GENOME THERAPEUTICS CORP
SC 13G/A, 1999-12-29
IN VITRO & IN VIVO DIAGNOSTIC SUBSTANCES
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<PAGE>

                       SECURITIES AND EXCHANGE COMMISSION
                              WASHINGTON, DC 20549


                                  SCHEDULE 13G
                                 (RULE 13d-102)


             INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT
           TO RULES 13d-1(b), (c) AND (d) AND AMENDMENTS THERETO FILED
                                PURSUANT TO 13d-2
                               (AMENDMENT NO. 1)1


                         GENOME THERAPEUTICS CORPORATION
                         -------------------------------
                                (Name of Issuer)

                                  COMMON STOCK
                         ------------------------------
                         (Title of Class of Securities)

                                   372430 10 8
                                 (CUSIP NUMBER)

                                December 22, 1999
                                -----------------
             (Date of Event Which Requires Filing of this Statement)


Check the appropriate box to designate the rule pursuant to which this Schedule
is filed:

                  / /      Rule 13d-1(b)
                  /X/      Rule 13d-1(c)
                  / /      Rule 13d-1(d)

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

(1)      The remainder of this cover page shall be filled out for a reporting
person's initial filing on this form with respect to the subject class of
securities, and for any subsequent amendment containing information which would
alter disclosures provided in a prior cover page.

         The information required on the remainder of this cover page shall not
be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange
Act of 1934 or otherwise subject to the liabilities of that section of the Act
but shall be subject to all other provisions of the Act (however, SEE the
NOTES).


<PAGE>


- ------------------------------                   -------------------------------
CUSIP NO. 372430 10 8                 13G                PAGE 2 OF 8 PAGES
- ------------------------------                   -------------------------------


- --------------------------------------------------------------------------------
   1       NAME OF REPORTING PERSON:
                    BIOTECHNOLOGY VALUE FUND, L.P.
           I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

- --------------------------------------------------------------------------------
   2       CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) /X/ (b) / /
- --------------------------------------------------------------------------------
   3       SEC USE ONLY

- --------------------------------------------------------------------------------
   4       CITIZENSHIP OR PLACE OF ORGANIZATION
                    DELAWARE
- --------------------------------------------------------------------------------
    NUMBER            5      SOLE VOTING POWER
      OF                          0
    SHARES           ----------------------------------------------------------
 BENEFICIALLY         6      SHARED VOTING POWER
   OWNED BY                       322,940
     EACH            ----------------------------------------------------------
  REPORTING           7      SOLE DISPOSITIVE POWER
    PERSON                        0
     WITH            ----------------------------------------------------------
                      8      SHARED DISPOSITIVE POWER
                                  322,940
- --------------------------------------------------------------------------------
   9       AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                    322,940
- --------------------------------------------------------------------------------
   10      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
           CERTAIN SHARES*                                               / /
- --------------------------------------------------------------------------------
   11      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                    1.8%
- --------------------------------------------------------------------------------
   12      TYPE OF REPORTING PERSON*
                    PN
- --------------------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!

<PAGE>

- ------------------------------                   -------------------------------
CUSIP NO. 372430 10 8                 13G                PAGE 3 OF 8 PAGES
- ------------------------------                   -------------------------------


- --------------------------------------------------------------------------------
   1       NAME OF REPORTING PERSON:
                    BIOTECHNOLOGY VALUE FUND II, L.P.
           I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

- --------------------------------------------------------------------------------
   2       CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) /X/ (b) / /
- --------------------------------------------------------------------------------
   3       SEC USE ONLY

- --------------------------------------------------------------------------------
   4       CITIZENSHIP OR PLACE OF ORGANIZATION
                    DELAWARE
- --------------------------------------------------------------------------------
    NUMBER            5      SOLE VOTING POWER
      OF                          0
    SHARES           ----------------------------------------------------------
 BENEFICIALLY         6      SHARED VOTING POWER
   OWNED BY                       282,515
     EACH            ----------------------------------------------------------
  REPORTING           7      SOLE DISPOSITIVE POWER
    PERSON                        0
     WITH            ----------------------------------------------------------
                      8      SHARED DISPOSITIVE POWER
                                  282,515
- --------------------------------------------------------------------------------
   9       AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON
                    282,515
- --------------------------------------------------------------------------------
   10      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
           CERTAIN SHARES*                                               / /
- --------------------------------------------------------------------------------
   11      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                    1.5%
- --------------------------------------------------------------------------------
   12      TYPE OF REPORTING PERSON*
                    PN
- --------------------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!


<PAGE>

- ------------------------------                   -------------------------------
CUSIP NO. 372430 10 8                 13G                PAGE 4 OF 8 PAGES
- ------------------------------                   -------------------------------


- --------------------------------------------------------------------------------
   1       NAME OF REPORTING PERSON:
                    BVF PARTNERS L.P.
           I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY):

- --------------------------------------------------------------------------------
   2       CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) /X/ (b) / /
- --------------------------------------------------------------------------------
   3       SEC USE ONLY

- --------------------------------------------------------------------------------
   4       CITIZENSHIP OR PLACE OF ORGANIZATION
                    DELAWARE
- --------------------------------------------------------------------------------
    NUMBER            5      SOLE VOTING POWER
      OF                          0
    SHARES           ----------------------------------------------------------
 BENEFICIALLY         6      SHARED VOTING POWER
   OWNED BY                       780,185
     EACH            ----------------------------------------------------------
  REPORTING           7      SOLE DISPOSITIVE POWER
    PERSON                        0
     WITH            ----------------------------------------------------------
                      8      SHARED DISPOSITIVE POWER
                                  780,185
- --------------------------------------------------------------------------------
   9       AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING
           PERSON
                    780,185
- --------------------------------------------------------------------------------
   10      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
           CERTAIN SHARES*                                                 / /
- --------------------------------------------------------------------------------
   11      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                    4.3%
- --------------------------------------------------------------------------------
   12      TYPE OF REPORTING PERSON*
                    PN
- --------------------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!

<PAGE>

- ------------------------------                   -------------------------------
CUSIP NO. 372430 10 8                 13G                PAGE 5 OF 8 PAGES
- ------------------------------                   -------------------------------


- --------------------------------------------------------------------------------
   1       NAME OF REPORTING PERSON
                    BVF INC.
           I.R.S. IDENTIFICATION NO. OF ABOVE PERSON (ENTITIES ONLY)

- --------------------------------------------------------------------------------
   2       CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                               (a) /X/ (b) / /
- --------------------------------------------------------------------------------
   3       SEC USE ONLY

- --------------------------------------------------------------------------------
   4       CITIZENSHIP OR PLACE OF ORGANIZATION
                    DELAWARE
- --------------------------------------------------------------------------------
    NUMBER            5      SOLE VOTING POWER
      OF                          0
    SHARES            ----------------------------------------------------------
 BENEFICIALLY         6      SHARED VOTING POWER
   OWNED BY                       780,185
     EACH             ----------------------------------------------------------
  REPORTING           7      SOLE DISPOSITIVE POWER
    PERSON                        0
     WITH             ----------------------------------------------------------
                      8      SHARED DISPOSITIVE POWER
                                  780,185
- --------------------------------------------------------------------------------
    9      AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING
           PERSON
                    780,185
- --------------------------------------------------------------------------------
   10      CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES
           CERTAIN SHARES*                                                 / /
- --------------------------------------------------------------------------------
   11      PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9
                    4.3%
- --------------------------------------------------------------------------------
   12      TYPE OF REPORTING PERSON*
                    IA, CO
- --------------------------------------------------------------------------------

                     * SEE INSTRUCTIONS BEFORE FILLING OUT!

<PAGE>

- ------------------------------                   -------------------------------
CUSIP NO. 372430 10 8                 13G                PAGE 6 OF 8 PAGES
- ------------------------------                   -------------------------------


ITEM 1(a).    NAME OF ISSUER:

              Genome Therapeutics Corp.

ITEM 1(b).    ADDRESS OF ISSUER'S PRINCIPAL EXECUTIVE OFFICES:

              100 Beaver Street
              Waltham, MA  02154

ITEM 2(a)     NAME OF PERSON FILING:

              This amendment to Schedule 13G is being filed on behalf of the
              following persons*:

                  (i)      Biotechnology Value Fund, L.P. ("BVF")
                  (ii)     Biotechnology Value Fund II, L.P. ("BVF2")
                  (iii)    BVF Partners, L.P.  ("Partners")
                  (iv)     BVF Inc. ("BVF Inc.")

                  *        Attached as Exhibit A is a copy of an agreement
                           between the Persons filing (as specified hereinabove)
                           that this amendment to Schedule 13G is being filed
                           on behalf of each of them.

ITEM 2(b).    ADDRESS OF PRINCIPAL BUSINESS OFFICE:

              The principal business office of the persons comprising the
group filing this Schedule 13G is located at 227 West Monroe Street, Suite 4800,
Chicago, Illinois 60606.

ITEM 2(c).    CITIZENSHIP:

              BVF:                       a Delaware limited partnership
              BVF2:                      a Delaware limited partnership
              Partners:                  a Delaware limited partnership
              BVF Inc.:                  a Delaware corporation

ITEM 2(d).    TITLE OF CLASS OF SECURITIES:

              The class of securities beneficially owned by the persons
filing this amendment to Schedule 13G is common stock.

ITEM 2(e).    CUSIP NUMBER:

              372430 10 8

ITEM 3.       IF THIS STATEMENT IS FILED PURSUANT TO RULE 13d-1(C), CHECK
              THIS BOX: /X/


<PAGE>

- ------------------------------                   -------------------------------
CUSIP NO. 372430 10 8                 13G                PAGE 7 OF 8 PAGES
- ------------------------------                   -------------------------------


ITEM 4.       OWNERSHIP:

              The information in items 1 and 5 through 11 on the cover pages
(pp.2 - 5) on this amendment to Schedule 13G is hereby incorporated by
reference.

ITEM 5.  OWNERSHIP OF FIVE PERCENT OR LESS OF A CLASS:

              If this statement is being filed to report the fact that as of
the date hereof the reporting person has ceased to be the beneficial owner of
more than five percent of the class of securities check the following. /X/

ITEM 6.       OWNERSHIP OF MORE THAN FIVE PERCENT ON BEHALF OF ANOTHER PERSON:

              BVF shares voting and dispositive power over the shares of the
Stock it beneficially owns with Partners. BVF2 also shares voting and
dispositive power over the shares of the stock it beneficially owns with
Partners. Partners and BVF Inc. share voting and dispositive power over the
shares of the Stock they beneficially own with, in addition to BVF and BVF2,
certain managed accounts on whose behalf Partners, as investment manager,
purchased such shares. BVF Inc. also shares voting and dispositive power over
the shares of the Stock they beneficially own with, in addition to BVF, BVF2
and Partners, certain other managed accounts on whose behalf BVF Inc., as
investment manager, purchased such shares. None of the managed accounts
individually own more than 5% of the Stock of the Issuer.

ITEM 7.       IDENTIFICATION AND CLASSIFICATION OF THE SUBSIDIARY WHICH
              ACQUIRED THE SECURITY BEING REPORTED ON BY THE PARENT HOLDING
              COMPANY:

              Not applicable.

ITEM 8.       IDENTIFICATION AND CLASSIFICATION OF MEMBERS OF A
              GROUP:

              Not applicable.

ITEM 9.       NOTICE OF DISSOLUTION OF GROUP:

              Not applicable.

<PAGE>

- ------------------------------                   -------------------------------
CUSIP NO. 372430 10 8                 13G                PAGE 8 OF 8 PAGES
- ------------------------------                   -------------------------------


ITEM 10.      CERTIFICATION

              By signing below I certify that, to the best of my knowledge
and belief, the securities referred to above were not acquired and are not held
for the purpose of or with the effect of changing or influencing the control of
the issuer of the securities and were not acquired and are not held in
connection with or as a participant in any transaction having that purpose or
effect.


              After reasonable inquiry and to the best of my knowledge and
belief, I certify that the information set forth in this statement is true,
complete and correct.

Dated:   December 29, 1999


                  BIOTECHNOLOGY VALUE FUND, L.P.

                  By:      BVF Partners L.P., its general partner

                           By:      BVF Inc., its general partner


                                    By: /s/Mark N. Lampert
                                       -----------------------------
                                            Mark N. Lampert
                                            President



                  BIOTECHNOLOGY VALUE FUND II, L.P.

                  By:      BVF Partners L.P., its general partner

                           By:      BVF Inc., its general partner


                                    By: /s/Mark N. Lampert
                                       -----------------------------
                                            Mark N. Lampert
                                            President



                  BVF PARTNERS L.P.

                  By:      BVF Inc., its general partner


                           By: /s/Mark N. Lampert
                               ----------------------------
                                    Mark N. Lampert
                                    President

                  BVF INC.


                  By: /s/Mark N. Lampert
                     -------------------------------
                           Mark N. Lampert
                           President



<PAGE>

                                                                   EXHIBIT 99.1

                                    EXHIBIT A

                        AGREEMENT REGARDING JOINT FILING


         The undersigned, Biotechnology Value Fund, L.P., a Delaware limited
partnership, Biotechnology Value Fund II, L.P., a Delaware limited
partnership, and BVF Partners L.P., a Delaware limited partnership, and BVF
Inc., a Delaware corporation, hereby agree and acknowledge that the
information required by Amendment 1 to Schedule 13G, to which this Agreement
is attached as an exhibit, is filed on behalf of each of them. The
undersigned further agree that any further amendments or supplements thereto
shall also be filed on behalf of each of them.

Dated:  December 29, 1999

                  BIOTECHNOLOGY VALUE FUND, L.P.

                  By:      BVF Partners L.P., its general partner

                           By:      BVF Inc., its general partner


                                    By: /s/Mark N. Lampert
                                       -----------------------------
                                            Mark N. Lampert
                                            President



                  BIOTECHNOLOGY VALUE FUND II, L.P.

                  By:      BVF Partners L.P., its general partner

                           By:      BVF Inc., its general partner


                                    By: /s/Mark N. Lampert
                                       -----------------------------
                                            Mark N. Lampert
                                            President


                  BVF PARTNERS L.P.

                  By:      BVF Inc., its general partner


                           By: /s/Mark N. Lampert
                              -------------------------------
                                    Mark N. Lampert
                                    President

                  BVF INC.


                  By: /s/Mark N. Lampert
                     ------------------------------------
                           Mark N. Lampert
                           President



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