for the purchase of Series 1 nonconvertible preferred stock and the outstanding Series 1 nonconvertible preferred stock for which fair value is determined by Level 3 inputs:


	Warrant Liability			Series 1 Nonconvertible Preferred Stock
Balance, September 30, 2015	$	1,276		$	163
Decrease in fair value		(39	)		(5	)

Balance, June 30, 2016	$	1,237		$	158

- 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

Marketable Securities

9 Months Ended

Jun. 30, 2016

Investments, Debt and Equity Securities [Abstract]

Marketable Securities

4.	Marketable Securities

As of June 30, 2016 and September 30, 2015, the fair value of available-for-sale marketable securities by type of security was as follows:


	June 30, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Corporate bonds	$	79,259	$	75	$	(8	)	$	79,326
U.S. Treasury notes		62,558		100		—			62,658
Commercial paper		46,819		—		—			46,819
U.S. Agency bonds		31,047		20		—			31,067

	$	219,683	$	195	$	(8	)	$	219,870


	September 30, 2015
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Corporate bonds	$	151,012	$	77	$	(69	)	$	151,020
U.S. Agency bonds		36,652		45		—			36,697

	$	187,664	$	122	$	(69	)	$	187,717

As of June 30, 2016, marketable securities consisted of investments that mature within one year, with the exception of certain corporate bonds, which have maturities within three years and an aggregate fair value of $26,194.

- Definition

The entire disclosure for investments in certain debt and equity securities.

+ References + Details

Accrued Expenses and Other Long-Term Liabilities

9 Months Ended

Jun. 30, 2016

Payables and Accruals [Abstract]

Accrued Expenses and Other Long-Term Liabilities

5.	Accrued Expenses and Other Long-Term Liabilities

Accrued expenses and other current liabilities as well as other long-term liabilities consisted of the following as of June 30, 2016 and September 30, 2015:


	June 30, 2016		September 30, 2015
Accrued expenses:
Accrued preclinical and clinical expenses	$	1,696	$	237
Accrued payroll and related expenses		1,661		1,622
Accrued professional fees		517		338
Accrued other		419		371
Accrued vendor manufacturing		219		18
Capital lease obligation		71		69
Accrued fixed assets		—		1,307

	$	4,583	$	3,962

Other long-term liabilities:
Accrued rent expense	$	682	$	628
Uncertain tax positions		668		448
Capital lease obligation		478		529
Asset retirement obligation		135		108

	$	1,963	$	1,713

Ongoing Collaboration Agreements

9 Months Ended

Jun. 30, 2016

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Ongoing Collaboration Agreements

6.	Ongoing Collaboration Agreements

AbbVie Collaboration

The Company has a Collaborative Development and License Agreement (the “AbbVie Agreement”), as amended, with AbbVie Inc. to identify, develop and commercialize HCV NS3 and NS3/4A protease inhibitor compounds, including paritaprevir, under which it has received license payments, proceeds from a sale of preferred stock, research funding payments, milestone payments and royalties totaling $380,000 through June 30, 2016. As of June 30, 2016 the Company is eligible to receive additional milestone payments totaling up to $80,000 upon AbbVie’s achievement of commercialization regulatory approval in the U.S. and other selected world markets for any additional protease inhibitor commercialized by AbbVie. Since the Company completed all its performance obligations under the AbbVie Agreement by the end of fiscal 2011, any milestone payments received since then have been and will be recognized as revenue when the milestones are achieved by AbbVie. The Company is also receiving annually tiered royalties per product ranging from the low double digits up to twenty percent, or on a blended basis from the low double digits up to the high teens, on calendar year net sales by AbbVie allocated to the collaboration’s protease inhibitors. Beginning with each January 1, the cumulative net sales of a given royalty-bearing product start at zero for purposes of calculating the tiered royalties.

During the three and nine months ended June 30, 2016, the Company earned and recognized milestone revenue of $0 and $30,000 respectively, upon AbbVie’s achievement of commercialization regulatory approval of a paritaprevir-containing regimen in Japan in November 2015. During the three and nine months ended June 30, 2015, the Company earned and recognized milestone revenue of $0 and $125,000 respectively, upon AbbVie’s achievement of commercialization regulatory approval of VIEKIRAX in Europe in January 2015 and VIEKIRA PAK in the U.S in December 2014.

Warrants to Purchase Series 1 Nonconvertible Preferred Stock and Series 1 Nonconvertible Preferred Stock

9 Months Ended

Jun. 30, 2016

Equity [Abstract]

Warrants to Purchase Series 1 Nonconvertible Preferred Stock and Series 1 Nonconvertible Preferred Stock

7.	Warrants to Purchase Series 1 Nonconvertible Preferred Stock and Series 1 Nonconvertible Preferred Stock

In October and November 2010, the Company issued warrants to purchase up to a total of 1,999,989 shares of Series 1 nonconvertible preferred stock, which expire on October 4, 2017. As these warrants are free-standing financial instruments that may require the Company to transfer assets upon exercise, these warrants are classified as liabilities. The Company is required to remeasure the fair value of these preferred stock warrants at each reporting date, with any adjustments recorded within the change in fair value of warrant liability included in other income (expense), net, in the consolidated statement of operations.

- Definition

The entire disclosure for shareholders' equity comprised of portions attributable to the parent entity and noncontrolling interest, including other comprehensive income. Includes, but is not limited to, balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings, accumulated balance for each classification of other comprehensive income and amount of comprehensive income.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-Section S99
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-Name Accounting Standards Codification
-Topic 505
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-Section 50
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-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21484-112644

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-Section S99
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-Paragraph 1
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Reference 7: http://www.xbrl.org/2003/role/presentationRef
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Reference 8: http://www.xbrl.org/2003/role/presentationRef
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-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02(30))
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
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-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21506-112644

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
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-URI http://asc.fasb.org/extlink&oid=26873400&loc=d3e23780-122690

Reference 11: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 505
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-Section S99
-Paragraph 1
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-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187085-122770

Reference 12: http://www.xbrl.org/2003/role/presentationRef
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-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6405834&loc=d3e23285-112656

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21475-112644

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Preferred Stock
-URI http://asc.fasb.org/extlink&oid=6521494

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21463-112644

Reference 16: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section 50
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=6928386&loc=d3e21564-112644

+ Details

Stock-Based Awards

9 Months Ended

Jun. 30, 2016

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

Stock-Based Awards

8.	Stock-Based Awards

The Company may grant stock-based awards under its existing 2012 Equity Incentive Plan (the “2012 Plan”) and its Employee Stock Purchase Plan (the “ESPP”). The Company also has outstanding stock-based awards under its 1995 Equity Incentive Plan (the “1995 Plan”), but is no longer granting awards under this plan. As of June 30, 2016, 491,511 shares of common stock are available for issuance under the 2012 Plan. As of June 30, 2016, a total of 185,614 shares of common stock are available for issuance under the ESPP. As of June 30, 2016, the Company had not commenced any offering under the ESPP and no shares have been issued.

The Company applies the fair value recognition provisions for all stock-based awards granted or modified in accordance with authoritative guidance. Under this guidance the Company records compensation costs over the requisite service period of the award based on the grant-date fair value. The straight-line method is applied to all grants with service conditions, while the graded vesting method is applied to all grants with both service and performance conditions.

In March 2013, the Company granted to certain executive officers 167,052 options that vest upon achievement of certain performance-based targets. The aggregate fair value of these performance options ranges between $0 and $2,479. During the three and nine months ended June 30, 2016, certain performance-based targets were achieved and the Company recorded compensation expense of $206 and $412, respectively, in the consolidated statements of operations.


	Shares Issuable Under Options			Weighted Average Exercise Price		Weighted Average Remaining Contractual Term in years		Aggregate Intrinsic Value
Outstanding as of September 30, 2015		1,752,010		$	23.76		7.2	$	25,093
Granted		495,780			30.52
Exercised		(318,929	)		3.21
Forfeited		(38,530	)		32.17

Outstanding, June 30, 2016		1,890,331		$	28.81		7.8	$	4,989

Options vested and expected to vest as of June 30, 2016		1,751,653		$	29.84		7.9	$	3,979

Options exercisable as of June 30, 2016		836,313		$	25.01		7.0	$	3,894

In December 2015, the Company awarded certain executive officers a total of 50,000 share units consisting of 25,000 performance share units, or PSUs, and 25,000 relative total shareholder return units, or rTSRUs. The number of units represents the target number of shares of common stock that may be earned; however, the actual number of shares that may be earned ranges from 0% to 200% of the target number. The PSUs will vest and result in issuance, or settlement, of common shares, based upon continued employment and achievement of specified research and development milestones on or before December 31, 2017. The aggregate grant date fair value of the 25,000 PSUs ranges between $0 and $1,602. During the three and nine months ended June 30, 2016, the Company recorded no compensation expense related to the PSU awards as none of the performance-based targets was probable of being achieved during this period.

The rTSRUs will vest and result in the issuance of common stock based on continuing employment and the relative ranking of the total shareholder return, or TSR, of the Company’s common stock in relation to the TSR of the component companies in the NASDAQ Biotech Index over a two-year period based on a comparison of average closing stock prices in November 2015 and December 2017. The number of market-based rTSRUs awarded represents the target number of shares of common stock that may be earned; however, the actual number of shares that may be earned ranges from 0% to 200% of the target number.

The Company used a Monte Carlo simulation model to estimate that the aggregate grant-date fair value of the rTSRUs was $942. The table below sets forth the assumptions used to value the awards and the estimated grant-date fair value:


Risk-free interest rate		0.97	%
Dividend yield		0	%
Expected volatility		63.95	%
Remaining performance period (years)		2.03
Estimated fair value per share of rTSRUs granted	$	37.67

The fair value related to the rTSRUs will be recorded as compensation expense over the period from date of grant to December 2017 regardless of whether the target relative total shareholder returns are reached.

In addition, in December 2015, the Company awarded an executive officer 5,250 share units consisting of 2,625 PSUs and 2,625 rTSRUs. The number of units represents the target number of shares of common stock that may be earned; however, the actual number of shares that may be earned ranges from 0% to 200% of the target number.

The PSUs will vest and result in issuance, or settlement, of common shares, based upon continued employment and achievement of specified research and development milestones on or before December 31, 2016. The aggregate grant date fair value of the 2,625 PSUs ranges between $0 and $168. During the three and nine months ended June 30, 2016, the Company recorded no compensation expense related to the PSU awards as none of the performance-based targets was probable of being achieved during this period.

The rTSRUs will vest and result in the issuance of common stock based on continuing employment and the relative ranking of the total shareholder return, or TSR, of the Company’s common stock in relation to the TSR of the component companies in the NASDAQ Biotech Index over a two-year period based on a comparison of average closing stock prices in December 2014 and December 2016. The number of market-based rTSRUs awarded represents the target number of shares of common stock that may be earned; however, the actual number of shares that may be earned ranges from 0% to 200% of the target number.

The Company used a Monte Carlo simulation model to estimate that the aggregate grant-date fair value of the rTSRUs was $44. The table below sets forth the assumptions used to value the awards and the estimated grant-date fair value:


Risk-free interest rate		0.65	%
Dividend yield		0	%
Expected volatility		72.30	%
Remaining performance period (years)		1.03
Estimated fair value per share of rTSRUs granted	$	16.90

The fair value related to the rTSRUs will be recorded as compensation expense over the period from date of grant to December 2016 regardless of whether the target relative total shareholder returns are reached.

The Company recognized stock-based compensation expense on all awards in the following expense categories:


	Three Months ended June 30,				Nine Months ended June 30,
	2016		2015		2016		2015
Research and development	$	790	$	468	$	2,092	$	1,106
General and administrative		1,680		1,116		4,752		2,935

	$	2,470	$	1,584	$	6,844	$	4,041

As of June 30, 2016, the Company had an aggregate of $24,680 unrecognized stock-based compensation cost, which is expected to be recognized over a weighted average period of 2.4 years.

- Definition

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

+ References + Details

Net Income (Loss) Per Share

9 Months Ended

Jun. 30, 2016

Earnings Per Share [Abstract]

Net Income (Loss) Per Share

9.	Net Income (Loss) Per Share

Basic and diluted net income (loss) per share attributable to common stockholders was calculated as follows for the three and nine months ended June 30, 2016 and 2015:


	Three Months Ended June 30,					Nine Months Ended June 30,
	2016			2015		2016		2015
Basic net income (loss) per share:
Numerator:
Net income (loss)	$	(1,076	)	$	2,418	$	23,468	$	73,180
Denominator:
Weighted average common shares outstanding—basic		18,982,825			18,697,104		18,892,627		18,659,742

Net income (loss) per share allocable to common shareholders—basic	$	(0.06	)	$	0.13	$	1.24	$	3.92

Diluted net income (loss) per share:
Numerator:
Net income (loss)	$	(1,076	)	$	2,418	$	23,468	$	73,180
Denominator:
Weighted average common shares outstanding—basic		18,982,825			18,697,104		18,892,627		18,659,742
Dilutive effect of common stock equivalents		—			580,862		330,732		617,025

Weighted average common shares outstanding—diluted		18,982,825			19,277,966		19,223,359		19,276,767

Net income (loss) per share allocable to common shareholders—diluted	$	(0.06	)	$	0.13	$	1.22	$	3.80

Antidilutive common stock equivalents excluded from above		1,619,987			700,679		1,250,330		599,384

The impact of certain common stock equivalents were excluded from the calculation of diluted net income (loss) per share for the three months ended June 30, 2016 because the impact would have been anti-dilutive for the period. The impact of dilutive common stock equivalents of 237,796 were excluded from the calculation of diluted earnings per share for the three months ended June 30, 2016 as the effect would be anti-dilutive.

As of June 30, 2016 the Company excluded 97,050 and 125,291 of unvested restricted stock units and performance based options, respectively, from the calculation of diluted net income per share attributable to common stockholders as these awards contain performance and market conditions that would not have been achieved as of June 30, 2016 had the measurement period been as of that date.

Income Taxes

9 Months Ended

Jun. 30, 2016

Income Tax Disclosure [Abstract]

Income Taxes

10.

Income Taxes

For the three months ended June 30, 2016 and 2015, the Company recorded an income tax (expense) benefit of $(434) and $428 respectively. The income tax (expense) benefit for the three months ended June 30, 2016 and 2015 was primarily attributable to the Company’s domestic operations. During the three months ended June 30, 2016, the Company increased its estimate of its annual effective tax rate, which resulted in an income tax expense despite a pre-tax loss for the quarter. For the three months ended June 30, 2015, the Company’s effective tax rate of 21.5% differs from the statutory rate of 35.0% primarily due to a research and development tax credit study performed in the quarter which resulted in an incremental tax benefit upon its completion in June 2015.

For the nine months ended June 30, 2016 and 2015, the Company recorded an income tax (expense) of $(11,720) and $(48,092), respectively, representing an effective tax rate of 33.3% and 39.7%, respectively. For the nine months ended June 30, 2016, the Company’s effective tax rate differs from the statutory rate of 35.0% primarily due to reinstatement of the federal research and development tax credits which are included in the Company’s annual effective tax rate. For the nine months ended June 30, 2015, the Company’s effective tax rate differs from the statutory rate of 35.0% primarily due to state income taxes and certain expenditures which are permanently not deductible for tax purposes.

The Company files tax returns as prescribed by the tax laws of the jurisdictions in which it operates. In the normal course of business, the Company is subject to examination by federal and state jurisdictions, where applicable. There are currently no pending income tax examinations. The Company’s tax years are still open under statute from 2008 to the present. Earlier years may be examined to the extent that tax credit or net operating loss carryforwards are used in future periods.

The Company had an unrecognized tax benefit of $668 and $448 as of June 30, 2016 and September 30, 2015, respectively. Unrecognized tax benefits represent tax positions for which reserves have been established. The Company’s policy is to record interest and penalties related to uncertain tax positions as part of its income tax provision.

Commitments and Contingencies

9 Months Ended

Jun. 30, 2016

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

11.

Commitments and Contingencies

Leases

The Company has an office and laboratory lease that expires in September 2022. Payment escalation as specified in the lease agreement is accrued such that rent expense is recognized on a straight-line basis over the term of occupancy. The Company recorded rent expense of $506 and $341 for the three months ended June 30, 2016 and 2015, respectively, and $1,519 and $821 for the nine months ended June 30, 2016 and 2015, respectively.

In connection with the lease, the Company has outstanding a $608 letter of credit, collateralized by a money market account. As of June 30, 2016 and September 30, 2015, the Company classified the $608 related to the letter of credit as restricted cash. Additionally, the lease, as amended, included a $598 tenant improvement allowance from the landlord, which allowance is accounted for as a capital lease obligation.

Intellectual Property Licenses

The Company has a non-exclusive intellectual property license agreement with a third party, under which the Company is required to pay (1) annual maintenance fees of $105 for each year that the agreement remains in effect, commencing on the first anniversary of the agreement, in order to maintain the right to use the license, and (2) a one-time fee of $50 in each circumstance in which the Company provides the licensed intellectual property to one of its collaborators with the prior consent of the licensor.

The Company also has a non-exclusive license with respect to patents it uses in its HCV research. Under the license, the Company is obligated to pay milestones totaling up to $5,000 plus low single digit royalties, for the development and regulatory approval of each HCV product outside of the Company’s collaboration with AbbVie and any other collaboration it may enter into in the future with a partner that has already licensed these patents. During the nine months ended June 30, 2016, the Company made a $500 milestone payment under this license agreement upon its filing to commence clinical development of its cyclophilin inhibitor candidate. During the three and nine months ended June 30, 2015, no events triggering such payment occurred.

Litigation and Contingencies Related to Use of Intellectual Property

From time to time, the Company may become subject to legal proceedings, claims and litigation arising in the ordinary course of business. The Company currently is not a party to any threatened or pending litigation. However, third parties might allege that the Company or its collaborators are infringing their patent rights or that the Company is otherwise violating their intellectual property rights. Such third parties may resort to litigation against the Company or its collaborators, which the Company has agreed to indemnify. With respect to some of these patents, the Company expects that it will be required to obtain licenses and could be required to pay license fees or royalties, or both. These licenses may not be available on acceptable terms, or at all. A costly license, or inability to obtain a necessary license, would have a material adverse effect on the Company’s financial condition, results of operations or cash flows. The Company accrues contingent liabilities when it is probable that future expenditures will be made and such expenditures can be reasonably estimated.

Indemnification Agreements

In the ordinary course of business, the Company may provide indemnifications of varying scope and terms to customers, vendors, lessors, business partners, and other parties with respect to certain matters including, but not limited to, losses arising out of breach of such agreements, from services to be provided by the Company, or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with members of its board of directors and its executive officers that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors or officers. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is, in many cases, unlimited. To date, the Company has not incurred any material costs as a result of such indemnifications. In addition, the Company maintains officers and directors insurance coverage. The Company does not believe that the outcome of any claims under indemnification arrangements will have a material effect on its financial position, results of operations or cash flows, and it has not accrued any liabilities related to such obligations in its financial statements as of June 30, 2016.

Summary of Significant Accounting Policies (Policies)	9 Months Ended
Summary of Significant Accounting Policies (Policies)	Jun. 30, 2016
Accounting Policies [Abstract]
Use of Estimates	Use of Estimates The preparation of consolidated financial statements in conformity with 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 consolidated financial statements, and the reported amounts of revenues and expenses during the reporting period. Significant estimates and assumptions reflected in these consolidated financial statements include, but are not limited to, management’s judgments of separate units of accounting and best estimate of selling price of those units of accounting within its revenue arrangements; valuation of stock-based awards; the useful lives of property and equipment; and the accounting for income taxes, including uncertain tax positions and the valuation of net deferred tax assets. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Actual results could differ from the Company’s estimates.
Recently Issued Accounting Pronouncements	Recently Issued Accounting Pronouncements In May 2014, the Financial Accounting Standards Board (the “FASB”) issued ASU No. 2014-09, Revenue from Contracts with Customers (Topic 606), which supersedes all existing revenue recognition requirements, including most industry-specific guidance. The new standard requires a company to recognize revenue when it transfers goods or services to customers in an amount that reflects the consideration that the company expects to receive for those goods or services. In March 2016, the FASB issued ASU No. 2016-08, Revenue from Contracts with Customers: Principal versus Agent Considerations. The amendment includes indicators to assist an entity in determining whether it controls a specified good or service before it is transferred to the customers. In April 2016, the FASB issued ASU No. 2016-10, Revenue from Contracts with Customers: Identifying Performance Obligations and Licensing in April 2016 to clarify guidance from ASU 2014-09. Specifically, this amendment addresses an entity’s identification of its performance obligations in a contract, as well as an entity’s evaluation of the nature of its promise to grant a license of intellectual property and whether or not that revenue is recognized over time or at a point in time. The FASB also issued ASU No. 2016-12 Revenue from Contracts with Customers: Narrow-Scope Improvements and Practical Expedients, in May 2016. This amendment addresses collectability, non-cash consideration, presentation of sales tax and transitioning to the new standard. These new standards will be effective for the Company on October 1, 2018. The Company is currently evaluating the potential impact that Topic 606 may have on its financial position and results of operations. In November 2015, the FASB issued ASU No. 2015-17, Balance Sheet Classification of Deferred Taxes (“ASU 2015-17”), which simplifies the presentation of deferred income taxes by eliminating the need for entities to separate deferred income tax liabilities and assets into current and noncurrent amounts in a classified statement of financial position. This amendment is effective for the Company in the fiscal year beginning October 1, 2017, but early adoption is permissible. The Company is currently evaluating the potential impact that ASU 2015-17 may have on its financial position. In February 2016, the FASB issued ASU No. 2016-02, Leases (“ASU 2016-02”), which will replace the existing guidance in ASC 840, “Leases.” The updated standard aims to increase transparency and comparability among organizations by requiring lessees to recognize lease assets and lease liabilities on the balance sheet and requiring disclosure of key information about leasing arrangements. This amendment is effective for the Company in the fiscal year beginning October 1, 2019, but early adoption is permissible. The Company is currently evaluating the potential impact that ASU 2016-02 may have on its financial position and results of operations. In March 2016, the FASB issued ASU No. 2016-09, Improvements to Employee Share-Based Payment Accounting (“ASU 2016-09”), which intends to simplify several aspects of accounting for share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, an option to recognize gross stock compensation expense with actual forfeitures recognized as they occur, as well as certain classifications on the statement of cash flows. This amendment is effective for the Company in the fiscal year beginning October 1, 2017, but early adoption is permissible. The Company is currently evaluating the potential impact that ASU 2016-09 may have on its financial position and results of operations. Other accounting standards that have been issued or proposed by the FASB or other standards-setting bodies that do not require adoption until a future date are not expected to have a material impact on the Company’s financial statements upon adoption.

Fair Value of Financial Assets and Liabilities (Tables)

9 Months Ended

Jun. 30, 2016

Fair Value Disclosures [Abstract]

Financial Assets and Liabilities that were Subject to Fair Value Measurement on Recurring Basis


	Fair Value Measurements at June 30, 2016 Using:
	Level 1		Level 2		Level 3		Total
Assets:
U.S. Treasury notes	$	62,658	$	—	$	—	$	62,658
Cash equivalents		20,534		—		—		20,534
Corporate bonds		—		79,326		—		79,326
Commercial paper		—		46,819		—		46,819
U.S. Agency bonds		—		31,067		—		31,067

	$	83,192	$	157,212	$	—	$	240,404

Liabilities:
Warrant liability	$	—	$	—	$	1,237	$	1,237
Series 1 nonconvertible preferred stock		—		—		158		158

	$	—	$	—	$	1,395	$	1,395


	Fair Value Measurements at September 30, 2015 Using:
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents	$	21,327	$	—	$	—	$	21,327
Corporate bonds		—		151,020		—		151,020
U.S. Agency bonds		—		36,697		—		36,697

	$	21,327	$	187,717	$	—	$	209,044

Liabilities:
Warrant liability	$	—	$	—	$	1,276	$	1,276
Series 1 nonconvertible preferred stock		—		—		163		163

	$	—	$	—	$	1,439	$	1,439

Fair Value Measurements of the Company's Warrant Liability and Series 1 Nonconvertible Preferred Stock


	Unobservable Input	June 30, 2016 Range (Weighted Average)
Warrant liability and Series 1 nonconvertible preferred stock	Probabilities of payout	0% - 60%
	Periods in which payout is expected to occur	2016 – 2017
	Discount rate	4.50%
	Unobservable Input	September 30, 2015 Range (Weighted Average)
Warrant liability and Series 1 nonconvertible preferred stock	Probabilities of payout	5% - 60%
	Periods in which payout is expected to occur	2016 – 2017
	Discount rate	4.25%

Rollforward of Aggregate Fair Values of Warrants


	Warrant Liability			Series 1 Nonconvertible Preferred Stock
Balance, September 30, 2015	$	1,276		$	163
Decrease in fair value		(39	)		(5	)

Balance, June 30, 2016	$	1,237		$	158

Marketable Securities (Tables)

9 Months Ended

Jun. 30, 2016

Investments, Debt and Equity Securities [Abstract]

Fair Value of Available-for-Sale Marketable Securities by Type of Security

As of June 30, 2016 and September 30, 2015, the fair value of available-for-sale marketable securities by type of security was as follows:


	June 30, 2016
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Corporate bonds	$	79,259	$	75	$	(8	)	$	79,326
U.S. Treasury notes		62,558		100		—			62,658
Commercial paper		46,819		—		—			46,819
U.S. Agency bonds		31,047		20		—			31,067

	$	219,683	$	195	$	(8	)	$	219,870


	September 30, 2015
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
Corporate bonds	$	151,012	$	77	$	(69	)	$	151,020
U.S. Agency bonds		36,652		45		—			36,697

	$	187,664	$	122	$	(69	)	$	187,717

- Definition

Tabular disclosure of available-for-sale securities which includes, but is not limited to, changes in the cost basis and fair value, fair value and gross unrealized gain (loss), fair values by type of security, contractual maturity and classification, amortized cost basis, contracts to acquire securities to be accounted for as available-for-sale, debt maturities, transfers to trading, change in net unrealized holding gain (loss) net of tax, continuous unrealized loss position fair value, aggregate losses qualitative disclosures, other than temporary impairment (OTTI) losses or other disclosures related to available for sale securities.

+ References + Details

Accrued Expenses and Other Long-Term Liabilities (Tables)

9 Months Ended

Jun. 30, 2016

Payables and Accruals [Abstract]

Accrued Expenses and Other Current Liabilities as well as Other Long-Term Liabilities

Accrued expenses and other current liabilities as well as other long-term liabilities consisted of the following as of June 30, 2016 and September 30, 2015:


	June 30, 2016		September 30, 2015
Accrued expenses:
Accrued preclinical and clinical expenses	$	1,696	$	237
Accrued payroll and related expenses		1,661		1,622
Accrued professional fees		517		338
Accrued other		419		371
Accrued vendor manufacturing		219		18
Capital lease obligation		71		69
Accrued fixed assets		—		1,307

	$	4,583	$	3,962

Other long-term liabilities:
Accrued rent expense	$	682	$	628
Uncertain tax positions		668		448
Capital lease obligation		478		529
Asset retirement obligation		135		108

	$	1,963	$	1,713

Stock-Based Awards (Tables)

9 Months Ended

Jun. 30, 2016

Stock Option Activity

The straight-line method is applied to all grants with service conditions, while the graded vesting method is applied to all grants with both service and performance conditions.


	Shares Issuable Under Options			Weighted Average Exercise Price		Weighted Average Remaining Contractual Term in years		Aggregate Intrinsic Value
Outstanding as of September 30, 2015		1,752,010		$	23.76		7.2	$	25,093
Granted		495,780			30.52
Exercised		(318,929	)		3.21
Forfeited		(38,530	)		32.17

Outstanding, June 30, 2016		1,890,331		$	28.81		7.8	$	4,989

Options vested and expected to vest as of June 30, 2016		1,751,653		$	29.84		7.9	$	3,979

Options exercisable as of June 30, 2016		836,313		$	25.01		7.0	$	3,894

Stock-Based Compensation Expense

The Company recognized stock-based compensation expense on all awards in the following expense categories:


	Three Months ended June 30,				Nine Months ended June 30,
	2016		2015		2016		2015
Research and development	$	790	$	468	$	2,092	$	1,106
General and administrative		1,680		1,116		4,752		2,935

	$	2,470	$	1,584	$	6,844	$	4,041

RTSRUs [Member] | Certain Executives [Member]

Weighted Average Assumptions Used To Value Awards and Estimated Aggregate Grant Date Fair Value

The table below sets forth the assumptions used to value the awards and the estimated grant-date fair value:


Risk-free interest rate		0.97	%
Dividend yield		0	%
Expected volatility		63.95	%
Remaining performance period (years)		2.03
Estimated fair value per share of rTSRUs granted	$	37.67

RTSRUs [Member] | Executive Officer [Member]

Weighted Average Assumptions Used To Value Awards and Estimated Aggregate Grant Date Fair Value

The table below sets forth the assumptions used to value the awards and the estimated grant-date fair value:


Risk-free interest rate		0.65	%
Dividend yield		0	%
Expected volatility		72.30	%
Remaining performance period (years)		1.03
Estimated fair value per share of rTSRUs granted	$	16.90

Net Income (Loss) Per Share (Tables)

9 Months Ended

Jun. 30, 2016

Earnings Per Share [Abstract]

Basic and Diluted Net Income (Loss) Per Share Attributable to Common Stockholders

Basic and diluted net income (loss) per share attributable to common stockholders was calculated as follows for the three and nine months ended June 30, 2016 and 2015:


	Three Months Ended June 30,					Nine Months Ended June 30,
	2016			2015		2016		2015
Basic net income (loss) per share:
Numerator:
Net income (loss)	$	(1,076	)	$	2,418	$	23,468	$	73,180
Denominator:
Weighted average common shares outstanding—basic		18,982,825			18,697,104		18,892,627		18,659,742

Net income (loss) per share allocable to common shareholders—basic	$	(0.06	)	$	0.13	$	1.24	$	3.92

Diluted net income (loss) per share:
Numerator:
Net income (loss)	$	(1,076	)	$	2,418	$	23,468	$	73,180
Denominator:
Weighted average common shares outstanding—basic		18,982,825			18,697,104		18,892,627		18,659,742
Dilutive effect of common stock equivalents		—			580,862		330,732		617,025

Weighted average common shares outstanding—diluted		18,982,825			19,277,966		19,223,359		19,276,767

Net income (loss) per share allocable to common shareholders—diluted	$	(0.06	)	$	0.13	$	1.22	$	3.80

Antidilutive common stock equivalents excluded from above		1,619,987			700,679		1,250,330		599,384

Fair Value of Financial Assets and Liabilities - Financial Assets and Liabilities that were Subject to Fair Value Measurement on Recurring Basis (Detail) - USD ($) $ in Thousands	Jun. 30, 2016	Sep. 30, 2015
Liabilities:
Liabilities, Fair Value Disclosure, Total	$ 1,395	$ 1,439
Assets:
Cash equivalents	20,534	21,327
Available for sale securities, fair value	219,870	187,717
Assets, Fair Value Disclosure, Total	240,404	209,044
U.S. Treasury Notes [Member]
Assets:
Available for sale securities, fair value	62,658
Corporate Bonds [Member]
Assets:
Available for sale securities, fair value	79,326	151,020
Commercial Paper [Member]
Assets:
Available for sale securities, fair value	46,819
U.S. Agency Bonds [Member]
Assets:
Available for sale securities, fair value	31,067	36,697
Warrant Liability [Member]
Liabilities:
Liabilities	1,237	1,276
Series 1 Nonconvertible Preferred Stock [Member]
Liabilities:
Liabilities	158	163
Level 1 [Member]
Assets:
Cash equivalents	20,534	21,327
Assets, Fair Value Disclosure, Total	83,192	21,327
Level 1 [Member] \| U.S. Treasury Notes [Member]
Assets:
Available for sale securities, fair value	62,658
Level 2 [Member]
Assets:
Assets, Fair Value Disclosure, Total	157,212	187,717
Level 2 [Member] \| Corporate Bonds [Member]
Assets:
Available for sale securities, fair value	79,326	151,020
Level 2 [Member] \| Commercial Paper [Member]
Assets:
Available for sale securities, fair value	46,819
Level 2 [Member] \| U.S. Agency Bonds [Member]
Assets:
Available for sale securities, fair value	31,067	36,697
Level 3 [Member]
Liabilities:
Liabilities, Fair Value Disclosure, Total	1,395	1,439
Level 3 [Member] \| Warrant Liability [Member]
Liabilities:
Liabilities	1,237	1,276
Level 3 [Member] \| Series 1 Nonconvertible Preferred Stock [Member]
Liabilities:
Liabilities	$ 158	$ 163

Fair Value of Financial Assets and Liabilities - Additional Information (Detail) - USD ($)	3 Months Ended		9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Fair Value Disclosures [Abstract]
Transfers between Level 1, Level 2 and Level 3	$ 0	$ 0	$ 0	$ 0

Fair Value of Financial Assets and Liabilities - Fair Value Measurements of the Company's Warrant Liability and Series 1 Nonconvertible Preferred Stock (Detail) - Warrant Liability [Member] - Series 1 Nonconvertible Preferred Stock [Member]	9 Months Ended	12 Months Ended
	Jun. 30, 2016	Sep. 30, 2015
Fair Value Inputs, Liabilities, Quantitative Information [Line Items]
Periods in which payout is expected to occur, beginning	2016	2016
Periods in which payout is expected to occur, ending	2017	2017
Discount rate	4.50%	4.25%
Minimum [Member]
Fair Value Inputs, Liabilities, Quantitative Information [Line Items]
Probabilities of payout	0.00%	5.00%
Maximum [Member]
Fair Value Inputs, Liabilities, Quantitative Information [Line Items]
Probabilities of payout	60.00%	60.00%

Fair Value of Financial Assets and Liabilities - Rollforward of Aggregate Fair Values of Warrants (Detail) $ in Thousands	9 Months Ended
	Jun. 30, 2016 USD ($)
Series 1 Nonconvertible Preferred Stock [Member]
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Beginning Balance	$ 163
Decrease in fair value	(5)
Ending Balance	158
Warrant Liability [Member]
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Beginning Balance	1,276
Decrease in fair value	(39)
Ending Balance	$ 1,237

Marketable Securities - Fair Value of Available-for-Sale Marketable Securities by Type of Security (Detail) - USD ($) $ in Thousands	Jun. 30, 2016	Sep. 30, 2015
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 219,683	$ 187,664
Gross Unrealized Gains	195	122
Gross Unrealized Losses	(8)	(69)
Fair Value	219,870	187,717
Corporate Bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	79,259	151,012
Gross Unrealized Gains	75	77
Gross Unrealized Losses	(8)	(69)
Fair Value	79,326	151,020
U.S. Agency Bonds [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	31,047	36,652
Gross Unrealized Gains	20	45
Fair Value	31,067	$ 36,697
Commercial Paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	46,819
Fair Value	46,819
U.S. Treasury Notes [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	62,558
Gross Unrealized Gains	100
Fair Value	$ 62,658

Marketable Securities - Additional Information (Detail) - USD ($) $ in Thousands	Jun. 30, 2016	Sep. 30, 2015
Investments, Debt and Equity Securities [Abstract]
Marketable securities maturing in greater than one year, aggregate fair value	$ 26,194	$ 64,238

Accrued Expenses and Other Long-Term Liabilities - Accrued Expenses and Other Current Liabilities as well as Other Long-Term Liabilities (Detail) - USD ($) $ in Thousands	Jun. 30, 2016	Sep. 30, 2015
Accrued expenses:
Accrued preclinical and clinical expenses	$ 1,696	$ 237
Accrued payroll and related expenses	1,661	1,622
Accrued professional fees	517	338
Accrued other	419	371
Accrued vendor manufacturing	219	18
Capital lease obligation	71	69
Accrued fixed assets		1,307
Accrued expenses	4,583	3,962
Other long-term liabilities:
Accrued rent expense	682	628
Uncertain tax positions	668	448
Capital lease obligation	478	529
Asset retirement obligation	135	108
Other long-term liabilities	$ 1,963	$ 1,713

Ongoing Collaboration Agreements - Additional Information (Detail) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended		116 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone revenue recognized			$ 30,000	$ 125,000
AbbVie [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration agreement tiered royalty description			From the low double digits up to twenty percent, or on a blended basis from the low double digits up to the high teens, on calendar year net sales
Additional Funding Agreement Terms [Member] \| AbbVie [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone revenue payment received			$ 80,000
Milestone Payments [Member] \| AbbVie [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone revenue recognized		$ 0		$ 125,000
Milestone Payments [Member] \| Paritaprevir 3-DAA Regimen [Member] \| AbbVie [Member] \| JAPAN
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone revenue recognized	$ 0		$ 30,000
Milestone Payments and Royalties [Member] \| AbbVie [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Proceed received to fund research activities and preferred stock financing					$ 380,000

Warrants to Purchase Series 1 Nonconvertible Preferred Stock and Series 1 Nonconvertible Preferred Stock - Additional Information (Detail) - Series 1 Nonconvertible Preferred Stock [Member] - shares	9 Months Ended
	Jun. 30, 2016	Nov. 30, 2010
Class of Warrant or Right [Line Items]
Number of shares issuable upon exercise of the warrants		1,999,989
Warrant expiration date	Oct. 04, 2017

Stock-Based Awards - Additional Information (Detail) - USD ($)	1 Months Ended		3 Months Ended	9 Months Ended
	Dec. 31, 2015	Mar. 31, 2013	Jun. 30, 2016	Jun. 30, 2016
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Aggregate of unrecognized stock-based compensation cost			$ 24,680,000	$ 24,680,000
Weighted average recognition period				2 years 4 months 24 days
PSU [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation expenses			206,000	$ 412,000
Certain Executives [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares awarded	50,000
Certain Executives [Member] \| PSU [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares awarded	25,000	167,052
Compensation expenses			0	0
Certain Executives [Member] \| PSU [Member] \| Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Aggregate grant date fair value of award		$ 0		0
Certain Executives [Member] \| PSU [Member] \| Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Aggregate grant date fair value of award		$ 2,479,000		1,602,000
Certain Executives [Member] \| RTSRUs [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares awarded	25,000
Aggregate grant date fair value of award				$ 942,000
Certain Executives [Member] \| RTSRUs [Member] \| Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares range percentage	0.00%			0.00%
Certain Executives [Member] \| RTSRUs [Member] \| Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares range percentage	200.00%			200.00%
Executive Officer [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares awarded	5,250
Executive Officer [Member] \| PSU [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares awarded	2,625			2,625
Compensation expenses			$ 0	$ 0
Executive Officer [Member] \| PSU [Member] \| Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Aggregate grant date fair value of award				0
Executive Officer [Member] \| PSU [Member] \| Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Aggregate grant date fair value of award				168,000
Executive Officer [Member] \| RTSRUs [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares awarded	2,625
Aggregate grant date fair value of award				$ 44,000
Executive Officer [Member] \| RTSRUs [Member] \| Minimum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares range percentage	0.00%			0.00%
Executive Officer [Member] \| RTSRUs [Member] \| Maximum [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares range percentage	200.00%			200.00%
Employee Stock Purchase Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future grant			185,614	185,614
Shares issued				0
2012 Equity Incentive Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future grant			491,511	491,511

Stock-Based Awards - Stock Option Activity (Detail) - USD ($) $ / shares in Units, $ in Thousands		9 Months Ended
	Sep. 30, 2015	Jun. 30, 2016
Options
Outstanding as of beginning of period		1,752,010
Granted		495,780
Exercised		(318,929)
Forfeited		(38,530)
Outstanding as of end of period	1,752,010	1,890,331
Options vested and expected to vest as of end of period		1,751,653
Options exercisable as of end of period		836,313
Weighted Average Exercise Price
Outstanding	$ 23.76	$ 28.81
Granted		30.52
Exercised		3.21
Forfeited		32.17
Outstanding	$ 23.76	28.81
Options vested and expected to vest as of end of period		29.84
Options exercisable as of end of period		$ 25.01
Weighted Average Remaining Contractual Term
Outstanding as of end of period	7 years 2 months 12 days	7 years 9 months 18 days
Options vested and expected to vest as of end period		7 years 10 months 24 days
Options exercisable as of end of period		7 years
Aggregate Intrinsic Value
Outstanding as of beginning of period		$ 25,093
Outstanding as of end of period	$ 25,093	4,989
Options vested and expected to vest as of end of period		3,979
Options exercisable as of end of period		$ 3,894

Stock-Based Awards - Weighted Average Assumptions Used To Value Awards and Estimated Aggregate Grant Date Fair Value (Detail) - RTSRUs [Member]	9 Months Ended
	Jun. 30, 2016 $ / shares
Certain Executives [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	0.97%
Dividend yield	0.00%
Expected volatility	63.95%
Remaining performance period (years)	2 years 11 days
Estimated fair value per share of rTSRUs granted	$ 37.67
Executive Officer [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate	0.65%
Dividend yield	0.00%
Expected volatility	72.30%
Remaining performance period (years)	1 year 11 days
Estimated fair value per share of rTSRUs granted	$ 16.90

Stock-Based Awards - Stock-Based Compensation Expense (Detail) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation expense	$ 2,470	$ 1,584	$ 6,844	$ 4,041
Research and Development [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation expense	790	468	2,092	1,106
General and Administrative [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation expense	$ 1,680	$ 1,116	$ 4,752	$ 2,935

Net Income (Loss) Per Share - Basic and Diluted Net Income (Loss) Per Share Attributable to Common Stockholders (Detail) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Basic net income (loss) per share:
Net income (loss)	$ (1,076)	$ 2,418	$ 23,468	$ 73,180
Weighted average common shares outstanding-basic	18,982,825	18,697,104	18,892,627	18,659,742
Net income (loss) per share allocable to common shareholders-basic	$ (0.06)	$ 0.13	$ 1.24	$ 3.92
Diluted net income (loss) per share:
Net income (loss)	$ (1,076)	$ 2,418	$ 23,468	$ 73,180
Weighted average common shares outstanding-basic	18,982,825	18,697,104	18,892,627	18,659,742
Dilutive effect of common stock equivalents		580,862	330,732	617,025
Weighted average common shares outstanding-diluted	18,982,825	19,277,966	19,223,359	19,276,767
Net income (loss) per share allocable to common shareholders-diluted	$ (0.06)	$ 0.13	$ 1.22	$ 3.80
Antidilutive common stock equivalents excluded from above	1,619,987	700,679	1,250,330	599,384

Net Income (Loss) Per Share - Additional Information (Detail) - shares	3 Months Ended		9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Shares excluded from the computation of diluted net income per share	1,619,987	700,679	1,250,330	599,384
Common Stock Equivalents [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Shares excluded from the computation of diluted net income per share	237,796
Restricted Stock Units [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Shares excluded from the computation of diluted net income per share			97,050
PSU [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Shares excluded from the computation of diluted net income per share			125,291

Income Taxes - Additional Information (Detail) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Sep. 30, 2015
Income Tax Disclosure [Abstract]
Income tax (expense) benefit	$ (434)	$ 428	$ (11,720)	$ (48,092)
Federal statutory income tax rate		35.00%		35.00%
Effective income tax rate		21.50%	33.30%	39.70%
Unrecognized tax benefits	$ 668		$ 668		$ 448

Commitments and Contingencies - Additional Information (Detail) - USD ($)	3 Months Ended		9 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Sep. 30, 2015
Commitments and Contingencies Disclosure [Abstract]
Rent expense	$ 506,000	$ 341,000	$ 1,519,000	$ 821,000
Office lease expiration period			Sep. 30, 2022
Outstanding letter of credit	608,000		$ 608,000		$ 608,000
Restricted cash	$ 608,000		608,000		$ 608,000
Tenant improvement allowance			598,000
Maintenance fees			105,000
One-time fee			50,000
Company's obligation to pay			5,000,000
Milestone payment made		$ 0	$ 500,000	$ 0