Quarterly report pursuant to Section 13 or 15(d)

Significant Accounting Policies

v3.5.0.2
Significant Accounting Policies
3 Months Ended
Mar. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]  
Significant Accounting Policies
Significant Accounting Principles

Business    
    
Ligand is a biopharmaceutical company with a business model that is based upon the concept of developing or acquiring royalty revenue generating assets and coupling them with a lean corporate cost structure. We operate in one business segment: development and licensing biopharmaceutical assets.
 
Principles of Consolidation
    
The accompanying consolidated financial statements include Ligand and its wholly owned subsidiaries. All significant intercompany accounts and transactions have been eliminated in consolidation.

Basis of Presentation

The Company’s accompanying unaudited condensed consolidated financial statements as of March 31, 2016 and for the three months ended March 31, 2016 and 2015 have been prepared in accordance with GAAP for interim financial information. In the opinion of management, all adjustments (consisting of normal recurring adjustments) considered necessary for a fair presentation of the financial position and results of operations of the Company and its subsidiaries, have been included. Operating results for the three months ended March 31, 2016 are not necessarily indicative of the results that may be expected for the year ending December 31, 2016. These financial statements should be read in conjunction with the consolidated financial statements and notes therein included in the Company’s annual report on Form 10-K/A for the year ended December 31, 2015 filed on November 14, 2016.

Restatement
    
The Company has restated its financial statements for the year ended December 31, 2015 to correct errors relating to the Company's net operating loss (NOL) carryforward benefits in the United States which resulted in an overstatement of deferred tax assets (DTA) at December 31, 2015 and March 31, 2016.  In connection with three acquisitions that were completed prior to February 2010, the Company recognized DTAs for a portion of the NOLs, which included capitalized research and development expenses, obtained from the acquired businesses. From the time of the acquisitions until September 2015, there was a valuation allowance against all of the Company’s NOLs, including those obtained from the entities acquired. In September 2015, the Company concluded that it was more likely than not that a substantial portion of it deferred tax assets would be realized through future taxable income. As a result, the Company released the majority of its DTA valuation allowance in full, including $27.5 million related to NOLs recognized as part of the businesses acquired prior to February of 2010.

During the quarter ended September 30, 2016, the Company concluded that for accounting purposes the approximately $27.5 million of DTAs that were obtained upon acquiring the businesses prior to February of 2010 did not meet the more likely-than-not criterion for recognition in 2015 and that the related valuation allowance should not have been reversed. As a result, the Company's income tax benefit and net income for the year ended December 31, 2015 were overstated by $27.5 million each as were the Company's DTAs at March 31, 2016.

Based on the materiality guidelines contained in SEC Staff Accounting Bulletin No. 99, Materiality, and SEC Staff Accounting Bulletin No. 108, Considering the Effects of Prior Year Misstatements in Current Year Financial Statements, the Company believes that the income tax adjustment is material to its financial statements for periods subsequent to and including the year ended December 31, 2015. Accordingly, the Company determined that it would restate prior period financial statements and amend its previously filed affected filings, including its March 31, 2016 report on Form 10-Q and December 31, 2015 report on Form 10-K.

The Company also recorded adjustments as part of this restatement related to the classification of our 2019 Convertible Senior Notes. As of December 31, 2015, the Company's last reported sale price exceeded the 130% threshold described in Note 6 - "Financing Arrangements" and accordingly the 2019 Convertible Senior Notes have been reclassified as a current liability as of December 31, 2015. As a result, the related unamortized discount of $39.6 million previously classified within stockholder's equity was reclassified as temporary equity component of currently redeemable convertible notes on our Condensed Consolidated Balance Sheet.

The effects of these prior period corrections are as follows:

 
As of December 31, 2015
 
As Reported
 
Adjustments
 
As Restated
Deferred income taxes
$
216,564

 
$
(27,481
)
 
$
189,083

Total assets(1)
530,542

 
(27,481
)
 
503,061

2019 convertible senior notes, net - current

 
201,985

 
201,985

Total current liabilities
20,836

 
201,985

 
222,821

2019 convertible senior notes, net - long term(1)
201,985

 
(201,985
)
 

Equity component of currently redeemable convertible notes (Note 5)


 
39,628

 
39,628

Additional paid-in capital
701,478

 
(39,628
)
 
661,850

Accumulated deficit
(402,010
)
 
(27,481
)
 
(429,491
)
Total stockholders' equity
304,391

 
(67,109
)
 
237,282

Total liabilities and stockholders' equity(1)
530,542

 
(27,481
)
 
503,061

(1) $3.4 million of unamortized issuance cost was reclassified to debt discount in the concurrently filed 2015 10-K/A form that it is filed after the Company's retrospective adoption of ASU 2015-03, Interest-Imputation of Interest: Simplifying the Presentation of Debt Issuance Costs in Q1 2016.

 
As of March 31, 2016
 
As Reported
 
Adjustments
 
As Restated
Deferred income taxes
$
157,258

 
(27,481
)
 
$
129,777

Total assets
613,438

 
(27,481
)
 
585,957

Accumulated deficit
(395,402
)
 
(27,481
)
 
(422,883
)
Total stockholders' equity
392,077

 
(27,481
)
 
364,596

Total liabilities and stockholders' equity
613,438

 
(27,481
)
 
585,957


Use of Estimates

The preparation of condensed consolidated financial statements in conformity with GAAP requires the use of estimates and assumptions that affect the amounts reported in the condensed consolidated financial statements and the accompanying notes. Actual results may differ from those estimates.

Reclassifications

Certain reclassifications have been made to the previously issued balance sheet and statement of operations for the three months ended March 31, 2015 for comparability purposes. These reclassifications had no effect on the reported net income, stockholders' equity, and operating cash flows as previously reported.

Income Per Share

Basic income per share is calculated by dividing net income by the weighted-average number of common shares outstanding during the period. Diluted income per share is computed by dividing net income by the weighted-average number of common shares and common stock equivalents of all dilutive securities calculated using the treasury stock method and the if-converted method. The total number of potentially dilutive securities including stock options and warrants excluded from the computation of diluted income per share because their inclusion would have been anti-dilutive was 3.5 million and 4.5 million, as of March 31, 2016 and 2015, respectively.

The following table presents the computation of basic and diluted net income per share for the periods indicated (in thousands, except per share amounts):

 
Three months ended
 
March 31,
 
2016
 
2015
Net income from continuing operations
$
5,877

 
$
754

Net income from discontinued operations
731

 

Net income
$
6,608

 
$
754

 
 
 
 
Shares used to compute basic income per share
20,707,926

 
19,611,881

Dilutive potential common shares:
 
 
 
Restricted stock
66,736

 
61,538

     Stock options
759,581

 
957,369

     0.75% Convertible Senior Notes, Due 2019
749,736

 

Shares used to compute diluted income per share
22,283,979

 
20,630,788

 
 
 
 
Basic per share amounts:
 
 
 
Income from continuing operations
$
0.28

 
$
0.04

Income from discontinued operations
0.04

 

Basic net income per share
$
0.32

 
$
0.04

 
 
 
 
Diluted per share amounts:
 
 
 
Income from continuing operations
$
0.26

 
$
0.04

Income from discontinued operations
0.03

 

Diluted net income per share
$
0.30

 
$
0.04



Cash Equivalents
Cash equivalents consist of all investments with maturities of three months or less from the date of acquisition.
Short-term Investments
Short-term investments primarily consist of investments in debt securities that have effective maturities greater than three months and less than twelve months from the date of acquisition. The Company classifies its short-term investments as "available-for-sale". Such investments are carried at fair value, with unrealized gains and losses included in the statement of comprehensive income (loss). The Company determines the cost of investments based on the specific identification method.
Restricted Investments
Restricted investments consist of certificates of deposit held with a financial institution as collateral under a facility lease and third-party service provider arrangements.
The following table summarizes the various investment categories at March 31, 2016 and December 31, 2015 (in thousands):

 
Amortized cost
 
Gross unrealized
gains
 
Gross unrealized
losses
 
Estimated
fair value
March 31, 2016
 
 
 
 
 
 
 
Short-term investments
 
 
 
 
 
 


     Bank deposits
$
42,376

 
$
87

 
$

 
$
42,463

     Corporate bonds
24,268

 
84

 
(2
)
 
24,350

     Commercial paper
8,401

 
2

 

 
8,403

     Asset backed securities
2,067

 
1

 
(1
)
 
2,067

     Corporate equity securities
1,811

 
2,814

 

 
4,625

 
$
78,923

 
$
2,988

 
$
(3
)
 
$
81,908

December 31, 2015
 
 
 
 
 
 
 
Short-term investments
 
 
 
 
 
 
 
     Bank deposits
$
43,043

 
$

 
$
(4
)
 
$
43,039

     Corporate bonds
41,238

 
$

 
(35
)
 
41,203

     Commercial paper
1,747

 
$

 

 
1,747

     Asset backed securities
10,020

 
$

 
(5
)
 
10,015

     Corporate equity securities
1,843

 
$
4,944

 

 
6,787

 
$
97,891

 
$
4,944

 
$
(44
)
 
$
102,791




Inventory

Inventory, which consists of finished goods, is stated at the lower of cost or market value. The Company determines cost using the first-in, first-out method. Inventory levels are analyzed periodically and written down to its net realizable value if it has become obsolete, has a cost basis in excess of its expected net realizable value or is in excess of expected requirements. There were no write downs related to obsolete inventory recorded for the three months ended March 31, 2016 and 2015.

Goodwill and Other Identifiable Intangible Assets

Goodwill and other identifiable intangible assets consist of the following (in thousands):

 
March 31,
 
December 31,
 
2016
 
2015
Indefinite lived intangible assets
 
 
 
     Acquired IPR&D
$
12,556

 
$
12,556

     Goodwill
72,997

 
12,238

Definite lived intangible assets
 
 
 
     Complete technology
182,267

 
15,267

          Less: Accumulated amortization
(5,883
)
 
(3,762
)
     Trade name
2,642

 
2,642

          Less: Accumulated amortization
(685
)
 
(652
)
     Customer relationships
29,600

 
29,600

          Less: Accumulated amortization
(7,674
)
 
(7,304
)
Total goodwill and other identifiable intangible assets, net
$
285,820

 
$
60,585



As Discussed in Note 2-Business Combination, on January 8, 2016, the Company completed its acquisition of OMT. As a result of the transaction, the Company recorded $167.0 million of intangibles with definite lives and goodwill of $60.8 million. Amortization of definite-lived intangible assets is computed using the straight-line method over the estimated useful life of the asset of 20 years. Amortization expense of $2.5 million was recognized for the three months ended March 31, 2016 and amortization expense of $0.6 million was recognized for the three months ended March 31, 2015. Estimated amortization expense for the year ending December 31, 2016 is $10.6 million and estimated amortization expense for the years ended December 31, 2017 through 2020 is $10.7 million per year. For each of the three months ended March 31, 2016 and 2015, there was no impairment of IPR&D or goodwill.

Commercial License Rights
    
Commercial license rights represent a portfolio of future milestone and royalty payment rights acquired from Selexis in April 2013 and April 2015. Individual commercial license rights acquired under the agreement are carried at allocated cost and approximate fair value. The carrying value of the license rights will be reduced on a pro-rata basis as revenue is realized over the term of the agreement. Declines in the fair value of individual license rights below their carrying value that are deemed to be other than temporary are reflected in earnings in the period such determination is made. As of March 31, 2016, management does not believe there have been any events or circumstances indicating that the carrying amount of its commercial license rights may not be recoverable.

Property and Equipment

Property and equipment is stated at cost and consists of the following (in thousands):

 
March 31,
 
December 31,
 
2016
 
2015
Lab and office equipment
$
2,482

 
$
2,248

Leasehold improvements
273

 
273

Computer equipment and software
636

 
632

 
3,391

 
3,153

Less accumulated depreciation and amortization
(2,824
)
 
(2,781
)
     Total property and equipment, net
$
567

 
$
372



Depreciation of equipment is computed using the straight-line method over the estimated useful lives of the assets, which range from three to ten years. Leasehold improvements are amortized using the straight-line method over the shorter of the estimated useful lives or the related lease term. Depreciation expense of $0.1 million was recognized for each of the three months ended March 31, 2016 and 2015, respectively, which is included in operating expenses.

Other Current Assets

Other current assets consist of the following (in thousands):

 
March 31,
 
December 31,
 
2016
 
2015
Prepaid expenses
$
1,087

 
$
1,177

Other receivables
475

 
731

     Total other current assets
$
1,562

 
$
1,908


 
    
Accrued Liabilities

Accrued liabilities consist of the following (in thousands):

 
March 31,
 
December 31,
 
2016
 
2015
Compensation
$
854

 
$
1,711

Professional fees
754

 
726

Amounts owed to former licensees
695

 
915

Royalties owed to third parties
937

 
823

Other
429

 
1,222

     Total accrued liabilities
$
3,669

 
$
5,397



Other Long-Term Liabilities

Other long-term liabilities consist of the following (in thousands):

 
March 31,
 
December 31,
 
2016
 
2015
Deposits
$
298

 
$
268

Deferred rent
107

 

Other
41

 
29

     Total other long-term liabilities
$
446

 
$
297


Contingent Liabilities
    
In connection with the Company’s acquisition of CyDex in January 2011, the Company recorded a contingent liability, for amounts potentially due to holders of the CyDex CVRs and former license holders. The liability is periodically assessed based on events and circumstances related to the underlying milestones, royalties and material sales. Any change in fair value is recorded in the Company’s consolidated statement of operations. The carrying amount of the liability may fluctuate significantly and actual amounts paid under the CVR agreements may be materially different than the carrying amount of the liability. The fair value of the liability at March 31, 2016 and December 31, 2015 was $6.9 million and $9.5 million, respectively. The Company recorded a fair-value adjustment to increase the liability by $0.2 million and $1.2 million for the three months ended March 31, 2016 and 2015, respectively. There was a revenue-sharing payment of $2.8 million and $3.2 million to CyDex CVR holders during the three months ended March 31, 2016 and 2015, respectively.

In connection with the Company’s acquisition of Metabasis in January 2010, the Company issued to Metabasis stockholders four tradable CVRs, one CVR from each of four respective series of CVR, for each Metabasis share. The CVRs will entitle Metabasis stockholders to cash payments as frequently as every six months as cash is received by the Company from proceeds from the sale or partnering of any of the Metabasis drug development programs, among other triggering events. The fair values of the CVRs are remeasured at each reporting date through the term of the related agreement. Any change in fair value is recorded in the Company’s consolidated statement of operations. The carrying amount of the liability may fluctuate significantly based upon quoted market prices and actual amounts paid under the agreements may be materially different than the carrying amount of the liability. The fair value of the liability was estimated to be $2.4 million and $4.0 million as of March 31, 2016 and December 31, 2015, respectively. The Company recorded an increase in the liability for Metabasis-related CVRs of $1.1 million and an decrease of $1.2 million for the three months ended March 31, 2016 and 2015, respectively. The Company paid Metabasis CVR holders $2.6 million for the three months ended March 31, 2016. No payments were made to Metabasis CVR holders for the three months ended March 31, 2015.

Revenue Recognition

Royalties on sales of products commercialized by the Company’s partners are recognized in the quarter reported to Ligand by the respective partner. Generally, the Company receives royalty reports from its licensees approximately one quarter in arrears due to the fact that its agreements require partners to report product sales between 30 and 60 days after the end of the quarter. The Company recognizes royalty revenues when it can reliably estimate such amounts and collectability is reasonably assured. Under this accounting policy, the royalty revenues reported are not based upon estimates and such royalty revenues are typically reported to the Company by its partners in the same period in which payment is received.
Revenue from material sales of Captisol is recognized upon transfer of title, which normally passes upon shipment to the customer, provided all other revenue recognition criteria have been met. All product returns are subject to the Company's credit and exchange policy, approval by the Company and a 20% restocking fee. To date, product returns by customers have not been material to net material sales in any related period. The Company records revenue net of product returns, if any, and sales tax collected and remitted to government authorities during the period.

The Company analyzes its revenue arrangements and other agreements to determine whether there are multiple elements that should be separated and accounted for individually or as a single unit of accounting. For multiple element contracts, arrangement consideration is allocated at the inception of the arrangement to all deliverables on the basis of relative selling price, using a hierarchy to determine selling price. Management first considers VSOE, then TPE and if neither VSOE nor TPE exist, the Company uses its best estimate of selling price.
Many of the Company's revenue arrangements for Captisol involve a license agreement with the supply of manufactured Captisol product. Licenses may be granted to pharmaceutical companies for the use of Captisol product in the development of pharmaceutical compounds. The supply of the Captisol product may be for all phases of clinical trials and through commercial availability of the host drug or may be limited to certain phases of the clinical trial process. Management believes that the Company's licenses have stand-alone value at the outset of an arrangement because the customer obtains the right to use Captisol in its formulations without any additional input by the Company.
Other nonrefundable, upfront license fees are recognized as revenue upon delivery of the license, if the license is determined to have standalone value that is not dependent on any future performance by the Company under the applicable collaboration agreement. Nonrefundable contingent event-based payments are recognized as revenue when the contingent event is met, which is usually the earlier of when payments are received or collections are assured, provided that it does not require future performance by the Company. The Company occasionally has sub-license obligations related to arrangements for which it receives license fees, milestones and royalties. The Company evaluates the determination of gross versus net reporting based on each individual agreement.
Sales-based contingent payments from partners are accounted for similarly to royalties, with revenue recognized upon achievement of the sales targets assuming all other revenue recognition criteria for milestones are met. Revenue from development and regulatory milestones is recognized when earned, as evidenced by written acknowledgement from the collaborator, provided that (1) the milestone event is substantive, its achievability was not reasonably assured at the inception of the agreement, and the Company has no further performance obligations relating to that event, and (2) collectability is reasonably assured. If these criteria are not met, the milestone payment is recognized over the remaining period of the Company’s performance obligations under the arrangement.    
Revenue from research funding under our collaboration agreements is earned and recognized on a percentage-of completion basis as research hours are incurred in accordance with the provisions of each agreement.

Stock-Based Compensation

Stock-based compensation expense for awards to employees and non-employee directors is recognized on a straight-line basis over the vesting period until the last tranche vests. The following table summarizes stock-based compensation expense recorded as components of research and development expenses and general and administrative expenses for the periods indicated (in thousands):

 
Three months ended
 
 
March 31,
 
 
2016
 
2015
 
Stock-based compensation expense as a component of:
 
 
 
 
Research and development expenses
$
1,585

 
$
920

 
General and administrative expenses
2,533

 
1,994

 
 
$
4,118

 
$
2,914

 


The fair-value for options that were awarded to employees and directors was estimated at the date of grant using the Black-Scholes option valuation model with the following weighted-average assumptions:

 
Three months ended
 
 
March 31,
 
 
2016
 
2015
 
Risk-free interest rate
1.5%
 
1.8%
 
Dividend yield
 
 
Expected volatility
50%
 
58%
 
Expected term
6.6
 
6.6
 
Forfeiture rate
5.0%
 
8.5%
 



Income Taxes

                Income taxes are accounted for under the liability method.  This approach requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of differences between the tax basis of assets or liabilities and their carrying amounts in the consolidated financial statements. The Company provides a valuation allowance for deferred tax assets if it is more likely than not that these items will expire before we are able to realize their benefit. The Company calculates the valuation allowance in accordance with the authoritative guidance relating to income taxes under ASC 740, Income Taxes, which requires an assessment of both positive and negative evidence that is available regarding the reliability of these deferred tax assets, when measuring the need for a valuation allowance.   Developing the provision for income taxes requires significant judgment and expertise in federal and state income tax laws, regulations and strategies, including the determination of deferred tax assets and liabilities and, if necessary, any valuation allowances that may be required for deferred tax assets.  The Company's judgments and tax strategies are subject to audit by various taxing authorities.  While management believes the Company has provided adequately for its income tax liabilities in its consolidated financial statements, adverse determinations by these taxing authorities could have a material adverse effect on the Company's consolidated financial condition and results of operations. 




Variable Interest Entities

The Company identifies an entity as a VIE if either: (1) the entity does not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support, or (2) the entity's equity investors lack the essential characteristics of a controlling financial interest. The Company performs ongoing qualitative assessments of its VIEs to determine whether the Company has a controlling financial interest in any VIE and therefore is the primary beneficiary. If the Company is the primary beneficiary of a VIE, it consolidates the VIE under applicable accounting guidance. If the Company is no longer the primary of a VIE or the entity is no longer considered as a VIE as facts and circumstances changed, it deconsolidates the entity under the applicable accounting guidance. Beginning May 2015, the Company deconsolidated Viking, a previously reported VIE, and elected to record its investment in Viking under the equity method of accounting as Viking is no longer considered a VIE and the Company does not have voting control or other elements of control that would require consolidation. The investment is subsequently adjusted for the Company’s share of Viking's operating results, and if applicable, cash contributions and distributions, which is reported on a separate line in our condensed consolidated statement of operations called “Equity in net losses of Viking Therapeutics”. On the condensed consolidated balance sheet, the Company reports its investment in Viking on a separate line in the non-current assets section called “Investment in Viking Therapeutics”. See Note 3, Investment in Viking Therapeutics, for additional details.
 

Convertible Debt

In August 2014, the Company completed a $245.0 million offering of 2019 Convertible Senior Notes, which bear interest at 0.75%. The Company accounts for the 2019 Convertible Senior Notes by separating the liability and equity components of the instrument in a manner that reflects the Company's nonconvertible debt borrowing rate. As a result, the Company assigned a value to the debt component of the 2019 Convertible Senior Notes equal to the estimated fair value of similar debt instruments without the conversion feature, which resulted in the Company recording the debt instrument at a discount. The Company is amortizing the debt discount over the life of the 2019 Convertible Senior Notes as additional non-cash interest expense utilizing the effective interest method.
Recent Accounting Pronouncements
    
In May 2014, FASB issued ASU 2014-09, Revenue from Contracts with Customers. ASU 2014-09 is effective for annual periods beginning after December 15, 2016 and interim periods within those annual periods. The revenue standard’s core principle is built on the contract between a vendor and a customer for the provision of goods and services. It attempts to depict the exchange of rights and obligations between the parties in the pattern of revenue recognition based on the consideration to which the vendor is entitled. To accomplish this objective, the standard requires five basic steps: (1) identify the contract with the customer, (2) identify the performance obligations in the contract, (3) determine the transaction price, (4) allocate the transaction price to the performance obligations in the contract, (5) recognize revenue when (or as) the entity satisfies a performance obligation. Management is currently evaluating the effect the adoption of this standard will have on the Company's financial statements.
    
In April 2015, FASB issued ASU 2015-03, Interest-Imputation of Interest: Simplifying the Presentation of Debt Issuance Costs. This update was issued to simplify the presentation for debt issuance costs. Upon adoption, such costs shall be presented on our consolidated balance sheets as a direct deduction from the carrying amount of the related debt liability and not as a deferred charge presented in Other assets on our consolidated balance sheets. This amendment will be effective for interim and annual periods beginning on January 1, 2016, and is required to be retrospectively adopted. During the three-month period ended March 31, 2016, management adopted the change in the presentation on our consolidated balance sheets accordingly (see Note 6 for details).

In January 2016, the FASB issued ASU 2016-01 Recognition and Measurement of Financial Assets and Financial Liabilities that amends the accounting and disclosures of financial instruments, including a provision that requires equity investments (except for investments accounted for under the equity method of accounting) to be measured at fair value with changes in fair value recognized in current earnings. The new standard is effective for interim and annual periods beginning on January 1, 2018. We are currently evaluating the impact that this new standard will have on our consolidated financial statements.

In February 2016, the FASB issued a new accounting standard that amends the guidance for the accounting and disclosure of leases. This new standard requires that lessees recognize the assets and liabilities that arise from leases on the balance sheet and disclose qualitative and quantitative information about their leasing arrangements. The new standard is effective for interim and annual periods beginning on January 1, 2019. We are currently evaluating the impact that this new standard will have on our consolidated financial statements.

In March 2016, the FASB issued ASU 2016-09, Compensation – Stock Compensation, which identifies areas for simplification involving several aspects of accounting for stock-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, an option to recognize gross stock compensation expense with actual forfeitures recognized as they occur, as well as certain classifications on the statement of cash flows. ASU No. 2016-09 is effective for reporting periods beginning after December 31, 2016.  Early adoption is permitted. We are currently assessing the potential impact that the adoption of ASU No. 2016-09 will have in our condensed consolidated financial statements.