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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

FORM 10-Q
(Mark One)
☑ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the quarterly period ended September 30, 2019
or
☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the transition period from to
Commission file number: 001-35969
PTC Therapeutics, Inc.
(Exact name of registrant as specified in its charter)

Delaware |  | 04-3416587
(State or other jurisdiction of incorporation or organization) |  | (I.R.S. Employer Identification No.)

100 Corporate Court |  |
South Plainfield, | NJ |  | 07080
(Address of principal executive offices) |  | (Zip Code)

(908) 222-7000
(Registrant’s telephone number, including area code)
Securities registered pursuant to Section 12(b) of the Act:

Title of each class | Trading Symbol(s) | Name of each exchange on which registered
Common Stock, $0.001 par value per share | PTCT | Nasdaq Global Select Market

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes þ No ☐
Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes þ No ☐
Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer”, “accelerated filer,” “smaller reporting company,” and "emerging growth company" in Rule 12b-2 of the Exchange Act.

Large accelerated filer | þ | Accelerated filer | ☐
Non-accelerated filer | ☐ | Smaller reporting company | ☐
|  | Emerging growth company | ☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐
Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No þ
As of October 25, 2019, there were 61,630,979 shares of Common Stock, $0.001 par value per share, outstanding.

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TABLE OF CONTENTS
PTC Therapeutics, Inc.
| Page No.
PART I—FINANCIAL INFORMATION
Item 1. Financial Statements (unaudited) | 4
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations | 40
Item 3. Quantitative and Qualitative Disclosures About Market Risk | 55
Item 4. Controls and Procedures | 55
PART II—OTHER INFORMATION
Item 1. Legal Proceedings | 56
Item 1A. Risk Factors | 56
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds | 56
Item 6. Exhibits | 57

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FORWARD-LOOKING STATEMENTS
This Quarterly Report on Form 10-Q contains forward-looking statements that involve substantial risks and uncertainties. All statements, other than statements of historical facts, contained in this Quarterly Report on Form 10-Q, including statements regarding our strategy, future operations, future financial position, future revenues, projected costs, prospects, plans and objectives of management, are forward-looking statements. The words “anticipate,” “believe,” “estimate,” “expect,” “intend,” “may,” “might,” “plan,” “predict,” “project,” “target,” “potential,” “will,” “would,” “could,” “should,” “continue,” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words.
The forward-looking statements in this Quarterly Report on Form 10-Q include, among other things, statements about:

• | Our ability to realize the anticipated benefits of our acquisition of Agilis Biotherapeutics, Inc., or Agilis, including the possibility that the expected impact of benefits from the acquisition, including with respect to the business of Agilis and our expectations with respect to the potential achievement of development, regulatory and sales milestones and our contingent payments to the former Agilis equityholders with respect thereto, will not be realized or will not be realized within the expected time period, significant transaction costs, our ability to obtain marketing approval of our gene therapy for the treatment of Aromatic L-Amino Acid Decarboxylase, or AADC, deficiency, or PTC-AADC, and other product candidates we acquired from Agilis, unknown liabilities, the risk of litigation and/or regulatory actions related to the acquisition, and other business effects, including the effects of industry, market, economic, political or regulatory conditions;

• | our ability to negotiate, secure and maintain adequate pricing, coverage and reimbursement terms and processes on a timely basis, or at all, with third-party payors for Emflaza™ (deflazacort) for the treatment of Duchenne muscular dystrophy, or DMD, in the United States and for Translarna™ (ataluren) for the treatment of nonsense mutation DMD, or nmDMD, in the European Economic Area, or EEA, and other countries in which we have or may obtain regulatory approval, or in which there exist significant reimbursed early access programs, or EAP programs;

• | our ability to maintain our marketing authorization of Translarna for the treatment of nmDMD in the EEA (which is subject to the specific obligation to conduct and submit the results of Study 041 to the European Medicines Agency, or EMA, and annual review and renewal by the European Commission following reassessment of the benefit-risk balance of the authorization by the EMA);

• | our ability to enroll, fund, and complete Study 041, a multicenter, randomized, double-blind, 18-month, placebo-controlled clinical trial of Translarna for the treatment of nmDMD followed by an 18-month open label extension, according to the protocol agreed with the EMA, and by the trial’s deadline;

• | the anticipated period of market exclusivity for Emflaza for the treatment of DMD in the United States under the Orphan Drug Act of 1983, or the Orphan Drug Act, the Drug Price Competition and Patent Term Restoration Act of 1984, or the Hatch-Waxman Act;

• | our ability to complete the United States Food and Drug Administration, or FDA, post-marketing requirements to the marketing authorization of Emflaza;

• | our ability to complete any dystrophin study necessary in order to resolve the matters set forth in the FDA’s denial of our appeal to the Complete Response Letter we received from the FDA in connection with our New Drug Application, or NDA, for Translarna for the treatment of nmDMD, and our ability to perform additional clinical trials, non-clinical studies or CMC assessments or analyses at significant cost;

• | the timing and scope of our continued commercialization of Translarna as a treatment for nmDMD in the EEA or other territories outside of the United States;

• | our ability to obtain additional and maintain existing reimbursed named patient and cohort EAP programs for Translarna for the treatment of nmDMD on adequate terms, or at all;

• | our expectations and the potential financial impact and benefits related to our Collaboration and Licensing Agreement with Akcea Therapeutics, Inc., or Akcea, including with respect to the timing of regulatory approval of TegsediTM (inotersen) and WaylivraTM (volanesorsen) in countries in which we are licensed to commercialize them, the potential commercialization of Tegsedi and Waylivra, and our expectations with respect to contingent payments to Akcea based on the potential achievement of certain regulatory milestones and royalty payments by us to Akcea based on our potential achievement of certain net sales thresholds;

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• | our expectations with respect to the development and regulatory status of our product candidates and program directed against spinal muscular atrophy in collaboration with F. Hoffmann La Roche Ltd and Hoffmann La Roche Inc., which we refer to collectively as Roche, and the Spinal Muscular Atrophy Foundation, or the SMA Foundation, and our estimates regarding future revenues from achievement of milestones in that program;

• | our estimates regarding the potential market opportunity for Translarna, Emflaza, PTC-AADC, Tegsedi, Waylivra, risdiplam or any other product candidate, including the size of eligible patient populations and our ability to identify such patients;

• | our estimates regarding expenses, future revenues, third-party discounts and rebates, capital requirements and needs for additional financing, including our ability to maintain the level of our expenses consistent with our internal budgets and forecasts and to secure additional funds on favorable terms or at all;

• | the timing and conduct of our ongoing, planned and potential future clinical trials and studies of Translarna for the treatment of nmDMD, aniridia, and Dravet syndrome/CDKL5, each caused by nonsense mutations, and Emflaza for the treatment of limb-girdle 2I, as well as studies in our gene therapy, splicing and oncology programs, including the timing of initiation, enrollment and completion of the trials and the period during which the results of the trials will become available;

• | the rate and degree of market acceptance and clinical utility of Translarna, Emflaza, PTC-AADC, Tegsedi, Waylivra and risdiplam;

• | the ability and willingness of patients and healthcare professionals to access Translarna through alternative means if pricing and reimbursement negotiations in the applicable territory do not have a positive outcome;

• | the timing of, and our ability to obtain additional marketing authorizations for, Translarna, Tegsedi and our other product candidates;

• | the ability of Translarna, Emflaza, PTC-AADC, Tegsedi, Waylivra and risdiplam and our other product candidates to meet existing or future regulatory standards;

• | our ability to maintain the current labeling under the marketing authorization in the EEA or expand the approved product label of Translarna for the treatment of nmDMD in non-ambulatory patients or otherwise;

• | the potential receipt of revenues from future sales of Translarna, Emflaza, and other product candidates, including our ability to earn a profit from sales or licenses of Translarna for the treatment of nmDMD in the countries in which we have or may obtain regulatory approval and of Emflaza for the treatment of DMD in the United States;

• | the potential impact that enrollment, funding and completion of Study 041 may have on our revenue growth;

• | our sales, marketing and distribution capabilities and strategy, including the ability of our third-party manufacturers to manufacture and deliver Translarna and Emflaza in clinically and commercially sufficient quantities and the ability of distributors to process orders in a timely manner and satisfy their other obligations to us;

• | our ability to establish and maintain arrangements for the manufacture of Translarna, Emflaza and our other product candidates that are sufficient to meet clinical trial and commercial launch requirements;

• | our ability to increase our manufacturing capabilities for our gene therapy platform;

• | our expectations with respect to the potential financial impact of our leased biologics facility and our ability to satisfy our obligations under the terms of the lease agreement for such facility;

• | our ability to satisfy our obligations under the terms of the credit and security agreement with MidCap Financial Trust, or MidCap Financial, as administrative agent and MidCap Financial and certain other financial institutions as lenders thereunder;

• | our other regulatory submissions, including with respect to timing and outcome of regulatory review;

• | our plans to pursue development of Translarna and Emflaza for additional indications;

• | our ability to advance our earlier stage programs and pursue research and development of other product candidates, including our splicing, gene therapy and oncology programs;

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• | whether we may pursue business development opportunities, including potential collaborations, alliances, and acquisition or licensing of assets and our ability to successfully develop or commercialize any assets to which we may gain rights pursuant to such business development opportunities;

• | the potential advantages of Translarna, Emflaza, PTC-AADC, Tegsedi, Waylivra and risdiplam and any other product candidate;

• | our intellectual property position;

• | the impact of government laws and regulations;

• | the impact of litigation that has been or may be brought against us or of litigation that we are pursuing against others; and

• | our competitive position.

We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements, and you should not place undue reliance on our forward-looking statements. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements we make. We have included important factors in the cautionary statements included in this Quarterly Report on Form 10-Q, particularly in Part II, Item 1A. Risk Factors as well as in Part I, Item 1A. Risk Factors in our Annual Report on Form 10-K for the year ended December 31, 2018, that we believe could cause actual results or events to differ materially from the forward-looking statements that we make. Our forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, joint ventures or investments we may make.
You should read this Quarterly Report on Form 10-Q and the documents that we have filed as exhibits to this Quarterly Report on Form 10-Q and our Annual Report on Form 10-K for the year ended December 31, 2018 completely and with the understanding that our actual future results may be materially different from what we expect. We do not assume any obligation to update any forward-looking statements whether as a result of new information, future events or otherwise, except as required by applicable law.
In this Quarterly Report on Form 10-Q, unless otherwise stated or the context otherwise requires, references to “PTC,” “PTC Therapeutics,” “the Company,” “we,” “us,” “our,” and similar references refer to PTC Therapeutics, Inc. and, where appropriate, its subsidiaries. The trademarks, trade names and service marks appearing in this Quarterly Report on Form 10-Q are the property of their respective owners.
All website addresses given in this Quarterly Report on Form 10-Q are for information only and are not intended to be an active link or to incorporate any website information into this document.
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PART I—FINANCIAL INFORMATION
Item 1. Financial Statements.
PTC Therapeutics, Inc.
Consolidated Balance Sheets (unaudited)
In thousands (except per share data)

|  | September 30, 2019 |  | December 31, 2018
Assets |  |  |  |  |
Current assets: |  |  |  |  |
Cash and cash equivalents |  | $ | 523,577 |  |  | $ | 169,498 |
Marketable securities |  | 185,072 |  |  | 58,088 |
Trade receivables, net |  | 60,383 |  |  | 67,907 |
Inventory, net |  | 17,107 |  |  | 16,117 |
Prepaid expenses and other current assets |  | 20,723 |  |  | 9,247 |
Total current assets |  | 806,862 |  |  | 320,857 |
Fixed assets, net |  | 18,484 |  |  | 12,694 |
Intangible assets, net |  | 702,910 |  |  | 701,031 |
Goodwill |  | 82,341 |  |  | 82,341 |
Deposits and other assets |  | 30,889 |  |  | 2,299 |
Total assets |  | $ | 1,641,486 |  |  | $ | 1,119,222 |
Liabilities and stockholders’ equity |  |  |  |  |
Current liabilities: |  |  |  |  |
Accounts payable and accrued expenses |  | $ | 128,150 |  |  | $ | 128,199 |
Current portion of long-term debt |  | 20,000 |  |  | 11,667 |
Deferred revenue |  | 8,810 |  |  | 3,716 |
Other current liabilities |  | 6,840 |  |  | 3,814 |
Deferred consideration payable |  | 19,700 |  |  | 19,400 |
Total current liabilities |  | 183,500 |  |  | 166,796 |
Deferred revenue |  | 5,496 |  |  | 9,722 |
Long-term debt |  | 293,149 |  |  | 141,347 |
Contingent consideration payable |  | 344,900 |  |  | 310,240 |
Deferred consideration payable |  | 19,300 |  |  | 18,300 |
Deferred tax liability |  | 122,032 |  |  | 122,032 |
Other long-term liabilities |  | 9,455 |  |  | 58 |
Total liabilities |  | 977,832 |  |  | 768,495 |
Stockholders’ equity: |  |  |  |  |
Common stock, $0.001 par value. Authorized 125,000,000 shares; issued and outstanding 61,578,992 shares at September 30, 2019. Authorized 125,000,000 shares; issued and outstanding 50,606,147 shares at December 31, 2018. |  | 61 |  |  | 51 |
Additional paid-in capital |  | 1,775,799 |  |  | 1,288,137 |
Accumulated other comprehensive income |  | 616 |  |  | 1,462 |
Accumulated deficit |  | (1,112,822 | ) |  | (938,923 | )
Total stockholders’ equity |  | 663,654 |  |  | 350,727 |
Total liabilities and stockholders’ equity |  | $ | 1,641,486 |  |  | $ | 1,119,222 |

See accompanying unaudited notes.
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PTC Therapeutics, Inc.
Consolidated Statements of Operations (unaudited)
In thousands (except per share data)

|  | Three Months Ended September 30, |  | Nine Months Ended September 30,
|  | 2019 |  | 2018 |  | 2019 |  | 2018
Revenues: |  |  |  |  |  |  |  |  |  |  |  |
Net product revenue |  | $ | 71,369 |  |  | $ | 53,021 |  |  | $ | 209,899 |  |  | $ | 177,172 |
Collaboration and grant revenue |  | 47 |  |  | 570 |  |  | 622 |  |  | 1,224 |
Total revenues |  | 71,416 |  |  | 53,591 |  |  | 210,521 |  |  | 178,396 |
Operating expenses: |  |  |  |  |  |  |  |  |  |  |  |
Cost of product sales, excluding amortization of acquired intangible assets |  | 3,006 |  |  | 3,292 |  |  | 8,593 |  |  | 8,909 |
Amortization of acquired intangible assets |  | 7,025 |  |  | 5,793 |  |  | 19,677 |  |  | 16,815 |
Research and development |  | 63,076 |  |  | 54,368 |  |  | 175,621 |  |  | 118,337 |
Selling, general and administrative |  | 49,284 |  |  | 38,368 |  |  | 139,044 |  |  | 104,882 |
Change in the fair value of deferred and contingent consideration |  | 9,500 |  |  | — |  |  | 35,960 |  |  | — |
Total operating expenses |  | 131,891 |  |  | 101,821 |  |  | 378,895 |  |  | 248,943 |
Loss from operations |  | (60,475 | ) |  | (48,230 | ) |  | (168,374 | ) |  | (70,547 | )
Interest expense, net |  | (2,666 | ) |  | (3,118 | ) |  | (7,028 | ) |  | (9,306 | )
Other income, net |  | 2,800 |  |  | 734 |  |  | 2,509 |  |  | 1,066 |
Loss before income tax expense |  | (60,341 | ) |  | (50,614 | ) |  | (172,893 | ) |  | (78,787 | )
Income tax benefit (expense) |  | 344 |  |  | (355 | ) |  | (1,006 | ) |  | (964 | )
Net loss attributable to common stockholders |  | $ | (59,997 | ) |  | $ | (50,969 | ) |  | $ | (173,899 | ) |  | $ | (79,751 | )
Weighted-average shares outstanding: |  |  |  |  |  |  |  |  |  |  |  |
Basic and diluted (in shares) |  | 56,463,528 |  |  | 48,096,521 |  |  | 57,798,968 |  |  | 45,310,690 |
Net loss per share—basic and diluted (in dollars per share) |  | $ | (1.06 | ) |  | $ | (1.06 | ) |  | $ | (3.01 | ) |  | $ | (1.76 | )

See accompanying unaudited notes.
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PTC Therapeutics, Inc.
Consolidated Statements of Comprehensive Loss (unaudited)
In thousands

|  | Three Months Ended September 30, |  | Nine Months Ended September 30,
|  | 2019 |  | 2018 |  | 2019 |  | 2018
Net loss |  | $ | (59,997 | ) |  | $ | (50,969 | ) |  | $ | (173,899 | ) |  | $ | (79,751 | )
Other comprehensive (loss) income: |  |  |  |  |  |  |  |  |  |  |  |
Unrealized (loss) gain on marketable securities |  | (463 | ) |  | 33 |  |  | 435 |  |  | (50 | )
Foreign currency translation loss |  | (843 | ) |  | (260 | ) |  | (1,281 | ) |  | (2,291 | )
Comprehensive loss |  | $ | (61,303 | ) |  | $ | (51,196 | ) |  | $ | (174,745 | ) |  | $ | (82,092 | )

See accompanying unaudited notes.
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PTC Therapeutics, Inc.
Consolidated Statements of Stockholders' Equity (unaudited)
In thousands (except shares)

Three months ended September 30, 2019 | Common stock |  | Additional paid-in capital |  | Accumulated other comprehensive income (loss) |  | Accumulated deficit |  | Total stockholders’ equity
| Shares |  | Amount |  |  |  |
Balance, June 30, 2019 | 58,707,185 |  |  | $ | 58 |  |  | $ | 1,539,530 |  |  | $ | 1,922 |  |  | $ | (1,052,825 | ) |  | $ | 488,685 |
Issuance of common stock related to equity offerings | 2,539,174 |  |  | 3 |  |  | 99,208 |  |  | — |  |  | — |  |  | 99,211 |
Equity component of the convertible notes issuance, net | — |  |  | — |  |  | 119,489 |  |  | — |  |  | — |  |  | 119,489 |
Exercise of options | 334,433 |  |  | — |  |  | 7,088 |  |  | — |  |  | — |  |  | 7,088 |
Restricted stock vesting and issuance, net | (1,800 | ) |  | — |  |  | — |  |  | — |  |  | — |  |  | — |
Share-based compensation expense | — |  |  | — |  |  | 10,484 |  |  | — |  |  | — |  |  | 10,484 |
Net loss | — |  |  | — |  |  | — |  |  | — |  |  | (59,997 | ) |  | (59,997 | )
Comprehensive loss | — |  |  | — |  |  | — |  |  | (1,306 | ) |  | — |  |  | (1,306 | )
Balance, September 30, 2019 | 61,578,992 |  |  | $ | 61 |  |  | $ | 1,775,799 |  |  | $ | 616 |  |  | $ | (1,112,822 | ) |  | $ | 663,654 |

Three months ended September 30, 2018 | Common stock |  | Additional paid-in capital |  | Accumulated other comprehensive income (loss) |  | Accumulated deficit |  | Total stockholders’ equity
| Shares |  | Amount |  |  |  |
Balance, June 30, 2018 | 46,680,482 |  |  | $ | 47 |  |  | $ | 1,105,124 |  |  | $ | 1,855 |  |  | $ | (839,624 | ) |  | $ | 267,402 |
Issuance of common stock related to equity offerings | — |  |  | — |  |  | 42 |  |  | — |  |  | — |  |  | 42 |
Issuance of common stock related to acquisition | 3,500,907 |  |  | 4 |  |  | 155,857 |  |  | — |  |  | — |  |  | 155,861 |
Exercise of options | 251,266 |  |  | — |  |  | 5,039 |  |  | — |  |  | — |  |  | 5,039 |
Share-based compensation expense | — |  |  | — |  |  | 8,942 |  |  | — |  |  | — |  |  | 8,942 |
Net loss | — |  |  | — |  |  | — |  |  | — |  |  | (50,969 | ) |  | (50,969 | )
Comprehensive loss | — |  |  | — |  |  | — |  |  | (227 | ) |  | — |  |  | (227 | )
Balance, September 30, 2018 | 50,432,655 |  |  | $ | 51 |  |  | $ | 1,275,004 |  |  | $ | 1,628 |  |  | $ | (890,593 | ) |  | $ | 386,090 |

Nine months ended September 30, 2019 | Common stock |  | Additional paid-in capital |  | Accumulated other comprehensive income (loss) |  | Accumulated deficit |  | Total stockholders’ equity
| Shares |  | Amount |  |  |  |
Balance, December 31, 2018 | 50,606,147 |  |  | $ | 51 |  |  | $ | 1,288,137 |  |  | $ | 1,462 |  |  | $ | (938,923 | ) |  | $ | 350,727 |
Issuance of common stock related to equity offering | 10,102,899 |  |  | 10 |  |  | 323,746 |  |  | — |  |  | — |  |  | 323,756 |
Equity component of the convertible notes issuance, net | — |  |  | — |  |  | 119,489 |  |  | — |  |  | — |  |  | 119,489 |
Exercise of options | 645,435 |  |  | — |  |  | 12,195 |  |  | — |  |  | — |  |  | 12,195 |
Restricted stock vesting and issuance, net | 169,792 |  |  | — |  |  | — |  |  | — |  |  | — |  |  | — |
Issuance of common stock in connection with an employee stock purchase plan | 54,719 |  |  | — |  |  | 1,564 |  |  | — |  |  | — |  |  | 1,564 |
Share-based compensation expense | — |  |  | — |  |  | 30,668 |  |  | — |  |  | — |  |  | 30,668 |
Net loss | — |  |  | — |  |  | — |  |  | — |  |  | (173,899 | ) |  | (173,899 | )
Comprehensive loss | — |  |  | — |  |  | — |  |  | (846 | ) |  | — |  |  | (846 | )
Balance, September 30, 2019 | 61,578,992 |  |  | $ | 61 |  |  | $ | 1,775,799 |  |  | $ | 616 |  |  | $ | (1,112,822 | ) |  | $ | 663,654 |

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Nine months ended September 30, 2018 | Common stock |  | Additional paid-in capital |  | Accumulated other comprehensive income (loss) |  | Accumulated deficit |  | Total stockholders’ equity
| Shares |  | Amount |  |  |  |
Balance, December 31, 2017 | 41,612,395 |  |  | $ | 42 |  |  | $ | 966,534 |  |  | $ | 3,969 |  |  | $ | (814,108 | ) |  | $ | 156,437 |
Adjustments to accumulated deficit and other | — |  |  | $ | — |  |  | — |  |  | $ | — |  |  | $ | 3,266 |  |  | $ | 3,266 |
Issuance of common stock related to equity offering | 4,600,000 |  |  | 4 |  |  | 117,911 |  |  | — |  |  | — |  |  | 117,915 |
Issuance of common stock related to acquisition | 3,500,907 |  |  | 4 |  |  | 155,857 |  |  | — |  |  | — |  |  | 155,861 |
Exercise of options | 512,145 |  |  | 1 |  |  | 8,630 |  |  | — |  |  | — |  |  | 8,631 |
Restricted stock vesting and issuance | 119,691 |  |  | — |  |  | — |  |  | — |  |  | — |  |  | — |
Issuance of common stock in connection with an employee stock purchase plan | 87,517 |  |  | — |  |  | 1,299 |  |  | — |  |  | — |  |  | 1,299 |
Share-based compensation expense | — |  |  | — |  |  | 24,773 |  |  | — |  |  | — |  |  | 24,773 |
Net loss | — |  |  | — |  |  | — |  |  |  |  |  | (79,751 | ) |  | $ | (79,751 | )
Comprehensive loss | — |  |  | — |  |  | — |  |  | (2,341 | ) |  | — |  |  | (2,341 | )
Balance, September 30, 2018 | 50,432,655 |  |  | $ | 51 |  |  | $ | 1,275,004 |  |  | $ | 1,628 |  |  | $ | (890,593 | ) |  | $ | 386,090 |

See accompanying unaudited notes.
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PTC Therapeutics, Inc. Consolidated Statements of Cash Flows (unaudited) In thousands |  |  |  |
|  | Nine Months Ended September 30,
|  | 2019 |  | 2018
Cash flows from operating activities |  |  |  |  |  |
Net loss |  | $ | (173,899 | ) |  | $ | (79,751 | )
Adjustments to reconcile net loss to net cash used in operating activities: |  |  |  |  |  |
Depreciation and amortization |  | 22,903 |  |  | 19,316 |
Change in valuation of warrant liability |  | — |  |  | 3 |
Change in valuation of deferred and contingent consideration |  | 35,960 |  |  | — |
Unrealized gain on MRI investment |  | (2,529 | ) |  | — |
Non-cash interest expense |  | 6,583 |  |  | 5,563 |
Loss on disposal of asset |  | — |  |  | 2 |
Amortization of discounts on investments, net |  | (1,374 | ) |  | (354 | )
Amortization of debt issuance costs |  | 434 |  |  | 390 |
Share-based compensation expense |  | 30,668 |  |  | 24,773 |
Unrealized foreign currency transaction losses (gains), net |  | 205 |  |  | (977 | )
Changes in operating assets and liabilities: |  |  |  |  |  |
Inventory |  | (1,574 | ) |  | (3,252 | )
Prepaid expenses and other current assets |  | (11,771 | ) |  | (1,301 | )
Trade receivables, net |  | 5,879 |  |  | (2,681 | )
Deposits and other assets |  | (14,747 | ) |  | (385 | )
Accounts payable and accrued expenses |  | 695 |  |  | 18,606 |
Other liabilities |  | 12,553 |  |  | 1,617 |
Deferred revenue |  | 1,581 |  |  | 5,933 |
Net cash used in operating activities |  | (88,433 | ) |  | (12,498 | )
Cash flows from investing activities |  |  |  |  |  |
Purchases of fixed assets |  | (9,104 | ) |  | (2,489 | )
Purchases of equity investment in MRI |  | (4,000 | ) |  | — |
Purchases of marketable securities |  | (239,386 | ) |  | (28,656 | )
Sale and redemption of marketable securities |  | 114,500 |  |  | 65,923 |
Acquisition of product rights and licenses |  | (20,250 | ) |  | (3,903 | )
Business acquisition, net of cash acquired |  | — |  |  | (48,892 | )
Net cash used in investing activities |  | (158,240 | ) |  | (18,017 | )
Cash flows from financing activities |  |  |  |  |  |
Proceeds from exercise of options |  | 12,195 |  |  | 8,631 |
Net proceeds from public offerings |  | 324,262 |  |  | 117,915 |
Proceeds from issuance of convertible notes, net |  | 279,571 |  |  | — |
Proceeds from shares issued under employee stock purchase plan |  | 1,564 |  |  | 1,299 |
Repayment of senior secured term loan |  | (6,667 | ) |  | — |
Net cash provided by financing activities |  | 610,925 |  |  | 127,845 |
Effect of exchange rate changes on cash |  | (2,673 | ) |  | (2,209 | )
Net increase in cash and cash equivalents |  | 361,579 |  |  | 95,121 |
Cash and cash equivalents, and restricted cash beginning of period |  | 169,498 |  |  | 111,792 |
Cash and cash equivalents, and restricted cash end of period |  | $ | 531,077 |  |  | $ | 206,913 |
Supplemental disclosure of cash information |  |  |  |  |  |
Cash paid for interest |  | $ | 7,042 |  |  | $ | 6,927 |
Cash paid for income taxes |  | $ | 1,931 |  |  | $ | 919 |
Supplemental disclosure of non-cash investing and financing activity |  |  |  |
Change in unrealized gain (loss) on marketable securities, net of tax |  | $ | 435 |  |  | $ | (50 | )

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Right-of-use assets obtained in exchange for lease obligations |  | $ | 16,120 |  |  | $ | — |
Acquisition of product rights and licenses |  | $ | 7,432 |  |  | $ | 4,530 |
Accrued transaction costs related to public offerings |  | $ | 506 |  |  | $ | — |
Accrued transaction costs related to issuance of convertible notes |  | $ | 298 |  |  | $ | — |

See accompanying unaudited notes.
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PTC Therapeutics, Inc.
Notes to Consolidated Financial Statements (unaudited)
September 30, 2019
In thousands (except per share data unless otherwise noted)

1. | The Company

PTC Therapeutics, Inc. (the “Company” or “PTC”) is a science-led global biopharmaceutical company focused on the discovery, development and commercialization of clinically-differentiated medicines that provide benefits to patients with rare disorders. The Company’s ability to globally commercialize products is the foundation that drives its continued investment in a robust pipeline of transformative medicines and its mission to provide access to best-in-class treatments for patients who have an unmet medical need.
The Company has two products, Translarna™ (ataluren) and Emflaza™ (deflazacort), for the treatment of Duchenne muscular dystrophy, or DMD, a rare, life threatening disorder. Translarna received marketing authorization from the European Commission in August 2014 for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in ambulatory patients aged five years and older in the 31 member states of the European Economic Area, or EEA. In July 2018, the European Commission approved a label-extension request to the marketing authorization for Translarna in the EEA to include patients from two to up to five years of age. Emflaza is approved in the United States for the treatment of DMD in patients two years and older.
The Company has a pipeline of gene therapy product candidates, including PTC-AADC for the treatment of Aromatic L-Amino Acid Decarboxylase, or AADC, deficiency, or AADC deficiency. The Company is preparing a biologics license application, or BLA, for PTC-AADC for the treatment of AADC deficiency in the United States, which it anticipates submitting to the U.S. Food and Drug Administration, or FDA, in late 2019, with anticipated commercial launch in 2020, subject to approval. The Company is also preparing a marketing authorization application, or MAA, for PTC-AADC for the treatment of AADC deficiency in the European Union, or EU, for submission to the European Medicines Agency, or EMA, which will follow its BLA submission to the FDA.
The Company holds the rights for the commercialization of Tegsedi™ (inotersen) and Waylivra™ (volanesorsen) for the treatment of rare diseases in countries in Latin America and the Caribbean. Tegsedi has received marketing authorization in the U.S., EU and Canada for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hATTR amyloidosis. Tegsedi also received marketing authorization from ANVISA in October 2019 for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hATTR amyloidosis in Brazil. Waylivra has received conditional marketing authorization in the EU for the treatment of familial chylomicronemia syndrome, or FCS.
The Company also has a spinal muscular atrophy ("SMA") collaboration with F. Hoffman-La Roche Ltd and Hoffman-La Roche Inc., referred to collectively as Roche, and the Spinal Muscular Atrophy Foundation, or SMA Foundation. Currently, its collaboration has two pivotal clinical trials ongoing to evaluate the safety and effectiveness of risdiplam (RG7916, RO7034067), the lead compound in the SMA program. Roche is preparing an NDA and a MAA for risdiplam for the treatment of SMA in the United States and the EU, respectively, which Roche anticipates submitting to the FDA in the second half of 2019 and the EMA in the first half of 2020. In addition, the Company has a pipeline of product candidates and discovery programs that are in early clinical, pre-clinical and research and development stages focused on the development of new treatments for multiple therapeutic areas, including rare diseases and oncology.
The Company’s marketing authorization for Translarna in the EEA is subject to annual review and renewal by the European Commission following reassessment by the EMA of the benefit-risk balance of the authorization, which the Company refers to as the annual EMA reassessment. This marketing authorization is further subject to the specific obligation to conduct and submit the results of a multi-center, randomized, double-blind, 18-month, placebo-controlled trial, followed by an 18-month open-label extension, according to an agreed protocol, in order to confirm the efficacy and safety of Translarna. The final report on the trial and open-label extension is to be submitted by the Company to the EMA by the end of the third quarter of 2022. The Company refers to the trial and open-label extension together as Study 041.
The marketing authorization in the EEA was last renewed in July 2019 and is effective, unless extended, through August 5, 2020. The renewal was based on the Company’s commitment to conduct Study 041 and the totality of the clinical data available from its trials and studies of Translarna for the treatment of nmDMD, including the safety and efficacy results of the Phase 2b and Phase 3 clinical trials. The primary efficacy endpoint was not achieved in either trial within the pre-specified level of statistical significance.
In June 2014, the Company initiated reimbursed early access programs, or EAP programs, for Translarna for nmDMD patients in selected territories in the EEA and recorded its first sales of Translarna in the third quarter of 2014 pursuant to an EAP program. In December 2014, the Company recorded its first commercial sales in Germany. As of September 30, 2019, Translarna was available in over 40 countries on a commercial basis or pursuant to an EAP program. The Company expects to expand its commercial
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activities across the EEA pursuant to the marketing authorization granted by the EMA throughout 2019 and future years, subject to continued renewal of its marketing authorization following annual EMA reassessments and successful completion of pricing and reimbursement negotiations. Concurrently, the Company plans to continue to pursue EAP programs in select countries where those mechanisms exist, both within the EEA and in other countries that will reference the marketing authorization in the EEA.
Translarna is an investigational new drug in the United States. During the first quarter of 2017, the Company filed a New Drug Application, or NDA, over protest with the FDA, for which the FDA granted a standard review. In October 2017, the Office of Drug Evaluation I of the FDA issued a complete response letter for the NDA, stating that it was unable to approve the application in its current form. In response, the Company filed a formal dispute resolution request with the Office of New Drugs of the FDA. In February 2018, the Office of New Drugs of the FDA denied PTC’s appeal of the Complete Response Letter. In its response, the Office of New Drugs recommended a possible path forward for the ataluren NDA submission based on the accelerated approval pathway. This would involve a re-submission of an NDA containing the current data on effectiveness of ataluren with new data to be generated on dystrophin production in nmDMD patients’ muscles. The Company intends to follow the FDA’s recommendation and will collect, using newer technologies via procedures and methods that the Company designed, such dystrophin data in a new study, Study 045, which the Company initiated in the fourth quarter of 2018. The Company expects that a potential re-submission of an NDA could occur in 2020. Additionally, should a re-submission of an NDA receive accelerated approval, the Office of New Drugs stated that Study 041, which is currently enrolling, could serve as the confirmatory post-approval trial required in connection with the accelerated approval framework.
Emflaza was initially approved in the United States for the treatment of DMD in patients five years and older. In June 2019, the FDA approved the Company's label expansion request for Emflaza for patients two to five years of age.
On April 20, 2017, the Company completed its acquisition of all rights to Emflaza, or the Transaction. Emflaza is approved in the United States for the treatment of DMD in patients two years and older. The Transaction was completed pursuant to an asset purchase agreement, dated March 15, 2017, as amended on April 20, 2017, (the "Asset Purchase Agreement"), by and between the Company and Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC), or Marathon. The Transaction was accounted for as an asset acquisition. The assets acquired by the Company in the Transaction include intellectual property rights related to Emflaza, inventories of Emflaza, and certain contractual rights related to Emflaza. The Company assumed certain liabilities and obligations in the Transaction arising out of, or relating to, the assets acquired in the Transaction.
Upon the closing of the Transaction, the Company paid to Marathon total upfront consideration comprised of $75.0 million in cash, funded through cash on hand, and 6,683,598 shares of the Company’s common stock. The number of shares of common stock issued at closing was determined by dividing $65.0 million by the volume-weighted average price per share of the Company’s common stock on the Nasdaq Stock Market for the 15 trading-day period ending on the third trading day immediately preceding the closing. Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza, up to a specified aggregate maximum amount over the expected commercial life of the asset, and a single $50.0 million sales-based milestone, in each case subject to the terms and conditions of the Asset Purchase Agreement.
On August 23, 2018, the Company completed its acquisition of Agilis Biotherapeutics, Inc., or Agilis, pursuant to an Agreement and Plan of Merger, dated as of July 19, 2018 (the “Merger Agreement”), by and among the Company, Agility Merger Sub, Inc., a Delaware corporation and the Company's wholly owned, indirect subsidiary, Agilis and, solely in its capacity as the representative, agent and attorney-in-fact of the equityholders of Agilis, Shareholder Representative Services LLC (the "Merger").
Upon the closing of the Merger, the Company paid to Agilis equityholders total upfront consideration comprised of $49.2 million in cash and 3,500,907 shares of the Company’s common stock (the “Closing Stock Consideration”). The Closing Stock Consideration was determined by dividing $150.0 million by the volume-weighted average price per share of the Company’s common stock on the Nasdaq Global Select Market for the 10 consecutive trading-day period ending on the second trading-day immediately preceding the closing of the Merger. Agilis equityholders may become entitled to receive contingent payments from the Company based on the achievement of certain development, regulatory and net sales milestones as well as based upon a percentage of net sales of certain products. Under the Merger Agreement, the Company is required to pay $40.0 million of the development milestone payments no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved.
As of September 30, 2019, the Company had an accumulated deficit of approximately $1,112.8 million. The Company has financed its operations to date primarily through the private offerings in September 2019 of 1.5% convertible senior notes due 2026 and in August 2015 of 3.0% convertible senior notes due 2022 (see Note 11), public offerings of common stock in February 2014, October 2014, April 2018, January 2019, and September 2019, "at the market offerings" of its common stock, its initial public offering of common stock in June 2013, private placements of its convertible preferred stock, collaborations, bank debt, grant funding and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease area addressed by the Company’s product candidates. Since 2014, the Company has also relied on revenue generated from net sales of Translarna for the treatment of nmDMD in territories outside of the United States, and since May 2017, the Company has generated revenue
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from net sales of Emflaza for the treatment of DMD in the United States. The Company expects that cash flows from the sales of its products, together with the Company's cash, cash equivalents and marketable securities, will be sufficient to fund its operations for at least the next twelve months.

2. | Summary of significant accounting policies

The Company’s complete listing of significant accounting policies is set forth in Note 2 of the notes to the Company’s audited financial statements as of December 31, 2018 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (the "SEC") on March 1, 2019 (the "2018 Form 10-K"). Additional significant accounting policies adopted during the nine month period ended September 30, 2019 are discussed in further detail below.
Basis of presentation
The accompanying financial information as of September 30, 2019 and for the three and nine months ended September 30, 2019 and 2018 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States ("GAAP") have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2018 and notes thereto included in the 2018 Form 10-K.
In the opinion of management, the unaudited financial information as of September 30, 2019 and for the three and nine months ended September 30, 2019 and 2018 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations, stockholders' equity, and cash flows. The results of operations for the three and nine month period ended September 30, 2019 are not necessarily indicative of the results to be expected for the year ended December 31, 2019 or for any other interim period or for any other future year.
Use of estimates
The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, certain accruals related to the Company’s research and development expenses, stock-based compensation, valuation procedures for the convertible notes, allowance for doubtful accounts, inventory, acquired intangible assets, fair value of the contingent consideration, and the provision for or benefit from income taxes. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known.
Restricted cash
Restricted cash included in deposits and other assets on the consolidated balance sheet relates to an unconditional, irrevocable and transferable letter of credit that was entered into during the three-month period ended September 30, 2019 in connection with obligations under a facility lease for our leased biologics facility in Hopewell Township, New Jersey. The amount of the letter of credit is $7.5 million, is to be maintained for a term of not less than five years and has the potential to be reduced to $3.8 million if after five years the Company is not in default of its lease. The amount is classified within deposits and other assets on the consolidated balance sheet due to the long-term nature of the letter of credit.
The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet that sum to the total of the same amounts shown in the statement of cash flows:

|  | Beginning of period- December 31, 2018 |  | End of period- September 30, 2019
Cash and cash equivalents |  | $ | 169,498 |  |  | $ | 523,577 |
Restricted cash included in deposits and other assets |  | — |  |  | 7,500 |
Total Cash, cash equivalents and restricted cash per statement of cash flows |  | $ | 169,498 |  |  | $ | 531,077 |

Inventory and cost of product sales
Inventory
Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis by product. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization
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is considered probable and the future economic benefit is expected to be realized. Translarna and Emflaza product which may be used in clinical development programs are included in inventory and charged to research and development expense when the product enters the research and development process and no longer can be used for commercial purposes. Inventory used for marketing efforts are charged to selling, general and administrative expense.
The following table summarizes the components of the Company’s inventory for the periods indicated:

|  | September 30, 2019 |  | December 31, 2018
Raw materials |  | $ | 1,853 |  |  | $ | 1,431 |
Work in progress |  | 10,870 |  |  | 9,324 |
Finished goods |  | 4,384 |  |  | 5,362 |
Total inventory |  | $ | 17,107 |  |  | $ | 16,117 |

The Company periodically reviews its inventories for excess amounts or obsolescence and writes down obsolete or otherwise unmarketable inventory to its estimated net realizable value. No write downs were recorded for the three and nine month periods ended September 30, 2019. The Company recorded a $1.6 million inventory write down for the three month period ended September 30, 2018, primarily related to inventory labeling changes. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the three and nine month periods ended September 30, 2019 and 2018, these amounts were immaterial.
Cost of product sales
Costs of product sales consists of the cost of inventory sold, manufacturing and supply chain costs, including personnel costs, storage costs, amortization of the acquired intangible asset and royalty payments associated with net product sales.
Revenue recognition
In May 2014, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) No. 2014-9, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-9 eliminated transaction- and industry-specific revenue recognition guidance under FASB Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition-Products (Topic 605) and replaced it with a principle-based approach for determining revenue recognition. ASC Topic 606 requires entities to recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services.
Net product revenue
The Company's net product revenue primarily consists of sales of Translarna in territories outside of the U.S. for the treatment of nmDMD and sales of Emflaza in the U.S. for the treatment of DMD. The Company recognizes revenue when its performance obligations with its customers have been satisfied. The Company’s performance obligations are to provide Translarna or Emflaza based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when the Company’s customer obtains control of either Translarna or Emflaza, which is typically upon delivery. The Company invoices its customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of the invoice date. The Company determines the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods the Company has yet to provide. As the Company has identified only one distinct performance obligation, the transaction price is allocated entirely to either product sales of Translarna or Emflaza. In determining the transaction price, a significant financing component does not exist since the timing from when the Company delivers product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month.
The Company records product sales net of any variable consideration, which includes discounts, allowances, rebates and distribution fees. The Company uses the expected value or most likely amount method when estimating its variable consideration, unless discount or rebate terms are specified within contracts. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors and may impact such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained.
In relation to customer contracts, the Company incurs costs to fulfill a contract but does not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred.
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Upon adoption of ASC Topic 606 on January 1, 2018, the Company elected the following practical expedients:

• | Portfolio Approach - the Company applied the Portfolio Approach to contract reviews within its identified revenue streams that have similar characteristics and the Company believes this approach would not differ materially than if applying ASC Topic 606 to each individual contract.

• | Significant Financing Component - the Company expects the period between when it transfers a promised good to a customer and when the customer pays for the good or service to be one year or less.

• | Immaterial Performance Obligations - the Company disregards promises deemed to be immaterial in the context of the contract.

• | Shipping and Handling Activities - the Company considers any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise.

Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense.
Collaboration revenue
The terms of these agreements typically include payments to the Company of one or more of the following: nonrefundable, upfront license fees; milestone payments; research funding and royalties on future product sales. In addition, the Company generates service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events.
At the inception of a collaboration arrangement, the Company needs to first evaluate if the arrangement meets the criteria in ASC Topic 808 “Collaborative Arrangements” to then determine if ASC Topic 606 is applicable by considering whether the collaborator meets the definition of a customer. If the criteria are met, the Company assesses the promises in the arrangement to identify distinct performance obligations.
For licenses of intellectual property, the Company assesses, at contract inception, whether the intellectual property is distinct from other performance obligations identified in the arrangement. If the licensing of intellectual property is determined to be distinct, revenue is recognized for nonrefundable, upfront license fees when the license is transferred to the customer and the customer can use and benefit from the license. If the licensing of intellectual property is determined not to be distinct, then the license will be bundled with other promises in the arrangement into one distinct performance obligation. The Company needs to determine if the bundled performance obligation is satisfied over time or at a point in time. If the Company concludes that the nonrefundable, upfront license fees will be recognized over time, the Company will need to assess the appropriate method of measuring proportional performance.
For milestone payments, the Company assesses, at contract inception, whether the development or sales-based milestones are considered probable of being achieved. If it is probable that a significant revenue reversal will occur, the Company will not record revenue until the uncertainty has been resolved. Milestone payments that are contingent upon regulatory approval are not considered probable of being achieved until the applicable regulatory approvals or other external conditions are obtained as such conditions are not within the Company's control. If it is probable that a significant revenue reversal will not occur, the Company will estimate the milestone payments using the most likely amount method. The Company will re-assess the development and sales-based milestones each reporting period to determine the probability of achievement.
The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of research and development expenses as the Company has the risks and rewards as the principal in the research and development activities.
Allowance for doubtful accounts
The Company maintains an allowance for estimated losses resulting from the inability of its customers to make required payments. The Company estimates uncollectible amounts based upon current customer receivable balances, the age of customer receivable balances, the customer’s financial condition and current economic trends. The allowance for doubtful accounts was $0.3 million as of September 30, 2019 and $0.7 million as of December 31, 2018. Bad debt expense was immaterial for the three and nine month periods ended September 30, 2019 and 2018.
Indefinite-lived intangible assets
Indefinite-lived intangible assets consist of in-process research and development ("IPR&D"). IPR&D acquired directly in a transaction other than a business combination is capitalized if the projects will be further developed or have an alternative future use; otherwise they are expensed. The fair values of IPR&D projects acquired in business combinations are capitalized. Several
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methods may be used to determine the estimated fair value of the IPR&D acquired in a business combination. The Company utilizes the "income method” and uses estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, patent protection, and expected pricing and industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets are amortized over the remaining useful life or written off, as appropriate. IPR&D intangible assets that are determined to have had a drop in their fair value are adjusted downward and an impairment is recognized in the statement of operations. These assets are tested at least annually or sooner when a triggering event occurs that could indicate a potential impairment.
Goodwill
Goodwill represents the amount of consideration paid in excess of the fair value of net assets acquired as a result of the Company’s business acquisitions accounted for using the acquisition method of accounting. Goodwill is not amortized and is subject to impairment testing on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired.
Income Taxes
On December 22, 2017, the U.S. government enacted the 2017 Tax Cuts and Jobs Act ("the 2017 Tax Act"), which significantly revises U.S. tax law by, among other provisions, lowering the U.S. federal statutory income tax rate to 21%, imposing a mandatory one-time transition tax on previously deferred foreign earnings, and eliminating or reducing certain income tax deductions. The Global Intangible Low-tax Income ("GILTI") provisions of the 2017 Tax Act require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the period ended September 30, 2019.
Deferred tax assets and liabilities are recognized for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and net operating loss and credit carryforwards. Deferred tax assets and liabilities are measured at rates expected to apply to taxable income in the years in which those temporary differences and carryforwards are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in the statement of operations in the period that includes the enactment date. A valuation allowance is recorded when it is not more likely than not that all or a portion of the net deferred tax assets will be realized.
The Company recorded a deferred tax liability in conjunction with the Merger of $122.0 million related to the tax basis difference in the IPR&D indefinite-lived intangibles acquired. The Company's policy is to record a deferred tax liability related to acquired IPR&D which may eventually be realized either upon amortization of the asset when the research is completed and a product is successfully launched or the write-off of the asset if it is abandoned or unsuccessful.
Leases
In February 2016, the FASB issued ASU No. 2016-2, “Leases (Topic 842)” along with other amendments issued in 2017 and 2018. Topic 842 supersedes the lease accounting requirements in Accounting Standards Codification Topic 840, Leases (Topic 840). Topic 842 requires organizations to recognize leased assets and liabilities on the balance sheet. The standard also requires disclosures to help investors and other financial statement users better understand the amount, timing and uncertainty of cash flows arising from leases.
The Company determines if an arrangement is a lease at inception. This determination generally depends on whether the arrangement conveys to the Company the right to control the use of an explicitly or implicitly identified fixed asset for a period of time in exchange for consideration. Control of an underlying asset is conveyed to the Company if the Company obtains the rights to direct the use of and to obtain substantially all of the economic benefits from using the underlying asset. The Company has lease agreements which include lease and non-lease components, which the Company accounts for as a single lease component for all leases.
Under the standard, operating leases are classified as right of use ("ROU") assets, short term lease liabilities, and long term lease liabilities. Operating lease ROU assets and lease liabilities are recognized at the commencement date based on the present value of lease payments over the lease term. ROU assets are amortized and lease liabilities accrete to yield straight-line expense over the term of the lease. Lease payments included in the measurement of the lease liability are comprised of fixed payments.
Variable lease payments associated with the Company’s leases are recognized when the event, activity, or circumstance in the lease agreement on which those payments are assessed occurs. Variable lease payments are presented in the Company’s consolidated statements of operations in the same line item as expense arising from fixed lease payments for operating leases.
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Leases with an initial term of 12 months or less are not recorded on the consolidated balance sheet and the Company recognizes lease expense for these leases on a straight-line basis over the lease term. The Company applies this policy to all underlying asset categories.
Topic 842 requires a lessee to discount its unpaid lease payments using the interest rate implicit in the lease or, if that rate cannot be readily determined, its incremental borrowing rate. As most of the Company’s leases do not provide an implicit rate, the Company uses its incremental borrowing rate based on the information available at the commencement date in determining the present value of lease payments. The Company gives consideration to its recent debt issuances as well as publicly available data for instruments with similar characteristics when calculating its incremental borrowing rates.
The lease term for all of the Company’s leases includes the non-cancellable period of the lease plus any additional periods covered by either a Company option to extend (or not to terminate) the lease that the Company is reasonably certain to exercise, or an option to extend (or not to terminate) the lease controlled by the lessor. Leasehold improvements are capitalized and depreciated over the lesser of useful life or lease term.
See the "Impact of recently adopted accounting pronouncements" section within this Note below and Note 3 Leases for additional information. The information presented for periods prior to January 1, 2019 has not been adjusted and is reported under Topic 840.
Recently issued accounting standards
In June 2016, the FASB issued ASU No. 2016-13, “Financial Instruments — Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments”. This standard requires financial assets measured at amortized cost basis to be presented at the net amount expected to be collected. This standard is effective for public companies who are SEC filers for fiscal years beginning after December 15, 2019, including interim periods within those years. The Company expects to adopt this guidance when effective and is assessing what effect the adoption of ASU 2016-13 will have on its consolidated financial statements and accompanying notes with a focus on the potential impact on its accounts receivables and its available for sale debt securities.
In August 2018, the FASB issued ASU 2018-13, "Fair Value Measurement (Topic 820), Disclosure Framework—Changes to the Disclosure Requirements for Fair Value Measurement". This standard eliminates certain disclosure requirements for fair value measurements for all entities, requires public entities to disclose certain new information and modifies some disclosure requirements. The new guidance is effective for all entities for fiscal years beginning after December 15, 2019 and for interim periods within those fiscal years. An entity is permitted to early adopt either the entire standard or only the provisions that eliminate or modify requirements. Entities can elect to early adopt in interim periods, including periods for which they have not yet issued financial statements or made their financial statements available for issuance. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-13 will have on its consolidated financial statements and accompanying notes.
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 requires a customer in a cloud computing arrangement that is a service contract to follow the internal-use software guidance in Accounting Standards Codification 350-40 to determine which implementation costs to defer and recognize as an asset. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2019. For all other entities, it is effective for annual periods beginning after December 15, 2020 and interim periods in annual periods beginning after December 15, 2021. Early adoption is permitted, including adoption in any interim period for all entities. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-13 will have on its consolidated financial statements and accompanying notes.
In November 2018, the FASB issued ASU 2018-18,"Collaborative Arrangements (Topic 808): Clarifying the Interaction between Topic 808 and Topic 606”. ASU 2018-18 provides guidance on whether certain transactions between collaborative arrangement participants should be accounted for with revenue under Topic 606. For public business entities, the guidance is effective for annual periods, and interim periods within those annual periods, beginning after December 15, 2019. For all other entities, it is effective for annual periods beginning after December 15, 2020 and interim periods in annual periods beginning after December 15, 2021. Early adoption is permitted, including adoption in any interim period for all entities. The Company expects to adopt this guidance when effective and is currently assessing what effect the adoption of ASU No. 2018-18 will have on its consolidated financial statements and accompanying notes.
Impact of recently adopted accounting pronouncements
In February 2016, the FASB issued ASU No. 2016-2, “Leases (Topic 842)”. This standard requires organizations that lease assets with lease terms of more than 12 months to recognize assets and liabilities for the rights and obligations created by those leases on their balance sheets. The ASU also requires new qualitative and quantitative disclosures to help investors and other financial
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statement users better understand the amount, timing, and uncertainty of cash flows arising from leases. The standard is effective for public companies for fiscal years, and interim periods within those fiscal years, beginning after December 15, 2018, with early adoption permitted. Additionally, in March 2019, the FASB issued ASU 2019-01,"Leases (Topic 842): Codification Improvements”. ASU 2019-01 clarifies the transition guidance related to interim disclosures provided in the year of adoption. The Company adopted the new guidance on January 1, 2019 using the modified retrospective method. Prior period results were not adjusted and continue to be presented under Topic 840 based on the accounting standards originally in effect for such periods. As part of the adoption, the Company has elected to utilize practical expedients including the package of practical expedients permitted under the transition guidance within the new standard, which among other things, allowed the Company to: 1) carry forward the historical determination of contracts as leases, lease classification and not reassess initial direct costs for historical lease arrangements, 2) not separate non-lease components from lease components and instead to account for each separate lease component and the non-lease components associated with that lease component as a single lease component (the Company elected to apply this practical expedient to all underlying asset classes), 3) not apply the recognition requirements in ASC 842 to short-term leases, and 4) not record an ROU asset or ROU liability for leases with an asset or liability balance that would be considered immaterial. Upon adoption, the Company recorded an operating lease liability with a corresponding operating lease ROU asset of $11.3 million. The adoption did not have a material impact on the consolidated results of operations, stockholder's equity, and cash flows for the three and nine month periods ended September 30, 2019. As the Company is not a lessor, the aspects of the new guidance pertaining to lessors was not applicable for the Company.
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". This standard permits the reclassification of tax effects stranded in other comprehensive income as a result of tax reform to retained earnings related to the change in federal tax rate in addition to other stranded effects that relate to the 2017 Tax Act but do not directly relate to the change in the federal rate. ASU 2018-02 is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years with early adoption permitted for periods for which financial statements have not yet been issued or made available for issuance. The Company adopted this guidance on January 1, 2019 and elected not to reclassify the tax effects in other comprehensive income related to the 2017 Tax Act, as these amounts were immaterial. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.
In June 2018, the FASB issued ASU 2018-07, "Compensation — Stock Compensation (Topic 718), Improvements to Nonemployee Share-Based Payment Accounting". This standard expands the scope of ASC 718 to include share-based payments granted to nonemployees in exchange for goods or services used or consumed in the entity’s own operations and supersedes the guidance in ASC 505-50. The ASU retains the existing cost attribution guidance, which requires entities to recognize compensation cost for nonemployee awards in the same period and in the same manner they would if they paid cash for the goods or services, but it moves the guidance to ASC 718. ASU 2018-07 is effective for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years with early adoption permitted for periods for which financial statements have not yet been issued or made available for issuance. The Company adopted this guidance on January 1, 2019. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.
In May 2014, the FASB issued ASU No. 2014-09, “Revenue from Contracts with Customers (Topic 606)”. ASU No. 2014-09 eliminated transaction- and industry-specific revenue recognition guidance under FASB Accounting Standards Codification (“ASC”) Subtopic 605-15, Revenue Recognition-Products and replaced it with a principle-based approach for determining revenue recognition. ASC Topic 606 requires entities to recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. On January 1, 2018, the Company adopted ASC Topic 606 using the modified retrospective approach and applied this approach only to contracts that were not completed as of January 1, 2018. The Company calculated a one-time transition adjustment of $3.3 million, which was recorded on January 1, 2018 to deferred revenue and accumulated deficit, related to the product sales of Emflaza.
In January 2016, the FASB issued ASU No. 2016-01, “Financial Instruments — Overall (Subtopic 825-10): Recognition and Measurement of Financial Assets and Financial Liabilities”. This standard enhances the reporting model for financial instruments, which includes amendments to address aspects of recognition, measurement, presentation and disclosure. The new guidance affects all reporting organizations (whether public or private) that hold financial assets or owe financial liabilities. The Company adopted the guidance on January 1, 2018. In March 2018, the FASB issued ASU 2018-04, "Investments - Debt Securities (Topic 320) and Regulated Operations (Topic 980): Amendments to SEC Paragraphs Pursuant to the SEC Staff Accounting Bulletin ("SAB") No. 117 and SEC Release No. 33-9273 (SEC Update)". This standard supersedes SEC paragraphs in ASC 320, Investments- Debt Securities, as a result of the issuance of SAB 117 and also updates the Codification for a 2011 SEC release and is effective when a registrant adopts ASU 2016-01, which in the case of the Company was on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.
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In August 2016, the FASB issued ASU No. 2016-15, “Statement of Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments”. This standard clarifies the presentation of certain specific cash flow issues in the Statement of Cash Flows. The Company adopted the guidance on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.
In November 2016, the FASB issued ASU 2016-16, “Intra-Entity Transfers of Assets Other Than Inventory”. ASU 2016-16 requires companies to account for the income tax effects of intercompany transfers of assets other than inventory (e.g., intangible assets) when the transfer occurs. The Company adopted the guidance on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.
In November 2016, the FASB issued ASU No. 2016-18, “Statement of Cash Flows (Topic 230): Restricted Cash”. This standard requires entities to show the changes in the total of cash, cash equivalents, restricted cash and restricted cash equivalents in the statement of cash flows and no longer present transfers between cash and cash equivalents and restricted cash and restricted cash equivalents in the statement of cash flows. The Company adopted the guidance on January 1, 2018. Upon adoption, the guidance did not have a material impact on the consolidated financial statements and accompanying notes. During the three-month period ended September 30, 2019, the Company entered into an unconditional, irrevocable and transferable letter of credit in connection with obligations under a facility lease for our leased biologics facility. Accordingly, the Company updated its disclosures around restricted cash above within this footnote, including the nature and amount of restricted cash, its classification on the consolidated balance sheet, and a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet to the statement of cash flows.
In May 2017, the FASB issued ASU No. 2017-09, "Stock Compensation (Topic 718): Scope of Modification Accounting". This standard clarifies when changes to the terms or conditions of a share-based payment award must be accounted for as a modification, with entities applying the modification accounting guidance if the value, vesting conditions or classification of the award changes. In addition to all disclosures about modifications that are required under the current guidance, entities will also be required to disclose that compensation expense has not changed if applicable. The Company adopted the guidance on January 1, 2018. The adoption of the guidance did not have a material impact on the consolidated financial statements and accompanying notes.

3. | Leases

The Company leases office space in South Plainfield, New Jersey for its principal office under three noncancelable operating leases through May 2022 and August 2024, in addition to office space in various countries for international employees primarily through workspace providers. The Company also leases certain vehicles, lab equipment, and office equipment under operating leases. The Company’s operating leases have remaining lease terms ranging from 0.2 years to 6.7 years and certain of the leases include renewal options to extend the lease for up to 10 years.
The components of lease expense were as follows:

| Three Months Ended September 30, 2019 |  | Nine Months Ended September 30, 2019
Operating Lease Cost |  |  |
Fixed lease cost | $ | 1,431 |  |  | $ | 3,078 |
Variable lease cost | 184 |  |  | 488 |
Short-term lease cost | 94 |  |  | 235 |
Total operating lease cost | $ | 1,709 |  |  | $ | 3,801 |

Total operating lease cost is a component of operating expenses on the consolidated statements of operations.
Supplemental balance sheet information related to leases was as follows:

| September 30, 2019
Operating lease ROU asset | $ | 13,708 |
Operating lease liabilities- current | $ | 4,605 |
Operating lease liabilities- noncurrent | 9,455 |
Total operating lease liability | $ | 14,060 |

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Operating lease ROU asset is a component of deposits and other assets on the consolidated balance sheet. The current portion of operating lease liability is a component of other current liabilities on the consolidated balance sheet. The long term portion of operating lease liabilities is a component of other long term liabilities on the consolidated balance sheet.
Supplemental lease term and discount rate information related to leases was as follows:

| September 30, 2019
Weighted-average remaining lease terms - operating leases (years) | 3.58 |
Weighted-average discount rate - operating leases | 7.05 | %

Supplemental cash flow information related to leases was as follows:

| Nine Months Ended September 30, 2019
Cash paid for amounts included in the measurement of lease liabilities: |
Operating cash flows from operating leases | $ | 2,751 |
Right-of-use assets obtained in exchange for lease obligations: |
Operating leases | $ | 16,120 |

Future minimum lease payments under non-cancelable leases as of September 30, 2019 were as follows:

| Operating Leases |
2019 (Excludes the nine months ended September 30, 2019) | $ | 1,336 |
2020 | 5,463 |
2021 | 3,705 |
2022 | 2,110 |
2023 and thereafter | 2,124 |
Total lease payments | 14,738 |
Less: Imputed Interest | 678 |
Total | $ | 14,060 |

As of September 30, 2019, the Company had one operating lease that had not yet commenced, and accordingly, is not reflected in the tables above. On August 4, 2019, the Company and Bristol-Myers Squibb Company, (the “Landlord”), entered into a Lease Agreement (the “Lease”), relating to the lease of approximately 185,000 square feet of office, production and laboratory space at a facility located in Hopewell Township, New Jersey (the “Campus”).
The rental term of the Lease is currently estimated to commence on July 1, 2020 (the “Commencement Date”). Upon the Commencement Date, the Lease has an initial term of fifteen years (the “Initial Term”), with two consecutive 10 years renewal periods at the Company’s option.
The aggregate rent for the Initial Term will be approximately $88.1 million. The rental rate for the renewal periods will be 95% of the Prevailing Market Rate (as defined in the Lease) and determined at the time of the exercise of the renewal. The Company is also responsible for maintaining certain insurance and the payment of proportional taxes, utilities and common area operating expenses. The Lease contains customary events of default, representations, warranties and covenants.
Subject to the terms of the Lease, the Company has a right of first refusal to rent certain other space of the Campus, which would be triggered upon the Landlord’s issuance of a second round proposal or letter of intent to another tenant for such space. The Company also may seek to build a new separate building on the Campus, which may not contain less than 75,000 square feet (the “New Building”). Upon receipt of notice of the Company’s intention to build the New Building, the Landlord may, in its sole discretion, construct and lease the New Building to the Company or enter into a ground lease with the Company permitting the Company to construct the New Building. Rent terms for the New Building would be determined based on the land value, construction and project costs subject to whether the Landlord or Company constructs the New Building.
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4. Acquisitions
On August 23, 2018, the Company completed its acquisition of Agilis pursuant to the Merger Agreement. Agilis was a privately-held biotechnology company advancing an innovative gene therapy platform for rare monogenic diseases that affect the central nervous system. Upon completion of the Merger, the Company acquired Agilis's lead product candidate, PTC-AADC, for the treatment of AADC deficiency, as well as three other gene therapies that were part of the Agilis platform.
Upon the closing of the Merger, the Company paid to Agilis equityholders total upfront consideration comprised of 49.2 million in cash and 3,500,907 shares of the Company’s common stock (the “Closing Stock Consideration”). The Closing Stock Consideration was determined by dividing $150.0 million by the volume-weighted average price per share of the Company’s common stock on The Nasdaq Global Select Market for the 10 consecutive trading-day period ending on the second trading-day immediately preceding the closing of the Merger. The fair value of the stock on the acquisition date was determined to be $155.9 million.
Pursuant to the Merger Agreement, Agilis equityholders may become entitled to receive contingent consideration payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million, (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million, and (iv) a percentage of annual net sales for Friedreich Ataxia and Angelman Syndrome during specified terms, ranging from 2%-6%. The fair value of the contingent consideration payments at the acquisition date was estimated to be $290.5 million. Under the Merger Agreement, the Company is required to pay $40.0 million of the development milestone payments mentioned above no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The fair value of the deferred consideration payments at the closing date was estimated to be $38.1 million. Refer to Footnote 5 for further fair value considerations.
The Company evaluated the acquisition of Agilis under ASU No. 2017-01, Business Combinations: Clarifying the Definition of a Business. Because the business contained both inputs and processes necessary to manage products and provide economic benefits directly to its owners and substantially all the value of the acquisition did not relate to a similar group of assets, it was determined that the acquisition represents a business combination. Therefore, the transaction has been accounted for using the acquisition method of accounting. Under the acquisition method of accounting, the total purchase price of the acquisition is allocated to the net tangible and identifiable intangible assets acquired and liabilities assumed based on their fair values as of the date of acquisition.
The fair value of consideration totaled approximately $533.7 million summarized as follows:

| Fair Value
Cash consideration | $ | 49,221 |
Fair value of PTC common stock issued | 155,860 |
Estimated fair value of deferred consideration payable | 38,100 |
Estimated fair value of contingent consideration payable | 290,500 |
Total consideration | $ | 533,681 |

The Company recorded the assets acquired and liabilities assumed as of the date of acquisition based on the information available at that time. The Company finalized its accounting for the Merger during the three month period ended December 31, 2018. The following table presents the preliminary allocation of the purchase price to the estimated fair values of the assets acquired and liabilities assumed as of the acquisition date of August 23, 2018, the measurement period adjustments recorded during the period from the acquisition date through December 31, 2018, and the final allocation of the purchase price as of December 31, 2018.
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| Preliminary Allocation as of the acquisition date of August 23, 2018 |  | Measurement Period Adjustments |  | Final Allocation as of December 31, 2018
Cash and cash equivalents | $ | 328 |  |  | — |  |  | $ | 328 |
Prepaid expenses and other current assets | 181 |  |  | — |  |  | 181 |
Fixed assets | 153 |  |  | — |  |  | 153 |
Other assets | 38 |  |  | — |  |  | 38 |
Intangible assets - in process research and development (“IPRD”) | 480,000 |  |  | 96,500 |  |  | 576,500 |
Accounts payable and accrued expenses | (3,828 | ) |  | — |  |  | (3,828 | )
Deferred tax liability | (115,200 | ) |  | (6,832 | ) |  | (122,032 | )
Fair value of net assets acquired | $ | 361,672 |  |  | $ | 89,668 |  |  | $ | 451,340 |
Goodwill | 100,309 |  |  | (17,968 | ) |  | 82,341 |
Total purchase price | $ | 461,981 |  |  | $ | 71,700 |  |  | $ | 533,681 |

The Company incurred approximately $1.5 million in acquisition related expenses as of September 30, 2018, which were included in selling, general and administrative expenses in the consolidated statement of operations. The results of Agilis’s operations have been included in the consolidated statements of operations beginning on the acquisition date of August 23, 2018.
The fair value of the IPR&D was capitalized as of the acquisition date and accounted for as indefinite-lived intangible assets until disposition of the assets or completion or abandonment of the associated research and development efforts. Accordingly, during the development period after the completion of the acquisition, these assets will not be amortized into earnings; rather, these assets will be subject to periodic impairment testing. Upon successful completion of the development efforts, the useful lives of the IPR&D assets will be determined and the assets will be considered definite-lived intangible assets and amortized over their expected useful lives.
The goodwill recorded is the excess of the purchase price of the net assets acquired net of any deferred tax adjustments. The Company currently has a deferred tax liability for the indefinite lived IPR&D intangible assets, which have no tax basis and, therefore, will not result in a future tax deduction. The goodwill is not deductible for income tax purposes.
The net loss of Agilis included in the consolidated statement of operations for the period August 23, 2018 through September 30, 2018 was $1.9 million.
Pro-Forma Financial Information Associated with the Agilis Acquisition (Unaudited)
The following table summarizes certain supplemental pro forma financial information for the three and nine-month periods ended September 30, 2018 as if the Merger had occurred as of January 1, 2018. The unaudited pro-forma financial information for the three month and nine month periods ended September 30, 2018 reflects adjustments of $0.8 million and $1.5 million , respectively, related to acquisition fees that are non-recurring in nature.

| Three Months Ended September 30, |  | Nine Months Ended September 30,
| 2018 |  | 2018
Revenues | $ | 53,591 |  |  | $ | 178,396 |
Net loss attributable to common stockholders | $ | (52,458 | ) |  | $ | (89,976 | )

Bridge Loan
In connection with the Merger Agreement, on July 19, 2018, the Company also entered into a Bridge Loan and Security Agreement, or the Bridge Loan Agreement, by and among the Company, Agilis and certain of Agilis’s domestic subsidiaries, as guarantors. Under the Bridge Loan Agreement, the Company made a term loan advance to Agilis on July 23, 2018 in an original principal amount of $10.0 million. In connection with the closing of the Merger, the original principal amount of $10.0 million plus all accrued and unpaid interest thereon was credited against the cash portion of the upfront consideration paid by the Company pursuant to the terms of the Merger Agreement in satisfaction of Agilis’s outstanding payment obligations under the Bridge Loan Agreement, and the Company has no further obligation to extend any further loan amounts under the Bridge Loan Agreement.
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5. Fair value of financial instruments and marketable securities
The Company follows the fair value measurement rules, which provide guidance on the use of fair value in accounting and disclosure for assets and liabilities when such accounting and disclosure is called for by other accounting literature. These rules establish a fair value hierarchy for inputs to be used to measure fair value of financial assets and liabilities. This hierarchy prioritizes the inputs to valuation techniques used to measure fair value into three levels: Level 1 (highest priority), Level 2, and Level 3 (lowest priority).

· | Level 1—Unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the balance sheet date.

· | Level 2—Inputs other than quoted prices included within Level 1 that are observable for the asset or liability, either directly or indirectly. Level 2 inputs include quoted prices for similar assets and liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, inputs other than quoted prices that are observable for the asset or liability (i.e., interest rates, yield curves, etc.), and inputs that are derived principally from or corroborated by observable market data by correlation or other means (market corroborated inputs).

· | Level 3—Inputs are unobservable and reflect the Company’s assumptions as to what market participants would use in pricing the asset or liability. The Company develops these inputs based on the best information available.

Cash equivalents and investments are reflected in the accompanying financial statements at fair value. The carrying amount of receivables and accounts payable and accrued expenses approximates fair value due to the short-term nature of those instruments. The carrying amounts for borrowings under the credit and security agreement with MidCap Financial approximate fair value based on market activity for other debt instruments with similar characteristics and comparable risk.
In May 2019, the Company purchased $4.0 million of shares of MRI Interventions, Inc.'s ("MRI") common stock, at a purchase price of $3.10 per share, in connection with a securities purchase agreement that the Company entered into with MRI, a publicly traded medical device company. The Company determined that the equity investment represents a financial instrument and therefore, recorded it at fair value, which is readily determinable. The equity investment is a component of deposits and other assets on the consolidated balance sheet. During the three and nine month periods ended September 30, 2019, the Company recorded an unrealized gain of $2.4 million and $2.5 million, respectively, which are components of other (expense) income, net within the consolidated statement of operations. The fair value of the equity investment was $6.5 million as of September 30, 2019. The Company classifies its equity investment in MRI as a Level 1 asset within the fair value hierarchy, as the value is based on a quoted market price in an active market, which is not adjusted.
Fair value of certain marketable securities is based upon market prices using quoted prices in active markets for identical assets quoted on the last day of the period. In establishing the estimated fair value of the remaining investments, the Company used the fair value as determined by its investment advisors using observable inputs other than quoted prices.
The Company reviews its investments on a periodic basis for other-than-temporary impairments. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may have a significant adverse effect on the fair value of the investment.
The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2019 and December 31, 2018:

|  | September 30, 2019
|  | Total |  | Quoted prices in active markets for identical assets (level 1) |  | Significant other observable inputs (level 2) |  | Significant unobservable inputs (level 3)
Marketable securities |  | $ | 185,072 |  |  | $ | — |  |  | $ | 185,072 |  |  | $ | — |
Equity investment in MRI |  | $ | 6,529 |  |  | $ | 6,529 |  |  | $ | — |  |  | $ | — |
Stock appreciation rights liability |  | $ | 2,235 |  |  | $ | — |  |  | $ | — |  |  | $ | 2,235 |
Deferred consideration payable |  | $ | 39,000 |  |  | $ | — |  |  | $ | 39,000 |  |  | $ | — |
Contingent consideration payable- development and regulatory milestones |  | $ | 285,300 |  |  | $ | — |  |  | $ | — |  |  | $ | 285,300 |
Contingent consideration payable- net sales milestones and royalties |  | $ | 59,600 |  |  | $ | — |  |  | $ | — |  |  | $ | 59,600 |

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|  | December 31, 2018
|  | Total |  | Quoted prices in active markets for identical assets (level 1) |  | Significant other observable inputs (level 2) |  | Significant unobservable inputs (level 3)
Marketable securities |  | $ | 58,088 |  |  | $ | — |  |  | $ | 58,088 |  |  | $ | — |
Stock appreciation rights liability |  | $ | 3,814 |  |  | $ | — |  |  | $ | — |  |  | $ | 3,814 |
Deferred consideration payable |  | $ | 37,700 |  |  | $ | — |  |  | $ | 37,700 |  |  | $ | — |
Contingent consideration payable- development and regulatory milestones |  | $ | 257,040 |  |  | $ | — |  |  | $ | — |  |  | $ | 257,040 |
Contingent consideration payable- net sales milestones and royalties |  | $ | 53,200 |  |  | $ | — |  |  | $ | — |  |  | $ | 53,200 |

No transfers of assets between Level 1, Level 2, or Level 3 of the fair value measurement hierarchy occurred during the periods ended September 30, 2019 and December 31, 2018.
The following is a summary of marketable securities accounted for as available-for-sale securities at September 30, 2019 and December 31, 2018:

|  | September 30, 2019
|  | Amortized Cost |  | Gross Unrealized |  | Fair Value
|  |  | Gains |  | Losses |
Commercial paper |  | $ | 47,898 |  |  | $ | 80 |  |  | $ | — |  |  | $ | 47,978 |
Corporate debt securities |  | 115,109 |  |  | 612 |  |  | (4 | ) |  | 115,717 |
Asset-backed securities |  | 21,310 |  |  | 67 |  |  | — |  |  | 21,377 |
Total |  | $ | 184,317 |  |  | $ | 759 |  |  | $ | (4 | ) |  | $ | 185,072 |

|  | December 31, 2018
|  | Amortized Cost |  | Gross Unrealized |  | Fair Value
|  |  | Gains |  | Losses |
Commercial paper |  | $ | 31,657 |  |  | $ | 43 |  |  | $ | (1 | ) |  | $ | 31,699 |
Corporate debt securities |  | 26,399 |  |  | — |  |  | (10 | ) |  | 26,389 |
Total |  | $ | 58,056 |  |  | $ | 43 |  |  | $ | (11 | ) |  | $ | 58,088 |

At September 30, 2019 and December 31, 2018, the Company held securities with an unrealized loss position that were not considered to be other-than-temporarily impaired as the Company has the ability to hold such investments until recovery of their fair value. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. As of September 30, 2019 and December 31, 2018, the Company did not have any realized gains/losses from the sale of marketable securities.
The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of September 30, 2019 are as follows:

|  | September 30, 2019
|  | Securities in an unrealized loss position less than 12 months |  | Securities in an unrealized loss position greater than 12 months |  | Total
|  | Unrealized losses |  | Fair Value |  | Unrealized losses |  | Fair Value |  | Unrealized losses |  | Fair Value
Corporate debt securities |  | (4 | ) |  | 3,017 |  |  | — |  |  | — |  |  | (4 | ) |  | 3,017 |
Total |  | $ | (4 | ) |  | $ | 3,017 |  |  | $ | — |  |  | $ | — |  |  | $ | (4 | ) |  | $ | 3,017 |

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The unrealized losses and fair values of available-for-sale securities that have been in an unrealized loss position for a period of less than and greater than 12 months as of December 31, 2018 are as follows:

|  | December 31, 2018
|  | Securities in an unrealized loss position less than 12 months |  | Securities in an unrealized loss position greater than 12 months |  | Total
|  | Unrealized losses |  | Fair Value |  | Unrealized losses |  | Fair Value |  | Unrealized losses |  | Fair Value
Commercial paper |  | $ | (1 | ) |  | $ | 1,993 |  |  | $ | — |  |  | $ | — |  |  | $ | (1 | ) |  | $ | 1,993 |
Corporate debt securities |  | (7 | ) |  | 14,230 |  |  | (3 | ) |  | 10,087 |  |  | (10 | ) |  | 24,317 |
Total |  | $ | (8 | ) |  | $ | 16,223 |  |  | $ | (3 | ) |  | $ | 10,087 |  |  | $ | (11 | ) |  | $ | 26,310 |

Marketable securities on the balance sheet at September 30, 2019 and December 31, 2018 mature as follows:

|  | September 30, 2019
|  | Less Than 12 Months |  | More Than 12 Months
Commercial paper |  | $ | 47,978 |  |  | $ | — |
Corporate debt securities |  | 58,533 |  |  | 57,184 |
Asset-backed securities |  | 21,377 |  |  | — |
Total Marketable securities |  | $ | 127,888 |  |  | $ | 57,184 |

|  | December 31, 2018
|  | Less Than 12 Months |  | More Than 12 Months
Commercial paper |  | $ | 31,699 |  |  | $ | — |
Corporate debt securities |  | 26,389 |  |  | — |
Total Marketable securities |  | $ | 58,088 |  |  | $ | — |

The Company classifies all of its securities as current as they are all available for sale and are available for current operations.
Convertible senior notes
In August 2015, the Company issued $150.0 million of 3.0% convertible senior notes due August 15, 2022 (the “2022 Convertible Notes”). In September 2019, the Company issued $287.5 million of 1.5% convertible senior notes due September 15, 2026 (the “2026 Convertible Notes,” together with the “2022 Convertible Notes,” the “Convertible Notes”). The Company separately accounted for the liability and equity components of the Convertible Notes by allocating the proceeds between the liability component and equity component, as further discussed in Note 11. The fair value of the Convertible Notes, which differs from their carrying values, is influenced by interest rates, the Company’s stock price and stock price volatility and is determined by prices for the Convertible Notes observed in market trading which are Level 2 inputs. The estimated fair value of the 2022 Convertible Notes at September 30, 2019 and December 31, 2018 was $156.4 million and $146.6 million, respectively. The estimated fair value of the 2026 Convertible Notes at September 30, 2019 was $273.8 million.
Deferred consideration payable
Pursuant to the Merger Agreement, Agilis equityholders may become entitled to receive contingent consideration payments from the Company based on the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million and the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million. The Company is required to pay $40.0 million of development milestone payments no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The fair value of the deferred consideration payable at September 30, 2019 was estimated to be $39.0 million by applying a discounted cash flow approach. The discount rates are estimated utilizing Corporate B rated bonds maturing in the years of expected payments based on the Company’s estimated development timelines for the acquired product candidates. As of September 30, 2019, $19.7 million of the deferred consideration payable was classified as current on the balance sheet.
Level 3 valuation
The stock appreciation rights ("SARs") liability is classified in other liabilities on the Company’s consolidated balance sheets. The SARs liability is marked-to-market each reporting period with the change in fair value recorded as compensation expense on
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the Company’s consolidated statements of operations until the SARs vest. The fair value of the SARs liability is determined at each reporting period by utilizing the Black-Scholes option pricing model.
The contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss in the consolidated statements of operations. The fair value of the development and regulatory milestones is estimated utilizing a probability adjusted, discounted cash flow approach. The discount rates are estimated utilizing Corporate B rated bonds maturing in the years of expected payments based on the Company’s estimated development timelines for the acquired product candidate. The fair value of the net sales milestones and royalties is determined utilizing an option pricing model with Monte Carlo simulation to simulate a range of possible payment scenarios, and the average of the payments in these scenarios is then discounted to calculate present fair value.
The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the SARs liability, and the contingent consideration payable for the period ended September 30, 2019. The changes in the fair value of the Company's Level 3 valuations for the period ended September 30, 2018 were immaterial.

|  | Level 3 liabilities
|  | SARs |  | Contingent consideration payable- development and regulatory milestones | Contingent consideration payable- net sales milestones and royalties
Beginning balance as of December 31, 2018 |  | $ | 3,814 |  |  | $ | 257,040 |  | $ | 53,200 |
Additions |  | — |  |  | — |  | — |
Change in fair value |  | 2,236 |  |  | 28,260 |  | 6,400 |
Payments |  | (3,815 | ) |  | $ | — |  | — |
Ending balance as of September 30, 2019 |  | $ | 2,235 |  |  | $ | 285,300 |  | $ | 59,600 |

The following significant unobservable inputs were used in the valuation of the SARs liability, and the contingent consideration payable for the periods ended September 30, 2019 and December 31, 2018:

|  | September 30, 2019
|  | Fair Value |  | Valuation Technique |  | Unobservable Input |  | Range
SARs |  | $2,235 | Option-pricing model | Volatility | 43.23%
Risk free interest rate | 1.88%
Strike price | $6.76 - $30.86
Fair value of common stock | $33.82
Expected life | 0.26 years
Contingent consideration payable- development and regulatory milestones | $285,300 | Probability-adjusted discounted cash flow | Potential development and regulatory milestones | $0 - $555 million
Probabilities of success | 25% - 94%
Discount rates | 2.7% - 5.1%
Projected years of payments | 2020 - 2026
Contingent considerable payable- net sales milestones and royalties | $59,600 | Option-pricing model with Monte Carlo simulation | Potential net sales milestones | $0 - $150 million
Probabilities of success | 25% - 89%
Potential percentage of net sales for royalties | 2% - 6%
Discount rate | 14.0%
Projected years of payments | 2021 - 2038

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|  | December 31, 2018
|  | Fair Value |  | Valuation Technique |  | Unobservable Input |  | Range
SARs |  | $3,814 | Option-pricing model | Volatility | 46.53% - 59.59%
Risk free interest rate | 2.44% - 2.63%
Strike price | $6.76 - $30.86
Fair value of common stock | $34.32
Expected life | 0.01 - 1.01 years
Contingent consideration payable- development and regulatory milestones | $257,040 | Probability-adjusted discounted cash flow | Potential development and regulatory milestones | $0 - $555 million
Probabilities of success | 25% - 94%
Discount rates | 5.8% - 8.0%
Projected years of payments | 2020 - 2026
Contingent considerable payable- net sales milestones and royalties | $53,200 | Option-pricing model with Monte Carlo simulation | Potential net sales milestones | $0 - $150 million
Probabilities of success | 25% - 89%
Potential percentage of net sales for royalties | 2% - 6%
Discount rate | 14.0%
Projected years of payments | 2021 - 2038

The contingent consideration is classified as a Level 3 liability as its valuation requires substantial judgment and estimation of factors that are not currently observable in the market. If different assumptions were used for the various inputs to the valuation approach, including but not limited to, assumptions involving probability adjusted sales estimates for the Agilis platform and estimated discount rates, the estimated fair value could be significantly higher or lower than the fair value determined.

6. | Other comprehensive income (loss) and accumulated other comprehensive items

Other comprehensive income (loss) includes changes in equity that are excluded from net income (loss), such as unrealized gains and losses on marketable securities.
The following tables summarize other comprehensive income (loss) and the changes in accumulated other comprehensive items for the three and nine months ended September 30, 2019:

|  | Unrealized Gains/(Losses) On Marketable Securities, net of tax |  | Foreign Currency Translation |  | Total Accumulated Other Comprehensive Items
Balance at June 30, 2019 |  | $ | 929 |  |  | $ | 993 |  |  | $ | 1,922 |
Other comprehensive loss before reclassifications |  | (463 | ) |  | (843 | ) |  | (1,306 | )
Amounts reclassified from other comprehensive items |  | — |  |  | — |  |  | — |
Other comprehensive loss |  | (463 | ) |  | (843 | ) |  | (1,306 | )
Balance at September 30, 2019 |  | $ | 466 |  |  | $ | 150 |  |  | $ | 616 |

|  | Unrealized Gains/(Losses) On Marketable Securities, net of tax |  | Foreign Currency Translation |  | Total Accumulated Other Comprehensive Items
Balance at December 31, 2018 |  | $ | 31 |  |  | $ | 1,431 |  |  | $ | 1,462 |
Other comprehensive income (loss) before reclassifications |  | 435 |  |  | (1,281 | ) |  | (846 | )
Amounts reclassified from other comprehensive items |  | — |  |  | — |  |  | — |
Other comprehensive income (loss) |  | 435 |  |  | (1,281 | ) |  | (846 | )
Balance at September 30, 2019 |  | $ | 466 |  |  | $ | 150 |  |  | $ | 616 |

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7. | Accounts payable and accrued expenses

Accounts payable and accrued expenses at September 30, 2019 and December 31, 2018 consist of the following:

|  | September 30, 2019 |  | December 31, 2018
Employee compensation, benefits, and related accruals |  | $ | 25,800 |  |  | $ | 27,629 |
Consulting and contracted research |  | 2,356 |  |  | 11,267 |
Professional fees |  | 10,300 |  |  | 5,574 |
Sales allowance and other costs |  | 37,129 |  |  | 29,417 |
Sales rebates and royalties |  | 33,645 |  |  | 31,874 |
Accounts payable |  | 8,959 |  |  | 6,001 |
Other |  | 9,961 |  |  | 16,437 |
Balance at September 30, 2019 |  | $ | 128,150 |  |  | $ | 128,199 |

8. | Capitalization

In January 2019, the Company closed an underwritten public offering of its common stock pursuant to a registration statement on Form S-3. The Company issued and sold an aggregate of 7,563,725 shares of common stock under the registration statement at a public offering price of $30.20 per share, including 843,725 shares issued upon exercise by the underwriter of its option to purchase additional shares in February 2019. The Company received net proceeds of $224.2 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.
In August 2019, the Company entered into an At the Market Offering Sales Agreement (the “Sales Agreement”) with Cantor Fitzgerald and RBC Capital Markets, LLC (together, the “Sales Agents”), pursuant to which, the Company may offer and sell shares of its common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended. During the three month period ending September 30, 2019, the Company issued and sold an aggregate of 63,926 shares of common stock pursuant to the Sales Agreement at a weighted average public offering price of $46.60 per share. The Company received net proceeds of $2.6 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.
In September 2019, the Company closed an underwritten public offering of its common stock pursuant to a registration statement on Form S-3. The Company issued and sold an aggregate of 2,475,248 shares of common stock under the registration statement at a public offering price of $40.40 per share. The offering included an option to purchase up to an additional 371,287 shares for a period of 30 days following the offering. This option was not exercised by the underwriter. The Company received net proceeds of $97.0 million after deducting underwriting discounts and commissions and other offering expenses payable by the Company.
Warrants
During the three month period ended September 30, 2019, all of the Company’s outstanding warrants expired, and the Company wrote off the remaining liability, which was immaterial.
As of December 31, 2018, all of the Company's outstanding warrants were classified as liabilities because they contained non-standard antidilution provisions. The fair value of the warrants as of December 31, 2018 was immaterial.
The following is a summary of the Company’s outstanding warrants as of December 31, 2018:

|  | Warrant shares |  | Exercise price |  | Expiration
Common stock |  | 7,030 |  |  | $ | 128.00 |  |  | September 2019
Common stock |  | 130 |  |  | $ | 2,520.00 |  |  | August 2019

9. Net loss per share
Basic earnings per share is computed by dividing net loss by the weighted-average number of common shares outstanding. Diluted earnings per share is computed by dividing net loss by the weighted-average number of common shares plus the effect of any dilutive potential common shares outstanding during the period.
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The following tables set forth the computation of basic and diluted net loss per share:

| Three Months Ended September 30, |  | Nine Months Ended September 30, |
| 2019 |  | 2018 |  | 2019 |  | 2018 |
Numerator |  |  |  |  |  |  |  |  |  |  |  |
Net loss | $ | (59,997 | ) |  | $ | (50,969 | ) |  | $ | (173,899 | ) |  | $ | (79,751 | ) |
Denominator |  |  |  |  |  |  |  |  |  |  |  |
Denominator for basic and diluted net loss per share | 56,463,528 |  |  | 48,096,521 |  |  | 57,798,968 |  |  | 45,310,690 |  |
Net loss per share: |  |  |  |  |  |  |  |  |  |  |  |
Basic and diluted | $ | (1.06 | ) | * | $ | (1.06 | ) | * | $ | (3.01 | ) | * | $ | (1.76 | ) | *

*In the three and nine months ended September 30, 2019 and 2018, the Company experienced a net loss and therefore did not report any dilutive share impact.
The following table shows historical dilutive common share equivalents outstanding, which are not included in the above historical calculation, as the effect of their inclusion is anti-dilutive during each period.

| As of September 30,
| 2019 |  | 2018
Stock Options | 10,743,181 |  |  | 9,545,522 |
Unvested restricted stock awards and units | 650,103 |  |  | 580,347 |
Total | 11,393,284 |  |  | 10,125,869 |

10. | Stock award plan

On March 5, 2013, the Company’s Board of Directors approved the 2013 Stock Incentive Plan, which provides for the granting of stock option awards, stock appreciation rights, restricted stock, restricted stock units and other stock-based awards in the aggregate of 739,937 shares of common stock. On March 5, 2013, the Company's Board of Directors approved a grant of 735,324 shares of restricted stock and 4,613 stock options. There are no additional shares available for issuance under this plan.
In 2009, the Company’s shareholders approved the 2009 Equity and Long-Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards, subject to certain adjustments and annual increases. In May 2013, the Company’s Board of Directors and stockholders increased by 2,500,000 the number of shares authorized under the 2009 Equity and Long Term Incentive Plan, which provides for the granting of stock option awards, restricted stock awards, and other stock-based and cash-based awards. There are no additional shares available for issuance under this plan.
In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long Term Incentive Plan, which became effective upon the closing of the Company’s initial public offering. The 2013 Long Term Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards. The number of shares of common stock reserved for issuance under the 2013 Long Term Incentive Plan is the sum of (1) 122,296 shares of common stock available for issuance under the Company’s 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan, (2) the number of shares (up to 3,040,444 shares) equal to the sum of the number of shares of common stock subject to outstanding awards under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan and 2013 Stock Incentive Plan that expire, terminate or are otherwise surrendered, canceled, forfeited or repurchased by the Company at their original issuance price pursuant to a contractual repurchase right plus (3) an annual increase, to be added on the first day of each fiscal year until the expiration of the 2013 Long Term Incentive Plan, equal to the lowest of 2,500,000 shares of common stock, 4% of the number of shares of common stock outstanding on the first day of the fiscal year and an amount determined by the Company’s Board of Directors. As of September 30, 2019, awards for 453,992 shares of common stock are available for issuance.
From January 1, 2019 through September 30, 2019, the Company issued a total of 3,265,220 stock options to various employees. Of those, 999,300 were inducement grants for non-statutory stock options. The inducement grant awards were made pursuant to the Nasdaq Listing Rule 5635(c)(4) inducement grant exception as a material component of the Company's new hires’ employment compensation and not under the 2013 Long Term Incentive Plan.
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A summary of stock option activity is as follows:

|  | Number of options |  | Weighted- average exercise price |  | Weighted- average remaining contractual term |  | Aggregate intrinsic value (in thousands)
Outstanding at December 31, 2018 |  | 8,534,358 |  |  | $ | 28.58 |  |  |  |  |  |
Granted |  | 3,265,220 |  |  | $ | 34.68 |  |  |  |  |  |
Exercised |  | (645,435 | ) |  | $ | 18.91 |  |  |  |  |  |
Forfeited/Cancelled |  | (410,962 | ) |  | $ | 32.54 |  |  |  |  |  |
Outstanding at September 30, 2019 |  | 10,743,181 |  |  | $ | 30.85 |  |  | 7.39 years |  | $ | 75,022 |
Vested or Expected to vest at September 30, 2019 |  | 5,138,949 |  |  | $ | 30.27 |  |  | 8.89 years |  | $ | 27,358 |
Exercisable at September 30, 2019 |  | 5,220,799 |  |  | $ | 31.32 |  |  | 5.80 years |  | $ | 46,228 |

The fair value of grants made in the nine months ended September 30, 2019 was contemporaneously estimated on the date of grant using the following assumptions:

|  | Nine months ended September 30, 2019
Risk-free interest rate |  | 1.71 - 2.63%
Expected volatility |  | 61.90 - 91.75%
Expected term |  | 5.75 - 6.11 years

The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the nine-month period ended September 30, 2019 was $21.49 per share.
Prior to the three-month period ended September 30, 2019, the Company used the “simplified method” to determine the expected term of options. Under this method, the expected term represents the average of the vesting period and the contractual term. During the three-month period ended September 30, 2019, the Company determined that it had sufficient exercise history to be able to estimate the expected term of its options. Accordingly, for the three-month period ended September 30, 2019, the expected term of options was estimated based on the Company's historical exercise data.
Prior to the three-month period ended September 30, 2019, the expected volatility of share options was estimated based on a historical volatility analysis of peers that were similar to the Company with respect to industry, stage of life cycle, size, and financial leverage. During the three-month period ended September 30, 2019, the Company determined that it had sufficient Company stock volatility history to be able to estimate the expected volatility of its options. Accordingly, for the three-month period ended September 30, 2019, the expected volatility of options was estimated based on the Company's historical stock volatility.
The risk-free rate of the option is based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option.
Restricted Stock Awards—Restricted stock awards are granted subject to certain restrictions, including in some cases service or time conditions (restricted stock). The grant-date fair value of restricted stock awards, which has been determined based upon the market value of the Company’s shares on the grant date, is expensed over the vesting period.
Restricted Stock Units—Restricted stock units are granted subject to certain restrictions, including in some cases service or time conditions (restricted stock). The grant-date fair value of restricted stock units, which has been determined based upon the market value of the Company’s shares on the grant date, is expensed over the vesting period.
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The following table summarizes information on the Company’s restricted stock awards and units:

|  | Restricted Stock Awards and Units
|  | Number of Shares |  | Weighted Average Grant Date Fair Value
January 1, 2019 |  | 571,479 |  |  | $ | 17.61 |
Granted |  | 306,549 |  |  | $ | 32.97 |
Vested |  | (180,827 | ) |  | $ | 17.56 |
Forfeited |  | (47,098 | ) |  | $ | 22.34 |
Unvested at September 30, 2019 |  | 650,103 |  |  | $ | 24.54 |

Stock Appreciation Rights—SARs entitle the holder to receive, upon exercise, an amount of the Company's common stock or cash (or a combination thereof) determined by reference to appreciation, from and after the date of grant, in the fair market value of a share of the Company's common stock over the measurement price based on the exercise date.
In May 2016, a total of 897,290 SARs were granted to non-executive employees (the "2016 SARs"). The 2016 SARs will vest annually in equal installments over four years and will be settled in cash on each vest date, requiring the Company to remeasure the SARs at each reporting period until vesting occurs. For the nine month period ended September 30, 2019, a total of 157,930 SARs vested. For the three and nine month periods ended September 30, 2019, the Company recorded $0.4 million and $2.3 million, respectively, in compensation expense related to the 2016 SARs.
Employee Stock Purchase Plan—In June 2016, the Company established an Employee Stock Purchase Plan (“ESPP” or the "Plan”) for certain eligible employees. The Plan is administered by the Company’s Board of Directors or a committee appointed by the Company's Board of Directors. The total number of shares available for purchase under the Plan is one million shares of the Company’s common stock. Employees may participate over a six-month period through payroll withholdings and may purchase, at the end of the six-month period, the Company’s common stock at a purchase price of at least 85% of the closing price of a share of the Company’s common stock on the first business day of the offering period or the closing price of a share of the Company’s common stock on the last business day of the offering period, whichever is lower. No participant will be granted a right to purchase the Company’s common stock under the Plan if such participant would own more than 5% of the total combined voting power of the Company or any subsidiary of the Company after such purchase. For the three and nine month periods ended September 30, 2019, the Company recorded $0.3 million and $0.9 million, respectively, in compensation expense related to the ESPP.
The Company recorded share-based compensation expense in the statement of operations related to incentive stock options, nonstatutory stock options, restricted stock awards, restricted stock units and the ESPP as follows:

|  | Three Months Ended September 30, |  | Nine Months Ended September 30,
|  | 2019 |  | 2018 |  | 2019 |  | 2018
Research and development |  | $ | 4,988 |  |  | $ | 4,431 |  |  | $ | 15,191 |  |  | $ | 12,109 |
Selling, general and administrative |  | 5,496 |  |  | 4,511 |  |  | 15,477 |  |  | 12,664 |
Total |  | $ | 10,484 |  |  | $ | 8,942 |  |  | $ | 30,668 |  |  | $ | 24,773 |

As of September 30, 2019, there was approximately $104.0 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the 2009 Equity and Long Term Incentive Plan, the 2013 Long Term Incentive Plan and equity awards made pursuant to the Nasdaq Listing Rule 5635(c)(4) inducement grant exception for new hires. This cost is expected to be recognized as share-based compensation expense over the weighted average remaining service period of approximately 3.03 years.
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11. Debt
2017 Credit Facility
In May 2017, the Company entered into a credit and security agreement (the "Credit Facility") with MidCap Financial, a Delaware statutory trust, as administrative agent and MidCap Financial and certain other financial institutions as lenders thereunder (the “Credit Agreement”) that provides for a senior secured term loan facility of $60.0 million, of which $40.0 million was drawn by the Company on May 5, 2017. The Company's ability to draw on the remaining $20.0 million under the senior secured term loan facility expired on December 31, 2018. The Company capitalized approximately $0.4 million of debt issuance costs, which were netted against the carrying value of the Credit Facility and will be amortized over the term of the Credit Facility. As of September 30, 2019, the Company had made loan repayments of $6.7 million on the Credit Facility.
Borrowings under the Credit Agreement bear interest at a rate per annum equal to the London Interbank Offered Rate, or LIBOR, (with a LIBOR floor rate of 1.00%) plus 6.15%. The Company was obligated to make interest only payments (payable monthly in arrears) through April 30, 2019. Commencing on May 1, 2019 and continuing for the remaining twenty-four months of the facility, the Company is required to make monthly interest payments and monthly principal payments. The principal payments are to be made based on straight-line amortization of the principal over the twenty-four month period. The maturity date of the Credit Agreement is May 1, 2021, unless terminated earlier.
The Credit Facility is subject to certain financial covenants. As of September 30, 2019, the Company was in compliance with all required covenants.
2026 Convertible Notes
In September 2019, the Company issued, at par value, $287.5 million aggregate principal amount of 1.5% convertible senior notes due 2026, which included an option to purchase up to an additional $37.5 million in aggregate principal amount of the 2026 Convertible Notes. The 2026 Convertible Notes bear cash interest at a rate of 1.5% per year, payable semi-annually on March 15 and September 15 of each year, beginning on March 15, 2020. The 2026 Convertible Notes will mature on September 15, 2026, unless earlier repurchased or converted. The net proceeds to the Company from the offering were $279.3 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by the Company.
The 2026 Convertible Notes are governed by an indenture (the "2026 Convertible Notes Indenture") with U.S Bank National Association as trustee (the "2026 Convertible Notes Trustee").
Holders may convert their 2026 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding March 15, 2026 only under the following circumstances:
· during any calendar quarter commencing on or after December 31, 2019 (and only during such calendar quarter), if the last reported sale price of the Company’s common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day 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 (the “measurement period”) in which the trading price (as defined in the 2026 Convertible Notes Indenture) per $1,000 principal amount of 2026 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day;
· during any period after the Company has issued notice of redemption until the close of business on the scheduled trading day immediately preceding the relevant redemption date; or
· upon the occurrence of specified corporate events.
On or after March 15, 2026, until the close of business on the business day immediately preceding the maturity date, holders may convert their 2026 Convertible Notes at any time, regardless of the foregoing circumstances. Upon conversion, the Company will pay or deliver, as the case may be, cash, shares of the Company's common stock or any combination thereof at the Company's election.
The conversion rate for the 2026 Convertible Notes was initially, and remains, 19.0404 shares of the Company’s common stock per $1,000 principal amount of the 2026 Convertible Notes, which is equivalent to an initial conversion price of approximately $52.52 per share of the Company’s common stock. The conversion rate may be subject to adjustment in some events but will not be adjusted for any accrued and unpaid interest.
The Company is not permitted to redeem the 2026 Convertible Notes prior to September 20, 2023. The Company may redeem for cash all or any portion of the 2026 Convertible Notes, at its option, if the last reported sale price of its common stock has been
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at least 130% of the conversion price then in effect on the last trading day of, and for at least 19 other trading days (whether or not consecutive) during, any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption, at a redemption price equal to 100% of the principal amount of the 2026 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the 2026 Convertible Notes, which means that the Company is not required to redeem or retire the 2026 Convertible Notes periodically.
If the Company undergoes a “fundamental change” (as defined in the 2026 Convertible Notes Indenture), subject to certain conditions, holders of the 2026 Convertible Notes may require the Company to repurchase for cash all or part of their 2026 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2026 Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date.
The 2026 Convertible Notes Indenture contains customary events of default with respect to the 2026 Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the 2026 Convertible Notes when due and payable) occurring and continuing, the 2026 Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding 2026 Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the 2026 Convertible Notes Trustee at the request of such holders (subject to the provisions of the 2026 Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 2026 Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the 2026 Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately.
The Company accounts for the 2026 Convertible Notes as a liability and equity component where the carrying value of the liability component will be valued based on a similar instrument. In accounting for the issuance of the 2026 Convertible Notes, the Company separated the 2026 Convertible Notes into liability and equity components. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The carrying amount of the equity component representing the conversion option was determined by deducting the fair value of the liability component from the par value of the 2026 Convertible Notes as a whole. The excess of the principal amount of the liability component over its carrying amount, referred to as the debt discount, is amortized to interest expense over the seven-year term of the 2026 Convertible Notes. The equity component is not re-measured as long as it continues to meet the conditions for equity classification. The equity component recorded at issuance related to the 2026 Convertible Notes is $123.0 million and was recorded in additional paid-in capital.
In accounting for the transaction costs related to the issuance of the 2026 Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the 2026 Convertible Notes based on their relative values. Transaction costs attributable to the liability component are amortized to interest expense over the seven-year term of the 2026 Convertible Notes, and transaction costs attributable to the equity component are netted with the equity components in stockholders’ equity. Additionally, the Company initially recorded a net deferred tax liability of $25.3 million in connection with the 2026 Convertible Notes.
The 2026 Convertible Notes consist of the following:

Liability component |  | September 30, 2019
Principal |  | $ | 287,500 |
Less: Debt issuance costs |  | (4,692 | )
Less: Debt discount, net(1) |  | (122,618 | )
Net carrying amount |  | $ | 160,190 |

(1) Included in the consolidated balance sheets within convertible senior notes (due 2026) and amortized to interest expense over the remaining life of the 2026 Convertible Notes using the effective interest rate method.
As of September 30, 2019, the remaining contractual life of the 2026 Convertible Notes is approximately 7.0 years.
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The following table sets forth total interest expense recognized related to the 2026 Convertible Notes:

|  | Three Months Ended September 30, |  | Nine Months Ended September 30,
|  | 2019 |  | 2019
Contractual interest expense |  | $ | 130 |  |  | $ | 130 |
Amortization of debt issuance costs |  | 15 |  |  | 15 |
Amortization of debt discount |  | 391 |  |  | 391 |
Total |  | $ | 536 |  |  | $ | 536 |
Effective interest rate of the liability component |  | 10.2 | % |  | 10.2 | %

2022 Convertible Notes
In August 2015, the Company issued, at par value, $150.0 million aggregate principal amount of 3.0% convertible senior notes due 2022. The 2022 Convertible Notes bear cash interest at a rate of 3.0% per year, payable semi-annually on February 15 and August 15 of each year, beginning on February 15, 2016. The 2022 Convertible Notes will mature on August 15, 2022, unless earlier repurchased or converted. The net proceeds to the Company from the offering were $145.4 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by the Company.
The 2022 Convertible Notes are governed by an indenture (the "2022 Convertible Notes Indenture") with U.S Bank National Association as trustee (the "2022 Convertible Notes Trustee").
Holders may convert their 2022 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding February 15, 2022 only under the following circumstances:
· during any calendar quarter commencing on or after September 30, 2015 (and only during such calendar quarter), if the last reported sale price of the Company’s common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day 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 (the “measurement period”) in which the trading price (as defined in the 2022 Convertible Notes Indenture) per $1,000 principal amount of 2022 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day;
· during any period after the Company has issued notice of redemption until the close of business on the scheduled trading day immediately preceding the relevant redemption date; or
· upon the occurrence of specified corporate events.
On or after February 15, 2022, until the close of business on the business day immediately preceding the maturity date, holders may convert their 2022 Convertible Notes at any time, regardless of the foregoing circumstances. Upon conversion, the Company will pay cash up to the aggregate principal amount of the 2022 Convertible Notes to be converted and deliver shares of its common stock in respect of the remainder, if any, of its conversion obligation in excess of the aggregate principal amount of 2022 Convertible Notes being converted.
The conversion rate for the 2022 Convertible Notes was initially, and remains, 17.7487 shares of the Company’s common stock per $1,000 principal amount of the 2022 Convertible Notes, which is equivalent to an initial conversion price of approximately $56.34 per share of the Company’s common stock. The conversion rate may be subject to adjustment in some events but will not be adjusted for any accrued and unpaid interest.
The Company was not permitted to redeem the 2022 Convertible Notes prior to August 20, 2018. As of August 20, 2018, the Company may redeem for cash all or any portion of the 2022 Convertible Notes, at its option, if the last reported sale price of its common stock has been at least 130% of the conversion price then in effect on the last trading day of, and for at least 19 other trading days (whether or not consecutive) during, any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption, at a redemption price equal to 100% of the principal amount of the 2022 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the 2022 Convertible Notes, which means that the Company is not required to redeem or retire the 2022 Convertible Notes periodically. There have been no redemptions to date.
If the Company undergoes a “fundamental change” (as defined in the 2022 Convertible Notes Indenture), subject to certain conditions, holders of the 2022 Convertible Notes may require the Company to repurchase for cash all or part of their 2022
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Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2022 Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date.
The 2022 Convertible Notes Indenture contains customary events of default with respect to the 2022 Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the 2022 Convertible Notes when due and payable) occurring and continuing, the 2022 Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding 2022 Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the 2022 Convertible Notes Trustee at the request of such holders (subject to the provisions of the 2022 Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 2022 Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the 2022 Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately.
The Company accounts for the 2022 Convertible Notes as a liability and equity component where the carrying value of the liability component will be valued based on a similar instrument. In accounting for the issuance of the 2022 Convertible Notes, the Company separated the 2022 Convertible Notes into liability and equity components. The carrying amount of the liability component was calculated by measuring the fair value of a similar liability that does not have an associated convertible feature. The carrying amount of the equity component representing the conversion option was determined by deducting the fair value of the liability component from the par value of the 2022 Convertible Notes as a whole. The excess of the principal amount of the liability component over its carrying amount, referred to as the debt discount, is amortized to interest expense over the seven-year term of the 2022 Convertible Notes. The equity component is not re-measured as long as it continues to meet the conditions for equity classification. The equity component recorded at issuance related to the 2022 Convertible Notes is $57.5 million and was recorded in additional paid-in capital.
In accounting for the transaction costs related to the issuance of the 2022 Convertible Notes, the Company allocated the total costs incurred to the liability and equity components of the 2022 Convertible Notes based on their relative values. Transaction costs attributable to the liability component are amortized to interest expense over the seven-year term of the 2022 Convertible Notes, and transaction costs attributable to the equity component are netted with the equity components in stockholders’ equity. Additionally, the Company initially recorded a net deferred tax liability of $22.3 million in connection with the 2022 Convertible Notes.
The 2022 Convertible Notes consist of the following:

Liability component |  | September 30, 2019 |  | December 31, 2018
Principal |  | $ | 150,000 |  |  | $ | 150,000 |
Less: Debt issuance costs |  | (1,438 | ) |  | (1,746 | )
Less: Debt discount, net(1) |  | (28,862 | ) |  | (35,054 | )
Net carrying amount |  | $ | 119,700 |  |  | $ | 113,200 |

(1) Included in the consolidated balance sheets within convertible senior notes (due 2022) and amortized to interest expense over the remaining life of the 2022 Convertible Notes using the effective interest rate method.
As of September 30, 2019, the remaining contractual life of the 2022 Convertible Notes is approximately 2.9 years.
The following table sets forth total interest expense recognized related to the 2022 Convertible Notes:

|  | Three Months Ended September 30, |  | Nine Months Ended September 30,
|  | 2019 |  | 2018 |  | 2019 |  | 2018
Contractual interest expense |  | $ | 1,134 |  |  | $ | 1,134 |  |  | $ | 3,375 |  |  | $ | 3,375 |
Amortization of debt issuance costs |  | 106 |  |  | 95 |  |  | 308 |  |  | 277 |
Amortization of debt discount |  | 2,137 |  |  | 1,919 |  |  | 6,192 |  |  | 5,563 |
Total |  | $ | 3,377 |  |  | $ | 3,148 |  |  | $ | 9,875 |  |  | $ | 9,215 |
Effective interest rate of the liability component |  | 11.0 | % |  | 11.0 | % |  | 11.0 | % |  | 11.0 | %

12. | Commitments and contingencies

Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited
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("Wellcome Trust") for the research and development of small molecule compounds in connection with the Company's oncology and antibacterial programs. As the Company has discontinued development under its antibacterial program, it no longer expects that milestone and royalty payments from the Company to Wellcome Trust will apply under that agreement, resulting in a change to the total amount of development and regulatory milestone payments the Company may become obligated to pay for this program. Under the oncology program funding agreement, to the extent that the Company develops and commercializes program intellectual property on a for-profit basis itself or in collaboration with a partner (provided the Company retains overall control of worldwide commercialization), the Company may become obligated to pay to Wellcome Trust development and regulatory milestone payments and single-digit royalties on sales of any research program product. The Company’s obligation to pay such royalties would continue on a country-by-country basis until the longer of the expiration of the last patent in the program intellectual property in such country covering the research program product and the expiration of market exclusivity of such product in such country. The Company’s first such milestone payment of $0.8 million payable to Wellcome Trust occurred in the second quarter of 2016. Additional milestone payments of up to an aggregate of $22.4 million may become payable by the Company to Wellcome Trust under this agreement.
The Company has also entered into a collaboration agreement with the SMA Foundation. The Company may become obligated to pay the SMA Foundation single-digit royalties on worldwide net product sales of any collaboration product that is successfully developed and subsequently commercialized or, if the Company outlicenses rights to a collaboration product, a specified percentage of certain payments the Company receives from its licensee. The Company is not obligated to make such payments unless and until annual sales of a collaboration product exceed a designated threshold. The Company’s obligation to make such payments would end upon the Company's payment to the SMA Foundation of a specified amount.
Pursuant to the Merger Agreement with Agilis, Agilis equityholders may become entitled to receive contingent consideration payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million, (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million, and (iv) a percentage of annual net sales for Friedreich Ataxia and Angelman Syndrome during specified terms, ranging from 2%-6%. The Company is required to pay $40.0 million of the development milestone payments no later than the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved.
The Company also has a Collaboration and License Agreement with Akcea Therapeutics, Inc. ("Akcea") for the commercialization of Tegsedi and Waylivra, and products containing those compounds in countries in Latin America and the Caribbean (the "Akcea Collaboration and License Agreement"). Pursuant to the agreement, the Company paid Akcea an upfront licensing fee, which included an initial payment of $12.0 million. An additional $6.0 million was paid to Akcea in the three month period ended June 30, 2019 upon regulatory approval of Waylivra from the EMA. In addition, Akcea is eligible to receive milestone payments, on a Product-by-Product basis, of $4.0 million upon receipt of regulatory approval for a product from ANVISA, subject to a maximum aggregate amount of $8.0 million for all such products. Akcea is also entitled to receive royalty payments subject to certain terms set forth in the Akcea Collaboration and License Agreement.
The Company has employment agreements with certain employees which require the funding of a specific level of payments, if certain events, such as a change in control or termination without cause, occur. Additionally, the Company has royalty payments associated with Translarna and Emflaza product net sales, payable quarterly or annually in accordance with the terms of the related agreements.
From time to time in the ordinary course of its business, the Company is subject to claims, legal proceedings and disputes, including as a result of patients seeking to participate in the Company's clinical trials or otherwise gain access to its product candidates. The Company is not currently aware of any material legal proceedings against it.
13. Revenue recognition
Net product sales
The Company views its operations and manages its business in one operating segment. During the three months ended September 30, 2019 and 2018, net product sales in the United States were $22.9 million and $22.6 million respectively, consisting solely of Emflaza, and net product sales not in the United States were $48.5 million and $30.4 million, respectively, consisting of Translarna and Tegsedi. During the nine months ended September 30, 2019 and 2018, net product sales in the United States were $68.3 million and $62.2 million respectively, consisting solely of Emflaza, and net product sales not in the United States were $141.6 million and $115.0 million, respectively, consisting of Translarna and Tegsedi.
The following table presents changes in the Company’s contract liabilities from December 31, 2018 to September 30, 2019 and December 31, 2017 to September 30, 2018:
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|  | Balance as of December 31, 2018 |  | Additions |  | Deductions |  | ASC 606 Adjustment |  | Balance as of September 30, 2019
Deferred Revenue |  | $ | 12,938 |  |  | $ | 3,801 |  |  | $ | (2,433 | ) |  | $ | — |  |  | $ | 14,306 |

|  | Balance as of December 31, 2017 |  | Additions |  | Deductions |  | ASC 606 Adjustment |  | Balance as of September 30, 2018
Deferred Revenue |  | $ | 11,891 |  |  | $ | 4,706 |  |  | $ | — |  |  | $ | (3,937 | ) |  | $ | 12,660 |

The Company did not have any contract assets for the three and nine month periods ended September 30, 2019 and 2018.
During the three and nine month periods ended September 30, 2019 and 2018, the Company recognized revenue in the period from:

|  | Three Months Ended September 30, 2019 |  | Three Months Ended September 30, 2018 |  | Nine Months Ended September 30, 2019 | Nine Months Ended September 30, 2018
Amounts included in contract liabilities at the beginning of the period |  | $ | 2,269 |  |  | $ | — |  |  | $ | 2,269 |  | $ | — |
Performance obligations satisfied in current period |  | 69,100 |  |  | 53,021 |  |  | 207,630 |  | 177,172 |
Total product revenue |  | $ | 71,369 |  |  | $ | 53,021 |  |  | $ | 209,899 |  | $ | 177,172 |

The Company has not made significant changes to the judgments made in applying ASC Topic 606 for the three and nine month periods ended September 30, 2019 and 2018.
Remaining performance obligations
Remaining performance obligations represent the transaction price for goods the Company has yet to provide. As of September 30, 2019 and 2018, the aggregate amount of transaction price allocated to remaining performance obligations relating to Translarna net product revenue was $14.3 million and $12.7 million, respectively. The Company expects to recognize revenue over the next one to two years as the specific timing for satisfying the performance obligations is contingent upon a number of factors, including customers’ needs and schedules.
Collaboration revenue
The Company has ongoing collaborations with the SMA Foundation and Roche and early stage discovery arrangements with other institutions. The following are the key terms to the Company’s (i) ongoing collaborations and (ii) early stage discovery and development arrangements.
Roche and SMA Foundation
In November 2011, the Company and the SMA Foundation entered into a licensing and collaboration agreement with Roche for an SMA program. Under the terms of the agreement, Roche acquired an exclusive worldwide license to the Company’s SMA program, which includes three compounds currently in preclinical development, as well as potential back-up compounds. The Company received a nonrefundable upfront cash payment of $30.0 million during the research term, which was terminated effective December 31, 2014, after which Roche provided the Company with funding, based on an agreed- upon full-time equivalent rate, for an agreed-upon number of full-time equivalent employees that the Company contributed to the research program.
The Company identified two material promises in the collaboration agreement, the license and the research activities. The Company evaluated whether these material promises are distinct and determined that the license does not have standalone functionality and there is a significant integration of the license and research activities. As such, both promises were bundled into one distinct performance obligation. As a result, the Company deferred the $30.0 million upfront payment which was recognized over the estimated performance period of two years, which was the contracted research period. As of adoption of ASC Topic 606 on January 1, 2018, all performance obligations had been satisfied and the balance of the remaining deferred upfront payment was fully recognized.
Under the agreement, the Company is eligible to receive additional payments from Roche if specified events are achieved with respect to each licensed product, including up to $135.0 million in research and development event milestones, up to $325.0 million in sales milestones upon achievement of specified sales events, and up to double digit royalties on worldwide annual net sales of a commercial product.
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In August 2013, a lead development compound, RG7800, was selected to move into IND-enabling studies, which triggered a milestone payment to the Company from Roche of $10.0 million. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2013.
In January 2014, the Company announced the initiation of a Phase 1 clinical program in its SMA collaboration with Roche and the SMA Foundation which triggered a $7.5 million milestone payment from Roche. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014.
In November 2014, the Company announced the initiation of a Phase 2 study in adult and pediatric patients in its SMA collaboration with Roche and the SMA Foundation which triggered a $10 million payment from Roche. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2014.
In October 2017, the Company announced that the Sunfish, a two-part clinical trial in pediatric and adult type 2 and type 3 SMA initiated in the fourth quarter of 2016 with Roche and SMA Foundation, had transitioned into the pivotal second part of its study. The achievement of this milestone triggered a $20.0 million payment to the Company from Roche. Under ASC Topic 605, the Company considered this milestone event substantive because the applicable criteria of its revenue recognition policy would be satisfied and recorded it as collaboration revenue for the year ended December 31, 2017.
The remaining potential research and development event milestones that can be received as of September 30, 2019 is $87.5 million. The remaining potential sales milestones as of September 30, 2019 is $325.0 million upon achievement of certain sales events. In addition, the Company is eligible to receive up to double digit royalties on worldwide annual net sales of a commercial product.
For the three months ended September 30, 2019 and 2018, the Company recognized revenue related to the licensing and collaboration agreement with Roche of $0.1 million and $0.1 million, respectively. For the nine months ended September 30, 2019 and 2018, the Company recognized revenue related to the licensing and collaboration agreement with Roche of $0.1 million and $0.2 million, respectively.
Early stage collaboration and discovery agreements
From time to time, the Company has arrangements with several organizations pursuant to which the Company uses its discovery technologies to help identify potential drug candidates. The Company does not take ownership of the potential compounds, but rather provides research services to the collaborator using its specialized technology platform.
Generally, these arrangements are structured such that the collaborator and the Company work together to jointly select targets from which to apply its discovery technologies. The research period for the Company to apply its technology is generally three to four years. The Company will typically receive a nonrefundable, upfront cash payment and the collaborator agrees to provide funding for research activities performed on its behalf.
Generally, the two material promises in these arrangements are the license and the research activities. The Company evaluated whether these material promises are distinct and determined that the license does not have standalone functionality and there is a significant integration of the license and research activities. As such, both promises are bundled into one distinct performance obligation. As of adoption of ASC Topic 606 on January 1, 2018, all deferred revenue related to these arrangements had been recognized. For the three and nine months ended September 30, 2019 and 2018, the Company did not recognize any revenue related to discovery agreements.
The Company is eligible to receive additional payments from its early stage discovery research arrangements if the discovery compounds are ultimately developed and commercialized. The aggregate potential payments the Company is eligible for if all products are developed is $143.0 million and up to $252.0 million in sales milestones upon achievement of specified sales events and up to double digit royalties on worldwide annual net sales of the licensed product. The Company will recognize revenue when it is probable the milestones will be achieved (see Note 2). For the three and nine months ended September 30, 2019 and 2018, the Company did not recognize any revenue related to early stage collaborations.

14. | Intangible assets and goodwill

Definite-lived intangibles
On April 20, 2017, the Company completed its previously announced acquisition of all rights to Emflaza pursuant to the Asset Purchase Agreement, dated March 15, 2017, and amended on April 20, 2017, by and between the Company and Marathon. The assets acquired by the Company in the Transaction include intellectual property rights related to Emflaza, inventories of Emflaza,
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and certain contractual rights related to Emflaza. In accordance with ASU No. 2017-01, the Company determined that substantially all of the fair value is concentrated in the Emflaza rights intangible asset and as such accounted for the transaction as an asset acquisition under ASC 805-50 and recorded an intangible asset of $148.4 million.
The Emflaza rights intangible asset is being amortized to cost of product sales over its expected useful life of approximately seven years on a straight line basis.
Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza up to a specified aggregate maximum amount over the expected commercial life of the asset. In accordance with the guidance for an asset acquisition, the Company will record the milestone payment when it becomes payable to Marathon and increase the cost basis for the Emflaza rights intangible asset. For the three month periods ended September 30, 2019 and 2018, milestone payments of $7.4 million and $4.5 million were recorded, respectively.
Pursuant to the Akcea Collaboration and License Agreement, in May 2019 the Company made a $6.0 million milestone payment to Akcea upon regulatory approval of Waylivra from the EMA. The payment was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life of approximately ten years on a straight line basis. Akcea is also entitled to receive royalty payments subject to certain terms set forth in the Akcea Collaboration and License Agreement related to sales of Waylivra. In accordance with the guidance for an asset acquisition, the Company will record royalty payments when they become payable to Akcea and increase the cost basis for the Waylivra intangible asset.
For the three month periods ended September 30, 2019 and 2018, the Company recognized amortization expense of $7.0 million and $5.8 million, respectively, related to the Emflaza rights and Waylivra intangible assets. For the nine month periods ended September 30, 2019 and 2018, the Company recognized amortization expense of $19.7 million and $16.8 million, respectively, related to the Emflaza rights and Waylivra intangible assets.
The estimated future amortization of the Emflaza rights and Waylivra intangible asset is expected to be as follows:

|  | As of September 30, 2019
2019 |  | $ | 7,034 |
2020 |  | 28,136 |
2021 |  | 28,136 |
2022 |  | 28,136 |
2023 and thereafter |  | 34,968 |
Total |  | $ | 126,410 |

Indefinite-lived intangibles
In connection with the acquisition of Agilis, the Company acquired rights to PTC-AADC, for the treatment of AADC deficiency. AADC deficiency is a rare CNS disorder arising from reductions in the enzyme AADC that result from mutations in the dopa decarboxylase gene. The Agilis platform also includes a gene therapy asset targeting Friedreich ataxia, a rare and life-shortening neurodegenerative disease caused by a single defect in the FXN gene which causes reduced production of the frataxin protein. An investigational new drug ("IND") submission with the FDA for this program is expected mid-year 2020. Additionally, the Agilis platform includes two other gene therapy programs targeting CNS disorders, including Angelman syndrome, a rare, genetic, neurological disorder characterized by severe developmental delays.
In accordance with the acquisition method of accounting, the Company allocated the acquisition cost for the Merger to the underlying assets acquired and liabilities assumed, based upon the estimated fair values of those assets and liabilities at the date of acquisition. The Company classified the fair value of the acquired IPR&D as indefinite lived intangible assets until the successful completion or abandonment of the associated research and development efforts. The value allocated to the indefinite lived intangible assets was $576.5 million.
Goodwill
As a result of the Merger on August 23, 2018, the Company recorded $82.3 million of goodwill. There were no changes to the recorded value of goodwill for the three and nine month periods ended September 30, 2019.
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15. Subsequent events
Acquisition of BioElectron Technology Corporation
On October 25, 2019, the Company completed the acquisition of substantially all of the assets of BioElectron Technology Corporation (“BioElectron”), a Delaware corporation, (the “Acquisition”) pursuant to an Asset Purchase Agreement by and between the Company and BioElectron, dated October 1, 2019 (the “Acquisition Agreement”).
Upon the closing of the Acquisition, the Company paid to BioElectron total upfront consideration of $10.0 million, funded with cash on hand, less (i) transaction expenses incurred by BioElectron, (ii) the amount of outstanding indebtedness of BioElectron including a $4.0 million loan advance to BioElectron plus accrued and unpaid interest thereon and (iii) $1.5 million to be held in an escrow account to secure potential indemnification obligations owed to the Company. The loan advance was included in prepaid expenses and other current assets on the consolidated balance sheet as of September 30, 2019. Subject to the terms and conditions of the Acquisition Agreement, BioElectron may become entitled to receive contingent milestone payments of up to $200.0 million (in cash or in shares of the Company’s common stock, as determined by the Company) from the Company based on the achievement of certain regulatory and net sales milestones. Subject to the terms and conditions of the Acquisition Agreement, BioElectron may also become entitled to receive contingent payments of a low single digit percentage of net sales of certain products.
Tegsedi Approval in Brazil
Tegsedi received marketing authorization from ANVISA in October 2019 for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hATTR amyloidosis in Brazil. Refer to Note 12 for further details regarding our commitments and contingencies related to Tegsedi.
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations.
The following discussion of our financial condition and results of operations should be read in conjunction with our financial statements and the notes to those financial statements appearing elsewhere in this Quarterly Report on Form 10-Q and the audited consolidated financial statements and notes thereto and management’s discussion and analysis of financial condition and results of operations for the year ended December 31, 2018 included in our Annual Report on Form 10-K filed with the Securities and Exchange Commission on March 1, 2019, or our 2018 Annual Report. This discussion contains forward-looking statements that involve significant risks and uncertainties. As a result of many factors, such as those set forth in Part II, Item 1A. (Risk Factors) of this Quarterly Report on Form 10-Q and Part I, Item 1A. (Risk Factors) of our 2018 Annual Report, and our actual results may differ materially from those anticipated in these forward-looking statements.
Our Company
We are a science-led global biopharmaceutical company focused on the discovery, development and commercialization of clinically-differentiated medicines that provide benefits to patients with rare disorders. Our ability to commercialize products is the foundation that drives our continued investment in a robust pipeline of transformative medicines and our mission to provide access to best-in-class treatments for patients who have an unmet medical need. Our strategy is to bring best-in-class therapies with differentiated clinical benefit to patients affected by rare disorders and to leverage our global commercial infrastructure to maximize value for our patients and other stakeholders.
Corporate Updates
DMD Franchise
We have two products, Translarna™ (ataluren) and Emflaza™ (deflazacort), for the treatment of Duchenne muscular dystrophy, or DMD, a rare, life threatening disorder. Translarna received marketing authorization from the European Commission in August 2014 for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in ambulatory patients aged five years and older in the 31 member states of the European Economic Area, or EEA. In July 2018, the European Commission approved a label-extension request to our marketing authorization for Translarna in the EEA to include patients from two to up to five years of age. During the quarter ended September 30, 2019, we recognized $48.3 million in net sales from Translarna. Translarna is currently available for the treatment of nmDMD in over 40 countries on a commercial basis or through a reimbursed early access program, or EAP program. We hold worldwide commercialization rights to Translarna for all indications in all territories. Emflaza is approved in the United States for the treatment of DMD in patients two years and older. During the quarter ended September 30, 2019, Emflaza achieved net sales of $22.9 million.
Our marketing authorization for Translarna in the EEA is subject to annual review and renewal by the European Commission following reassessment by the European Medicines Agency, or EMA, of the benefit-risk balance of the authorization, which we refer to as the annual EMA reassessment. In July 2019, the European Commission renewed our marketing authorization, making
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it effective, unless extended, through August 5, 2020. This marketing authorization is further subject to a specific obligation to conduct and submit the results of an 18-month, placebo-controlled trial, followed by an 18-month open-label extension, which we refer to together as Study 041. The final report on the trial and open-label extension is to be submitted by us to the EMA by the end of the third quarter of 2022.
In September 2018, we submitted to the EMA a label-extension request to our marketing authorization in the EEA to include patients who are non-ambulatory. In June 2019, the Committee for Medicinal Products for Human Use, or CHMP, of the EMA informed us that it had adopted a negative opinion of our label-extension request. We requested a re-examination of the procedure and in October 2019 the negative opinion was affirmed.
In April 2019 we received approval for marketing authorization for Translarna in Brazil from ANVISA, the Brazilian health regulatory authority, for the treatment of nmDMD in ambulatory patients aged five years and older.
Each country, including each member state of the EEA, has its own pricing and reimbursement regulations. In order to commence commercial sale of product pursuant to our Translarna marketing authorization in any particular country in the EEA, we must finalize pricing and reimbursement negotiations with the applicable government body in such country. As a result, our commercial launch will continue to be on a country-by-country basis. We also have made, and expect to continue to make, product available under EAP programs, both in countries in the EEA and other territories. Our ability to negotiate, secure and maintain reimbursement for product under commercial and EAP programs can be subject to challenge in any particular country and can also be affected by political, economic and regulatory developments in such country.
There is substantial risk that if we are unable to renew our EEA marketing authorization during any annual renewal cycle, or if our product label is materially restricted, or if Study 041 does not provide the data necessary to maintain our marketing authorization, we would lose all, or a significant portion of, our ability to generate revenue from sales of Translarna in the EEA and other territories.
Translarna is an investigational new drug in the United States. During the first quarter of 2017, we filed a New Drug Application, or NDA, for Translarna for the treatment of nmDMD over protest with the United States Food and Drug Administration, or FDA. In October 2017, the Office of Drug Evaluation I of the FDA issued a Complete Response Letter for the NDA, stating that it was unable to approve the application in its current form. In response, we filed a formal dispute resolution request with the Office of New Drugs of the FDA. In February 2018, the Office of New Drugs of the FDA denied our appeal of the Complete Response Letter. In its response, the Office of New Drugs recommended a possible path forward for the ataluren NDA submission based on the accelerated approval pathway. This would involve a re-submission of an NDA containing the current data on effectiveness of ataluren with new data to be generated on dystrophin production in nmDMD patients’ muscles. We intend to follow the FDA’s recommendation and will collect, using newer technologies via procedures and methods that we designed, such dystrophin data in a new study, Study 045, which we initiated in the fourth quarter of 2018. We expect that a potential re-submission of an NDA could occur in 2020. Additionally, should a re-submission of an NDA receive accelerated approval, the Office of New Drugs stated that Study 041, which is currently enrolling, could serve as the confirmatory post-approval trial required in connection with the accelerated approval framework.
There is substantial risk that Study 045, or any other studies we may use to collect the dystrophin data, will not provide the necessary data to support a marketing approval for Translarna for the treatment of nmDMD in the U.S.
Emflaza was initially approved in the United States for the treatment of DMD in patients five years and older. In June 2019, the FDA approved our label expansion request for Emflaza for patients two to five years of age.
Gene Therapy Platform
We have a pipeline of gene therapy product candidates for rare monogenic diseases that affect the central nervous system, or CNS, including PTC-AADC for the treatment of Aromatic L-Amino Acid Decarboxylase, or AADC, deficiency, or AADC deficiency, a rare CNS disorder arising from reductions in the enzyme AADC that result from mutations in the dopa decarboxylase gene. We are preparing a biologics license application, or BLA, for PTC-AADC for the treatment of AADC deficiency in the United States, which we anticipate submitting to the FDA in late 2019, with an anticipated commercial launch in 2020. We are also preparing a marketing authorization application, or MAA, for PTC-AADC for the treatment of AADC deficiency in the European Union, or EU, for submission to the EMA, which will follow our BLA submission to the FDA.
Our gene therapy platform also includes a gene therapy asset targeting Friedreich ataxia, a rare and life-shortening neurodegenerative disease caused by a single defect in the FXN gene which causes reduced production of the frataxin protein. We expect to submit an investigational new drug application, or IND, to the FDA for this program mid-year 2020.
Akcea Partnership
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We hold the rights for the commercialization of Tegsedi™ (inotersen) and Waylivra™ (volanesorsen) for the treatment of rare diseases in countries in Latin America and the Caribbean, or the PTC Territory, pursuant to our collaboration and license agreement with Akcea Therapeutics, Inc, or the Akcea Agreement.
Tegsedi has received marketing authorization in the U.S., EU and Canada for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hATTR amyloidosis. Tegsedi also received marketing authorization from ANVISA in October 2019 for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hATTR amyloidosis in Brazil.
Waylivra has received conditional marketing authorization in the EU for the treatment of familial chylomicronemia syndrome, or FCS. In connection with the conditional marketing approval for Waylivra in the EU, the European Commission is requiring Akcea to provide results of a study based on a registry of patients to investigate how blood checks and adjustments to frequency of injections are carried out in practice and how well they work to prevent thrombocytopenia and bleeding in FCS patients taking Waylivra. Waylivra is not currently approved for marketing in the PTC Territory.
Splicing Platform
We also have a spinal muscular atrophy, or SMA, collaboration with F. Hoffman-La Roche Ltd. and Hoffman-La Roche Inc., which we refer to collectively as Roche, and the Spinal Muscular Atrophy Foundation, or SMA Foundation. Currently, our collaboration has two pivotal clinical trials ongoing to evaluate the safety and effectiveness of risdiplam (RG7916, RO7034067), the lead compound in the SMA program. Roche is preparing an NDA and an MAA for risdiplam for the treatment of SMA in the United States and the EU, respectively, which Roche anticipates submitting to the FDA in the second half of 2019 and the EMA in the first half of 2020.
In collaboration with Massachusetts General Hospital and New York University, we had identified the splicing compound PTC258, which is a splicing modifier that restores IKAP levels, targeting Familial Dysautonomia. Based on initial feedback from the FDA on the difficulty for a clinical pathway for the small population of patients, the Familial Dysautonomia oral splicing program has been discontinued.
Pre-clinical and other programs
In addition, we have a pipeline of product candidates and discovery programs that are in early clinical, pre-clinical and research and development stages focused on the development of new treatments for multiple therapeutic areas, including rare diseases and oncology.
Funding
The success of our products, product candidates and any other product candidates we may develop, depends largely on obtaining and maintaining reimbursement from governments and third-party insurers. Our revenues are primarily generated from sales of Translarna for the treatment of nmDMD in territories where we are permitted to distribute Translarna under our EAP programs and in countries in the EEA where we were able to obtain acceptable commercial pricing and reimbursement terms, and from sales of Emflaza for the treatment of DMD in the United States.
To date, we have financed our operations primarily through our offering of 3.0% convertible senior notes due August 15, 2022, or the 2022 Convertible Notes, our offering of 1.5% convertible senior notes due September 15, 2026, or the 2026 Convertible Notes, and together with the 2022 Convertible Notes, the Convertible Notes, our public offerings of common stock in February 2014, October 2014, April 2018, January 2019, and September 2019, "at the market offerings" of our common stock, our initial public offering of common stock in June 2013, private placements of our preferred stock, collaborations, bank debt, a credit and security agreement, or the Credit Agreement, with MidCap Financial Trust, or MidCap Financial, as administrative agent and MidCap Financial and other certain institutions as lenders thereto, and grants and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease areas addressed by our product candidates. Since 2014, we have also relied on revenue generated from net sales of Translarna for the treatment of nmDMD in territories outside of the United States, and in May 2017, we began to recognize revenue generated from net sales of Emflaza for the treatment of DMD in the United States.
The Credit Agreement provides for a senior secured term loan facility of $60 million, of which $40 million was drawn by us on May 5, 2017. Our ability to draw on the remaining $20 million under the senior secured term loan facility expired on December 31, 2018. The maturity date of the Credit Agreement is May 1, 2021, unless terminated earlier. As of September 30, 2019, we made loan repayments of $6.7 million on the Credit Facility.
In January 2019, we closed an underwritten public offering of our common stock pursuant to a registration statement on Form S-3. We issued and sold an aggregate of 7,563,725 shares of common stock under the registration statement at a public offering price of $30.20 per share, including 843,725 shares issued upon exercise by the underwriter of its option to purchase additional shares in February 2019. We received net proceeds of approximately $224.2 million after deducting underwriting discounts and commissions and other offering expenses payable by us.
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In August 2019, we entered into an At the Market Offering Sales Agreement, or the Sales Agreement, with Cantor Fitzgerald and RBC Capital Markets, LLC, or together, the Sales Agents, pursuant to which, we may offer and sell shares of our common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended, or the Securities Act. During the three month period ending September 30, 2019, we issued and sold an aggregate of 63,926 shares of common stock pursuant to the Sales Agreement at a weighted average public offering price of $46.60 per share. We received net proceeds of $2.6 million after deducting underwriting discounts and commissions and other offering expenses payable by us.
In September 2019, we closed an underwritten public offering of our common stock pursuant to a registration statement on Form S-3. We issued and sold an aggregate of 2,475,248 shares of common stock under the registration statement at a public offering price of $40.40 per share. The offering included an option to purchase up to an additional 371,287 shares for a period of 30 days following the offering. This option was not exercised by the underwriter. We received net proceeds of $97.0 million after deducting underwriting discounts and commissions and other offering expenses payable by us.
In September 2019, we issued $287.5 million aggregate principal amount of 2026 Convertible Notes, which included an option to purchase up to an additional $37.5 million in aggregate principal amount of the 2026 Convertible Notes. The 2026 Convertible Notes bear cash interest at a rate of 1.5% per year, payable semi-annually on March 15 and September 15 of each year, beginning on March 15, 2020. The 2026 Convertible Notes will mature on September 15, 2026, unless earlier repurchased or converted. We received net proceeds of $279.3 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by us.
As of September 30, 2019, we had an accumulated deficit of $1,112.8 million. We had a net loss of $173.9 million and $79.8 million for the nine month periods ended September 30, 2019 and 2018, respectively.
We anticipate that our expenses will continue to increase in connection with our commercialization efforts in the United States, the EEA, Latin America and other territories, including the expansion of our infrastructure and corresponding sales and marketing, legal and regulatory, distribution and manufacturing and administrative and employee-based expenses. In addition to the foregoing, we expect to continue to incur significant costs in connection with Study 041 and Study 045 and our open label extension trials of Translarna for the treatment of nmDMD as well as our studies for nonsense mutation aniridia and nonsense mutation Dravet syndrome/CDKL5 and our FDA post-marketing requirements with respect to Emflaza in the United States and studies for limb-girdle 2I. We also expect to incur ongoing research and development expenses for our other product candidates, including our gene therapy, splicing and oncology programs. In addition, we may incur substantial costs in connection with our efforts to advance our regulatory submissions. We have begun seeking and intend to continue to seek marketing authorization for Translarna for the treatment of nmDMD in territories outside of the EEA and we may also seek marketing authorization for Translarna for other indications. In late 2019, we plan to submit a request for marketing authorization for PTC-AADC with the FDA, followed by a request for marketing authorization for PTC-AADC with the EMA. These efforts may significantly impact the timing and extent of our commercialization expenses.
We may seek to continue to expand and diversify our product pipeline through opportunistically in-licensing or acquiring the rights to products, product candidates or technologies and we may incur expenses, including with respect to transaction costs, subsequent development costs or any upfront, milestone or other payments or other financial obligations associated with any such transaction, which would increase our future capital requirements.
With respect to our outstanding 2022 and 2026 Convertible Notes, cash interest payments are payable on a semi-annual basis in arrears, which require total funding of $8.8 million annually. Additionally, under the terms of our Credit Agreement cash interest and principal payments are payable monthly in arrears. Furthermore, as a result of our initial public offering in June 2013, we have incurred and expect to continue to incur additional costs associated with operating as a public company including significant legal, accounting, investor relations and other expenses.
We have never been profitable and we will need to generate significant revenues to achieve and sustain profitability, and we may never do so. Accordingly, we may need to obtain substantial additional funding in connection with our continuing operations. Adequate additional financing may not be available to us on acceptable terms, or at all. If we are unable to raise capital when needed or on attractive terms, we could be forced to delay, reduce or eliminate our research and development programs or our commercialization efforts.
Financial operations overview
To date, our net product sales have consisted primarily of sales of Translarna for the treatment of nmDMD in territories outside of the United States and sales of Emflaza for the treatment of DMD in the United States. Our process for recognizing revenue is described below under “Critical accounting policies and significant judgments and estimates—Revenue recognition”.
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Roche and the SMA Foundation Collaboration. In November 2011, we entered into a license and collaboration agreement, or licensing agreement, with Roche and the SMA Foundation pursuant to which we are collaborating with Roche and the SMA Foundation to further develop and commercialize compounds identified under our SMA program with the SMA Foundation. The research component of this agreement terminated effective December 31, 2014. The licensing agreement included a $30 million upfront payment made in 2011 which was recognized on a deferred basis over the research term, and the potential for up to $460 million in milestone payments and royalties on net sales.
In August 2013, we announced the selection of a development candidate. The achievement of this milestone triggered a $10.0 million payment to us from Roche, which we recorded as collaboration revenue for the year ended December 31, 2013.
In January 2014, we initiated a Phase 1 clinical program, which triggered a $7.5 million milestone payment to us from Roche which we recorded as collaboration revenue for the year ended December 31, 2014.
In November 2014, we announced that our joint development program in SMA with Roche and the SMA Foundation had started a Phase 2 study in adult and pediatric patients. The achievement of this milestone triggered a $10.0 million payment to us from Roche which we recorded as collaboration revenue for the year ended December 31, 2014.
In October 2017, we announced that the joint development program in SMA with Roche and SMA Foundation had transitioned into the pivotal second part of its study evaluating the efficacy and safety of RG7916 in pediatric and adult Type 2/3 SMA patients. The achievement of this milestone triggered a $20.0 million payment to us from Roche which we recorded as collaboration revenue at time of achievement.
Grant revenue. From time to time, we receive grant funding from various institutions and governmental bodies. The grants are typically for early discovery research, and generally such grant programs last from two to five years.
Research and development expense
Research and development expenses consist of the costs associated with our research activities, as well as the costs associated with our drug discovery efforts, conducting preclinical studies and clinical trials, manufacturing development efforts and activities related to regulatory filings. Our research and development expenses consist of:
· external research and development expenses incurred under agreements with third-party contract research organizations and investigative sites, third-party manufacturing organizations and consultants;
· employee-related expenses, which include salaries and benefits, including share-based compensation, for the personnel involved in our drug discovery and development activities; and
· facilities, depreciation and other allocated expenses, which include direct and allocated expenses for rent and maintenance of facilities, IT, human resources and other support functions, depreciation of leasehold improvements and equipment, and laboratory and other supplies.
We use our employee and infrastructure resources across multiple research projects, including our drug development programs. We track expenses related to our clinical programs and certain preclinical programs on a per project basis.
We expect our research and development expenses to fluctuate in connection with our ongoing activities, particularly in connection with Study 041 and other studies for Translarna for the treatment of nmDMD, our studies of Translarna in nonsense mutation aniridia and nonsense mutation Dravet syndrome/CDKL5, our studies of Emflaza in limb-girdle 2I, activities under our gene therapy, splicing and oncology programs, and performance of our FDA post-marketing requirements with respect to Emflaza in the United States. The timing and amount of these expenses will depend upon the outcome of our ongoing clinical trials and the costs associated with our planned clinical trials. The timing and amount of these expenses will also depend on the costs associated with potential future clinical trials of our products or product candidates and the related expansion of our research and development organization, regulatory requirements, advancement of our preclinical programs, and product and product candidate manufacturing costs.
The following tables provide research and development expense for our most advanced principal product development programs, for the three and nine months ended September 30, 2019 and 2018.
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|  | Three Months Ended September 30,
|  | 2019 |  | 2018
|  | (in thousands)
Translarna (nmDMD, aniridia and Dravet) |  | $ | 25,239 |  |  | $ | 33,878 |
Gene Therapy |  | 17,016 |  |  | 1,928 |
Oncology |  | 3,944 |  |  | 3,495 |
Emflaza |  | 4,760 |  |  | 4,670 |
Other research and preclinical |  | 12,117 |  |  | 10,397 |
Total research and development |  | $ | 63,076 |  |  | $ | 54,368 |

|  | Nine Months Ended September 30,
|  | 2019 |  | 2018
|  | (in thousands)
Translarna (nmDMD, aniridia and Dravet) |  | $ | 53,354 |  |  | $ | 68,552 |
Gene Therapy |  | 44,418 |  |  | 1,928 |
Oncology |  | 17,769 |  |  | 8,467 |
Emflaza |  | 19,253 |  |  | 10,676 |
Other research and preclinical |  | 40,827 |  |  | 28,714 |
Total research and development |  | $ | 175,621 |  |  | $ | 118,337 |

The successful development of our products and product candidates is highly uncertain. This is due to the numerous risks and uncertainties associated with developing drugs, including the uncertainty of:

· | the scope, rate of progress and expense of our clinical trials and other research and development activities;

· | the potential benefits of our products and product candidates over other therapies;

· | our ability to market, commercialize and achieve market acceptance for any of our products or product candidates that we are developing or may develop in the future, including our ability to negotiate pricing and reimbursement terms acceptable to us and to obtain and maintain marketing authorizations we currently have or may receive in the future for our products and product candidates;

· | clinical trial results;

· | the terms and timing of regulatory approvals; and

· | the expense of filing, prosecuting, defending and enforcing patent claims and other intellectual property rights.

A change in the outcome of any of these variables with respect to the development of our products or product candidates could mean a significant change in the costs and timing associated with the development of that product or product candidate. For example, if the EMA or FDA or other regulatory authority were to require us to conduct clinical trials beyond those which we currently anticipate will be required for the completion of clinical development of Translarna or any other product candidate or if we experience significant delays in enrollment in any of our clinical trials, we could be required to expend significant additional financial resources and time on the completion of clinical development.
Selling, general and administrative expense
Selling, general and administrative expenses consist primarily of salaries and other related costs for personnel, including share-based compensation expenses, in our executive, legal, business development, commercial, finance, accounting, information technology and human resource functions. Other selling, general and administrative expenses include facility-related costs not otherwise included in research and development expense; advertising and promotional expenses; costs associated with industry and trade shows; and professional fees for legal services, including patent-related expenses, accounting services and miscellaneous selling costs.
We expect that selling, general and administrative expenses will increase in future periods in connection with our continued efforts to commercialize Emflaza in the United States, our continued efforts to commercialize Translarna for the treatment of nmDMD in territories outside the United States, our efforts to commercialize Waylivra and Tegsedi in Latin America and the Caribbean and to support our operations, including increased payroll, expanded infrastructure, commercial operations, increased consulting, legal, accounting and investor relations expenses.
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Interest expense, net
Interest expense, net consists of interest income earned on investments and interest expense from the Convertible Notes outstanding and interest expense from the Credit Agreement.
Critical accounting policies and significant judgments and estimates
Our management’s discussion and analysis of our financial condition and results of operations is based on our financial statements, which we have prepared in accordance with generally accepted accounting principles in the United States. The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements, as well as the reported revenues and expenses during the reporting periods. Actual results may differ from these estimates under different assumptions or conditions.
During the three and nine months ended September 30, 2019, there were no material changes to our critical accounting policies as reported in our 2018 Annual Report on Form 10-K, other than those disclosed below.
Restricted cash
Restricted cash included in deposits and other assets on the consolidated balance sheet relates to an unconditional, irrevocable and transferable letter of credit that was entered into during the three-month period ended September 30, 2019 in connection with obligations under a facility lease for our leased biologics facility in Hopewell Township, New Jersey. The amount of the letter of credit is $7.5 million, is to be maintained for a term of not less than five years and has the potential to be reduced to $3.8 million if after five years the Company is not in default of its lease. The amount is classified within deposits and other assets on the consolidated balance sheet due to the long-term nature of the letter of credit.
Revenue recognition
Net Product Revenue
Our net product revenue primarily consists of sales of Translarna in territories outside of the U.S. for the treatment of nmDMD and sales of Emflaza in the U.S. for the treatment of DMD. We recognize revenue when performance obligations with customers have been satisfied. Our performance obligations are to provide Translarna or Emflaza based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when our customer obtains control of either Translarna or Emflaza, which is typically upon delivery. We invoice customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of invoice date. We determine the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods not yet provided. As we have identified only one distinct performance obligation, the transaction price is allocated entirely to either product sales of Translarna or Emflaza. In determining the transaction price, a significant financing component does not exist since the timing from when we deliver product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month.
We record product sales net of any variable consideration, which includes discounts, allowances, rebates and distribution fees. We use the expected value or most likely amount method when estimating variable consideration, unless discount or rebate terms are specified within contracts. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors and may impact such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained.
In relation to customer contracts, we incur costs to fulfill a contract but do not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred.
Upon adoption of ASC Topic 606 on January 1, 2018, we have elected the following practical expedients:

• | Portfolio Approach - We applied the Portfolio Approach to contract reviews within identified revenue streams that have similar characteristics and we believe this approach would not differ materially than if applying ASC Topic 606 to each individual contract.

• | Significant Financing Component - We expect the period between when we transfer a promised good or service to a customer and when the customer pays for the good or service to be one year or less.

• | Immaterial Performance Obligations - We disregard promises deemed to be immaterial in the context of the contract.

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• | Shipping and Handling Activities - We consider any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise.

Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense.
Collaboration Revenue
The terms of these agreements typically include payments to us of one or more of the following: nonrefundable, upfront license fees; milestone payments; research funding and royalties on future product sales. In addition, we generate service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events.
At the inception of a collaboration arrangement, we need to first evaluate if the arrangement meets the criteria in ASC Topic 808 “Collaborative Arrangements” to then determine if ASC Topic 606 is applicable by considering whether the collaborator meets the definition of a customer. If the criteria are met, we assess the promises in the arrangement to identify distinct performance obligations.
For licenses of intellectual property, we assess, at contract inception, whether the intellectual property is distinct from other performance obligations identified in the arrangement. If the licensing of intellectual property is determined to be distinct, revenue is recognized for nonrefundable, upfront license fees when the license is transferred to the customer and the customer can use and benefit from the license. If the licensing of intellectual property is determined not to be distinct, then the license will be bundled with other promises in the arrangement into one distinct performance obligation. We determine if the bundled performance obligation is satisfied over time or at a point in time. If we conclude that the nonrefundable, upfront license fees will be recognized over time, we assess the appropriate method of measuring proportional performance.
For milestone payments, we assess, at contract inception, whether the development or sales-based milestones are considered probable of being achieved. If it is probable that a significant revenue reversal will occur, we will not record revenue until the uncertainty has been resolved. Milestone payments that are contingent upon regulatory approval are not considered probable of being achieved until the applicable regulatory approvals or other external conditions are obtained as such conditions are not within our control. If it is probable that a significant revenue reversal will not occur, we will estimate the milestone payments using the most likely amount method. We will re-assess the development and sales-based milestones each reporting period to determine the probability of achievement.
We recognize revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. We record these reimbursements as revenue and not as a reduction of research and development expenses as we have the risks and rewards as the principal in the research and development activities.
Leases
In February 2016, the FASB issued ASU No. 2016-2, “Leases (Topic 842)” along with other amendments issued in 2017 and 2018. Topic 842 supersedes the lease accounting requirements in Accounting Standards Codification Topic 840, Leases (Topic 840). Topic 842 requires organizations to recognize leased assets and liabilities on the balance sheet. The standard also requires disclosures to help investors and other financial statement users better understand the amount, timing and uncertainty of cash flows arising from leases.
We determine if an arrangement is a lease at inception. This determination generally depends on whether the arrangement conveys to us the right to control the use of an explicitly or implicitly identified fixed asset for a period of time in exchange for consideration. Control of an underlying asset is conveyed to us if we obtain the rights to direct the use of and to obtain substantially all of the economic benefits from using the underlying asset. We have lease agreements which include lease and non-lease components, which we account for as a single lease component for all leases.
Under the standard, operating leases are classified as right of use ("ROU") assets, short term lease liabilities, and long term lease liabilities. Operating lease ROU assets and lease liabilities are recognized at the commencement date based on the present value of lease payments over the lease term. ROU assets are amortized and lease liabilities accrete to yield straight-line expense over the term of the lease. Lease payments included in the measurement of the lease liability are comprised of fixed payments.
Variable lease payments associated with our leases are recognized when the event, activity, or circumstance in the lease agreement on which those payments are assessed occurs. Variable lease payments are presented in our consolidated statements of operations in the same line item as expense arising from fixed lease payments for operating leases.
Leases with an initial term of 12 months or less are not recorded on the consolidated balance sheet and we recognize lease expense for these leases on a straight-line basis over the lease term. We apply this policy to all underlying asset categories.
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Topic 842 requires a lessee to discount its unpaid lease payments using the interest rate implicit in the lease or, if that rate cannot be readily determined, its incremental borrowing rate. As most of our leases do not provide an implicit rate, we use our incremental borrowing rate based on the information available at the commencement date in determining the present value of lease payments. We give consideration to our recent debt issuances as well as publicly available data for instruments with similar characteristics when calculating our incremental borrowing rates.
The lease term for all of our leases includes the non-cancellable period of the lease plus any additional periods covered by either our option to extend (or not to terminate) the lease that we are reasonably certain to exercise, or an option to extend (or not to terminate) the lease controlled by the lessor.
Results of operations
Three months ended September 30, 2019 compared to three months ended September 30, 2018
The following table summarizes revenues and selected expense and other income data for the three months ended September 30, 2019 and 2018.

|  | Three Months Ended September 30, |  | Change 2019 vs. 2018
(in thousands) |  | 2019 |  | 2018 |
Net product revenue |  | $ | 71,369 |  |  | $ | 53,021 |  |  | $ | 18,348 |
Collaboration and grant revenue |  | 47 |  |  | 570 |  |  | (523 | )
Cost of product sales, excluding amortization of acquired intangible asset |  | 3,006 |  |  | 3,292 |  |  | (286 | )
Amortization of acquired intangible asset |  | 7,025 |  |  | 5,793 |  |  | 1,232 |
Research and development expense |  | 63,076 |  |  | 54,368 |  |  | 8,708 |
Selling, general and administrative expense |  | 49,284 |  |  | 38,368 |  |  | 10,916 |
Change in the fair value of deferred and contingent consideration |  | 9,500 |  |  | — |  |  | 9,500 |
Interest expense, net |  | (2,666 | ) |  | (3,118 | ) |  | 452 |
Other income, net |  | 2,800 |  |  | 734 |  |  | 2,066 |
Income tax benefit (expense) |  | 344 |  |  | (355 | ) |  | 699 |

Net product revenues. Net product revenues were $71.4 million for the three months ended September 30, 2019, an increase of $18.3 million, or 35%, from $53.0 million for the three months ended September 30, 2018. The increase in net product revenue was primarily due to the increase in net product sales in existing markets where Translarna is available as well as continued geographic expansion into new territories.
Collaboration and grant revenues. Collaboration and grant revenues were $0.1 million for the three months ended September 30, 2019, a decrease of $0.5 million, or 92%, from $0.6 million for the three months ended September 30, 2018. The decrease in collaboration and grant revenues is related to our ongoing collaboration arrangements.
Cost of product sales, excluding amortization of acquired intangible asset. Cost of product sales, excluding amortization of acquired intangible asset, were $3.0 million for the three months ended September 30, 2019, a decrease of $0.3 million, or 9%, from $3.3 million for the three months ended September 30, 2018. Cost of product sales consist primarily of royalty payments associated with Emflaza and Translarna net product sales, excluding contingent payments to Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC) or Marathon, and costs associated with Emflaza and Translarna product sold during the period.
Amortization of acquired intangible asset. Amortization of our intangible assets was $7.0 million for the three months ended September 30, 2019, an increase of $1.2 million, or 21%, from $5.8 million for the three months ended September 30, 2018. These amounts are related to the acquisition of all rights to Emflaza acquired in May 2017, Marathon contingent payments, and the Waylivra intangible asset. The increase is primarily related to additional Marathon contingent payments. The amount allocated to the Emflaza intangible asset is amortized on a straight-line basis over its estimated useful life of approximately seven years from the date of the completion of the acquisition of all rights to Emflaza, the period of estimated future cash flows. The Marathon contingent payments are amortized prospectively as incurred, straight-line, over the remaining useful life of the Emflaza intangible asset. The Waylivra asset is amortized on a straight-line basis over its estimated useful life of approximately ten years.
Research and development expense. Research and development expense was $63.1 million for the three months ended September 30, 2019, an increase of $8.7 million, or 16%, from $54.4 million for the three months ended September 30, 2018. The increase
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reflects costs associated with advancing the gene therapy platform and increased investment in research programs as well as advancement of the clinical pipeline.
Selling, general and administrative expense. Selling, general and administrative expense was $49.3 million for the three months ended September 30, 2019, an increase of $10.9 million, or 28%, from $38.4 million for the three months ended September 30, 2018. The increase was primarily due to continued investment to support our commercial activities including our expanding commercial portfolio.
Change in the fair value of deferred and contingent consideration. The change in the fair value of deferred and contingent consideration was $9.5 million for the three months ended September 30, 2019. The change is related to the fair valuation of the potential future consideration to be paid to former equity holders of Agilis Biotherapeutics, Inc., or Agilis, as a result of our merger with Agilis which closed in August 2018. Changes in the fair value were due to the re-calculation of discounted cash flows for the passage of time and changes to certain other estimated assumptions.
Interest expense, net. Interest expense, net was $2.7 million for the three months ended September 30, 2019, a decrease of $0.5 million, or 14%, from $3.1 million for the three months ended September 30, 2018. The decrease in interest expense, net was primarily due to increased interest income from investments, which partially offset current year interest expense recorded from the 2022 and 2026 Convertible Notes and the Credit Agreement.
Other income, net. Other income, net was $2.8 million for the three months ended September 30, 2019, an increase of $2.1 million, or 281%, from other income, net of $0.7 million for the three months ended September 30, 2018. The increase in other income, net resulted primarily from an unrealized gain on our equity investment in MRI Interventions, Inc. of $2.4 million, partially offset by exchange rate changes in the current period.
Income tax benefit (expense). Income tax benefit was $0.3 million for the three months ended September 30, 2019 compared to income tax expense of $0.4 million for the three months ended September 30, 2018. We incurred income tax expense in various foreign jurisdictions, and our foreign tax liabilities are largely dependent upon the distribution of pre-tax earnings among these different jurisdictions. We are paying minimum income taxes in the United States because of incurred losses in the various state jurisdictions.
Nine months ended September 30, 2019 compared to nine months ended September 30, 2018
The following table summarizes revenues and selected expense and other income data for the nine months ended September 30, 2019 and 2018.

|  | Nine Months Ended September 30, |  | Change 2019 vs. 2018
(in thousands) |  | 2019 |  | 2018 |
Net product revenue |  | $ | 209,899 |  |  | $ | 177,172 |  |  | $ | 32,727 |
Collaboration and grant revenue |  | 622 |  |  | 1,224 |  |  | (602 | )
Cost of product sales, excluding amortization of acquired intangible asset |  | 8,593 |  |  | 8,909 |  |  | (316 | )
Amortization of acquired intangible asset |  | 19,677 |  |  | 16,815 |  |  | 2,862 |
Research and development expense |  | 175,621 |  |  | 118,337 |  |  | 57,284 |
Selling, general and administrative expense |  | 139,044 |  |  | 104,882 |  |  | 34,162 |
Change in the fair value of deferred and contingent consideration |  | 35,960 |  |  | — |  |  | 35,960 |
Interest expense, net |  | (7,028 | ) |  | (9,306 | ) |  | 2,278 |
Other income, net |  | 2,509 |  |  | 1,066 |  |  | 1,443 |
Income tax expense |  | (1,006 | ) |  | (964 | ) |  | (42 | )

Net product revenues. Net product revenues were $209.9 million for the nine months ended September 30, 2019 an increase of $32.7 million, or 18%, from $177.2 million for the nine months ended September 30, 2018. The increase in net product revenue was primarily due to the increase in net product sales in existing markets where Translarna is available as well as continued geographic expansion into new territories, in addition to an increase in net product sales of Emflaza.
Collaboration and grant revenues. Collaboration and grant revenues were $0.6 million for the nine months ended September 30, 2019, a decrease of $0.6 million, or 49%, from $1.2 million for the nine months ended September 30, 2018. The decrease in collaboration and grant revenues is related to our ongoing collaboration arrangements.
Cost of product sales, excluding amortization of acquired intangible asset. Cost of product sales, excluding amortization of acquired intangible asset, were $8.6 million for the nine months ended September 30, 2019, a decrease of $0.3 million, or 4%, from $8.9 million for the nine months ended September 30, 2018. Cost of product sales consist primarily of royalty payments associated
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with Emflaza and Translarna net product sales, excluding contingent payments to Marathon, and costs associated with Emflaza and Translarna product sold during the period.
Amortization of acquired intangible asset. Amortization of our intangible assets were $19.7 million for the nine months ended September 30, 2019, an increase of $2.9 million, or 17%, from $16.8 million for the nine months ended September 30, 2018. These amounts are related to the acquisition of all rights to Emflaza acquired in May 2017, Marathon contingent payments, and our Waylivra intangible asset. The increase is primarily related to additional Marathon contingent payments. The amount allocated to the Emflaza intangible asset is amortized on a straight-line basis over its estimated useful life of approximately seven years from the date of the completion of the acquisition of all rights to Emflaza, the period of estimated future cash flows. The Marathon contingent payments are amortized prospectively as incurred, straight-line, over the remaining useful life of the Emflaza intangible asset. The Waylivra asset is amortized on a straight-line basis over its estimated useful life of approximately ten years.
Research and development expense. Research and development expense was $175.6 million for the nine months ended September 30, 2019, an increase of $57.3 million, or 48%, from $118.3 million for the nine months ended September 30, 2018. The increase reflects costs associated with advancing the gene therapy platform and increased investment in research programs as well as advancement of the clinical pipeline.
Selling, general and administrative expense. Selling, general and administrative expense was $139.0 million for the nine months ended September 30, 2019, an increase of $34.2 million, or 33%, from $104.9 million for the nine months ended September 30, 2018. The increase was primarily due to continued investment to support our commercial activities including our expanding commercial portfolio.
Change in the fair value of deferred and contingent consideration. The change in the fair value of deferred and contingent consideration was $36.0 million for the nine months ended September 30, 2019. The change is related to the fair valuation of the potential future consideration to be paid to former equity holders of Agilis, as a result of our merger with Agilis which closed in August 2018. Changes in the fair value were due to the re-calculation of discounted cash flows for the passage of time and changes to certain other estimated assumptions.
Interest expense, net. Interest expense, net was $7.0 million for the nine months ended September 30, 2019, a decrease of $2.3 million, or 24%, from $9.3 million for the nine months ended September 30, 2018. The decrease in interest expense, net was primarily due to increased interest income from investments, which partially offset current year interest expense recorded from the 2022 and 2026 Convertible Notes and the Credit Agreement.
Other income, net. Other income, net was $2.5 million for the nine months ended September 30, 2019, an increase of $1.4 million, or 135%, from other income, net of $1.1 million for the nine months ended September 30, 2018. The increase in other income, net resulted primarily from an unrealized gain on our equity investment in MRI Interventions, Inc. of $2.5 million, partially offset by exchange rate changes in the current period.
Income tax expense. Income tax expense was $1.0 million for the nine months ended September 30, 2019 and $1.0 million for the nine months ended September 30, 2018. We incurred income tax expense in various foreign jurisdictions, and our foreign tax liabilities are largely dependent upon the distribution of pre-tax earnings among these different jurisdictions. We are paying minimum income taxes in the United States because of incurred losses in the various state jurisdictions.
Liquidity and capital resources
Sources of liquidity
Since inception, we have incurred significant operating losses.
As a growing commercial-stage biopharmaceutical company, we are engaging in significant commercialization efforts for Translarna for nmDMD and Emflaza for the treatment of DMD while also devoting a substantial portion of our efforts on research and development related to our products, product candidates and other programs. To date, almost all of our product revenue has been attributable to sales of Translarna for the treatment of nmDMD in territories outside of the United States and from Emflaza for the treatment of DMD in the United States. Our ongoing ability to generate revenue from sales of Translarna for the treatment of nmDMD is dependent upon our ability to maintain our marketing authorization in the EEA and secure market access through commercial programs following the conclusion of pricing and reimbursement terms at sustainable levels in the member states of the EEA or through EAP programs in the EEA and other territories. The marketing authorization requires annual review and renewal by the European Commission following reassessment by the EMA of the benefit-risk balance of the authorization and is subject to the specific obligation to conduct Study 041. Our ability to generate product revenue from Emflaza will largely depend on the coverage and reimbursement levels set by governmental authorities, private health insurers and other third-party payors.
We have historically financed our operations primarily through the issuance and sale of our common stock in public offerings and “at the market offerings” of our common stock, the private placements of our preferred stock, collaborations, bank debt, convertible
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debt financings, the Credit Agreement and grants and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease areas addressed by our product candidates. Since 2014, we have also relied on revenues generated from net sales of Translarna for the treatment of nmDMD in territories outside of the United States, and since May 2017, we have recognized revenue generated from net sales of Emflaza for the treatment of DMD in the United States. Based on our current commercial, research and development plans, we expect to continue to incur significant operating expenses for the foreseeable future, which we anticipate will be partially offset by revenues generated from the sale of both Translarna and Emflaza, as well as Waylivra and Tegsedi once our commercialization efforts for them commence. As a result, while we expect to continue to generate operating losses in 2019, we anticipate that operating losses generated in future periods should decline versus prior periods. The net losses we incur may fluctuate significantly from quarter to quarter.
In August 2015, we closed a private offering of $150 million in aggregate principal amount of 3.0% convertible senior notes due 2022 including the exercise by the initial purchasers of an option to purchase an additional $25 million in aggregate principal amount of the 2022 Convertible Notes. The 2022 Convertible Notes bear cash interest payable on February 15 and August 15 of each year, beginning on February 15, 2016. The 2022 Convertible Notes are senior unsecured obligations of ours and will mature on August 15, 2022, unless earlier converted, redeemed or repurchased in accordance with their terms prior to such date. We received net proceeds from the offering of approximately $145.4 million, after deducting the initial purchasers’ discounts and commissions and the estimated offering expenses payable by us.
On May 5, 2017, we entered into the Credit Agreement with MidCap Financial, which provides for a senior secured term loan facility of $60 million, of which $40 million was drawn by us on May 5, 2017. Our ability to draw on the remaining $20 million under the senior secured term loan facility expired on December 31, 2018. The maturity date of the Credit Agreement is May 1, 2021, unless terminated earlier. The facility is structured to require only monthly interest payments for the initial two years with principal amortization beginning in years three and four. The facility bears interest at a rate per annum equal to the London Interbank Offered Rate, or LIBOR (with a LIBOR floor rate of 1.00%) plus 6.15%, as well as additional upfront and administrative fees and expenses.
In January 2019, we closed an underwritten public offering of our common stock pursuant to a registration statement on Form S-3. We issued and sold an aggregate of 7,563,725 shares of common stock under the registration statement at a public offering price of $30.20 per share, including 843,725 shares issued upon exercise by the underwriter of its option to purchase additional shares in February 2019. We received net proceeds of approximately $224.2 million after deducting underwriting discounts and commissions and other offering expenses payable by us.
In August 2019, we entered into the Sales Agreement, pursuant to which, we may offer and sell shares of our common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act. During the three month period ending September 30, 2019, we issued and sold an aggregate of 63,926 shares of common stock pursuant to the Sales Agreement at a weighted average public offering price of $46.60 per share. We received net proceeds of $2.6 million after deducting underwriting discounts and commissions and other offering expenses payable by us.
In September 2019, we closed a private offering of $287.5 million aggregate principal amount of 1.5% convertible senior notes due 2026 including the exercise by the initial purchasers of an option to purchase an additional $37.5 million in aggregate principal amount of the 2026 Convertible Notes. The 2026 Convertible Notes bear cash interest at a rate of 1.5% per year, payable semi-annually on March 15 and September 15 of each year, beginning on March 15, 2020. The 2026 Convertible Notes will mature on September 15, 2026, unless earlier repurchased or converted. We received net proceeds of $279.3 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by us.
In September 2019, we closed an underwritten public offering of our common stock pursuant to a registration statement on Form S-3. We issued and sold an aggregate of 2,475,248 shares of common stock under the registration statement at a public offering price of $40.40 per share. The offering included an option to purchase up to an additional 371,287 shares for a period of 30 days following the offering. This option was not exercised by the underwriter. We received net proceeds of $97.0 million after deducting underwriting discounts and commissions and other offering expenses payable by us.
Cash flows
As of September 30, 2019, we had cash, cash equivalents and marketable securities of $708.6 million.
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The following table provides information regarding our cash flows and our capital expenditures for the periods indicated.

|  | Nine Months Ended September 30,
(in thousands) |  | 2019 |  | 2018
Cash (used in) provided by: |  |  |  |  |  |
Operating activities |  | (88,433 | ) |  | (12,498 | )
Investing activities |  | (158,240 | ) |  | (18,017 | )
Financing activities |  | 610,925 |  |  | 127,845 |

Net cash used in operating activities was $88.4 million for the nine months ended September 30, 2019 and $12.5 million for the nine months ended September 30, 2018. The net cash used in operating activities primarily relates to supporting clinical development and commercial activities.
Net cash used in investing activities was $158.2 million for the nine months ended September 30, 2019. Cash used in investing activities for the nine months ended September 30, 2019 was primarily related to net purchases of marketable securities. Cash used in investing activities for the nine months ended September 30, 2018 was $18.0 million and was primarily related to our acquisition of Agilis, partially offset by net sales of marketable securities.
Net cash provided by financing activities was $610.9 million for the nine months ended September 30, 2019 and $127.8 million for the nine months ended September 30, 2018. Cash provided by financing activities for the nine months ended September 30, 2019 was primarily attributable to our equity offerings in January 2019 and September 2019, our at the market equity offering in August 2019, our convertible debt offering in September 2019, and the exercise of options. Cash provided by financing activities for the nine months ended September 30, 2018 was primarily attributable to our equity offering in April 2018 and the exercise of options.
Funding requirements
We anticipate that our expenses will continue to increase in connection with our commercialization efforts in the United States, the EEA, Latin America and other territories, including the expansion of our infrastructure and corresponding sales and marketing, legal and regulatory, distribution and manufacturing and administrative and employee-based expenses. In addition to the foregoing, we expect to continue to incur significant costs in connection with Study 041 and Study 045 and our open label extension trials of Translarna for the treatment of nmDMD as well as our studies for nonsense mutation aniridia and nonsense mutation Dravet syndrome/CDKL5 and our FDA post-marketing requirements with respect to Emflaza in the United States and our studies for limb-girdle 2I. We also expect to incur ongoing research and development expenses for our other product candidates, including our gene therapy, splicing and oncology programs. In addition, we may incur substantial costs in connection with our efforts to advance our regulatory submissions. We have begun seeking and intend to continue to seek marketing authorization for Translarna for the treatment of nmDMD in territories outside of the EEA and we may also seek marketing authorization for Translarna for other indications. In late 2019, we plan to submit a request for marketing authorization for PTC-AADC with the FDA, followed by a request for marketing authorization for PTC-AADC with the EMA. These efforts may significantly impact the timing and extent of our commercialization expenses.
In addition, our expenses will increase if and as we:

• | seek to satisfy contractual and regulatory obligations we assumed in connection with the Agilis acquisition;

• | seek to satisfy contractual and regulatory obligations in conjunction with the Akcea Agreement, including the potential commercialization of Tegsedi and Waylivra in the PTC Territory;

• | execute our strategy for Emflaza in the United States, including commercialization and integration efforts;

• | satisfy contractual and regulatory obligations that we assumed through the Emflaza acquisition;

• | are required to complete any additional clinical trials, non-clinical studies or CMC assessments or analyses in order to advance Translarna for the treatment of nmDMD in the United States or elsewhere;

• | are required to take other steps, in addition to Study 041, to maintain our current marketing authorization in the EEA for Translarna for the treatment of nmDMD or to obtain further marketing authorizations for Translarna for the treatment of nmDMD or other indications;

• | initiate or continue the research and development of Translarna and Emflaza for additional indications and of our other product candidates;

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• | seek to discover and develop additional product candidates;

• | seek to expand and diversify our product pipeline through strategic transactions;

• | maintain, expand and protect our intellectual property portfolio; and

• | add operational, financial and management information systems and personnel, including personnel to support our product development and commercialization efforts.

We believe that our cash flows from the sales of our products, together with existing cash, cash equivalents and marketable securities, will be sufficient to fund our operating expenses and capital expenditure requirements for at least the next twelve months. We have based this estimate on assumptions that may prove to be wrong, and we could use our capital resources sooner than we currently expect.
Our future capital requirements will depend on many factors, including:

• | our ability to commercialize and market Emflaza for the treatment of DMD in the United States;

• | our ability to negotiate, secure and maintain adequate pricing, coverage and reimbursement terms, on a timely basis, with third-party payors for Emflaza for the treatment of DMD in the United States and for Translarna for the treatment of nmDMD in the EEA and other territories outside of the United States;

• | our ability to maintain orphan exclusivity for, and successfully complete all FDA post-marketing requirements with respect to, Emflaza;

• | our ability to maintain the marketing authorization in the EEA for Translarna for the treatment of nmDMD, including whether the EMA determines on an annual basis that the benefit-risk balance of Translarna supports renewal of our marketing authorization in the EEA, on the current approved label;

• | the costs, timing and outcome of Study 041;

• | the costs, timing and outcome of our efforts to advance Translarna for the treatment of nmDMD in the United States, including, whether we will be required to perform additional clinical trials, non-clinical studies or CMC assessments or analyses at significant cost which, if successful, may enable FDA review of an NDA submission by us and, ultimately, may support approval of Translarna for nmDMD in the United States;

• | our ability to commercialize and market Tegsedi and Waylivra in the PTC Territory;

• | the progress and results of our open label extension clinical trials of Translarna for the treatment of nmDMD as well as our studies for nonsense mutation aniridia, nonsense mutation Dravet syndrome/CDKL5 and limb-girdle 2I and activities under our gene therapy, splicing and oncology programs;

• | the scope, costs and timing of our commercialization activities, including product sales, marketing, legal, regulatory, distribution and manufacturing, for both Emflaza for the treatment of DMD and Translarna for the treatment of nmDMD, for Tegsedi, for Waylivra and for any of our other product candidates that may receive marketing authorization or any additional indications or territories in which we receive authorization to market Translarna;

• | the costs, timing and outcome of regulatory review of our other product candidates, including those in our gene therapy and oncology programs, and Translarna in other territories or for indications other than nmDMD;

• | our ability to satisfy our obligations under the terms of the lease agreement for our leased biologics facility;

• | our ability to satisfy our obligations under the terms of the Credit Agreement with MidCap Financial;

• | the timing and scope of growth in our employee base;

• | the scope, progress, results and costs of preclinical development, laboratory testing and clinical trials for Translarna and Emflaza for additional indications and for our other product candidates, including those in our gene therapy and oncology programs;

• | revenue received from commercial sales of Translarna, Emflaza, Tegsedi, Waylivra, or any of our other product candidates;

• | our ability to obtain additional and maintain existing reimbursed named patient and cohort EAP programs for Translarna for the treatment of nmDMD on adequate terms, or at all;

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• | the ability and willingness of patients and healthcare professionals to access Translarna through alternative means if pricing and reimbursement negotiations in the applicable territory do not have a positive outcome;

• | the costs of preparing, filing and prosecuting patent applications, maintaining, and protecting our intellectual property rights and defending against intellectual property-related claims;

• | the extent to which we acquire or invest in other businesses, products, product candidates, and technologies, including the success of any acquisition, in-licensing or other strategic transaction we may pursue, and the costs of subsequent development requirements and commercialization efforts, including with respect to our acquisition of Emflaza, our acquisition of Agilis, and our licensing of Tegsedi and Waylivra; and

• | our ability to establish and maintain collaborations, including our collaborations with Roche and the SMA Foundation, and our ability to obtain research funding and achieve milestones under these agreements.

With respect to our outstanding Convertible Notes, cash interest payments are payable on a semi-annual basis in arrears, which require total funding of $8.8 million annually. Additionally, under the terms of our Credit Agreement cash interest and principal payments are payable monthly in arrears. Furthermore, as a result of our initial public offering in June 2013, we have incurred and expect to continue to incur additional costs associated with operating as a public company. These costs include significant legal, accounting, investor relations and other expenses that we did not incur as a private company.
We have never been profitable and we will need to generate significant revenues to achieve and sustain profitability, and we may never do so. We may need to obtain substantial additional funding in connection with our continuing operations. Until such time, if ever, as we can generate substantial product revenues, we expect to finance our cash needs primarily through a combination of equity offerings, debt financings, collaborations, strategic alliances, grants and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease areas addressed by our product and product candidates and marketing, distribution or licensing arrangements. Adequate additional financing may not be available to us on acceptable terms, or at all. To the extent that we raise additional capital through the sale of equity or convertible debt securities, our shareholders ownership interest will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of our common stockholders. Debt financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends. If we raise additional funds through collaborations, strategic alliances or marketing, distribution or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs or product candidates or to grant licenses on terms that may not be favorable to us.
If we are unable to raise additional funds through equity or debt financings when needed or on attractive terms, we may be required to delay, limit, reduce or terminate our product development or commercialization efforts or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves.
Off-Balance Sheet Arrangements
We did not have during the periods presented, and we do not currently have, any off-balance sheet arrangements, as defined under Securities and Exchange Commission rules.
Contractual obligations
During the period ended September 30, 2019, there were no material changes to our contractual obligations and commitments outside the ordinary course of business from those disclosed under the heading “Management’s Discussion and Analysis of Financial Condition and Results of Operations-Contractual Obligations” in our 2018 Annual Report, other than as disclosed below.

(in thousands) | Total |  | Less than 1 year |  | 1 - 3 years |  | 3 - 5 years |  | More than 5 years
Operating lease obligations (1) | $ | 88,121 |  |  | 1,065 |  |  | 9,451 |  |  | 10,913 |  |  | 66,692 |
Purchase commitments (2) | $ | 6,900 |  |  | 2,050 |  |  | 4,850 |  |  | — |  |  | — |
Total contractual obligations | $ | 95,021 |  |  | $ | 3,115 |  |  | $ | 14,301 |  |  | $ | 10,913 |  |  | $ | 66,692 |

(1) Obligations stem from lease agreement entered into with Bristol-Myers Squibb Company in August 2019 relating to the lease of approximately 185,000 square feet of office, production and laboratory space at a facility located in Hopewell Township, New Jersey.
(2) Purchase commitments related to a manufacturing arrangement entered into within the third quarter of 2019.
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Item 3. Quantitative and Qualitative Disclosures About Market Risk.
During the period ended September 30, 2019, there were no material changes in our market risk or how our market risk is managed, compared to those disclosed under the heading “Quantitative and Qualitative Disclosures about Market Risk” in our 2018 Annual Report.
Item 4. Controls and Procedures.
Evaluation of Disclosure Controls and Procedures
Our management, with the participation of our Chief Executive Officer and our Chief Financial Officer, evaluated the effectiveness of our disclosure controls and procedures as of September 30, 2019. The term “disclosure controls and procedures”, as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, or the Exchange Act, means controls and other procedures of a company that are designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported, within the time periods specified in the Securities and Exchange Commission’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is accumulated and communicated to the company’s management, including its principal executive and principal financial officers, as appropriate to allow timely decisions regarding required disclosure. Management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Based on the evaluation of our disclosure controls and procedures as of September 30, 2019, our Chief Executive Officer and Chief Financial Officer concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level.
Changes in Internal Control over Financial Reporting
In the first quarter of 2019, we implemented an enterprise resource planning (“ERP”) system, Oracle, on a worldwide basis, which is expected to improve the efficiency of certain financial and related transactional processes. We have completed the implementation of certain processes, including the financial consolidation and reporting, sales order to cash, fixed assets, supplier management and indirect procure-to-pay processes, and have revised and updated the related controls. These changes did not materially affect our internal control over financial reporting for the three and nine months ended September 30, 2019. As we implement the remaining functionality under this ERP system over the next several years, we will continue to assess the impact on our internal control over financial reporting. No other changes in our internal control over financial reporting occurred during the quarter ended September 30, 2019 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.
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PART II—OTHER INFORMATION
Item 1. Legal Proceedings.
From time to time in the ordinary course of our business, we are subject to claims, legal proceedings and disputes, including as a result of patients seeking to participate in our clinical trials or otherwise gain access to our product candidates. We are not currently aware of any material legal proceedings to which we are a party or of which any of our property is subject.
Item 1A. Risk Factors
We have set forth in Item 1A to our Annual Report on Form 10-K for the year ended December 31, 2018, risk factors relating to our business, our industry, our structure and our common stock. Readers of this Quarterly Report on Form 10-Q are referred to such Item 1A for a more complete understanding of risks concerning us. There have been no material changes in our risk factors since those published in such Form 10-K for the year ended December 31, 2018.
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds.
Recent Sales of Unregistered Securities
Inducement grant awards. Pursuant to the Nasdaq Listing Rule 5635(c)(4) inducement grant exception, during the quarter ended September 30, 2019, we issued options to purchase an aggregate of 419,600 shares of common stock to certain new hire employees at a weighted-average exercise price of $42.44 per share. The shares underlying these options will be registered on a Form S-8 registration statement prior to the first vesting event applicable to each such award.
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Item 6. Exhibits.

Exhibit Number |  | Description of Exhibit
4.1 |  | Indenture (including Form of Note), dated as of September 20, 2019, by and between PTC Therapeutics, Inc. and U.S. Bank National Association, a national banking association, as trustee (incorporated by reference to Exhibit 4.1 to the Current Report on Form 8-K filed by the Registrant on September 20, 2019)
10.1 |  | Amendment No. 2 to Credit and Security Agreement, dated as of August 7, 2019, by and among PTC Therapeutics, Inc., MidCap Financial Trust and the Lenders as defined therein
10.2 |  | Amendment No. 3 to Credit and Security Agreement, dated as of August 29, 2019, by and among PTC Therapeutics, Inc., MidCap Financial Trust and the Lenders as defined therein
10.3 |  | Amendment No. 4 to Credit and Security Agreement, dated as of September 17, 2019, by and among PTC Therapeutics, Inc., MidCap Financial Trust and the Lenders as defined therein
10.4 |  | Omnibus Amendment No. 5 and Joinder to Credit and Security Agreement and Amendment and Joinder to Pledge Agreement, dated as of October 1, 2019, by and among PTC Therapeutics, Inc., each of the subsidiaries listed therein as a New Borrower, MidCap Financial Trust and the Lenders as defined therein
10.5† |  | Lease Agreement dated as of August 3, 2019, by and between Bristol-Myers Squibb Company and PTC Therapeutics, Inc.
10.6 |  | Irrevocable Standby Letter of Credit, dated September 3, 2019, issued by HSBC Bank USA, N.A. in favor of Bristol-Myers Squibb Company for the Account of PTC Therapeutics, Inc., as amended
31.1 |  | Certification of Principal Executive Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
31.2 |  | Certification of Principal Financial Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002
32.1 |  | Certification of Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
32.2 |  | Certification of Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002
101.INS |  | Inline XBRL Instance Document*
101.SCH |  | Inline XBRL Taxonomy Extension Schema Document*
101.CAL |  | Inline XBRL Taxonomy Extension Calculation Linkbase Document*
101.LAB |  | Inline XBRL Taxonomy Extension Label Linkbase Database*
101.PRE |  | Inline XBRL Taxonomy Extension Presentation Linkbase Document*
101.DEF |  | Inline XBRL Taxonomy Extension Definition Linkbase Document*
104 |  | The cover page from this Quarterly Report on Form 10-Q, formatted in Inline XBRL

* Submitted electronically herewith.
† Portions of this exhibit have been omitted pursuant to Item 601(b)(10)(iv) of Regulation S-K.
In accordance with SEC Release 33-8238, Exhibits 32.1 and 32.2 are being furnished and not filed.
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SIGNATURES
Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

| PTC THERAPEUTICS, INC.
Date: October 29, 2019 | By: | /s/ Emily Hill
|  | Emily Hill
|  | Chief Financial Officer
|  | (Principal Financial Officer and Duly Authorized Signatory)

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