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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-Q

     
x   QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
     
 
    for the quarterly period ended June 30, 2003.

OR

     
o   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 0-22570

Lynx Therapeutics, Inc.

(Exact name of registrant as specified in its charter)
     
Delaware
(State or other jurisdiction of
incorporation or organization)
  94-3161073
(I.R.S. Employer
Identification No.)

25861 Industrial Blvd.
Hayward, CA 94545

(Address of principal executive offices)

(510) 670-9300
(Registrant’s telephone number, including area code)

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 x No o

Indicate by check mark whether the registrant is an accelerated filer (as defined in Rule 12b-2 of the Exchange Act). Yes o No x

The number of shares of common stock outstanding as of August 8, 2003 was 4,654,245.



 


TABLE OF CONTENTS

PART I. FINANCIAL INFORMATION
Item 1. Financial Statements
CONDENSED CONSOLIDATED BALANCE SHEETS
CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS
CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
NOTES TO UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations
Item 3. Quantitative and Qualitative Disclosures About Market Risk
Item 4. Controls and Procedures
PART II. OTHER INFORMATION
Item 1. Legal Proceedings
Item 2. Changes in Securities and Use of Proceeds
Item 3. Defaults Upon Senior Securities
Item 4. Submission of Matters to a Vote of Security Holders
Item 5. Other Information
Item 6. Exhibits and Reports on Form 8-K.
SIGNATURES
INDEX TO EXHIBITS
EXHIBIT 10.34.01
EXHIBIT 10.38
EXHIBIT 31.1
EXHIBIT 31.2
EXHIBIT 32.1


Table of Contents

Lynx Therapeutics, Inc.

FORM 10-Q
For the Quarter Ended June 30, 2003

INDEX

                 
            Page
           
PART I.  
FINANCIAL INFORMATION
       
Item 1.  
Financial Statements (unaudited)
       
       
Condensed Consolidated Balance Sheets —June 30, 2003 and December 31, 2002
    3  
       
Condensed Consolidated Statements of Operations — three months and six months ended June 30, 2003 and 2002
    4  
       
Condensed Consolidated Statements of Cash Flows — six months ended June 30, 2003 and 2002
    5  
       
Notes to Unaudited Condensed Consolidated Financial Statements
    6  
Item 2.  
Management’s Discussion and Analysis of Financial Condition and Results of Operations
    10  
Item 3.  
Quantitative and Qualitative Disclosures About Market Risk
    23  
Item 4.  
Controls and Procedures
    23  
PART II.  
OTHER INFORMATION
       
Item 1.  
Legal Proceedings
    24  
Item 2.  
Changes in Securities and Use of Proceeds
    24  
Item 3.  
Defaults Upon Senior Securities
    24  
Item 4.  
Submission of Matters to a Vote of Security Holders
    24  
Item 5.  
Other Information
    25  
Item 6.  
Exhibits and Reports on Form 8-K
    25  
Signatures     26  

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PART I. FINANCIAL INFORMATION

Item 1. Financial Statements

Lynx Therapeutics, Inc.
CONDENSED CONSOLIDATED BALANCE SHEETS
(In thousands)

                     
        June 30,   December 31,
        2003   2002
       
 
        (unaudited)   (*)
Assets
               
Current Assets:
               
 
Cash and cash equivalents
  $ 1,835     $ 11,735  
 
Restricted cash
    1,165        
 
Accounts receivable
    1,176       836  
 
Inventory
    1,012       1,030  
 
Other current assets
    431       714  
 
   
     
 
 
Total current assets
    5,619       14,315  
Property and equipment:
               
 
Leasehold improvements
    12,233       12,238  
 
Laboratory and other equipment
    23,222       22,972  
 
   
     
 
 
    35,455       35,210  
 
Less accumulated depreciation and amortization
    (21,503 )     (19,640 )
 
   
     
 
 
Net property and equipment
    13,952       15,570  
Investment in related party
    214       1,930  
Other non-current assets
    172       172  
 
   
     
 
 
  $ 19,957     $ 31,987  
 
   
     
 
Liabilities and Stockholders’ Equity
               
Current liabilities:
               
 
Accounts payable
  $ 1,200     $ 962  
 
Accrued compensation
    515       516  
 
Deferred revenue
    3,426       2,926  
 
Note payable
    1,675       2,250  
 
Other accrued liabilities
    413       604  
 
   
     
 
 
Total current liabilities
    7,229       7,258  
Deferred revenue
    6,064       10,634  
Note payable
    490       1,093  
Other non-current liabilities
    924       946  
Commitments and contingencies
               
Stockholders’ equity:
               
 
Common stock
    110,992       110,978  
 
Deferred compensation
          (9 )
 
Accumulated deficit
    (105,742 )     (98,913 )
 
   
     
 
   
Total stockholders’ equity
    5,250       12,056  
 
   
     
 
 
  $ 19,957     $ 31,987  
 
   
     
 


*   The balance sheet amounts at December 31, 2002 have been derived from audited financial statements at that date but do not include all of the information and footnotes required by generally accepted accounting principles for complete financial statements.

See accompanying notes.

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Lynx Therapeutics, Inc.
CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

(In thousands, except per share amounts)
(Unaudited)

                                     
        Three Months Ended   Six Months Ended
        June 30,   June 30,
       
 
        2003   2002   2003   2002
       
 
 
 
Net revenues:
                               
 
Technology access and service fees
  $ 4,187     $ 2,443     $ 7,187     $ 4,597  
 
License fees from related party
    190       190       380       380  
 
Collaborative research and other
    208       220       282       2,898  
 
   
     
     
     
 
Total revenues
    4,585       2,853       7,849       7,875  
 
   
     
     
     
 
Operating costs and expenses:
                               
   
Cost of services fees and other
    1,377       436       2,101       735  
   
Research and development
    3,196       5,406       6,761       12,293  
   
General and administrative
    1,893       1,408       3,678       3,142  
   
Restructuring charge for workforce reduction
          530       292       530  
 
   
     
     
     
 
Total operating costs and expenses
    6,466       7,780       12,832       16,700  
 
   
     
     
     
 
Loss from operations
    (1,881 )     (4,927 )     (4,983 )     (8,825 )
Equity in net loss of related party
    (891 )     (721 )     (1,716 )     (1,508 )
Interest expense, net
    (84 )     (24 )     (128 )     (124 )
Other income (expense), net
          (75 )           911  
 
   
     
     
     
 
Loss before provision for income taxes
    (2,856 )     (5,747 )     (6,827 )     (9,546 )
Income tax provision (benefit)
    1       (271 )     2       (310 )
 
   
     
     
     
 
Net loss
    (2,857 )     (5,476 )     (6,829 )     (9,236 )
 
   
     
     
     
 
Basic and diluted net loss per share
    (0.61 )     (1.61 )     (1.47 )     (3.44 )
 
   
     
     
     
 
Shares used in per share computation
    4,654       3,394       4,653       2,682  
 
   
     
     
     
 

See accompanying notes.

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Lynx Therapeutics, Inc.
CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(In thousands)
(Unaudited)

                     
        Six Months Ended
        June 30,
       
        2003   2002
       
 
Cash flows from operating activities:
               
Net loss
  $ (6,829 )   $ (9,236 )
Adjustments to reconcile net loss to net cash used in operating activities:
               
Depreciation and amortization of fixed assets and leasehold improvements
    1,863       2,279  
 
Amortization of deferred compensation
    9       489  
 
Equity in net loss of related party
    1,716       1,508  
 
Gain on sale of antisense business
          (1,008 )
 
Changes in operating assets and liabilities:
               
   
Accounts receivable
    (340 )     510  
   
Inventory
    18       628  
   
Other current assets
    283       97  
   
Accounts payable
    238       (613 )
   
Accrued liabilities
    (192 )     54  
   
Deferred revenue
    (4,070 )     (1,643 )
   
Other non-current liabilities
    (22 )     35  
 
   
     
 
Net cash used in operating activities
    (7,326 )     (6,900 )
Cash flows from investing activities:
               
Purchases of short-term investments
          (3,249 )
Proceeds from sale of equity securities
          2,180  
Purchases of property and equipment, net of proceeds from sale
    (245 )     (840 )
Payments received on notes receivable from officers and employees
          42  
 
   
     
 
Net cash used in investing activities
    (245 )     (1,867 )
Cash flows from financing activities:
               
Issuance of common stock, net of repurchases
    14       20,946  
Repayment of equipment loan
    (1,178 )     (798 )
 
   
     
 
Net cash provided by (used in) financing activities
    (1,164 )     20,148  
 
   
     
 
Net increase (decrease) in cash and cash equivalents
    (8,735 )     11,381  
Cash and cash equivalents at beginning of period
    11,735       3,199  
 
   
     
 
Cash, cash equivalents and restricted cash at end of period
  $ 3,000     $ 14,580  
 
   
     
 
Supplemental cash flow information:
               
Cash paid during the period for income taxes
  $ 2     $ 0  
 
   
     
 
Cash paid during the period for interest
  $ 134     $ 191  
 
   
     
 

See accompanying notes.

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Lynx Therapeutics, Inc.
NOTES TO UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

June 30, 2003

1. Nature of Business

     We believe that Lynx Therapeutics, Inc. (“Lynx” or the “Company”) is a leader in the development and application of novel genomics analysis solutions that provide comprehensive and quantitative digital gene expression information important to modern systems biology research in the pharmaceutical, biotechnology and agricultural industries. These solutions are based on Megaclone and Massively Parallel Signature Sequencing, or MPSS, Lynx’s unique and proprietary cloning and sequencing technologies. Gene expression refers to the number of genes and the extent a cell or tissue expresses those genes, and represents a way to move beyond DNA sequence data to understand the function of genes, the proteins that they encode and the role they play in health and disease. Systems biology is an approach in which researchers seek to gain a complete molecular understanding of biological systems in health and disease.

2. Basis of Presentation

     In January 2003, we received stockholder approval for, and effected, a reverse stock split of our common stock at a ratio of 1-for-7 (the “reverse stock split”). As a result of the reverse stock split, each outstanding share of common stock automatically converted into one-seventh of a share of common stock, with the par value of each share of common stock remaining at one cent ($.01) per share. Accordingly, common stock share and per share amounts for all periods presented have been adjusted to reflect the impact of the reverse stock split.

     The accompanying unaudited condensed consolidated financial statements included herein have been prepared by Lynx without audit, pursuant to the rules and regulations promulgated by the Securities and Exchange Commission (the “SEC”). Certain prior year amounts have been reclassified to conform to current year presentation. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles have been omitted pursuant to SEC rules and regulations; nevertheless, Lynx believes that the disclosures are adequate to make the information presented not misleading. In the opinion of management, the financial statements contain all adjustments, consisting only of normal recurring adjustments, necessary to present fairly the financial position, results of operations and cash flows of the Company for the interim periods presented. The results of operations for the six months ended June 30, 2003 are not necessarily indicative of the results for the full year.

     Our unaudited condensed consolidated financial statements have been presented on a basis that contemplates the realization of assets and satisfaction of liabilities in the normal course of business. We have experienced operating losses since our inception of $105.7 million, including net losses of $2.9 million and $6.8 million for the three and six months ended June 30, 2003, respectively. Net losses may continue for at least the next several years as we proceed with the commercialization and additional development of our technologies. The size of these losses will depend on the rate of growth, if any, in our revenues and on the level of our expenses. As of June 30, 2003, our cash and cash equivalents consisted of $1.8 million in unrestricted cash and restricted cash of $1.2 million, and our accounts receivable were $1.2 million. In July 2003, we received a cash payment of approximately $3.0 million from Takara Bio Inc. related to an amendment of our existing collaboration with Takara and the sale of three MPSS instruments. Depending on the success of our commercial efforts, we may require additional funding to continue our business activities for at least the next twelve months. We will be considering various options, which include securing additional equity financing and obtaining new collaborators and customers. If we raise additional capital by issuing equity or convertible debt securities, our existing stockholders may experience substantial dilution. If we require additional financing, there can be no assurance that it will be available on satisfactory terms, or at all. If we are unable to secure additional financing on reasonable terms, or are unable to generate sufficient new sources of revenue through arrangements with customers, collaborators and licensees, we may be forced to take substantial restructuring actions, which may include significantly reducing our anticipated

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level of expenditures, the sale of some or all of our assets, or obtaining funds by entering into financing or collaborative agreements on unattractive terms, or we will not be able to fund operations.

     The unaudited condensed consolidated financial statements include all accounts of Lynx and our wholly owned subsidiary, Lynx Therapeutics GmbH (“Lynx GmbH”), formed under the laws of the Federal Republic of Germany. All significant intercompany balances and transactions have been eliminated. Certain amounts in prior periods have been reclassified to conform to the current year presentation.

     These financial statements should be read in conjunction with Lynx’s audited consolidated financial statements and notes thereto for the year ended December 31, 2002, included in Lynx’s annual report on Form 10-K, filed with the SEC.

3. Summary of Significant Accounting Policies

Revenue Recognition

     Technology access fees have generally resulted from upfront payments from collaborators, customers and licensees who are provided access to our technologies for specified periods. We receive service fees from collaborators and customers for genomics discovery services performed by us on the biological samples they send to us. Collaborative research revenues are payments received under various agreements and include such items as milestone payments. Milestone payments are recognized as revenue pursuant to collaborative agreements upon the achievement of specified technology developments, representing the culmination of the earnings process. Other revenues include the proceeds from the sale of technology assets, the sale of proprietary instruments and reagents, and grant revenue.

     Technology access and license fees are deferred and recognized as revenue on a straight-line basis over the noncancelable term of the agreement to which they relate. Payments for services and/or materials provided by Lynx are recognized as revenues when earned over the period in which the services are performed and/or materials are delivered, provided that no other consequential obligations, refunds or credits to be applied to future work exist. Revenues from the sale of technology assets are recognized upon the transfer of the assets to the purchaser. Revenues from the sales of instruments and reagents are recognized upon shipment to the customer.

Inventory

     Inventory is stated at the lower of cost (which approximates first-in, first out cost) or market. The balances at June 30, 2003 and December 31, 2002 were classified as raw materials and consisted primarily of reagents and other chemicals utilized while performing genomics discovery services. Inventory used in providing genomics discovery services and for reagent sales is charged to cost of services fees and other as consumed. Reagents and chemicals purchased for internal development purposes are charged to research and development expense as incurred.

Net Loss Per Share

     Basic and diluted net loss per share have been computed using the weighted-average number of shares of common stock outstanding during the period. Basic and diluted net loss per share amounts are the same in each period as we have incurred a net loss for all periods presented. Had we been in a net income position, diluted earnings per share would have included the dilutive impact of outstanding options and warrants to purchase common stock. At June 30, 2003, options to purchase approximately 530,986 shares of common stock at a weighted-average exercise price of $40.08 per share and warrants to purchase 101,082 shares of common stock at an exercise price of $39.76 per share, 41,714 shares of common stock at an exercise price of $10.85 per share and 834,272 shares of common stock at an exercise price of $13.58 per share were excluded from the calculation of diluted loss per share for 2003 because the effect of inclusion would be antidilutive. The options and warrants will be included in the calculation at such time as the effect is no longer antidilutive, as calculated using the treasury stock method. At June 30, 2002, options to purchase approximately 418,277 shares of common stock at a weighted-average exercise price of $74.26 per share and warrants to purchase 101,082 shares of common stock at an exercise price of $39.76 per share, 41,714 shares of common stock at an exercise price of $10.85 per share and 834,272 shares of common stock

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at an exercise price of $13.58 per share were excluded from the calculation of diluted loss per share for 2002 because the effect of inclusion would be antidilutive.

Stock-Based Compensation

     We grant stock options for a fixed number of shares to employees with an exercise price equal to the fair value of the shares at the date of grant. We account for stock option grants in accordance with Accounting Principles Board (APB) Opinion No. 25, Accounting for Stock Issued to Employees (APB 25), and related Interpretations. Under APB 25, when the exercise price of our employee stock options equals the market price of the underlying stock on the date of grant, no compensation expense is recognized.

     All stock option awards to non-employees are accounted for at the fair value of the consideration received or the fair value of the equity instrument issued, as calculated using the Black-Scholes model, in accordance with Statement of Financial Accounting Standards No. 123, Accounting for Stock-based Compensation, (SFAS 123) and Emerging Issues Task Force Consensus No. 96-18, Accounting for Equity Instruments that are Issued to Other Than Employees for Acquiring, or in Conjunction with Selling, Goods or Services. The option arrangements with non-employees are subject to periodic remeasurement over their vesting terms. Pro forma information regarding net loss and net loss per share required by SFAS 123, as amended by Accounting for Stock-Based Compensation — Transition and Disclosure (SFAS 148), is presented below and has been determined as if we had accounted for awards under our stock option and employee stock purchase plans using the fair value method:

                                 
    Three Months Ended   Six Months Ended
    June 30,   June 30,
   
 
    2003   2002   2003   2002
   
 
 
 
Net loss, as reported
  $ (2,857 )   $ (5,476 )   $ (6,829 )   $ (9,236 )
Add: Stock-based employee compensation as reported
    0       489       9       489  
Deduct: Stock-based employee compensation as if fair value method applied to all awards
    (720 )     (1,138 )     (1,125 )     (2,587 )
 
   
     
     
     
 
Net loss, pro forma as if fair value method applied to all awards
  $ (3,577 )   $ (6,125 )   $ (7,945 )   $ (11,334 )
 
   
     
     
     
 
Basic and diluted net loss per share, as reported
  $ (0.61 )   $ (1.61 )   $ (1.47 )   $ (3.44 )
 
   
     
     
     
 
Basic and diluted net loss per share, pro forma as if fair value method applied to all awards
  $ (0.77 )   $ (1.80 )   $ (1.71 )   $ (4.23 )
 
   
     
     
     
 

Recent Accounting Pronouncements

     In January 2003, the FASB issued Interpretation No. 46 (FIN 46), “Consolidation of Variable Interest Entities.” In general, a variable interest entity is a corporation, partnership, trust, or any other legal structure used for business purposes that either (a) does not have equity investors with voting rights or (b) has equity investors that do not provide sufficient financial resources for the entity to support its activities. FIN 46 requires a variable interest entity to be consolidated by a company if that company is subject to a majority of the risk of loss from the variable interest entity’s activities or entitled to receive a majority of the entity’s residual returns or both. The consolidation requirements of FIN 46 apply immediately to variable interest entities created after January 31, 2003. The consolidation requirements apply to older entities in the first fiscal year or interim period beginning after June 15, 2003. Certain of the disclosure requirements apply in all financial statements issued after January 31, 2003, regardless of when the variable interest entity was established. The Company does not believe the adoption of FIN 46 will have a material impact on its financial position or results of operations.

     In November 2002, the Emerging Issues Task Force (EITF) reached a consensus regarding EITF Issue 00-21, Accounting for Revenue Arrangements with Multiple Deliverables. The consensus addresses not only when and how an arrangement involving multiple deliverables should be divided into separate units of accounting, but also how the arrangement’s consideration should be allocated among separate units. The pronouncement is effective for revenue

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arrangements entered into in fiscal periods beginning after June 15, 2003. We are in the process of evaluating the financial statement impact, if any, of adopting EITF Issue 00-21, but do not expect that the adoption of EITF Issue 00-21 will have a material effect on our results of operations or financial position.

     In May 2003, the FASB issued Statement of Financial Accounting Standards No. 150, Accounting for Certain Financial Instruments with Characteristics of both Liabilities and Equity (SFAS 150). The Statement establishes standards for classifying and measuring as liabilities certain financial instruments that embody obligations of the issuer and have characteristics of both liabilities and equity. The Statement is effective for all financial instruments created or modified after May 31, 2003, and to other instruments for periods beginning after June 15, 2003. We are currently evaluating the effects of SFAS 150, but do not expect that the adoption of SFAS 150 will have a material effect on our results of operations or financial position.

4. Comprehensive Loss

     The following are the components of comprehensive loss: (in thousands)

                 
    Three Months Ended
    June 30,
   
    2003   2002
   
 
Net loss
  $ (2,857 )   $ (5,476