<PAGE>

                                                                   EXHIBIT 10.27



                         REGISTRATION RIGHTS AGREEMENT

        REGISTRATION RIGHTS AGREEMENT (this "Agreement") is dated as of April
__, 2002 by and between Lynx Therapeutics, Inc., a Delaware corporation (the
"Company"), and the Persons listed on Schedule A hereto (each, an "Investor" and
collectively, the "Investors").

                                 R E C I T A L S

        A. The Investors have made an investment in the Company by acquiring
shares of the Company's common stock (the "Common Stock") and warrants to
acquire shares of Common Stock (the "Warrants") (collectively, the Common Stock
and Warrants together, the "Securities").

        B. In connection with such purchase of the Securities, and to induce the
Investors to consummate such purchase of the Securities, the Company has agreed
to enter into this Agreement and to grant to the Investors the rights set forth
herein.

                                    AGREEMENT

        NOW, THEREFORE, in consideration of the foregoing and of the mutual
promises and covenants contained herein, the Investors and the Company (each, a
"Party", and collectively, the "Parties") agree as follows:

        1. Definitions. For purposes of this Statement:

           "Exchange Act" means the Securities Exchange Act of 1934, as amended,
or any successor statute.

           "Holder" means (i) the Investors, (ii) the partners, members or
stockholders of each Investor collectively provided that such partners, members
or stockholders act through each such Investor or its successor and (iii) any
person or entity to whom an Investor or any person or entity identified in
clause (ii) of this definition sells, transfers or assigns any of such Person's
Registrable Securities, other than in a sale pursuant to Rule 144 under the
Securities Act or a registration effected pursuant to this Agreement.

           "Register," "registered," and "registration" refer to an underwritten
registration effected by preparing and filing with the Securities and Exchange
Commission (the "Commission") a registration statement or similar document in
compliance with the Securities Act, and the declaration or ordering by the
Commission of effectiveness of such registration statement or document.

           "Registration Expenses" means all expenses in connection with the
Company's performance of or compliance with its obligations under this
Agreement, including, without limitation, all (i) registration, qualification
and filing fees; (ii) fees, costs and expenses of compliance with securities or
blue sky laws (including reasonable fees, expenses and disbursements of counsel
in connection with blue sky qualifications of the Registrable Securities); (iii)
printing expenses; (iv) messenger, telephone and delivery expenses; (v) fees,


<PAGE>


expenses and disbursements of counsel for the Company and of all independent
certified public accountants retained by the Company (including the expenses of
any special audit and "cold comfort" letters required by or incident to such
performance); (vi) Securities Act liability insurance if the Company so desires;
(vii) fees, expenses and disbursements of any other individuals or entities
retained by the Company in connection with the registration of the Registrable
Securities; (viii) fees, costs and expenses incurred in connection with the
listing of the Registrable Securities on each national securities exchange or
automated quotation system on which the Company has made application for the
listing of its Common Stock; and (ix) internal expenses of the Company
(including, without limitation, all salaries and expenses of its officers and
employees performing legal or accounting duties and expenses of any annual
audit). Registration Expenses shall not include selling commissions, discounts
or other compensation paid to underwriters or other agents or brokers to effect
the sale of Registrable Securities.

           "Registrable Securities" means any shares of Common Stock of the
Company owned by any Holder or that may be acquired by any Holder upon the
exercise of any Warrant owned by any Holder.

           "Securities Act" means the Securities Act of 1933, as amended, or any
successor statute.

        2. Registration of the Securities. The Company shall:

           (a) within fifteen (15) days of the date of this Agreement, prepare
and file with the Commission a registration statement with respect to such
Registrable Securities on any form that may be utilized by the Company and that
shall permit the disposition of the Registrable Securities, and use its best
efforts to cause such registration statement to become effective within
forty-five (45) days of the date of this Agreement and remain effective
thereafter as provided herein; provided, that prior to filing a registration
statement or prospectus or any amendments or supplements thereto, including
documents incorporated by reference after the initial filing of any registration
statement, the Company will furnish to each of the Investors and their
respective counsel copies of all such documents proposed to be filed
sufficiently in advance of filing to provide them with a reasonable opportunity
to review such documents and comment thereon. If at the time the Company files
the registration statement registering the Registrable Securities pursuant to
this Section 2, the sale or other disposition of such Registrable Securities by
the Holders may be made pursuant to a registration statement on Form S-3 (or any
successor form that permits the incorporation by reference of future filings by
the Company under the Exchange Act), such registration statement shall be filed
as a "shelf" registration statement pursuant to Rule 415 under the Securities
Act (or any successor rule). Any such shelf registration shall cover the
disposition of all Registrable Securities in one or more underwritten offerings,
block transactions, broker transactions, at-market transactions and in such
other manner or manners as may be specified by the Investors. The Company shall
use its best efforts to keep such "shelf" registration continuously effective as
long as the delivery of a prospectus is required under the Securities Act in
connection with the disposition of the Registrable Securities registered thereby
and in furtherance of such obligation, shall supplement or amend such
registration statement if, as and when required by the rules, regulations and
instructions applicable to the form used by the Company for such registration or
by the Securities Act or by any other rules and regulations thereunder
applicable to shelf registrations;



                                      -2-
<PAGE>

           (b) prepare and file with the Commission such amendments (including
post-effective amendments) and supplements to such registration statement and
the prospectus used in connection therewith as may be necessary to keep such
registration statement effective and current and to comply with the provisions
of the Securities Act with respect to the sale or other disposition of all
Registrable Securities covered by such registration statement, including such
amendments (including post-effective amendments) and supplements as may be
necessary to reflect the intended method of disposition by the prospective
seller or sellers of such Registrable Securities;

           (c) subject to receiving reasonable assurances of confidentiality,
for so long as the registration statement remains effective, make available for
inspection by the selling holders of Registrable Securities being offered and
their respective counsel, such financial and other information and books and
records of the Company, and cause the officers, directors, employees, counsel
and independent certified public accountants of the Company to respond to such
inquiries as shall be reasonably necessary, in the judgment of such counsel, to
conduct a reasonable investigation within the meaning of Section 11 of the
Securities Act;

           (d) promptly notify the selling holders of Registrable Securities and
confirm such advice in writing, (i) when such registration statement or the
prospectus included therein or any prospectus amendment or supplement or
post-effective amendment has been filed, and, with respect to such registration
statement or any post-effective amendment, when the same has become effective,
(ii) of any comments by the Commission, by the National Association of
Securities Dealers Inc. ("NASD"), and by the blue sky or securities commissioner
or regulator of any state with respect thereto or any request by any such entity
for amendments or supplements to such registration statement or prospectus or
for additional information, (iii) of the issuance by the Commission of any stop
order suspending the effectiveness of such registration statement or the
initiation or threatening of any proceedings for that purpose, (iv) of the
receipt by the Company of any notification with respect to the suspension of the
qualification of the Registrable Securities for sale in any jurisdiction or the
initiation or threatening of any proceeding for such purpose, or (v) at any time
when a prospectus is required to be delivered under the Securities Act, that
such registration statement, prospectus, prospectus amendment or supplement or
post-effective amendment, or any document incorporated by reference in any of
the foregoing, contains an untrue statement of a material fact or omits to state
any material fact required to be stated therein or necessary to make the
statements therein, in light of the circumstances under which they are made, not
misleading;

           (e) furnish to each selling holder of Registrable Securities being
offered prospectuses or amendments or supplements thereto, in such quantities as
they may reasonably request and as soon as practicable, that update previous
prospectuses or amendments or supplements thereto;

           (f) use its best efforts to (i) register or qualify the Registrable
Securities to be included in a registration statement hereunder under such other
securities laws or blue sky laws of such jurisdictions within the United States
of America as any selling holder of such Registrable Securities shall reasonably
request, (ii) keep such registrations or qualifications in effect for so long as
the registration statement remains in effect and (iii) take any and all such
actions as may be reasonably necessary or advisable to enable such holder to
consummate the



                                      -3-
<PAGE>


disposition in such jurisdictions of such Registrable Securities owned by such
holder; provided, however, that the Company shall not be required for any such
purpose to (x) qualify generally to do business as a foreign corporation in any
jurisdiction wherein it would not otherwise be required to qualify but for the
requirements of this Section 2(h), (y) subject itself to taxation in any such
jurisdiction or (z) consent to general service of process in any such
jurisdiction;

           (g) cause all such Registrable Securities to be listed or accepted
for quotation on each securities exchange or automated quotation system on which
the Company's Common Stock then trades; and

           (h) otherwise use best efforts to comply with all applicable
provisions of the Securities Act, and rules and regulations of the Commission.

        3. Transfer of Shares After Registration; Suspension.

           (a) Except in the event that paragraph (b) below applies, the Company
shall: (i) if deemed necessary by the Company upon advice of counsel, prepare
and file from time to time with the Commission a post-effective amendment to the
registration statement or a supplement to the related prospectus or a supplement
or amendment to any document incorporated therein by reference or file any other
required document so that such registration statement will not contain an untrue
statement of a material fact or omit to state a material fact required to be
stated therein or necessary to make the statements therein not misleading, and
so that, as thereafter delivered to purchaser of the Registrable Securities
being sold thereunder, such prospectus will not contain an untrue statement of a
material fact or omit to state a material fact required to be stated therein or
necessary to make the statements therein, in light of the circumstances under
which they were made, not misleading; (ii) provide each Holder copies of any
documents filed pursuant to Section 3(a)(i); and (iii) inform each Holder that
the Company has complied with its obligations in Section 3(a)(i) (or that, if
the Company has filed a post-effective amendment to the registration statement
which has not yet been declared effective, the Company will notify each Holder
to that effect, will use its reasonable efforts to secure the effectiveness of
such post-effective amendment as promptly as possible and will promptly notify
each Holder pursuant to Section 3(a)(i) hereof when the amendment has become
effective).

           (b) Subject to paragraph (c) below, in the event: (i) of any request
by the Commission or any other federal or state governmental authority during
the period of effectiveness of the registration statement for amendments or
supplements to a registration statement or related prospectus or for additional
information; (ii) of the issuance by the Commission or any other federal or
state governmental authority of any stop order suspending the effectiveness of a
registration statement or the initiation of any proceedings for that purpose;
(iii) of the receipt by the Company of any notification with respect to the
suspension of the qualification or exemption from qualification of any of the
Registrable Securities for sale in any jurisdiction or the initiation of any
proceeding for such purpose; or (iv) of any event or circumstance which
necessitates the making of any changes in the registration statement or
prospectus, or any document incorporated or deemed to be incorporated therein by
reference, so that, in the case of the registration statement, it will not
contain any untrue statement of a material fact or any omission to state a
material fact required to be stated therein or necessary to make the statements
therein not misleading, and that in the case of the prospectus, it will not



                                      -4-
<PAGE>

contain any untrue statement of a material fact or any omission to state a
material fact required to be stated therein or necessary to make the statements
therein, in the light of the circumstances under which they were made, not
misleading; then the Company shall deliver a certificate in writing to each
Holder (the "Suspension Notice") to the effect of the foregoing and, upon
receipt of such Suspension Notice, a Holder will refrain from selling any
Registrable Securities pursuant to the registration statement (a "Suspension")
until such Holder's receipt of copies of a supplemented or amended prospectus
prepared and filed by the Company, or until it is advised in writing by the
Company that the current prospectus may be used, and has received copies of any
additional or supplemental filings that are incorporated or deemed incorporated
by reference in any such prospectus. In the event of any Suspension, the Company
will use its reasonable efforts to cause the use of the prospectus so suspended
to be resumed as soon as reasonably practicable after delivery of a Suspension
Notice to each such Holder.

           (c) Notwithstanding the foregoing paragraphs of this Section 3, a
Holder shall not be prohibited from selling the Registrable Securities under the
registration statement as a result of Suspensions on more than two occasions of
not more than 30 days each in any twelve-month period.

           (d) For so long as a Suspension is not then in effect, a Holder may
sell the Registrable Securities under the registration statement, provided that
it arranges for delivery of a current prospectus to the transferee of such
Registrable Securities. Upon receipt of a request therefor, the Company has
agreed to provide an adequate number of current prospectuses to such Holder and
to supply copies to any other parties requiring such prospectuses.

        4. Indemnification. With respect to the Registrable Securities included
in the registration statement pursuant to this Agreement:

           (a) the Company will indemnify each Holder who participates in such
registration, each of its officers and directors and partners and such Holder's
separate legal counsel and independent accountants, and each person controlling
such Holder within the meaning of Section 15 of the Securities Act, and each
underwriter, if any, and each person who controls any underwriter within the
meaning of Section 15 of the Securities Act, against all expenses, claims,
losses, damages or liabilities (or actions in respect thereof), including any of
the foregoing incurred in settlement of any litigation, commenced or threatened,
arising out of or based on any untrue statement (or alleged untrue statement) of
a material fact contained in any registration statement, prospectus, offering
circular or other document, or any amendment or supplement thereto, incident to
any such registration, qualification or compliance, or based on any omission (or
alleged omission) to state therein a material fact required to be stated therein
or necessary to make the statements therein, in light of the circumstances in
which they were made, not misleading, or any violation by the Company of any
rule or regulation promulgated under the Securities Act applicable to the
Company in connection with any such registration, qualification or compliance,
and the Company will reimburse each such Holder, each of its officers and
directors and partners and such Holder's separate legal counsel and independent
accountants and each person controlling such Holder, each such underwriter and
each person who controls any such underwriter, for any legal and any other
expenses reasonably incurred in connection with investigating, preparing or
defending any such claim, loss, damage, liability or action, provided that the
Company will not be liable in any such case to the extent that any such claim,
loss,



                                      -5-
<PAGE>

damage, liability or expense arises out of or is based on any untrue statement
or omission or alleged untrue statement or omission, made in reliance upon and
in conformity with written information furnished to the Company by an instrument
duly executed by such Holder or underwriter and stated to be specially for use
therein.

           (b) Each Holder will, if Registrable Securities held by such Holder
are included in the securities as to which such registration, qualification or
compliance is being effected, indemnify the Company, each of its directors and
officers and its legal counsel and independent accountants, each underwriter, if
any, of the Company's securities covered by such a registration statement, each
person who controls the Company or such underwriter within the meaning of
Section 15 of the Securities Act, and each such other Holder, each of its
officers and directors and each person controlling such Holder within the
meaning of Section 15 of the Securities Act, against all claims, losses, damages
and liabilities (or actions in respect thereof) arising out of or based on any
untrue statement (or alleged untrue statement) of a material fact contained in
any such registration statement, prospectus, offering circular or other
document, or any omission (or alleged omission) to state therein a material fact
required to be stated therein or necessary to make the statement therein not
misleading, and will reimburse the Company, such other Holders, such directors,
officers, persons, underwriters or control persons for any legal or any other
expenses reasonably incurred in connection with investigating or defending any
such claim, loss, damage, liability or action, in each case to the extent, but
only to the extent, that such untrue statement (or alleged untrue statement) or
omission (or alleged omission) is made in such registration statement,
prospectus, offering circular or other document in reliance upon and in
conformity with written information furnished to the Company by an instrument
duly executed by such Holder and stated to be specifically for use therein.

           (c) Each party entitled to indemnification under this Section 6 (the
"Indemnified Party") shall give notice to the party required to provide
indemnification (the "Indemnifying Party") promptly after such Indemnified Party
has actual knowledge of any claim as to which indemnity may be sought provided
that failure to give such prompt notice shall not relieve the Indemnifying Party
of its obligations hereunder unless it is materially prejudiced thereby, and
shall permit the Indemnifying Party to assume the defense of any such claim or
any litigation resulting therefrom, provided that counsel for the Indemnifying
Party, who shall conduct the defense of such claim or litigation, shall be
approved by the Indemnified Party (whose approval shall not unreasonably be
withheld). Such Indemnified Party shall have the right to employ separate
counsel in any such action and to participate in the defense thereof, but the
fees and expenses of such counsel shall be that of such Indemnified Party unless
(i) the Indemnifying Party has agreed to pay such fees and expenses or (ii) the
Indemnifying Party shall have failed to assume the defense of such action or
proceeding and employ counsel reasonably satisfactory to such Indemnified Party
in any such action or proceeding or (iii) the named parties to any such action
or proceeding (including any impleaded parties) include both such Indemnified
Party and the Indemnifying Party and such Indemnified Party shall have been
advised by counsel that there may be one or more legal defenses available to
such Indemnified Party which are different from or additional to those available
to the Indemnifying Party (in which case, if such Indemnified Party notifies the
Indemnifying Party in writing of an election to employ separate counsel at the
expense of the Indemnifying Party, the Indemnifying Party shall not have the
right to assume the defense of such action or proceeding on behalf of such
Indemnified Party, it being understood, however, that the Indemnifying Party
then shall have the right to employ separate counsel at its



                                      -6-
<PAGE>

own expense and to participate in the defense thereof, and shall not, in
connection with any one such action or proceeding or separate but substantially
similar or related actions or proceedings in the same jurisdiction arising out
of the same general allegations or circumstances, be liable for the reasonable
fees and expenses of more than one separate firm of attorneys at any time for
all Indemnified Parties, which firm shall be designated in writing by a majority
of the Indemnified Parties who are eligible to select such counsel). No
Indemnifying Party, in the defense of any such claim or litigation, shall,
except with the consent of each Indemnified Party, consent to entry of any
judgment or enter into any settlement which does not include as an unconditional
term thereof the giving by the claimant or plaintiff to such Indemnified Party
of a release from all liability in respect to such claim or litigation. No
Indemnified Party may consent to entry of any judgment or enter into any
settlement without the prior written consent of the Indemnifying Party.

           (d) If the indemnification provided for in this Section 6 is held by
a court of competent jurisdiction to be unavailable to an Indemnified Party with
respect to any loss, liability, claim, damage or expense referred to herein,
then the Indemnifying Party, in lieu of indemnifying the Indemnified Party,
shall contribute to the amount paid or payable by such Indemnified Party with
respect to such loss, liability, claim, damage or expenses in the proportion
that is appropriate to reflect the relative fault of the Indemnifying Party and
the Indemnified Party in connection with the statements or omissions that
resulted in such loss, liability, claim, damage, or expense, as well as any
other relevant equitable considerations. The relative fault of the Indemnifying
Party and the Indemnified Party shall be determined by reference to, among other
things, whether the untrue or alleged untrue statement of material fact or the
omission to state a material fact relates to information supplied by the
Indemnifying Party or by the Indemnified Party, and the parties' relative
intent, knowledge, access to information and opportunity to correct or prevent
such statement or omission.

        5. Rule 144 Reporting. With a view to making available the benefits of
certain rules and regulations of the Commission which may at any time permit the
sale of the Registrable Securities to the public without registration, after
such time as a public market exists for the Common Stock, the Company shall use
best efforts to:

           (a) Make and keep public information available, as those terms are
understood and defined in Rule 144 under the Securities Act, beginning ninety
(90) days after the Company registers a class of securities under Section 12 of
the Exchange Act or completes a registered offering under the Securities Act;

           (b) File with the Commission in a timely manner all reports and other
documents required of the Company under the Securities Act and the Exchange Act
(at any time after it has become subject to such reporting requirements); and

           (c) Furnish to any Holder promptly upon request a written statement
as to its compliance with the reporting requirements of Rule 144 (at any time
after ninety (90) days after the Company completes a registered offering under
the Securities Act), and of the Securities Act and the Exchange Act (at any time
after it has become subject to such reporting requirements), a copy of the most
recent annual or quarterly report of the Company, and such other reports and
documents of the Company and other information in the possession of or
reasonably obtainable



                                      -7-
<PAGE>

by the Company as an Holder may reasonably request in availing itself of any
rule or regulation of the Commission allowing an Holder to sell Registrable
Securities without registration.

        6. Termination of Registration Rights. No Holder shall be entitled to
exercise any right provided for in this Agreement after the earlier of (a) the
date all Registrable Securities have been effectively registered under the
Securities Act and sold or otherwise disposed of in accordance with the intended
method of disposition set forth in the registration statement covering such
Registrable Securities and (b), in the opinion of counsel of such Holder, the
date all Registrable Securities held by such Holder may be sold in a single
three-month period under Rule 144 under the Securities Act.

        7. Information To Be Provided by the Holders. Each Holder whose
Registrable Securities are included in any registration pursuant to this
Agreement shall furnish the Company such information regarding such Holder and
the distribution proposed by such Holder as may be reasonably requested in
writing by the Company and as shall be required in connection with such
registration or the registration or qualification of such securities under any
applicable state securities law.

        8. Expense of Registration. All Registration Expenses incurred in
connection with the registration and other obligations of the Company pursuant
to this Agreement shall be borne by the Company.

        9. Miscellaneous.

           (a) Notices. All notices, requests and other communications hereunder
shall be in writing and shall be deemed to have been duly given at the time of
receipt if delivered by hand or by facsimile transmission or three days after
being mailed, registered or certified mail, return receipt requested, with
postage prepaid, to the address or facsimile number (as the case may be) listed
below the signature of each Party on such Party's signature page hereto if any
Party shall have designated a different address or facsimile number by notice to
the other Parties given as provided above, then to the last address or facsimile
number so designated.

           (b) Severability. In the event one or more of the provisions of this
Agreement should, for any reason, be held to be invalid, illegal or
unenforceable in any respect, such invalidity, illegality or unenforceability
shall not affect any other provisions of this Agreement, and this Agreement
shall be construed and interpreted in such manner as to be effective and valid
under applicable law.

           (c) Waiver or Modification. Any amendment or modification of this
Agreement shall be effective only if evidenced by a written instrument executed
by the Company and by Investors that hold a majority of the total Registrable
Securities.

           (d) Governing Law. This Agreement shall be governed by and construed
in accordance with the laws of the Commonwealth of Virginia without regard to
the principles of conflicts of laws thereof.



                                      -8-
<PAGE>


           (e) Attorneys' Fees. In the event of any dispute involving the terms
hereof, the prevailing parties shall be entitled to collect legal fees and
expenses from the other party to the dispute.

           (f) Further Assurances. Each Party agrees to act in accordance
herewith and not to take any action that is designed to avoid the intention
hereof.

           (g) Successors and Assigns. This Agreement and the rights and
obligations of the Parties hereunder shall inure to the benefit of, and be
binding upon, their respective successors, assigns and legal representatives.


                  [Remainder of page intentionally left blank]



                                      -9-
<PAGE>


                            [COMPANY SIGNATURE PAGE]


        IN WITNESS WHEREOF, the undersigned Party has executed this Agreement as
of the day and year first above written.



                                       LYNX THERAPEUTICS, INC.

                                       By:
                                          --------------------------------
                                          Name:
                                          Title:


                                       ADDRESS FOR NOTICE:

                                       Lynx Therapeutics, Inc.
                                       25861 Industrial Blvd.
                                       Hayward, CA  94545
                                       Attention: Edward C. Albini
                                                  Chief Financial Officer
                                       Facsimile: (510) 670-9304


                                       with a copy to:


                                       Cooley Godward LLP
                                       Five Palo Alto Square
                                       3000 El Camino Real
                                       Palo Alto, CA  94306
                                       Attention: James C. Kitch, Esq.
                                       Facsimile: (650) 849-7400




                                      -10-
<PAGE>

                            [INVESTOR SIGNATURE PAGE]


        IN WITNESS WHEREOF, the undersigned Investor has executed this Agreement
as of the day and year first above written.


                                       INVESTOR


                                       By:
                                          --------------------------------
                                          Name:
                                          Title:



                                       ADDRESS FOR NOTICE:

                                       Investor
                                       [o]
                                       [o]
                                       [o]
                                       Attention:   [o]
                                       Facsimile:   (   ) ____-________

                                       with a copy to:



                                       Attention:
                                       Facsimile:



                                      -11-
<PAGE>


                                   SCHEDULE A


                          REGISTRATION RIGHTS AGREEMENT

                              SCHEDULE OF INVESTORS

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<S>                          <C>                      <C>                 <C>
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                                      -12-