GENOME THERAPEUTICS CORP
10-Q, 1997-04-15
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: March 1, 1997
                                           -------------

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

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

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

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

                        REGISTRANT'S TELEPHONE NUMBER: (617) 398-2300
                                                       --------------

     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                                    17,660,477
       --------------                           --------------------------
       $.10 PAR VALUE                           Outstanding April 11, 1997




<PAGE>   2



                    Genome Therapeutics Corp. and Subsidiaries


           Index to Financial Information (Unaudited) and Other Information

                                                                          Page
                                                                          -----
Part I
Financial Information  (Unaudited) :

     Consolidated Condensed Balance Sheets as of                           3
         August 31, 1996 and March 1, 1997

     Consolidated Condensed Statements of Operations                       4
         for the 26 week period ended February 24, 1996
         and March 1,1997

     Consolidated Statements of Cash Flows for the                         5
         26 week period ended February 24, 1996
         and March 1,1997

     Notes to Consolidated Condensed Financial                             6-10
         Statements for the 26 week period ended 
         February 24, 1996 and March 1,1997

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


Part II
Other Information:
         Other Information                                                18

         Signature                                                        19


                                       2

<PAGE>   3

GENOME THERAPEUTICS CORP. AND SUBSIDIARIES
<TABLE>
CONSOLIDATED CONDENSED BALANCE SHEETS
<CAPTION>
- -----------------------------------------------------------------------------------------------------
                                                                     August 31,              March 1,
                                                                          1996                  1997
                                                                               (Unaudited)
- -----------------------------------------------------------------------------------------------------
<S>                                                                <C>                   <C>        
ASSETS:
Current Assets:
   Cash and cash equivalents                                       $10,679,287           $15,365,723
   Marketable securities                                            17,429,488            26,336,305
   Interest receivable                                               1,296,657             1,231,255
   Accounts receivable                                               1,338,418               435,877
   Unbilled costs and fees                                             345,773               528,596
   Prepaid expenses and other current assets                           552,903               402,056
                                                                   -----------           -----------

        Total current assets                                        31,642,526            44,299,812

Equipment and leasehold improvements, at cost:
   Laboratory and scientific equipment                               6,403,221             9,863,132
   Leasehold improvements                                            1,939,545             1,945,748
   Office equipment and furniture                                      581,533               749,278
   Construction-in-progress                                             77,027               100,128
                                                                   -----------           -----------
                                                                     9,001,326            12,658,286
   Less-Accumulated depreciation
       and amortization                                              3,266,068             4,163,904
                                                                   -----------           -----------
                                                                     5,735,258             8,494,382

Restricted cash                                                        195,500               395,500
Long-term marketable securities                                     25,464,287            11,313,488
 
Other assets                                                           241,446               290,108
                                                                   -----------           -----------

        Total assets                                               $63,279,017           $64,793,290
                                                                   ===========           ===========


LIABILITIES AND SHAREHOLDERS' EQUITY:
Current Liabilities:
   Accounts payable                                                $   864,279           $   434,585
   Accrued expenses                                                  1,731,220             1,652,077
   Deferred contract revenue                                         1,035,504             2,459,938
   Current maturities of capital lease obligations                   2,106,882             2,833,696
                                                                   -----------           -----------
        Total current liabilities                                    5,737,885             7,380,296
                                                                   -----------           -----------

Capital lease obligations, net of current maturities                 3,228,374             4,479,496

Shareholders' equity                                                54,312,758            52,933,498
                                                                   -----------           -----------

        Total liabilities and shareholders' equity                 $63,279,017           $64,793,290
                                                                   ===========           ===========
</TABLE>



See Notes to Consolidated Condensed Financial Statements.


                                       3



<PAGE>   4

GENOME THERAPEUTICS CORP. AND SUBSIDIARIES
<TABLE>
CONSOLIDATED STATEMENTS OF OPERATIONS
<CAPTION>
- ---------------------------------------------------------------------------------------------------------------------------
                                                           Thirteen Weeks Ended                 Twenty-six Weeks Ended
                                                       February 24,         March 1,        February 24,           March 1,
                                                               1996            1997                1996               1997
                                                                 (Unaudited)                          (Unaudited)
- ---------------------------------------------------------------------------------------------------------------------------

<S>                                                     <C>              <C>                 <C>                <C>        
REVENUES:
  Collaborative research, license fees and royalties    $ 6,287,083      $ 4,787,798         $ 7,016,184        $ 6,828,835
  Government research                                     1,652,080        1,336,153           3,017,973          3,310,563
  Interest income                                           190,323          756,678             308,708          1,529,758
                                                        -----------      -----------         -----------        -----------

       Total revenues                                     8,129,486        6,880,629          10,342,865         11,669,156
                                                        -----------      -----------         -----------        -----------

COSTS AND EXPENSES:
  Research and development                                1,530,130        4,487,912           2,609,125          8,221,076
  Cost of government research                             1,637,420        1,429,670           2,920,104          3,277,316
  General, selling and administrative                       772,215        1,013,253           1,243,290          1,870,885
  Interest expense                                           42,744          145,553              83,302            271,479
  Noncash charge for stock option grants                  1,577,600           18,525           1,579,416             37,050
                                                        -----------      -----------         -----------        -----------
 
       Total costs and expenses                           5,560,109        7,094,913           8,435,237         13,677,806
                                                        -----------      -----------         -----------        -----------
                                                                                          
       NET INCOME (LOSS)                                $ 2,569,377      $  (214,284)        $ 1,907,628        $(2,008,650)
                                                        ===========      ===========         ===========        =========== 

NET INCOME (LOSS) PER COMMON SHARE:
  Primary                                                     $0.15           ($0.01)              $0.12             ($0.11)
                                                        ===========      ===========         ===========        =========== 
  Fully diluted                                               $0.15                -               $0.11                  -
                                                        ===========      ===========         ===========        =========== 
                                                                                                            
WEIGHTED AVERAGE NUMBER OF COMMON AND COMMON
EQUIVALENT SHARES OUTSTANDING:
  Primary                                                16,604,609       17,566,018          16,325,491         17,521,094
                                                        ===========      ===========         ===========        =========== 
  Fully diluted                                          16,861,637                -          16,650,695                  -
                                                        ===========      ===========         ===========        =========== 
</TABLE>


See Notes to Consolidated Condensed Financial Statements.


                                       4



<PAGE>   5

GENOME THERAPEUTICS CORP. AND SUBSIDIARIES
<TABLE>
CONSOLIDATED STATEMENTS OF CASH FLOWS
<CAPTION>
- -------------------------------------------------------------------------------------------------------------------------------
                                                                                                   Twenty-six Weeks Ended
                                                                                             February 24,             March 1,
                                                                                                     1996                 1997
                                                                                                        (Unaudited)
- -------------------------------------------------------------------------------------------------------------------------------
                                                                                                             
<S>                                                                                           <C>                 <C>          
Cash Flows from Operating Activities:
Net Income (loss)                                                                             $ 1,907,628         $ (2,008,650)
Adjustments to reconcile net loss to net
    cash used in operating activities:
      Depreciation and amortization                                                               313,140              981,286
      Deferred compensation                                                                     1,579,416               37,050
      Changes in assets and liabilities:                                                                     
          Interest receivable                                                                    (128,131)              65,402
          Accounts receivable                                                                    (158,573)             902,541
          Unbilled costs and fees                                                                 (82,183)            (182,823)
          Prepaid expenses and other current assets                                               (26,887)             150,847
          Accounts payable                                                                        638,822             (429,694)
          Accrued expenses                                                                        223,600              (79,143)
          Deferred contract revenue                                                                90,546            1,424,434
                                                                                              -----------          -----------

                   Total adjustments                                                            2,449,750            2,869,900
                                                                                              -----------          -----------

                   Net cash provided by operating activities                                    4,357,378              861,250
                                                                                              -----------          -----------

Cash Flows from Investing Activities:                                                   
  Purchases of marketable securities                                                           (6,070,048)          (8,105,018)
  Proceeds from sale of marketable securities                                                   1,595,000           13,349,000
  (Increase) decrease in restricted cash                                                           19,158             (200,000)
  Purchases of equipment and leasehold improvements                                                   418             (409,128)
  Increase in other assets                                                                              0              (56,064)
                                                                                              -----------          -----------

        Net cash provided by (used in) investing activities                                    (4,455,472)           4,578,790
                                                                                              -----------          -----------

Cash Flows from Financing Activities:
  Proceeds from sale of common stock and warrants                                              36,064,824                    0
  Proceeds from exercise of stock options and warrants                                            708,111              592,339
  Payments on capital lease obligations                                                          (262,371)          (1,345,943)
                                                                                              -----------          -----------

        Net cash provided by (used in) financing activities                                    36,510,564             (753,604)
                                                                                              -----------          -----------

Net Increase in Cash and Cash Equivalents                                                      36,412,470            4,686,436
Cash and Cash Equivalents, at beginning of period                                               5,886,184           10,679,287
                                                                                              -----------          -----------

Cash and Cash Equivalents, at end of period                                                   $42,298,654          $15,365,723
                                                                                              ===========          ===========

Supplemental Disclosure of Cash Flow Information:                                                            
  Taxes paid during period                                                                    $     1,350          $    23,798
                                                                                              ===========          ===========
  Interest paid during period                                                                 $    83,302          $   271,479
                                                                                              ===========          ===========

Supplemental Disclosure of Non-cash Investing Activities:
  Property and equipment acquired under capital leases                                        $ 1,385,275          $ 3,725,508
                                                                                              ===========          ===========
</TABLE>



See Notes to Consolidated Condensed Financial Statements.


                                       5



<PAGE>   6





NOTES TO CONSOLIDATED CONDENSED FINANCIAL STATEMENTS (UNAUDITED)
- ----------------------------------------------------------------


1.   BASIS OF PRESENTATION
     ---------------------

     The 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 condensed 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 March 1, 1997 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 27, 1996 and as amended on
     Form 10-K/A on December 4, 1996.


2.   NET INCOME (LOSS) PER COMMON AND COMMON EQUIVALENT 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 method. Net loss
     per share is computed by dividing the net loss by the weighted average
     number of common shares outstanding during the year.

3.   NEW ACCOUNTING STANDARD
     -----------------------

     In March 1997, the Financial Accounting Standards Board (FASB) issued SFAS
     No. 128, Earnings Per Share. SFAS No. 128 establishes standards for
     computing and presenting earnings per share and applies to entities with
     publicly held common stock or potential common stock. This statement is
     effective for fiscal years ending after December 15, 1997 and early
     adoption is not permitted. When adopted, the statement will require
     restatement of prior years' earnings per share. The Company will adopt this
     statement for its fiscal year ended August 31, 1998 and does not believe
     that the effect of the adoption of this standard would be materially
     different from the amounts presented in the accompanying statements of
     operations.


                                       6
<PAGE>   7



     In October 1995, FASB issued SFAS No. 123, Accounting for Stock-Based
     Compensation. The Company has determined that it will continue to account
     for stock-based compensation for employees under Accounting Principles
     Board (APB) Opinion No. 25 and elect the disclosure-only alternative under
     SFAS No. 123. The Company will be required to disclose the pro forma net
     income or loss and per share amounts in the notes to the financial
     statements using the fair-value-based method for year ending August 31,
     1997, with comparable disclosures for the year ended August 31, 1996. The
     Company has not determined the impact of these pro forma adjustments.

4.   CASH, CASH EQUIVALENTS AND MARKETABLE SECURITIES
     ------------------------------------------------

     The Company applies SFAS No. 115, Accounting for Certain Investments in
     Debt and Equity Securities. The Company's cash equivalents and marketable
     securities are classified as held-to-maturity, as the Company has the
     positive intent and ability to hold these securities to maturity. 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 market value, and
     consist of money market funds, repurchase agreements and debt securities.
     Marketable securities are recorded at amortized cost which approximates
     market value. The Company has not recorded any realized holding gains or
     losses on its marketable securities. Marketable securities consist of
     commercial paper and U.S. Government debt securities. The Company has
     restricted cash of $195,500 and $395,500 at August 31, 1996 and March 1,
     1997, respectively, in connection with certain capital lease obligations.

5.   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.

6.   CAPITAL LEASE OBLIGATIONS
     -------------------------

     On February 28, 1997, the Company entered into a leasing arrangement under
     which it can finance up to $6.0. million of laboratory, computer and office
     equipment. The lease is payable in 48 monthly installments at a variable
     interest rate of prime plus one-quarter of one percent (.25%). At any time
     during the term of this agreement, the Company may elect to convert to a
     fixed rate loan at the prevailing interest rate. The Company is required to
     maintain certain restricted cash balances, as defined (see Note 4). In
     addition, the Company is required to maintain certain financial ratios


                                       7
<PAGE>   8

     pertaining to minimum cash balances, tangible net worth and debt service
     coverage. The Company has approximately $5.3 million available under this
     capital lease agreement at March 1, 1997.

     The Company has other capital lease line arrangements under which it
     financed certain laboratory, computer and office equipment. These leases
     are payable in 36 monthly installments. The interest rates range from 7.52%
     to 11.42%. The Company is required to maintain certain restricted cash
     balances, as defined (see Note 4). 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 no funds available under these capital lease agreements at
     March 1, 1997.

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
     Company's Staph. aureus genomic database 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.

     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.


                                       8
<PAGE>   9



     The agreement grants Schering-Plough exclusive world wide rights to make,
     use and sell pharmaceutical and vaccine products based on the Company's
     Staph. aureus genomic database 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 Staph. aureus. 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.

     For the 13 week period and 26 week period ended March 1, 1997, the Company
     recorded revenue of $1.0 million and $1.8 million, respectively, under this
     agreement, which consisted of sponsored research funding. For the 13 week
     period and 26 week period ended February 24, 1996, the Company recorded
     revenue of $4.0 million under this agreement, which consisted of a license
     fee and a milestone payment.

     The Company entered into its second research collaboration agreement with
     Schering-Plough in December 1996. This agreement calls for the use of
     genomics to discover new therapeutics for treating asthma. As part of the
     agreement, the Company will employ its high-throughput positional cloning,
     bioinformatics, and genomics sequencing capabilities to identify genes and
     associated proteins that can be utilized by Schering-Plough to develop new
     pharmaceuticals. Under this agreement, the Company has granted
     Schering-Plough exclusive access to (i) certain gene sequence databases
     made available under this research program, (ii) information made available
     to the Company under certain third party research agreements, (iii) an
     exclusive worldwide right and license to make, use and sell pharmaceutical
     and vaccine products based on the technology developed in the course of the
     research program. The Company will retain all rights to develop and
     commercialize diagnostic products that may result from this collaboration.

     Under the agreement, Schering-Plough made an initial payment for a license
     fee and an expense allowance to the Company. Schering-Plough is also
     required to fund a research program for a minimum number of years with an
     option to extend. In addition, upon completion of certain scientific
     developments, Schering-Plough will make milestone payments to the Company,
     as well as pay royalties to the Company based upon sales of therapeutics
     products developed from this collaboration. If all milestones are met and
     the research program continues for its full term, total payments to the
     Company will approximate $67 million, excluding royalties. Of the total
     potential payments, approximately $22.5 million represents license fees and
     research payments and $44.5 million represents milestone payments based on
     achievement of research and product development objectives.


                                       9
<PAGE>   10



     For the 13 and 26 week periods ended March 1, 1997, the Company
     recorded revenue of $2.8 million under this agreement, which consisted
     primarily of a license fee, expense allowance and subcontract activity.

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 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.

     For the 13 week period ended March 1, 1997, the Company recorded revenue of
     $1.0 million, which consisted of sponsored research funding and a milestone
     payment. For the 13 week period ended February 24, 1996, the Company
     recorded revenue of $2.3 million under this agreement which also consisted
     of sponsored research funding and a milestone payment.

     For the 26 week period ended March 1, 1997, the Company recorded revenue of
     $1.6 million, which consisted of sponsored research funding and a milestone
     payment. For the 26 week period ended February 24, 1996, the Company
     recorded revenue of $2.9 million under this agreement which also consisted
     of sponsored research funding and a 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 have 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 Company's Staph. aureus genomic database to identify new
gene targets for the development of novel antibiotics. In December 1996, the
Company entered into its second research collaboration with Schering-Plough to
identify genes and associated proteins that can be utilized by Schering-Plough
to develop new pharmaceuticals for treating asthma.

As of March 1, 1997, the Company had outstanding approximately $3,900,000 of
government grants and research contracts under which services were yet to be
performed. These grants and contracts call for services to be performed over the
next 36 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 Congress.
As of March 1, 1997, the funded portion of these grants and contracts was
$3,737,000. For the 26 week periods ended February 24, 1996 and March 1, 1997,
revenue recognized pursuant to United States government grants and research
accounted for approximately 29% and 28%, respectively, of the Company's total
revenues. 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 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 to pursue this strategy successfully.


                                       11
<PAGE>   12



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 collaborators to conduct preclinical tests and 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.

The Company has incurred significant losses, since inception, with an
accumulated deficit of approximately $35,262,000 at March 1, 1997. 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 collaborative 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 MARCH 1, 1997
- --------------------------------------------------------------

REVENUE
- -------

Total revenues decreased 15% from $8,129,000 for the 13 week period ended
February 24, 1996 to $6,881,000 for the 13 week period ended March 1, 1997.
Collaborative research, license fees and royalties decreased 24% from $6,287,000
for the 13 week period ended February 24, 1996 to $4,788,000 for the 13 week
period ended March 1, 1997. The decrease was primarily due to $5,500,000 of
license fees and milestone payments received in the prior year under the
Company's collaboration agreements with Schering-Plough and Astra which began in
December 1995 and August 1995, respectively. This decrease was partially offset
by an increase in sponsored research revenue earned under the Company's
collaborative research programs, a milestone payment achieved under the Astra
agreement, as well as a license fee and expense allowance earned under the
Company's asthma program with Schering-Plough which began in December 1996.


                                       12
<PAGE>   13


Government research revenue decreased 19% from $1,652,000 for the 13 week period
ended February 24, 1996 to $1,336,000 for the 13 week period ended March 1,
1997. The decrease in government research revenue was primarily attributable to
a higher concentration of research effort on Company sponsored research and
development programs, particularly the microbial genetic database program.
Revenue derived from government research grants and contracts is generally based
upon direct cost such as labor, laboratory supplies, as well as an allocation
for reimbursement of a portion of overhead.

Interest income increased from $190,000 for the 13 week period ended February
24, 1996 to $757,000 for the 13 week period ended March 1, 1997 reflecting an
increase in funds available for investment as a result of proceeds received from
the sale of common stock through a public offering in February 1996.

COST AND EXPENSES
- -----------------

Total cost and expenses increased 28% from $5,560,000 for the 13 week period
ended February 24, 1996 to $7,095,000 for the 13 week period ended March 1,
1997. Research and development expense, which includes company-sponsored
research and development and research funded pursuant to arrangements with the
Company's corporate collaborators increased 193% from $1,530,000 for the 13 week
period ended February 24, 1996 to $4,488,000 for the 13 week period ended March
1, 1996. The increase in research and development cost was primarily related to
the Company's expansion of its pathogen, microbial genetic database and gene
discovery programs. 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, particularly with
respect to its human gene discovery and microbial genetic database programs.

The cost of government research decreased 13% from $1,637,000 for the 13 week
period ended February 24, 1996 to $1,430,000 for the 13 week period ended March
1, 1997. The decrease in cost of government research was due to an decrease in
work performed on existing government research programs. Cost of government
research, as a percentage of government research revenue, was 99% for the 13
week period ended February 24, 1996 and 107% for the 13 week period ended March
1, 1997. The increase was primarily due to an increase in overhead expenses
associated with the expansion of laboratory space, such as facility expenses
and related depreciation.

General, selling, and administrative expenses increased 31% from $772,000 for 
the 13 week period ended February 24, 1996 to $1,013,000 for the 13 week period
ended March 1, 1997. The increase in general, selling, and administrative
expenses was primarily due to increases in payroll and related expenses, legal
fees and facility expenses.

Interest expense increased from $43,000 for the 13 week period ended February
24, 1996 to $146,000 for the 13 week period ended March 1, 1997 reflecting an
increase in the Company's capital lease obligations from year to year.


                                       13
<PAGE>   14



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 deferred compensation 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
$19,000 and $1,578,000 of the $2,565,000, as compensation expense in the 13 week
periods ended March 1, 1997 and February 24, 1996, respectively.

TWENTY-SIX WEEK PERIOD ENDED FEBRUARY 24, 1996 AND MARCH 1, 1997
- ----------------------------------------------------------------

REVENUE
- -------

Total revenues increased 13% from $10,343,000 for the 26 week period ended
February 24, 1996 to $11,669,000 for the 26 week period ended March 1, 1997.
Collaborative research, license fees and royalties decreased slightly by 3% from
$7,016,000 for the 26 week period ended February 24, 1996 to $6,829,000 for the
26 week period ended March 1, 1997.

Government research revenue increased 10% from $3,018,000 for the 26 week period
ended February 24, 1996 to $3,311,000 for the 26 week period ended March 1,
1997. The increase in government research revenue was primarily attributable to
an increase in work performed on existing government grants and contracts,
primarily in the first quarter of this year. Revenue derived from government
research grants and contracts is generally based upon direct cost such as labor,
laboratory supplies, as well as an allocation for reimbursement of a portion of
overhead.

Interest income increased from $309,000 for the 26 week period ended February
24, 1996 to $1,530,000 for the 26 week period ended March 1, 1997 reflecting the
increase in funds available for investment as a result of proceeds received from
the sale of common stock through a public offering in February 1996.

COST AND EXPENSES
- -----------------

Total cost and expenses increased 62% from $8,435,000 for the 26 week period
ended February 24, 1996 to $13,678,000 for the 26 week period ended March 1,
1997. Research and development expense, which includes company-sponsored
research and development and research funded pursuant to arrangements with the
Company's corporate collaborators increased 215% from $2,609,000 for the 26 week
period ended February 24, 1996 to $8,221,000 for the 26 week period ended 
March 1, 1996. The increase in research and development cost was primarily 
related to the Company's expansion of its pathogen, microbial genetic database 
and gene discovery programs. The increase consisted primarily of increases in 
payroll and related expenses, laboratory supplies, and overhead expenses. 


                                       14
<PAGE>   15

The Company expects to continue to increase research and development
expenditures, particularly with respect to its human gene discovery and
microbial genetic database programs.

The cost of government research increased 12% from $2,920,000 for the 26 week
period ended February 24, 1996 to $3,277,000 for the 26 week period ended March
1, 1997. The increase in cost of government research was due to an increase in
work performed on existing government research programs, Cost of government
research, as a percentage of government research revenue, was 97% for the 26
week period ended February 24, 1996 and 99% for the 26 week period ended March
1, 1997.

General, selling, and administrative expenses increased 12% from $1,243,000 for
the 26 week period ended February 24, 1996 to $1,871,000 for the 26 week period
ended March 1, 1997. The increase in general, selling, and administrative
expenses was primarily due to increases in payroll and related expenses, legal
fees and facility expenses.

Interest expense increased from $83,000 for the 26 week period ended February
24, 1996 to $271,000 for the 26 week period ended March 1, 1997 reflecting an
increase in the Company's capital lease obligations from year to year.

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 deferred compensation 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
$37,000 and $1,578,000 of the $2,565,000, as compensation expense in the 26 week
periods ended March 1, 1997 and February 24, 1996, respectively.

LIQUIDITY AND CAPITAL RESOURCES
- -------------------------------

The Company's primary sources of cash have been revenue from government grants
and contract, revenue from collaborative research agreements, borrowing under
capital leases and proceeds from sale of equity securities. In August 1995, the
Company entered into a collaborative agreement with Astra under which it
received an up-front payment of $3,500,000.

In fiscal 1996, the Company received $4,421,000 in collaborative payments from
Astra consisting of a milestone payment and sponsored research. In December
1995, the Company entered into a collaborative agreement with Schering-Plough
under which it received a $7,250,000 consisting of an up-front license fee,
milestone payments and sponsored research through August 31, 1996.


                                       15
<PAGE>   16


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
$36,007,000, 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.
Additionally, the Company received proceeds of $1,311,000 from the issuance of
534,831 shares of common stock resulting from the exercise of stock options and
warrants during fiscal 1996.

In December 1996, the Company entered into a second collaborative agreement with
Schering-Plough under which it received a total of $4,041,000 in an up-front
license fee, expense allowance and sponsored research funding. The Company also
received $2,748,000 in sponsored research payments under its other collaborative
agreements with Schering-Plough and Astra for the 26 week period ended March 1,
1997.

As of March 1, 1997, the Company had cash, cash equivalents, restricted cash and
long and short-term marketable securities of approximately $53,411,000. The
Company has various arrangements under which it can finance certain office and
laboratory equipment and leasehold improvements. Under these arrangements, 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 March 1, 1997, the Company had
approximately $5,340,000 available under these arrangements and had an
outstanding balance of approximately $7,313,000 which is repayable over the four
year period ending December 2001.

The Company's operating activities provided cash of approximately $861,000 for
the 26 week period ended March 1, 1997 primarily from the up-front payment of
$4,041,000 received from Schering-Plough (described above), partially offset by
cash used to fund the Company's operations. The Company's operating activities
provided cash of approximately $4,357,000 for the 26 week period ended February
24, 1996 primarily from the up-front license fee from Schering-Plough, as well
as milestone payments from both Astra and Schering-Plough. These payments were
partially offset by cash used to fund the Company's operations.

The Company's investing activities provided cash of approximately $4,579,000 for
the 26 week period ended March 1, 1997 from the sale of marketable securities,
partially offset by purchases of marketable securities, and property and
equipment. The Company investing activities for the 26 week period ended
February 24, 1996 used cash of approximately $4,455,000 for purchases of
marketable securities.

Financing activities used cash of approximately $754,000 for the 26 week period
ended March 1, 1997 primarily for payments of capital lease obligations,
partially offset by the exercise of stock options. Financing activities provided
cash of approximately $36,511,000 for the 26 week period ended February 24, 1996
primarily from the sale of equity securities, exercise of stock options,
partially offset by the payments of capital lease obligations.


                                       16
<PAGE>   17


Capital expenditures totaled $3,741,000 during the 26 week period ended March 1,
1997. The Company currently estimates that it will acquire an additional
$2,054,000 in capital equipment in fiscal 1997, consisting primarily of
laboratory, computer and office equipment. The Company also plans to consolidate
its operations at its Beaver Street facility at an estimated cost of $6,000,000
which consists of laboratory and office renovations. The Company plans to
utilize capital lease arrangements to finance substantially all of these
capital expenditures which will be incurred through October 1997.

At August 31, 1996, the Company had net operating loss and tax credit
carryforwards of approximately $33,968,000 and $1,128,000 respectfully. 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 in
excess of 50%. The Company does not believe it has experienced 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 the foreseeable future. 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.

Statements in this Form 10Q that are not strictly historical are "forward
looking" statements as defined in the Private Securities Litigation Reform Act
of 1995. The actual results may differ from those projected in the forward
looking statement due to risks and uncertainties that exist in the Company's
operations and business environment, described more fully in the Company's
Annual Report on Forms 10-K and 10-K/A for the year ended August 31, 1996, filed
with the Securities and Exchange Commission.


                                       17
<PAGE>   18



                                     Part II
                                     -------


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
         -----------------

         None.

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

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

            None.

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

            None.



                                       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 Corp.
         
         
                                /s/ Fenel M. Eloi
                          -----------------------------
                                  Fenel M. Eloi
                          (Principal Financial Officer)
         
                              Date: April 15, 1997


                                       19
<PAGE>   20


                                    INSERT A
                                    --------



<TABLE>
The Company's Special Meeting in lieu of an Annual Meeting was held on February
7, 1997. At the meeting, shareholders took the following actions:

1) Election of Directors
<CAPTION>

                                                    Shares Voted
   Name of Nominee                            For           Withhold Authority
   ---------------                        ----------        ------------------
   <S>                                    <C>                    <C>   
   Robert J. Hennessey                    15,440,526              55,713
   Philip J. Leder                        15,390,476             105,763
   Lawrence Levy                          15,425,076              71,163
   Donald J. McCarren                     15,378,576             117,663
   Steven M. Rauscher                     15,431,526              64,713
</TABLE>

<TABLE>
2) To ratify the selection of Arthur Andersen LLP as the Company's auditors for
   the fiscal year ending August 31, 1997.
<CAPTION>

   For                       Against               Abstain           No Voting
   ----------                -------               -------           ---------
   <S>                       <C>                    <C>                  <C>
   15,282,726                135,869                77,644               0
</TABLE>




                                       20







WARNING: THE EDGAR SYSTEM ENCOUNTERED ERROR(S) WHILE PROCESSING THIS SCHEDULE.

<TABLE> <S> <C>

<ARTICLE> 5
<CIK> 0000356830
<NAME> 
<MULTIPLIER> 1,000
<CURRENCY> U.S.DOLLARS
       
<S>                             <C>
<PERIOD-TYPE>                   6-MOS
<FISCAL-YEAR-END>                          AUG-31-1997
<PERIOD-START>                             SEP-01-1996
<PERIOD-END>                               MAR-01-1997
<EXCHANGE-RATE>                                      1
<CASH>                                          15,366
<SECURITIES>                                    37,650
<RECEIVABLES>                                      436
<ALLOWANCES>                                         0
<INVENTORY>                                          0
<CURRENT-ASSETS>                                44,300
<PP&E>                                          12,658
<DEPRECIATION>                                   4,164
<TOTAL-ASSETS>                                  64,793
<CURRENT-LIABILITIES>                            7,380
<BONDS>                                              0
                                0
                                          0
<COMMON>                                         1,765
<OTHER-SE>                                      51,168
<TOTAL-LIABILITY-AND-EQUITY>                    64,793
<SALES>                                              0
<TOTAL-REVENUES>                                11,669
<CGS>                                                0
<TOTAL-COSTS>                                   13,407
<OTHER-EXPENSES>                                     0
<LOSS-PROVISION>                                     0
<INTEREST-EXPENSE>                                 271
<INCOME-PRETAX>                                      0
<INCOME-TAX>                                         0
<INCOME-CONTINUING>                                  0
<DISCONTINUED>                                       0
<EXTRAORDINARY>                                      0
<CHANGES>                                            0
<NET-INCOME>                                   (2,009)
<EPS-PRIMARY>                                   (0.11)
<EPS-DILUTED>                                        0
        

</TABLE>


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