GENOME THERAPEUTICS CORP
10-Q, 1996-04-09
IN VITRO & IN VIVO DIAGNOSTIC SUBSTANCES
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<PAGE>   1


                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                  ------------

                                    FORM 10-Q


                QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d)
                   OF THE SECURITIES AND EXCHANGE ACT OF 1934

                      For Quarter Ended: February 24, 1996
                                         -----------------

                           Commission File No: 0-10824
                                               -------

                         GENOME THERAPEUTICS CORPORATION
                         -------------------------------
             (EXACT NAME OF REGISTRANT AS SPECIFIED IN ITS CHARTER)

             MASSACHUSETTS                            04-2297484
             -------------                            ----------
    (STATE OR OTHER JURISDICTION         (I.R.S. EMPLOYER IDENTIFICATION NO.)
  OF INCORPORATION OR ORGANIZATION)        

  100 BEAVER STREET;  WALTHAM, MASSACHUSETTS                     02154
  ------------------  ----------------------                     -----
   (ADDRESS OF PRINCIPAL EXECUTIVE OFFICES)                   (ZIP CODE)

                  REGISTRANT'S TELEPHONE NUMBER: (617) 893-5007
                                                 --------------

     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
                                             -----   -----

     Indicate the number of shares outstanding of each of the issuer's classes
of common stock, as of the latest practicable date.

        COMMON STOCK                                    16,899,090
       --------------                             -------------------------
       $.10 PAR VALUE                             Outstanding April 8, 1996
       --------------

   SERIES B RESTRICTED STOCK                              57,512
   -------------------------                      -------------------------
       $.10 PAR VALUE                             Outstanding April 8, 1996
       --------------


<PAGE>   2



<TABLE>
                   Genome Therapeutics Corp. and Subsidiaries

        Index to Financial Information (Unaudited) and Other Information
<CAPTION>


                                                                          Page
                                                                          ----
<S>                                                                        <C>
Part I
Financial Information  (Unaudited) :

    Consolidated Condensed Balance Sheets as of                            3
       February 24, 1996 and August 31, 1995

    Consolidated Condensed Statements of Operations                        4
       for the 13 and 26 week periods ended
       February 24, 1996 and February 25, 1995

    Consolidated Statements of Cash Flows for the                          5
       26 week periods ended February 24, 1996
       and February 25, 1995

    Notes to Consolidated Condensed Financial                              6-10
       Statements for the 26 week periods ended
       February 24, 1996 and February 25, 1995


    Management's Discussion and Analysis of Financial
       Conditions and Results of Operations                                11-17


Part II
Other Information:

       Other Information                                                   18

       Signature                                                           19
</TABLE>


                                       2
<PAGE>   3

<TABLE>
GENOME THERAPEUTICS CORP. AND SUBSIDIARIES
CONSOLIDATED CONDENSED BALANCE SHEETS
- --------------------------------------------------------------------------------
<CAPTION>

                                                     August 31,    February 24,
                                                        1995           1996
                                                            (Unaudited)
- --------------------------------------------------------------------------------
<S>                                                 <C>           <C>        
Assets
Current Assets:
   Cash and Cash Equivalents                        $ 5,886,184   $42,298,654
   Marketable Securities                              2,340,592     6,815,640
   Accounts Receivable (net of allowances           
       for doubtful accounts)                           360,793       647,497
   Unbilled Costs and Fees                              259,005       341,188
   Prepaid Expenses and Other Current Assets             50,140        77,027
                                                    
                                                    -----------   -----------
        Total Current Assets                          8,896,714    50,180,006
                                                    
Equipment and Leasehold Improvements, at cost:      
   Laboratory and Scientific Equipment                1,464,987     2,138,262
   Leasehold Improvements                             1,597,069     1,611,537
   Office Equipment and Furniture                       903,946     1,785,733
   Construction-in-Progress                             206,103        13,552
                                                    -----------   -----------
                                                      4,172,105     5,549,084
   Less Accumulated Depreciation
       and Amortization                               2,451,632     2,749,492
                                                    -----------   -----------
                                                      1,720,473     2,799,592
                                                    
Restricted Cash                                         784,471       765,313
                                                    
Other Assets                                            127,016       119,614
                                                    
                                                    -----------   -----------
        Total Assets                                $11,528,674   $53,864,525
                                                    -----------   -----------
                                                    
                                                    
Liabilities and Shareholders' Equity                
Current Liabilities:                                
   Accounts Payable                                 $   409,282   $ 1,048,104
   Accrued Expenses                                   1,736,569     1,889,044
   Deferred Contract Revenue                            774,048       864,594
   Current Maturities of Capital Lease Obligation       478,033       973,407
                                                    -----------   -----------
        Total Current Liabilities                     3,397,932     4,775,149
                                                    -----------   -----------
                                                    
Capital Lease Obligations, net of Current Maturities    892,239     1,519,769
                                                    
Shareholders' Equity                                  7,238,503    47,569,607
                                                    
                                                    -----------   -----------
        Total Liabilities and Shareholders'Equity   $11,528,674   $53,864,525
                                                    -----------   -----------
</TABLE>

See Notes to Consolidated Condensed Financial Statements.

                                       3
<PAGE>   4

<TABLE>
GENOME THERAPEUTICS CORP. AND SUBSIDIARIES
CONSOLIDATED STATEMENTS OF OPERATIONS
- ---------------------------------------------------------------------------------------------------------------
<CAPTION>
                                                           Thirteen Weeks Ended       Twenty-six Weeks Ended
                                                        February 25,  February 24,  February 25,   February 24,
                                                           1995          1996           1995           1996
                                                                (Unaudited)                  (Unaudited)
- ---------------------------------------------------------------------------------------------------------------

<S>                                                      <C>           <C>            <C>           <C>
REVENUES:
  Government Research                                    $1,782,186    $1,652,080     $3,308,144    $3,017,973
  Collaborative Research, License Fees and Royalties        128,801     6,280,418        164,361     6,996,954
  Interest Income and Other                                  57,913       196,988        110,938       327,938

                                                         ----------    ----------     ----------    ----------
       TOTAL REVENUES                                     1,968,900     8,129,486      3,583,443    10,342,865
                                                         ----------    ----------     ----------    ----------

COSTS AND EXPENSES:
  Cost of Government Research                             1,590,143     1,637,420      2,914,411     2,920,104
  Research and Development                                  351,456     1,530,130        607,086     2,609,125
  General and Administrative                                477,038       814,959        955,195     1,326,592
  Noncash Charge for Stock Option Grants                      6,489     1,577,600         12,978     1,579,416
                                                         ----------    ----------     ----------    ----------
       Total Costs and Expenses Including Provision
           for Income Taxes                               2,425,126     5,560,109      4,489,670     8,435,237
                                                         ----------    ----------     ----------    ----------

       NET INCOME (LOSS)                                  ($456,226)   $2,569,377      ($906,227)   $1,907,628
                                                         ----------    ----------     ----------    ----------

NET INCOME (LOSS) PER COMMON SHARE:
  Primary                                                    ($0.04)        $0.15         ($0.08)        $0.12
                                                         ----------    ----------     ----------    ----------
  Fully Diluted                                              -              $0.15         -              $0.11
                                                         ----------    ----------     ----------    ----------

WEIGHTED AVERAGE NUMBER OF COMMON SHARES OUTSTANDING:
  Primary                                                11,778,946    16,604,609     11,778,946    16,325,491
                                                         ----------    ----------     ----------    ----------
  Fully Diluted                                              -         16,861,637         -         16,650,695
                                                         ----------    ----------     ----------    ----------
</TABLE>


See Notes to Consolidated Condensed Financial Statements.


                                       4
<PAGE>   5
<TABLE>
GENOME THERAPEUTICS CORP. AND SUBSIDIARIES
CONSOLIDATED STATEMENTS OF CASH FLOWS
- --------------------------------------------------------------------------------------------
<CAPTION>
                                                                   Twenty-six Weeks Ended
                                                                  February 25,  February 24,
                                                                      1995          1996
                                                                         (Unaudited)
- --------------------------------------------------------------------------------------------

<S>                                                                 <C>          <C>       
Cash Flows from Operating Activities:
Net Income (Loss)                                                   ($906,227)   $1,907,628
Adjustments to Reconcile Net Income (Loss) to Net
    Cash Provided by (Used in) Operating Activities:
      Depreciation and Amortization                                   144,380       313,140
      Deferred Compensation                                            12,978     1,579,416
      Changes in Assets and Liabilities:
          Accounts Receivable                                         (82,912)     (286,704)
          Unbilled Costs and Fees                                     (40,804)      (82,183)
          Prepaid Expenses and Other Current Assets                  (130,521)      (26,887)
          Accounts Payable                                            (45,776)      638,822
          Accrued Expenses                                            232,574       223,600
          Deferred Contract Revenue                                    18,334        90,546
                                                                   ----------  ------------

              Total Adjustments                                       108,253     2,449,750
                                                                   ----------  ------------

              Net Cash Provided by (Used) in Operating Activities    (797,974)    4,357,378
                                                                   ----------  ------------

Cash Flows from Investing Activities:
  Purchases of Marketable Securities                               (3,291,835)   (6,070,048)
  Proceeds from Sale of Marketable Securities                       5,500,000     1,595,000
  (Increase) Decrease in Restricted Cash                                    0        19,158
  Purchases of Equipment and Leasehold Improvements                   (68,844)          418
  (Increase) Decrease in Other Assets                                  (9,778)            0
                                                                   ----------  ------------

        Net Cash Provided by (Used in) Investing Activities         2,129,543    (4,455,472)
                                                                   ----------  ------------
     
Cash Flows from Financing Activities:
  Proceeds from Sale of Common Stock                                        0    36,064,824
  Proceeds from Exercise of Stock Options and Warrants                      0       708,111
  Payments on Capital Lease Obligations                              (150,497)     (262,371)
                                                                   ----------  ------------

        Net Cash Provided by (Used in) Financing Activities          (150,497)   36,510,564
                                                                   ----------  ------------

Net Increase in Cash and Cash Equivalents                           1,181,072    36,412,470
Cash and Cash Equivalents, at Beginning of Period                   1,208,836     5,886,184
                                                                   ----------  ------------

Cash and Cash Equivalents, at End of Period                        $2,389,908   $42,298,654
                                                                   ----------  ------------

Supplemental Disclosure of Cash Flow Information:
  Interest Paid during Period                                         $28,354       $83,302
                                                                   ----------  ------------

Supplemental Schedule of Non-cash Investing Activities:
  Property and Equipment Acquired under Capital Leases               $656,129    $1,385,275
                                                                   ----------  ------------
</TABLE>


See Notes to Consolidated Condensed Financial Statements.


                                       5



<PAGE>   6



Notes to Consolidated Condensed Financial Statements (Unaudited)
- ----------------------------------------------------------------


1.  Basis of Presentation
    ---------------------

The unaudited consolidated condensed financial statements included herein have 
been prepared by the Company, without audit, pursuant to the rules and 
regulations of the Securities and Exchange Commission. In the opinion of
management, the unaudited consolidated financial statements have been prepared
on the same basis as the audited consolidated financial statements and include
all adjustments (consisting only of normal recurring adjustments) necessary for
a fair presentation of interim period results. Certain information and footnote
disclosures normally included in the financial statements prepared in accordance
with generally accepted accounting principles have been condensed or omitted
pursuant to such rules and regulations. The Company believes, however, that its
disclosures are adequate to make the information presented not misleading. The
results of operations for the 26 week period ended February 24, 1996 are not
necessarily indicative of the results to be expected for the full fiscal year.
The accompanying consolidated condensed financial statements should be read in
conjunction with the Company's Form 10-K which was filed with the Securities and
Exchange Commission on November 29, 1995 and as amended on Form 10-K/A on
January 10, 1996.

2.  Net Income (Loss) Per Share
    ---------------------------

Net Income per common and common equivalent share is computed by dividing net 
income by the weighted average number of common and common equivalent shares 
outstanding during the period using the treasury stock method. Net loss per
share is computed by dividing net loss by the weighted average number of common
shares outstanding during the period. Common share equivalents have not been
included in the calculation of net loss per share, as their effects would be
anti-dilutive.

3.  Cash Equivalents and Marketable Securities
    ------------------------------------------

The Company applies Statement of Financial Accounting Standards (SFAS) No. 115,
Accounting for Certain Investments in Debt and Equity Securities. The Company's
cash equivalents and marketable securities are classified as available-for-
sale. Cash equivalents are short-term, highly liquid investments with original 
maturities of less than three months. Marketable securities are investment 
securities with original maturities of greater than three months. Cash 
equivalents are carried at cost which approximates fair market value and 
consist of money market funds, repurchase agreements and debt securities. 
Marketable securities are carried at fair market value which approximates 
amortized cost, accordingly unrealized


                                       6
<PAGE>   7

    holding gains and losses were immaterial. The Company has not recorded any
    realized holding gains or losses on its marketable securities. Marketable
    securities consist of commercial paper and medium term notes with an average
    maturity of nine to fourteen months. The Company has $784,471 and $765,313
    in restricted cash at August 31, 1995 and February 24, 1996, respectively,
    in connection with certain capital lease obligations.

4.  Use of Estimates in the Preparation of Financial Statements
    -----------------------------------------------------------

    The preparation of financial statements in conformity with generally
    accepted accounting principles requires management to make estimates and
    assumptions that affect the reported amounts of assets and liabilities and
    disclosure of contingent assets and liabilities at the date of the financial
    statements and the reported amounts of revenues and expenses during the
    reporting period. Actual results could differ from those estimates.

5.  Capital Lease Obligations
    -------------------------

    The Company has various capital lease line arrangements under which it can
    finance up to $4,000,000 of certain office and laboratory equipment. These
    leases are payable in 36 monthly installments. The interest rate ranges from
    prime (8.25% at February 24, 1996) plus 1% to 11.42%. The Company is
    required to maintain certain restricted cash balances, as defined (see Note
    3). In addition, the Company is required to maintain certain financial
    ratios pertaining to minimum cash balances, tangible net worth, debt to
    tangible net worth and maximum loss. The Company has approximately $692,000
    available under these various capital lease agreements at February 24, 1996.

    Additionally, in connection with its facilities lease, the Company issued a
    $100,000 note payable in September 1994 to its lessor to finance leasehold
    improvements. The note bears interest at 9% and is payable in 60 monthly
    payments of $2,076.

                                       7
<PAGE>   8



6.  Public Offering
    ---------------

    In February 1996, the Company closed a public offering of 3,000,000 shares
    of its Common Stock at $13.00 per share, resulting in proceeds of
    approximately $36,065,000, net of issuance costs. In March 1996, the Company
    sold an additional 450,000 shares of its Common Stock in the underwriter's
    over-allotment, resulting in proceeds of $5,515,000, net of issuance costs.

<TABLE>
    The following selected financial statement information reflects the exercise
    of the options, as described.
<CAPTION>

                                                   February        February
                                                   24, 1996        24, 1996
                                                  (Unaudited)     (Pro-forma)

    <S>                                           <C>             <C>
    Cash and Cash Equivalents                     $42,298,654     $47,814,079
    Total Current Assets                          $50,180,006     $55,695,431
    Total Assets                                  $53,864,525     $59,379,950
    Shareholders' Equity                          $47,569,607     $53,085,032
    Total Liabilities and Shareholders' Equity    $53,864,525     $59,379,950
</TABLE>



7.  Collaborative Agreements
    ------------------------

    Schering-Plough
    ---------------

    In December 1995, the Company entered into a collaboration and license
    agreement with Schering Corporation and Schering-Plough Ltd. (collectively,
    "Schering-Plough") providing for the use by Schering-Plough of the genomic
    sequence of a specified pathogen the Company is sequencing to identify new
    gene targets for development of antibiotics effective against drug-resistant
    infectious organisms. As part of this agreement, the Company granted
    Schering-Plough exclusive access to certain of the Company's genomic
    sequence databases. The Company also granted Schering-Plough a non-exclusive
    license to use the Company's bioinformatics systems for Schering-Plough's
    internal use in connection with the genomic databases licensed to
    Schering-Plough under the agreement and other genomic databases
    Schering-Plough develops or acquires. The Company also agreed to undertake
    certain research efforts to identify bacteria-specific genes essential to
    microbial survival and to develop biological assays to be used by
    Schering-Plough in screening natural product and compound libraries to
    identify antibiotics with new mechanisms of action.


                                       8
<PAGE>   9

    Under the agreement, Schering-Plough made an up-front payment to the Company
    of $3 million. In addition, upon completion of certain development
    milestones, Schering-Plough has agreed to pay the Company a minimum of an
    additional $10.3 million in expense allowances, research funding and
    milestone payments. Subject to the achievement of additional product
    development milestones and Schering-Plough's election to extend the research
    collaboration, Schering-Plough has agreed to pay the Company up to an
    additional approximately $40.5 million (inclusive of the $10.3 million
    referred to in the previous sentence) in expense allowances, research
    funding and milestone payments.

    The agreement grants Schering-Plough exclusive world wide rights to make,
    use and sell pharmaceutical and vaccine products based on the Company's
    genomic database of specified pathogen and on the technology developed in
    the course of the research program. The Company has also granted
    Schering-Plough a right of first negotiation if during the term of the
    research plan the Company desires to enter into a collaboration with a third
    party with respect to the development or sale of any compounds which are
    targeted against, as their primary indication, the pathogen that is the
    principal subject of the Company's agreement with Schering-Plough. The
    Company will be entitled to receive royalties on Schering-Plough's sale of
    therapeutic products and vaccines developed using the technology licensed
    from the Company. Subject to certain limitations, the Company retained the
    rights to make, use and sell diagnostic products developed based on the
    Company's database licensed to Schering-Plough or the technology developed
    in the course of the research program.

    In the 13 week period ended February 24, 1996, the Company recorded $4
    million in collaborative revenue under this agreement, which consisted of
    the $3 million up-front license fee and a $1 million milestone payment.

    Astra AB
    --------

    In August 1995, the Company entered into a collaboration agreement with
    Astra Hassle AB ("Astra") to develop pharmaceutical, vaccine and diagnostic
    products effective against gastrointestinal infection or any other disease
    caused by H. pylori. Under the terms of the agreement, the Company granted
    Astra exclusive access to its H. pylori genomic sequence database and agreed
    to undertake certain research efforts in exchange for a minimum of
    approximately $11 million and up to $22 million in license fees, expense
    allowances, research funding and milestone payments. The agreement granted
    Astra exclusive worldwide rights to make, use and sell products based on the
    Company's H. pylori technology and requires Astra to provide research
    funding to the Company over a minimum period of two and one- half years to
    further develop and annotate the Company's H. pylori genomic sequence
    database, identify therapeutic and vaccine targets and develop appropriate
    biological assays. The Company will also be entitled to receive royalties on
    Astra's sale of any products (i) protected by claims of patents

                                       9
<PAGE>   10

    licensed exclusively to Astra by the Company pursuant to the agreement, or
    (ii) the discovery of which were enabled in a significant manner by the
    genomic database licensed to Astra by the Company.

    In the 13 week period ended February 24, 1996, the Company recorded $2.3
    million in collaborative revenue under this agreement, which consisted of
    $.8 million of collaborative research funding and a $1.5 million milestone
    payment.

    In the 26 week period ended February 24, 1996, the Company recorded $2.9
    million in collaborative revenue under this agreement, which consisted of
    $1.4 million of collaborative research funding and a $1.5 million milestone
    payment.


                                       10



<PAGE>   11


                     Management's Discussion and Analysis of
                  Financial Condition and Results of Operations

OVERVIEW
- --------

The Company is engaged in the field of genomics -- the discovery and
characterization of genes. Currently, the Company's primary activity is genomic
research and development. For the past several years, the Company's primary
source of revenues has been government research grants and contracts and
collaborative agreements with pharmaceutical company partners. The Company
entered into corporate collaborations with Astra Hassle AB ("Astra") relating to
H. Pylori in August 1995 and with Schering Corporation and Schering-Plough, Ltd.
(collectively, "Schering-Plough") in December 1995 providing for the use by
Schering-Plough of the genomic sequence of a specific pathogen that the Company
is sequencing to identify new gene targets for the development of novel
antibiotics.

The Company will not receive significant product revenues on a sustained
basis until such time, if any, at which products based on the Company's research
efforts are commercialized. The Company's product development strategy is to
enter into collaborations with pharmaceutical and biotechnology companies
whereby these corporate partners will provide most of or all of the financial
and other resources required to complete the development and to commercialize
products based on the Company's genomics research in exchange for a variety of
license and milestone payments, research support and royalties. In order for a
product to be commercialized based on the Company's research, it will be
necessary for the collaboration to conduct pre-clinical trials, obtain
regulatory clearances and make manufacturing, distribution and marketing
arrangements. Accordingly, the Company does not expect to receive royalties
based on product revenues for many years.

As of February 24, 1996, the Company had outstanding approximately
$10,382,000 of government grants and research contracts under which services had
yet to be performed over approximately the next 18 to 24 months. The Company's
government grants and contracts are typically funded annually and are subject to
appropriation by the United States Congress each year. Funding may be
discontinued or reduced at any time by the United States Congress. As of
February 24, 1996, the funded portion of these grants and contracts was
$3,627,000. For the 26 week period ended February 25, 1995 and February 24, 1996
revenue recognized pursuant to United States government grants and research
accounted for approximately 92% and 29%, respectively of the Company's total
revenues. The decrease in government research revenue, as a percentage of total
revenues, for the 26 week period ended February 24, 1996 reflects a substantial
increase in revenue derived from the Company's collaborative partnerships. The
Company plans to continue to seek government grants and contracts in the
genomics field and to enter into additional corporate partnering arrangements
with the goal of advancing the 

                                       11

<PAGE>   12

Company's genomic technologies and gene discovery programs and of obtaining
revenues sufficient to cover a portion of the Company's cash requirements. There
can be no assurance that the Company will be able successfully to pursue this
strategy.

The Company has incurred significant losses, since inception, with an
accumulated deficit of approximately $33,267,000 at February 24, 1996. The
Company's results of operations have fluctuated from period to period and may
continue to fluctuate in the future based upon the timing and composition of
funding under existing and new government grants and contracts and collaboration
agreements. The Company is subject to risks common to companies in its industry
including unproven technology and business strategy, availability of, and
competition for, family resources, reliance upon collaborative partners and
others, reliance on United States government funding, history of operating
losses, need for future capital, competition, patent and proprietary rights,
dependence on key personnel, uncertainty of regulatory approval, uncertainty of
pharmaceutical pricing, health care reform and related matters, product
liability exposure, and volatility of the Company's stock price.

Results of Operations
- ---------------------

Thirteen Week Period Ended February 24, 1996 and February 25, 1995
- ------------------------------------------------------------------

Revenue
- -------

Total revenues increased 313% from $1,969,000 for the 13 week period ended
February 25, 1995 to $8,129,000 for the 13 week period ended February 24, 1996.
Government research revenue decreased approximately 7% from $1,782,000 for the
13 week period ended February 25, 1995 to $1,652,000 for the 13 week period
ended February 24, 1996. The decrease in government research revenue for the 13
week period ended February 24, 1996 was primarily attributable to a change in
the mix of government grants and contracts under which services were performed
under grants and contracts which contain provisions for lower overhead
reimbursement rates as well as reduced purchases of equipment. Revenue derived
from government research grants and contracts is generally based upon direct
cost such as labor and laboratory supplies as well as an allocation
for reimbursement of a portion of overhead.

Collaborative research, license fees and royalties increased from $129,000 for
the 13 week period ended February 25, 1995 to $6,280,000 for the 13 week period
ended February 24, 1996, primarily due to $2,253,000 and $4,000,000 in milestone
payments, license fee and sponsored research revenues received under the
Company's collaborations with Astra and Schering-Plough, respectively.


                                       12
<PAGE>   13

Interest and other income increased 240% from $58,000 for the 13 week period
ended February 25, 1995 to $197,000 for the 13 week period ended February 24,
1996 reflecting the increase in funds available for investment as a result of
the Company's payments received under the Astra and Schering-Plough
collaborations.

Cost and Expenses
- -----------------

Total cost and expenses, excluding a $1,578,000 noncash charge for stock option
grants, increased 65% from $2,419,000 for the 13 week period ended February 25,
1995 to $3,983,000 for the 13 week period ended February 24, 1996. Cost of
government and collaborative research consists of payroll and related costs,
laboratory supplies and overhead expenses (including facilities and equipment
expenses). The cost of government research increased 3% from $1,590,000 for the
13 week period ended February 25, 1995 to $1,637,000 for the 13 week period
ended February 24, 1996. Cost of government research, as a percentage of
government research revenue, was 99% for the 13 week period ended February 24,
1996 and 89% for the 13 week period ended February 25, 1995. This increase was
primarily due to a change in the mix of government grants and contracts under
which services were performed during the 13 week period ended February 24, 1996
to grants and contracts which contain provisions for lower overhead
reimbursement rates. Cost of government research, as a percentage of government
research revenue, fluctuates based upon the nature of the government contracts
and grants, the overhead reimbursement rates under such contracts and grants, as
well as changes in the Company's overhead structure.

Research and development expense, which includes both company-sponsored research
and development and research funded pursuant to arrangements with the Company's
corporate collaborators, increased 336% from $351,000 for the 13 week period
ended February 25, 1995 to $1,530,000 for the 13 week period ended February 24,
1996. This increase was primarily related to increased expenses related to the
Company's H. pylori and Staph. pathogen gene discovery programs and some of its
human gene discovery programs. The H. pylori program is currently funded under
the Company's collaborative agreement with Astra. The increase consisted
primarily of increases in payroll and related expenses, laboratory supplies and
overhead expenses. The Company expects to continue to increase research and
development expenditures in fiscal 1996, particularly with respect to its human
gene discovery programs.


                                       13
<PAGE>   14



General and administrative expenses increased 71% from $477,000 for the
13 week period ended February 25, 1995 to $815,000 for the 13 week period ended
February 24, 1996. The increase in general and administrative expenses
for the 13 week period ended February 24, 1996 was primarily due to an increase
in payroll and related expenses, interest expense, legal fees and other
corporate expenses.

In November and December 1995, the Company's Board of Directors granted certain
employees, officers, and directors options to purchase an aggregate of 440,000
shares of Common Stock which were subject to shareholder approval. The options
were granted at exercise prices ranging from $7.25 to $9.56 per share, in each
case, the fair market value of the Common Stock on the date the Company's Board
of Directors granted the option. The Company recorded a noncash deferred
compensation charge of $2,565,000 which represents an amount equal to the
difference between the fair market value of the Common Stock on February 16,
1996, the date of shareholder approval, and the per share exercise price of the
options. The Company recorded $1,578,000 of the $2,565,000 as compensation
expense in the 13 week period ended February 24, 1996. The Company will amortize
the remainder of the deferred compensation over the vesting period of the
underlying options.


Twenty-Six Week Period Ended February 24, 1996 and February 25, 1995
- --------------------------------------------------------------------

Revenue
- -------

Total revenues increased 189% from $3,583,000 for the 26 week period ended
February 25, 1995 to $10,343,000 for the 26 week period ended February 24, 1996.
Government research revenue decreased approximately 9% from $3,308,000 for the
26 week period ended February 25, 1995 to $3,018,000 for the 26 week period
ended February 24, 1996. The decrease in government research revenue for the 26
week period ended February 24, 1996 was primarily attributable to a change in
the mix of government grants and contracts under which services were performed
to grants and contracts which contain provisions for lower overhead
reimbursement rates as well as reduced purchases of equipment.

Collaborative research, license fees and royalties increased from $164,000 for
the 26 week period ended February 25, 1995 to $6,997,000 for the 26 week period
ended February 24, 1996, primarily due to $2,945,000 and $4,000,000 in milestone
payments, license fee and sponsored research revenues received under the
Company's collaboration with Astra and Schering-Plough which began in August
1995 and December 1995, respectively.


                                       14
<PAGE>   15

Interest and other income increased 195% from $111,000 for the 26 week period
ended February 25, 1995 to $328,000 for the 26 week period ended February 24,
1996 reflecting the increase in funds available for investment as a result of
payments received under the Astra and Schering-Plough collaboration agreements.

Cost and Expenses
- -----------------

Total cost and expenses, excluding a $1,579,000 noncash charge for stock option
grants, increased 53% from $4,477,000 for the 26 week period ended February 25,
1995 to $6,856,000 for the 26 week period ended February 24, 1996. Cost of
government and collaborative research consists of payroll and related costs,
laboratory supplies and overhead expenses (including facilities and equipment
expenses). The cost of government research remained relatively consistent from
$2,914,000 for the 26 week period ended November 25, 1994 to $2,920,000 for the
26 week period ended November 15, 1995. Cost of government research, as a
percentage of government research revenue, was 97% for the 26 week period ended
February 24, 1996 and 88% for the 26 week period ended February 25, 1995. This
increase was primarily due to a change in the mix of government grants and
contracts under which services were performed during the 26 week period ended
February 24, 1996 to grants and contracts which contain provisions for lower
overhead reimbursement rates.

Research and development expense, which includes both company-sponsored research
and development and research funded pursuant to arrangements with the Company's
corporate collaborators, increased 330% from $607,000 for the 26 week period
ended February 25, 1995 to $2,609,000 for the 26 week period ended February 24,
1996. This increase was primarily related to increased expenses related to the
Company's H. pylori and Staph. pathogen gene discovery programs and some of its
human gene discovery programs. The H. pylori program is funded currently under
the Company's collaborative agreement with Astra. The increase consisted
primarily of increases in payroll and related expenses, laboratory supplies and
overhead expenses. The Company expects to continue to increase research and
development expenditures in fiscal 1996, particularly with respect to its human
gene discovery programs.

General and administrative expenses increased 39% from $955,000 for the
26 week period ended February 25, 1995 to $1,327,000 for the 26 week period
ended February 24, 1996. The increase in general and administrative
expenses for the 26 week period ended February 24, 1996 was 


                                       15
<PAGE>   16

primarily due to an increase in payroll and related expenses, interest expense,
legal fees and other corporate expenses.

In November and December 1995, the Company's Board of Directors granted certain
employees, officers, and directors options to purchase an aggregate of 440,000
shares of Common Stock which were subject to shareholder approval. The options
were granted at exercise prices ranging from $7.25 to $9.56 per share, in each
case, the fair market value of the Common Stock on the date the Company's Board
of Directors granted the option. The Company recorded a noncash deferred
compensation charge of $2,565,000 which represents an amount equal to the
difference between the fair market value of the Common Stock on February 16,
1996, the date of shareholder approval, and the per share exercise price of the
options. The Company recorded $1,578,000 of the $2,565,000 as compensation
expense in the 26 week period ended February 24, 1996. The Company will amortize
the remainder of the deferred compensation over the vesting period of the
underlying options.

Liquidity and Capital Resources
- -------------------------------

Since September 1, 1992, the Company's primarily sources of cash have been
government grants and contract revenue, revenue from collaborative research
agreements, borrowing under capital leases and proceeds from sale of equity
securities. In fiscal 1995, the Company received net proceeds of approximately
$2,403,000 from the private sale of Common Stock and warrants and the exercise
of stock options. The Company also entered into a collaborative agreement in
August 1995 under which it received $3,500,000 from Astra.

In December 1995, the Company entered into a collaborative agreement under
which it received an up-front license fee of $3,000,000 and a $1,000,000
milestone payment in December 1995 and February 1996, respectively.

In February 1996, the Company closed a public offering of 3,000,000 shares
of its Common Stock at $13.00 per share, resulting in proceeds of approximately
$36,065,000, net of issuance costs. In March 1996, the Company sold an
additional 450,000 shares of its Common Stock in the underwriter's
over-allotment, resulting in proceeds of $5,515,000, net of issuance costs. In
the 26 week period ended February 24, 1996, the Company received proceeds of
$708,000 from the issuance of 327,829 shares of Common Stock resulting from the
exercise of stock options and warrants.

As of February 24, 1996, the Company had cash, cash equivalents and
marketable securities of approximately $49,880,000 (of which approximately
$765,000 is restricted in connection with certain capital lease obligations) and
working capital of approximately $45,405,000. The Company has various
arrangements under which it can finance up to $4,000,000 of certain office and
laboratory equipment and leasehold improvements. Under these arrangements, 


                                       16
<PAGE>   17


the Company is required to maintain certain financial ratios, including minimum
levels of tangible net worth, total indebtedness to tangible net worth, maximum
loss, and minimum restricted cash balances. At February 24, 1996, the Company
had approximately $692,000 available under these arrangements and had an
outstanding balance of approximately $2,493,000 which is repayable over the
three year period ending March 1999.

The Company's operating activities provided cash of approximately
$4,357,000 for the 26 week period ended February 24, 1996 reflecting primarily
the up-front license fee from Schering-Plough of $3,000,000 as well as
milestone payments from both Astra and Schering-Plough totaling $2,500,000.
These payments were partially offset by cash used to fund the Company's
operations. The Company's operating activities used cash of approximately
$798,000 for the 26 week period ended February 25, 1995 primarily to fund the
Company's operating losses.

The Company's investing activities used cash of approximately $4,455,000 for
the 26 week period ended February 24, 1996 for the purchases of marketable
securities. The Company's investing activities provided cash of approximately
$2,130,000 for the 26 week period ended February 25, 1995 primarily from sales
of marketable securities.

The Company's financing activities provided cash of approximately
$36,511,000 for the 26 week period ended February 24, 1996 from the sale of
equity securities and the exercise of stock options and warrants, net of
payments of capital lease obligations. The Company's financing activities for
the 26 week period ended February 25, 1995 used cash of approximately $150,000
primarily for the payment of capital lease obligations.

The Company estimates that it will acquire $1,500,000 of capital equipment
during fiscal 1996, consisting primarily of computer systems, laboratory
equipment and office equipment. The Company plans to utilize capital lease
arrangements to finance the acquisition of this equipment.

At August 31, 1995, the Company had net operating loss and tax credit
carryforwards of approximately $35,007,000 and $1,120,000 respectively. These
losses and tax credits are available to reduce federal taxable income and
federal income taxes, respectively, in future years, if any. These losses and
tax credits are subject to review and possible adjustment by the Internal
Revenue Service and may be limited in the event of certain cumulative changes in
ownership interests of significant shareholders over a three-year period excess
of 50%. The Company does not believe that it has experienced cumulative
ownership changes in excess of 50% or that the consummation of this offering
will result in a cumulative ownership change in excess of 50%. However, there
can be no assurance that ownership changes will not occur in future periods
which will limit the Company's ability to utilize the losses and tax credits.

The Company believes that its existing capital resources are adequate to meet
its cash requirements for at least the next 60 months. There is no assurance,
however, that changes in the Company's plans or events affecting the Company's
operations will not result in accelerated or unexpected expenditures.


The Company may seek additional funding through public or private financing and
expects additional funding through collaborative or other arrangements with
corporate partners. There can be no assurance, however, that additional
financing will be available from any of these sources or will be available on
terms acceptable to the Company.

                                       17
<PAGE>   18

<TABLE>
                                     Part II
                                     -------
<CAPTION>


<S>       <C>
Item 1.   Legal Proceedings
          -----------------

          None

Item 2.   Changes In Securities
          ---------------------

          None

Item 3.   Defaults Upon Senior Securities
          -------------------------------

          None

Item 4.   Submission of Matters to a Vote of Security Holders
          ---------------------------------------------------

          See Insert A

Item 5.   Other Information
          -----------------

          Subsequent to the quarter ended February 24, 1996, the options to
          purchase 450,000 shares of the Company's Common Stock, which were
          granted to the underwriter in connection with the public offering in
          February 1996, were exercised on March 1, 1996. Proforma information
          is included in Note 6 to the Notes to Consolidated Condensed Financial
          Statements.

Item 6.   Exhibits and Reports on Form 8-K
          --------------------------------

       a) Exhibits:
          --------

          None.

       b) Reports on Form 8-K
          -------------------

          None.
</TABLE>


                                       18


<PAGE>   19


                                    Signature



Pursuant to the requirements of the Securities Exchange Act of 1934, the
registrant has caused this report to be signed on its behalf by the undersigned
thereunto duly authorized who also serves in the capacity of principal financial
officer.



                                Genome Therapeutics Corporation


                                    /s/  Fenel M. Eloi
                                ----------------------------

                                        Fenel M. Eloi
                                (Principal Financial Officer)

                                    Date: April 9, 1996


                                       19

<TABLE> <S> <C>

<ARTICLE> 5
<MULTIPLIER> 1,000
<CURRENCY> U.S. DOLLARS
       
<S>                             <C>
<PERIOD-TYPE>                   6-MOS
<FISCAL-YEAR-END>                          AUG-31-1996
<PERIOD-START>                             SEP-01-1995
<PERIOD-END>                               FEB-24-1996
<EXCHANGE-RATE>                                      1
<CASH>                                          42,299
<SECURITIES>                                     6,816
<RECEIVABLES>                                      647
<ALLOWANCES>                                         0
<INVENTORY>                                          0
<CURRENT-ASSETS>                                50,180
<PP&E>                                           5,549
<DEPRECIATION>                                   2,749
<TOTAL-ASSETS>                                  53,865
<CURRENT-LIABILITIES>                            4,775
<BONDS>                                              0
<COMMON>                                         1,680
                                0
                                          0
<OTHER-SE>                                      45,890
<TOTAL-LIABILITY-AND-EQUITY>                    53,865
<SALES>                                         10,015
<TOTAL-REVENUES>                                10,343
<CGS>                                            5,529
<TOTAL-COSTS>                                    6,695
<OTHER-EXPENSES>                                 1,579
<LOSS-PROVISION>                                     0
<INTEREST-EXPENSE>                                  83
<INCOME-PRETAX>                                  1,986
<INCOME-TAX>                                        78
<INCOME-CONTINUING>                                  0
<DISCONTINUED>                                       0
<EXTRAORDINARY>                                      0
<CHANGES>                                            0
<NET-INCOME>                                     1,908
<EPS-PRIMARY>                                      .12
<EPS-DILUTED>                                      .11
        

</TABLE>


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