<PAGE>

                                                                 EXHIBIT 10.17.2

CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY BRACKETS,
HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.

June 30, 2003

Mr. Kevin Corcoran
President and Chief Executive Officer
Lynx Therapeutics, Inc.
25861 Industrial Blvd.
Hayward, CA 94545, USA

         Re: Amendment No. 2 to Collaboration Agreement

Dear Mr. Corcoran:

         This letter (the "Second Amendment") shall be effective on [ * ], 2003
("Effective Date") and will serve to confirm and memorialize our agreement to
amend, in certain respects, that certain Collaboration Agreement (the
"Collaboration Agreement"), effective as of October 1, 2000 between Takara Bio,
Inc. ("Takara Bio"), as successor-in-interest to Takara Shuzo Co., Ltd., and
Lynx Therapeutics, Inc. ("Lynx")(as amended by that certain Amendment No. 1 to
Collaboration Agreement, dated December 19, 2002 (the "First Amendment")).
Please note that all terms used herein, which are not otherwise defined, shall
be given the definition ascribed to such term in the Collaboration Agreement.

         1.       Lynx hereby grants to Takara Bio an exclusive, fully paid-up,
non-transferable, irrevocable, perpetual, royalty-free license to all of the
patents, technology and software which Lynx owns in the Territory relevant to
Megaclone(TM), Megasort(TM), and MPSS(TM), and all of the Lynx technology and
know-how listed in Exhibit 1 of the Collaboration Agreement for the purpose of
providing MPSS(TM) and Megasort(TM) services to customers in the Territory and
to permit Takara Bio to make or have made, import or distribute and sell
Microarrays containing nucleic acid sequences identified by Megasort(TM) or
MPSS(TM) technologies to customers in the Territory; all as more particularly
set forth on [ * ]. Lynx shall use its reasonable efforts to prosecute and
maintain such patents, and to transfer all current PCT applications to each
country

<PAGE>

comprising the Territory at Lynx' expense and for no additional consideration.
In the event that Lynx or any current or successor entity is unable to maintain
such patents and patent applications in the Territory, Lynx shall take or cause
to be taken all steps necessary to transfer to Takara Bio (or its designated
affiliate) all right, title and interest in and to these patents and patent
applications in the Territory. All language in the Collaboration Agreement,
which is contrary to or inconsistent with the rights granted in this paragraph,
is hereby deemed deleted.

         2.       Lynx agrees to provide Takara Bio, [ * ], with a total of [ *
] weeks of training and instruction in the use of the technology and know-how
related to the [ * ] on mutually agreeable dates in Hayward, California to
enable Takara Bio to [ * ]; provided that Takara Bio shall be responsible for
related travel and lodging costs incurred by Takara Bio in connection with the
training and instruction provided hereunder. In addition, Lynx agrees to provide
Takara Bio and Takara Bio is required to obtain directly from Lynx, on a first
priority basis after satisfying Lynx's internal needs, with the [ * ] necessary
for the [ * ] upon mutually agreed upon terms and conditions, which shall, in no
event, be less favorable than those accorded to any other commercial customers
of Lynx. In the event that Lynx is unable, for any reason whatsoever, to supply
such [ * ] to Takara Bio, Lynx shall, at its own expense, assist Takara in
arranging for a supply of the [ * ] from an alternate source, which is
reasonably acceptable to Takara Bio.

         3.       Lynx, as of the Effective Date of this Second Amendment,
hereby waives and releases Takara Bio from (i) the payment of the technology
access fee in the amount of US$1 million otherwise payable by Takara Bio on [ *
], 2003 pursuant to paragraph 4(b) of the First Amendment, (ii) the equity
investment in the amount of US$1 million which Takara Bio would otherwise be
required to make on [ * ], 2003 pursuant to paragraph 5(b) of the First
Amendment, (iii) the payment of the technology access fee in the amount of US$1
million otherwise payable by Takara Bio on [ * ], 2004 pursuant to paragraph
4(c) of the First Amendment, (iv) the equity investment in the amount of US$1
million which Takara Bio would otherwise be required to make on [ * ], 2004
pursuant to paragraph 5(c) of the First Amendment and (v) payment of the running
royalties which Takara Bio would otherwise be obligated to make pursuant to
Article

[ * ] = CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.

                                       2

<PAGE>

9.1(a) and (b) of the Collaboration Agreement for the remainder of the term of
the Collaboration Agreement.

         4.       Lynx shall provide Takara Bio with three [ * ] instruments for
MPSS analysis within [ * ] of the Effective Date of this Second Amendment.

         5.       Within [ * ] after the Effective Date, Lynx shall file a
registration statement under the Securities Act of 1933, as amended ("Securities
Act"), and use its best efforts to cause such registration statement to be
declared effective by the Securities and Exchange Commission as promptly
thereafter as is practicable to permit or facilitate the sale and distribution
of [ * ] Takara Bio's shares of Lynx common stock on a continuous basis pursuant
to Rule 415 under the Securities Act. No other shares of Lynx common stock or
other securities shall be included in such registration, whether held by other
stockholders or newly-issued by Lynx, without the prior written consent of
Takara Bio. Lynx shall, subject to applicable law or applicable interpretations
of the staff of the SEC, use its best efforts to keep the registration statement
continuously effective until two years after the last purchase of shares of Lynx
common stock by Takara Bio or such shorter period ending when (i) all shares of
Lynx common stock covered by the registration statement have been sold by Takara
Bio or otherwise cease to be outstanding or (ii) all such shares are eligible to
be sold pursuant to Rule 144(k) under the Securities Act and Lynx has complied
with all requirements that would permit such sale under Rule 144(k). Lynx shall
pay for all expenses incurred in connection with the registration including,
without limitation, all filing, registration and qualification fees, printing
expenses, and Lynx' legal and accounting fees. Takara Bio shall pay for all
expenses related to underwriting discounts and selling commissions, if any, in
connection with the sale of any shares of Lynx common stock by Takara Bio under
the registration statement.

         6.       In consideration of the rights granted herein, Takara Bio
agrees to make a payment of US$3 million to Lynx no later than [ * ] following
the Effective Date of this Second Amendment.

         If the foregoing is consistent with Lynx' understanding of our
agreement,

[ * ] = CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.

                                       3

<PAGE>

please execute the enclosed copy of this letter and return it to Takara Bio.

                                                 Very truly yours,

                                                 /s/ Ikunoshin Kato
                                                 -------------------------------
                                                 Ikunoshin Kato
                                                 President and C.E.O.
                                                 Takara Bio, Inc.

Confirmed and agreed to: Lynx Therapeutics, Inc.

By: /s/ Kevin P. Corcoran
    -------------------------------------
Kevin P. Corcoran
President & CEO
Lynx Therapeutics, Inc.

[ * ]

[ * ] = CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY
BRACKETS, HAS BEEN OMITTED AND FILED SEPARATELY WITH THE SECURITIES AND EXCHANGE
COMMISSION PURSUANT TO RULE 24b-2 OF THE SECURITIES EXCHANGE ACT OF 1934, AS
AMENDED.

                                       4