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Fair value of financial instruments and marketable securities | 3 Months Ended | 6 Months Ended
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Jun. 30, 2020 | Jun. 30, 2020
Fair Value Disclosures [Abstract] |  |
Fair value of financial instruments and marketable securities | 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 marketable securities 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 ClearPoint Neuro, Inc.'s ("ClearPoint"), formerly known as MRI Interventions, Inc., common stock, at a purchase price of $3.10 per share, in connection with a securities purchase agreement that the Company entered into with ClearPoint, 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 six month periods ended June 30, 2020, the Company recorded unrealized losses of $0.1 million and $1.6 million, respectively, which are components of other expense, net within the consolidated statement of operations. The fair value of the equity investment was $4.6 million as of June 30, 2020. The Company classifies its equity investment in ClearPoint 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. In January 2020, the Company purchased a $10.0 million convertible note from ClearPoint that the Company can convert into ClearPoint shares at a conversion rate of $6.00 per share at any point throughout the term of the loan, which matures five years from the purchase date. The Company determined that the convertible note represents an available for sale debt security and the Company has elected to record it at fair value under ASC 825. The Company classifies its ClearPoint convertible debt security as a Level 2 asset within the fair value hierarchy, as the value is based on inputs other than quoted prices that are observable. The fair value of the ClearPoint convertible debt security is determined at each reporting period by utilizing a Black-Scholes option pricing model, as well as a present value of expected cash flows from the debt security utilizing the risk free rate and the estimated credit spread as of the valuation date as the discount rate. During the three and six month periods ended June 30, 2020, the Company recorded an unrealized gain of $2.1 million and an unrealized loss of $0.7 million, respectively, which are components of other expense and other income, net within the consolidated statement of operations. The fair value of the convertible debt security was $9.3 million as of June 30, 2020. The convertible debt security is considered to be long term and is included as a component of deposits and other assets on the consolidated balance sheet. Other than the equity investment and the convertible debt security, no other items included in deposits and other assets on the consolidated balance sheets are fair valued. 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 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 June 30, 2020 and December 31, 2019:
|  | June 30, 2020 |  |  |  |  |  |
|  | Total |  | Quoted prices in active markets for identical assets (level 1) |  | Significant other observable inputs (level 2) |  | Significant unobservable inputs (level 3)
Marketable securities |  | $ | 340,430 |  |  | $ | — |  |  | $ | 340,430 |  |  | $ | — |
Equity investment in ClearPoint |  | $ | 4,594 |  |  | $ | 4,594 |  |  | $ | — |  |  | $ | — |
ClearPoint convertible debt security |  | $ | 9,251 |  |  | $ | — |  |  | $ | 9,251 |  |  | $ | — |
Deferred consideration payable |  | $ | 2,384 |  |  | $ | — |  |  | $ | 2,384 |  |  | $ | — |
Contingent consideration payable- development and regulatory milestones |  | $ | 136,100 |  |  | $ | — |  |  | $ | — |  |  | $ | 136,100 |
Contingent consideration payable- net sales milestones and royalties |  | $ | 89,600 |  |  | $ | — |  |  | $ | — |  |  | $ | 89,600 |
|  | December 31, 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 |  | $ | 398,535 |  |  | $ | — |  |  | $ | 398,535 |  |  | $ | — |
Equity investment in ClearPoint |  | $ | 6,194 |  |  | $ | 6,194 |  |  | $ | — |  |  | $ | — |
Stock appreciation rights liability |  | $ | 3,186 |  |  | $ | — |  |  | $ | — |  |  | $ | 3,186 |
Deferred consideration payable |  | $ | 40,000 |  |  | $ | — |  |  | $ | 40,000 |  |  | $ | — |
Contingent consideration payable- development and regulatory milestones |  | $ | 290,500 |  |  | $ | — |  |  | $ | — |  |  | $ | 290,500 |
Contingent consideration payable- net sales milestones and royalties |  | $ | 65,800 |  |  | $ | — |  |  | $ | — |  |  | $ | 65,800 |
No transfers of assets between Level 1, Level 2, or Level 3 of the fair value measurement hierarchy occurred during the periods ended June 30, 2020 and December 31, 2019. The following is a summary of marketable securities accounted for as available-for-sale securities at June 30, 2020 and December 31, 2019:
|  | June 30, 2020 |  |  |  |  |  |
|  | Amortized Cost |  | Gross Unrealized |  |  |  | Fair Value
|  |  |  | Gains |  | Losses |  |
Commercial paper |  | $ | 53,638 |  |  | $ | 178 |  |  | $ | — |  |  | $ | 53,816 |
Corporate debt securities |  | 221,068 |  |  | 2,882 |  |  | — |  |  | 223,950 |
Asset-backed securities |  | 44,492 |  |  | 332 |  |  | (1) |  |  | 44,823 |
Government obligations |  | 17,823 |  |  | 19 |  |  | (1) |  |  | 17,841 |
Total |  | $ | 337,021 |  |  | $ | 3,411 |  |  | $ | (2) |  |  | $ | 340,430 |
|  | December 31, 2019 |  |  |  |  |  |
|  | Amortized Cost |  | Gross Unrealized |  |  |  | Fair Value
|  |  |  | Gains |  | Losses |  |
Commercial paper |  | $ | 157,936 |  |  | $ | 162 |  |  | $ | — |  |  | $ | 158,098 |
Corporate debt securities |  | 188,778 |  |  | 576 |  |  | (20) |  |  | 189,334 |
Asset-backed securities |  | 51,062 |  |  | 49 |  |  | (8) |  |  | 51,103 |
Total |  | $ | 397,776 |  |  | $ | 787 |  |  | $ | (28) |  |  | $ | 398,535 |
For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security's amortized cost basis is written down to fair value. For the three month and six month periods ended June 30, 2020, no write downs occurred. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases, which may be maturity. The Company also reviews its available for sale debt securities in an unrealized loss position and evaluates whether the decline in fair value has resulted from credit losses or other factors. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may be related to credit issues. For the three month and six month periods ended June 30, 2020, no allowance was recorded for credit losses. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. For the three month and six month periods ended June 30, 2020, the Company had $0.2 million realized gains from the sale of marketable securities. Realized gains are reported as a component of interest expense, net in the consolidated statement of operations. 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 June 30, 2020 are as follows:
|  | June 30, 2020 |  |  |  |  |  |  |  |  |  |
|  | 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
Asset-backed securities |  | (1) |  |  | 594 |  |  | — |  |  | — |  |  | (1) |  |  | 594 |
Government obligations |  | (1) |  |  | 8,602 |  |  | — |  |  | — |  |  | (1) |  |  | 8,602 |
Total |  | $ | (2) |  |  | $ | 9,196 |  |  | $ | — |  |  | $ | — |  |  | $ | (2) |  |  | $ | 9,196 |
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, 2019 are as follows:
|  | December 31, 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 |  | $ | (20) |  |  | $ | 71,779 |  |  | $ | — |  |  | $ | — |  |  | $ | (20) |  |  | $ | 71,779 |
Asset-backed securities |  | (8) |  |  | 24,211 |  |  | — |  |  | — |  |  | (8) |  |  | 24,211 |
Total |  | $ | (28) |  |  | $ | 95,990 |  |  | $ | — |  |  | $ | — |  |  | $ | (28) |  |  | $ | 95,990 |
Marketable securities on the balance sheet at June 30, 2020 and December 31, 2019 mature as follows:
|  | June 30, 2020 |  |
|  | Less Than 12 Months |  | More Than 12 Months
Commercial paper |  | $ | 53,816 |  |  | $ | — |
Corporate debt securities |  | 168,250 |  |  | 55,700 |
Asset-backed securities |  | 26,320 |  |  | 18,503 |
Government obligations |  | 7,201 |  |  | 10,640 |
Total Marketable securities |  | $ | 255,587 |  |  | $ | 84,843 |
|  | December 31, 2019 |  |
|  | Less Than 12 Months |  | More Than 12 Months
Commercial paper |  | $ | 158,098 |  |  | $ | — |
Corporate debt securities |  | 139,596 |  |  | 49,738 |
Asset-backed securities |  | 44,724 |  |  | 6,379 |
Total Marketable securities |  | $ | 342,418 |  |  | $ | 56,117 |
The Company classifies all of its marketable 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 3.00% convertible senior notes due August 15, 2022 (the “2022 Convertible Notes”). In September 2019, the Company issued $287.5 million of 1.50% 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 June 30, 2020 and December 31, 2019 was $175.2 million and $171.2 million, respectively. The estimated fair value of the 2026 Convertible Notes at June 30, 2020 and December 31, 2019 was $343.8 million and $335.0 million, respectively. Deferred and contingent consideration payable Pursuant to the Merger Agreement, Agilis equityholders were previously 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 was required to pay $40.0 million of development milestone payments upon the passing of the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The $40.0 million of development milestones were classified as deferred consideration on the Company's consolidated balance sheets. Pursuant to the terms of the Rights Exchange Agreement, in the three month period ended June 30, 2020, the Company issued 2,821,176 shares of its common stock and paid $36.9 million in the aggregate, to Participating Rightholders, who in exchange have canceled and forfeited their rights under the Merger Agreement to receive (i) $174.0 million, in the aggregate, of potential milestone payments based on the achievement of certain regulatory milestones and (ii) $37.6 million, in the aggregate, of $40.0 million in development milestone payments, or the deferred consideration, that would have been due upon the passing of the second anniversary of the closing of the Merger. As a result of the Rights Exchange Agreement, the remaining deferred consideration payable at June 30, 2020 was $2.4 million, which was also determined to be the fair value. The Company did not apply a discount, as the milestones will be paid within one calendar year. Accordingly, as of June 30, 2020, the $2.4 million of the deferred consideration payable was classified as current on the balance sheet. As of result of the Rights Exchange Agreement, the Company recognized a gain of $0.7 million on the settlement of the development milestones and a loss of $11.3 million on the settlement of the regulatory milestones. The $0.7 million gain and $11.3 million loss are included in the settlement of deferred and contingent consideration in the Company’s statement of operations for the three and six month periods ended June 30, 2020. Additionally, as of the date of the Rights Exchange Agreement, the Company recognized a gain on the fair value of the contingent consideration of $1.0 million related to the portion of regulatory milestones that were forfeited, which is included in the change in fair value of the deferred and contingent liability within the Company’s statement of operations for the three and six month periods ended June 30, 2020. This non-recurring Level 3 fair value measurement was estimated using the same valuation methoolody and unobservable inputs for development and regulatory milestones in the Level 3 valuation section below. In conjunction with the Rights Exchange Agreement, the Company also incurred $2.0 million of transaction fees, which were included in other expense in the Company’s statement of operations for the three and six month periods ended June 30, 2020. 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 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 last payment of the SARs liability was made in the three month period ended March 31, 2020, and accordingly, the balance of the SARS liability as of June 30, 2020 was $0. The contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss within the change in the fair value of deferred and contingent consideration on 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. At June 30, 2020, the weighted average discount rate for the development and regulatory milestones was 5.4% and the weighted average probability of success was 43%. 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. At June 30, 2020, the weighted average discount rate for the net sales milestones and royalties was 12.0% and the weighted average probability of success for the net sales milestones was 50%. 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 periods ended June 30, 2020 and June 30, 2019.
|  | 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, 2019 |  | $ | 3,186 |  |  | $ | 290,500 |  |  | $ | 65,800 |
Additions |  | — |  |  | — |  |  | — |
Change in fair value |  | — |  |  | (15,220) |  |  | 23,800 |
Payments |  | (3,186) |  |  | — |  |  | — |
Rights Exchange settlement |  | — |  |  | (139,180) |  |  | — |
Ending balance as of June 30, 2020 |  | $ | — |  |  | $ | 136,100 |  |  | $ | 89,600 |
|  | 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 |  | 1,961 |  |  | 20,360 |  |  | 5,600 |
Payments |  | (3,815) |  |  | — |  |  | — |
Ending balance as of June 30, 2019 |  | $ | 1,960 |  |  | $ | 277,400 |  |  | $ | 58,800 |
The following significant unobservable inputs were used in the valuation of the contingent consideration payable for the periods ended June 30, 2020 and December 31, 2019 and of the SARs liability for the period ended December 31, 2019:
|  | June 30, 2020 |  |  |  |  |  |
|  | Fair Value |  | Valuation Technique |  | Unobservable Input |  | Range
Contingent consideration payable- development and regulatory milestones |  | $136,100 |  | Probability-adjusted discounted cash flow |  | Potential development and regulatory milestones |  | $0 - $381 million
|  |  |  |  |  | Probabilities of success |  | 25% - 94%
|  |  |  |  |  | Discount rates |  | 4.6% - 6.1%
|  |  |  |  |  | Projected years of payments |  | 2021 - 2027
Contingent considerable payable- net sales milestones and royalties |  | $89,600 |  | Option-pricing model with Monte Carlo simulation |  | Potential net sales milestones |  | $0 - $150 million
|  |  |  |  |  | Probabilities of success |  | 25% -94%
|  |  |  |  |  | Potential percentage of net sales for royalties |  | 2% - 6%
|  |  |  |  |  | Discount rate |  | 12.0%
|  |  |  |  |  | Projected years of payments |  | 2022 - 2039
|  | December 31, 2019 |  |  |  |  |  |
|  | Fair Value |  | Valuation Technique |  | Unobservable Input |  | Range
SARs |  | $3,186 |  | Option-pricing model |  | Volatility |  | 28.93%
|  |  |  |  |  | Risk free interest rate |  | 0.19%
|  |  |  |  |  | Strike price |  | $6.76 - $30.86
|  |  |  |  |  | Fair value of common stock |  | $48.03
|  |  |  |  |  | Expected life |  | 0.01 years
Contingent consideration payable- development and regulatory milestones |  | $290,500 |  | Probability-adjusted discounted cash flow |  | Potential development and regulatory milestones |  | $0- $555 million
|  |  |  |  |  | Probabilities of success |  | 25% - 94%
|  |  |  |  |  | Discount rates |  | 2.2% - 4.7%
|  |  |  |  |  | Projected years of payments |  | 2020 - 2026
Contingent considerable payable- net sales milestones and royalties |  | $65,800 |  | 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 |  | 14.5%
|  |  |  |  |  | Projected years of payments |  | 2021 - 2038
The contingent consideration payables are classified Level 3 liabilities as their 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 approaches, including but not limited to, assumptions involving probability adjusted sales estimates for the gene therapy platform and estimated discount rates, the estimated fair value could be significantly higher or lower than the fair value determined. | 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 marketable securities 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 ClearPoint Neuro, Inc.'s ("ClearPoint"), formerly known as MRI Interventions, Inc., common stock, at a purchase price of $3.10 per share, in connection with a securities purchase agreement that the Company entered into with ClearPoint, 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 six month periods ended June 30, 2020, the Company recorded unrealized losses of $0.1 million and $1.6 million, respectively, which are components of other expense, net within the consolidated statement of operations. The fair value of the equity investment was $4.6 million as of June 30, 2020. The Company classifies its equity investment in ClearPoint 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. In January 2020, the Company purchased a $10.0 million convertible note from ClearPoint that the Company can convert into ClearPoint shares at a conversion rate of $6.00 per share at any point throughout the term of the loan, which matures five years from the purchase date. The Company determined that the convertible note represents an available for sale debt security and the Company has elected to record it at fair value under ASC 825. The Company classifies its ClearPoint convertible debt security as a Level 2 asset within the fair value hierarchy, as the value is based on inputs other than quoted prices that are observable. The fair value of the ClearPoint convertible debt security is determined at each reporting period by utilizing a Black-Scholes option pricing model, as well as a present value of expected cash flows from the debt security utilizing the risk free rate and the estimated credit spread as of the valuation date as the discount rate. During the three and six month periods ended June 30, 2020, the Company recorded an unrealized gain of $2.1 million and an unrealized loss of $0.7 million, respectively, which are components of other expense and other income, net within the consolidated statement of operations. The fair value of the convertible debt security was $9.3 million as of June 30, 2020. The convertible debt security is considered to be long term and is included as a component of deposits and other assets on the consolidated balance sheet. Other than the equity investment and the convertible debt security, no other items included in deposits and other assets on the consolidated balance sheets are fair valued. 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 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 June 30, 2020 and December 31, 2019:
|  | June 30, 2020 |  |  |  |  |  |
|  | Total |  | Quoted prices in active markets for identical assets (level 1) |  | Significant other observable inputs (level 2) |  | Significant unobservable inputs (level 3)
Marketable securities |  | $ | 340,430 |  |  | $ | — |  |  | $ | 340,430 |  |  | $ | — |
Equity investment in ClearPoint |  | $ | 4,594 |  |  | $ | 4,594 |  |  | $ | — |  |  | $ | — |
ClearPoint convertible debt security |  | $ | 9,251 |  |  | $ | — |  |  | $ | 9,251 |  |  | $ | — |
Deferred consideration payable |  | $ | 2,384 |  |  | $ | — |  |  | $ | 2,384 |  |  | $ | — |
Contingent consideration payable- development and regulatory milestones |  | $ | 136,100 |  |  | $ | — |  |  | $ | — |  |  | $ | 136,100 |
Contingent consideration payable- net sales milestones and royalties |  | $ | 89,600 |  |  | $ | — |  |  | $ | — |  |  | $ | 89,600 |
|  | December 31, 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 |  | $ | 398,535 |  |  | $ | — |  |  | $ | 398,535 |  |  | $ | — |
Equity investment in ClearPoint |  | $ | 6,194 |  |  | $ | 6,194 |  |  | $ | — |  |  | $ | — |
Stock appreciation rights liability |  | $ | 3,186 |  |  | $ | — |  |  | $ | — |  |  | $ | 3,186 |
Deferred consideration payable |  | $ | 40,000 |  |  | $ | — |  |  | $ | 40,000 |  |  | $ | — |
Contingent consideration payable- development and regulatory milestones |  | $ | 290,500 |  |  | $ | — |  |  | $ | — |  |  | $ | 290,500 |
Contingent consideration payable- net sales milestones and royalties |  | $ | 65,800 |  |  | $ | — |  |  | $ | — |  |  | $ | 65,800 |
No transfers of assets between Level 1, Level 2, or Level 3 of the fair value measurement hierarchy occurred during the periods ended June 30, 2020 and December 31, 2019. The following is a summary of marketable securities accounted for as available-for-sale securities at June 30, 2020 and December 31, 2019:
|  | June 30, 2020 |  |  |  |  |  |
|  | Amortized Cost |  | Gross Unrealized |  |  |  | Fair Value
|  |  |  | Gains |  | Losses |  |
Commercial paper |  | $ | 53,638 |  |  | $ | 178 |  |  | $ | — |  |  | $ | 53,816 |
Corporate debt securities |  | 221,068 |  |  | 2,882 |  |  | — |  |  | 223,950 |
Asset-backed securities |  | 44,492 |  |  | 332 |  |  | (1) |  |  | 44,823 |
Government obligations |  | 17,823 |  |  | 19 |  |  | (1) |  |  | 17,841 |
Total |  | $ | 337,021 |  |  | $ | 3,411 |  |  | $ | (2) |  |  | $ | 340,430 |
|  | December 31, 2019 |  |  |  |  |  |
|  | Amortized Cost |  | Gross Unrealized |  |  |  | Fair Value
|  |  |  | Gains |  | Losses |  |
Commercial paper |  | $ | 157,936 |  |  | $ | 162 |  |  | $ | — |  |  | $ | 158,098 |
Corporate debt securities |  | 188,778 |  |  | 576 |  |  | (20) |  |  | 189,334 |
Asset-backed securities |  | 51,062 |  |  | 49 |  |  | (8) |  |  | 51,103 |
Total |  | $ | 397,776 |  |  | $ | 787 |  |  | $ | (28) |  |  | $ | 398,535 |
For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security's amortized cost basis is written down to fair value. For the three month and six month periods ended June 30, 2020, no write downs occurred. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases, which may be maturity. The Company also reviews its available for sale debt securities in an unrealized loss position and evaluates whether the decline in fair value has resulted from credit losses or other factors. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may be related to credit issues. For the three month and six month periods ended June 30, 2020, no allowance was recorded for credit losses. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity. For the three month and six month periods ended June 30, 2020, the Company had $0.2 million realized gains from the sale of marketable securities. Realized gains are reported as a component of interest expense, net in the consolidated statement of operations. 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 June 30, 2020 are as follows:
|  | June 30, 2020 |  |  |  |  |  |  |  |  |  |
|  | 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
Asset-backed securities |  | (1) |  |  | 594 |  |  | — |  |  | — |  |  | (1) |  |  | 594 |
Government obligations |  | (1) |  |  | 8,602 |  |  | — |  |  | — |  |  | (1) |  |  | 8,602 |
Total |  | $ | (2) |  |  | $ | 9,196 |  |  | $ | — |  |  | $ | — |  |  | $ | (2) |  |  | $ | 9,196 |
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, 2019 are as follows:
|  | December 31, 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 |  | $ | (20) |  |  | $ | 71,779 |  |  | $ | — |  |  | $ | — |  |  | $ | (20) |  |  | $ | 71,779 |
Asset-backed securities |  | (8) |  |  | 24,211 |  |  | — |  |  | — |  |  | (8) |  |  | 24,211 |
Total |  | $ | (28) |  |  | $ | 95,990 |  |  | $ | — |  |  | $ | — |  |  | $ | (28) |  |  | $ | 95,990 |
Marketable securities on the balance sheet at June 30, 2020 and December 31, 2019 mature as follows:
|  | June 30, 2020 |  |
|  | Less Than 12 Months |  | More Than 12 Months
Commercial paper |  | $ | 53,816 |  |  | $ | — |
Corporate debt securities |  | 168,250 |  |  | 55,700 |
Asset-backed securities |  | 26,320 |  |  | 18,503 |
Government obligations |  | 7,201 |  |  | 10,640 |
Total Marketable securities |  | $ | 255,587 |  |  | $ | 84,843 |
|  | December 31, 2019 |  |
|  | Less Than 12 Months |  | More Than 12 Months
Commercial paper |  | $ | 158,098 |  |  | $ | — |
Corporate debt securities |  | 139,596 |  |  | 49,738 |
Asset-backed securities |  | 44,724 |  |  | 6,379 |
Total Marketable securities |  | $ | 342,418 |  |  | $ | 56,117 |
The Company classifies all of its marketable 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 3.00% convertible senior notes due August 15, 2022 (the “2022 Convertible Notes”). In September 2019, the Company issued $287.5 million of 1.50% 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 June 30, 2020 and December 31, 2019 was $175.2 million and $171.2 million, respectively. The estimated fair value of the 2026 Convertible Notes at June 30, 2020 and December 31, 2019 was $343.8 million and $335.0 million, respectively. Deferred and contingent consideration payable Pursuant to the Merger Agreement, Agilis equityholders were previously 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 was required to pay $40.0 million of development milestone payments upon the passing of the second anniversary of the closing of the Merger, regardless of whether the applicable milestones have been achieved. The $40.0 million of development milestones were classified as deferred consideration on the Company's consolidated balance sheets. Pursuant to the terms of the Rights Exchange Agreement, in the three month period ended June 30, 2020, the Company issued 2,821,176 shares of its common stock and paid $36.9 million in the aggregate, to Participating Rightholders, who in exchange have canceled and forfeited their rights under the Merger Agreement to receive (i) $174.0 million, in the aggregate, of potential milestone payments based on the achievement of certain regulatory milestones and (ii) $37.6 million, in the aggregate, of $40.0 million in development milestone payments, or the deferred consideration, that would have been due upon the passing of the second anniversary of the closing of the Merger. As a result of the Rights Exchange Agreement, the remaining deferred consideration payable at June 30, 2020 was $2.4 million, which was also determined to be the fair value. The Company did not apply a discount, as the milestones will be paid within one calendar year. Accordingly, as of June 30, 2020, the $2.4 million of the deferred consideration payable was classified as current on the balance sheet. As of result of the Rights Exchange Agreement, the Company recognized a gain of $0.7 million on the settlement of the development milestones and a loss of $11.3 million on the settlement of the regulatory milestones. The $0.7 million gain and $11.3 million loss are included in the settlement of deferred and contingent consideration in the Company’s statement of operations for the three and six month periods ended June 30, 2020. Additionally, as of the date of the Rights Exchange Agreement, the Company recognized a gain on the fair value of the contingent consideration of $1.0 million related to the portion of regulatory milestones that were forfeited, which is included in the change in fair value of the deferred and contingent liability within the Company’s statement of operations for the three and six month periods ended June 30, 2020. This non-recurring Level 3 fair value measurement was estimated using the same valuation methoolody and unobservable inputs for development and regulatory milestones in the Level 3 valuation section below. In conjunction with the Rights Exchange Agreement, the Company also incurred $2.0 million of transaction fees, which were included in other expense in the Company’s statement of operations for the three and six month periods ended June 30, 2020. 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 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 last payment of the SARs liability was made in the three month period ended March 31, 2020, and accordingly, the balance of the SARS liability as of June 30, 2020 was $0. The contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss within the change in the fair value of deferred and contingent consideration on 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. At June 30, 2020, the weighted average discount rate for the development and regulatory milestones was 5.4% and the weighted average probability of success was 43%. 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. At June 30, 2020, the weighted average discount rate for the net sales milestones and royalties was 12.0% and the weighted average probability of success for the net sales milestones was 50%. 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 periods ended June 30, 2020 and June 30, 2019.
|  | 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, 2019 |  | $ | 3,186 |  |  | $ | 290,500 |  |  | $ | 65,800 |
Additions |  | — |  |  | — |  |  | — |
Change in fair value |  | — |  |  | (15,220) |  |  | 23,800 |
Payments |  | (3,186) |  |  | — |  |  | — |
Rights Exchange settlement |  | — |  |  | (139,180) |  |  | — |
Ending balance as of June 30, 2020 |  | $ | — |  |  | $ | 136,100 |  |  | $ | 89,600 |
|  | 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 |  | 1,961 |  |  | 20,360 |  |  | 5,600 |
Payments |  | (3,815) |  |  | — |  |  | — |
Ending balance as of June 30, 2019 |  | $ | 1,960 |  |  | $ | 277,400 |  |  | $ | 58,800 |
The following significant unobservable inputs were used in the valuation of the contingent consideration payable for the periods ended June 30, 2020 and December 31, 2019 and of the SARs liability for the period ended December 31, 2019:
|  | June 30, 2020 |  |  |  |  |  |
|  | Fair Value |  | Valuation Technique |  | Unobservable Input |  | Range
Contingent consideration payable- development and regulatory milestones |  | $136,100 |  | Probability-adjusted discounted cash flow |  | Potential development and regulatory milestones |  | $0 - $381 million
|  |  |  |  |  | Probabilities of success |  | 25% - 94%
|  |  |  |  |  | Discount rates |  | 4.6% - 6.1%
|  |  |  |  |  | Projected years of payments |  | 2021 - 2027
Contingent considerable payable- net sales milestones and royalties |  | $89,600 |  | Option-pricing model with Monte Carlo simulation |  | Potential net sales milestones |  | $0 - $150 million
|  |  |  |  |  | Probabilities of success |  | 25% -94%
|  |  |  |  |  | Potential percentage of net sales for royalties |  | 2% - 6%
|  |  |  |  |  | Discount rate |  | 12.0%
|  |  |  |  |  | Projected years of payments |  | 2022 - 2039
|  | December 31, 2019 |  |  |  |  |  |
|  | Fair Value |  | Valuation Technique |  | Unobservable Input |  | Range
SARs |  | $3,186 |  | Option-pricing model |  | Volatility |  | 28.93%
|  |  |  |  |  | Risk free interest rate |  | 0.19%
|  |  |  |  |  | Strike price |  | $6.76 - $30.86
|  |  |  |  |  | Fair value of common stock |  | $48.03
|  |  |  |  |  | Expected life |  | 0.01 years
Contingent consideration payable- development and regulatory milestones |  | $290,500 |  | Probability-adjusted discounted cash flow |  | Potential development and regulatory milestones |  | $0- $555 million
|  |  |  |  |  | Probabilities of success |  | 25% - 94%
|  |  |  |  |  | Discount rates |  | 2.2% - 4.7%
|  |  |  |  |  | Projected years of payments |  | 2020 - 2026
Contingent considerable payable- net sales milestones and royalties |  | $65,800 |  | 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 |  | 14.5%
|  |  |  |  |  | Projected years of payments |  | 2021 - 2038
The contingent consideration payables are classified Level 3 liabilities as their 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 approaches, including but not limited to, assumptions involving probability adjusted sales estimates for the gene therapy platform and estimated discount rates, the estimated fair value could be significantly higher or lower than the fair value determined.

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- Definition The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information. + References Reference 1: http://www.xbrl.org/2003/role/disclosureRef -Publisher FASB -Name Accounting Standards Codification -Topic 820 -SubTopic 10 -Section 50 -Paragraph 2 -URI http://asc.fasb.org/extlink&oid=117815213&loc=d3e19207-110258 + Details
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