Document:

exv10w37w2

 

Exhibit 10.37.2

Amendment To

Executive Employment Agreement for John S. West

     This Amendment To Executive Employment Agreement for John S. West (the “Amendment”)
is made and entered into, as of May 19, 2006 (the “Effective Date”), by and between Solexa,
Inc., a Delaware corporation (“Company”), and John S. West (“Executive”). Effective
as of the Effective Date, the Company and Executive hereby amend that certain Executive
Employment Agreement for John S. West between them entered into as of June 23, 2005 (the
“Employment Agreement”), a copy of which is attached hereto as Exhibit A, as follows:

     1. Amendment of Section 2.1 of Employment Agreement.  Section 2.1 of the
Employment Agreement is amended to state that Executive’s annual base salary is increased to Three
Hundred Sixty-Seven Thousand, Five Hundred Dollars ($367,500), retroactive to January 1, 2006.

     2. Amendment of Section (d) of Exhibit B. Section (d) of Exhibit B to the
Employment Agreement is superseded and replaced with the following new Section (d) of Exhibit B:

          (d) Alternative One-Time Bonuses. Executive will be eligible for one of the following two
alternative one-time bonuses, subject to the terms and conditions set forth herein. If the terms
and conditions are met for one of these bonuses at any time, Executive will not earn or be eligible
to receive any additional such bonus, and will not earn or be eligible to receive the other
one-time bonus, even if the applicable terms and conditions subsequently are met. In addition,
because the alternative one-time bonuses are intended to incentivize Executive with respect to his
employment services and continued employment with the Company, in order to earn and be eligible to
receive either of the below alternative one-time bonuses, Executive must remain an employee in good
standing of the Company (or a successor entity) as of the date that such bonus is earned. The
alternative one-time bonuses are as follows:

               (i) One-Time Market Capitalization Bonus. In the event that the closing price of the
Company’s common stock equals or exceeds twenty-seven dollars and sixty cents ($27.60) per share
(as presently constituted) for each of twenty-five (25) consecutive public trading days (the
“Trading Period”), Executive will be entitled to receive a one-time bonus of three hundred eight
thousand, six hundred and five (308,605) shares of the Company’s common stock (as adjusted for
stock splits, stock dividends or the like) pursuant to the Company’s 2005 Equity Incentive Plan
(the “Plan”) (the “Market Capitalization Bonus”). If it is reasonably determined by the Company
that it would be inadvisable or impractical for Executive to sell or otherwise dispose of a portion
of the common stock constituting the Market Capitalization Bonus for the purposes of paying
applicable taxes, the Company may at its election provide cash compensation to Executive in lieu of
a portion of the common stock sufficient to pay, valued based on the average of the per share
closing prices during the Trading Period, the taxes applicable to the Market Capitalization Bonus,
with the remaining portion of the Market Capitalization Bonus to be provided as Company common
stock pursuant to the Plan. The Market Capitalization Bonus shall be provided to Executive within
forty-five (45) days after the Trading Period. Notwithstanding the preceding sentence, at
Executive’s written election, delivery of all or a portion of the Market Capitalization Bonus will
be delayed until January 15 of the tax year following the year in which the bonus is earned,
without any interest or additional consideration being owed to Executive. The Company shall make
all determinations and calculations regarding whether and when the Market Period Capitalization
Bonus has been earned and the amount of the Market Capitalization Bonus.

 

 

               (ii) One-Time Change in Control Bonus. In the event of a Change in Control (as defined in
Section 6), Executive shall be eligible to receive a bonus equivalent to one percent (1%) of the
amount by which the consideration received by the Company’s stockholders as a direct result of the
Change in Control exceeds the sum of One Hundred Fifty Million Dollars ($150,000,000) plus the
aggregate gross proceeds received by Solexa through sales of equity securities after the Effective
Date (the “Change in Control Bonus”). The Change in Control Bonus will be provided to Executive in
the same form as the consideration received by the Company’s stockholders as a direct result of the
Change in Control. For example, if cash is the consideration provided to the Company’s
stockholders as a direct result of the Change in Control, Executive shall be provided a cash Change
in Control Bonus; and if the consideration provided to the Company’s stockholders as a direct
result of the Change in Control consists of securities or other non-cash consideration,
Executive’s Change in Control Bonus shall be paid in such form and determined based on the value
thereof established in the Change in Control, provided that, notwithstanding the preceding, the
Company may in its sole discretion elect to substitute cash for all or any portion of the
securities or other non-cash consideration that would otherwise be payable based on the value
thereof established in the Change in Control. The Company shall make all determinations and
calculations regarding whether the Change in Control Bonus has been earned and the amount of the
Change in Control Bonus.

     3. Miscellaneous. This Amendment constitutes the complete, final and
exclusive embodiment of the entire agreement between the Company and Executive with regard to
amendment of the Employment Agreement. It is entered into without reliance on any promise or
representation, written or oral, other than those expressly contained herein, and it supersedes any
other such promises, warranties or representations. Any provisions of the Employment Agreement
contrary to this Amendment are hereby superseded and replaced, and the remaining portions of the
Employment Agreement remain in full force and effect. This Amendment may not be modified or
amended except in a writing signed by Executive and a duly authorized officer of the Company. This
Amendment will bind the heirs, personal representatives, successors and assigns of both Executive
and the Company, and inure to the benefit of both Executive and the Company, their heirs,
successors and assigns. If any provision of this Amendment is determined to be invalid or
unenforceable, in whole or in part, this determination shall not affect any other provision of this
Amendment and the provision in question shall be modified so as to be rendered enforceable in a
manner consistent with the intent of the parties insofar as possible under applicable law. This
Amendment shall be construed and enforced in accordance with the laws of the State of California
without regard to conflicts of law principles. Any ambiguity in this Amendment shall not be
construed against either party as the drafter. Any waiver of a breach of this Amendment, or rights
hereunder, shall be in writing and shall not be deemed to be a waiver of any successive breach or
rights hereunder. This Amendment may be executed in counterparts which shall be deemed to be part
of one original, and facsimile signatures shall be equivalent to original signatures.

 

 

     IN WITNESS WHEREOF, the parties have executed this Amendment as of the date first written
above.

	 	 	 	 	 	 	 	 	 
	Solexa, Inc.	 	 	 	John S. West	 	 
	A Delaware Corporation	 	 	 	An Individual	 	 
	 
	 	 	 	 	 	 	 	 
	By:
	 	/s/ Craig C. Taylor	 	 	 	/s/ John West	 	 
	 

	 	 

	 	 
	 	 

	 	 
	Name:
	 	Craig C. Taylor	 	 	 	 	 	 
	 

	 	 

	 	 	 	 	 	 
	Title:
	 	Chairman of the Board	 	 	 	 	 	 
	 

	 	 

	 	 	 	 	 	 

 

 

Exhibit A

EXECUTIVE EMPLOYMENT AGREEMENT

FOR

JOHN S. WEST

 

 

EXECUTIVE EMPLOYMENT AGREEMENT

FOR

John S. West

This Executive Employment Agreement (the “Agreement”) is entered into as of June 23, 2005
and effective as of the Closing (as defined below), by and between John S. West
(“Executive”) and Solexa, Inc., a Delaware corporation (“Solexa”).

WHEREAS, Solexa has employed Executive effective upon the First Closing Date (as defined in the
Acquisition Agreement) (“Closing”) of the business combination transaction between Solexa
and Solexa Limited, a company registered in England and Wales (“Solexa UK”) pursuant to
that certain Acquisition Agreement dated September 28, 2004 (“Acquisition Agreement”), in
accordance with which Executive’s Solexa UK stock options have been exchanged for Solexa stock
options and in which the acquisition of Solexa UK’s goodwill is a key asset motivating the
participation of Solexa in the Acquisition Agreement.

NOW, THEREFORE, in consideration of the mutual promises and covenants contained herein, it is
hereby agreed by and among the parties as follows:

1. EMPLOYMENT BY SOLEXA .

     1.1 Title and Responsibilities. Subject to the terms set forth herein, Solexa agrees
to employ Executive effective on Closing in the position of Chief Executive Officer, and Executive
hereby accepts such employment and office. It is also anticipated that Executive will be nominated
with the support Solexa management for election by Solexa’s stockholders to serve on the board of
directors of Solexa (the “Board”). During his employment with Solexa, Executive will
devote substantially all of his business time and attention (except for vacation periods and
reasonable periods of illness or other incapacity permitted by the Solexa’s general employment
policies) to the business of Solexa and its affiliated entities (“Affiliates”). In
addition to any additional reasonable duties and responsibilities delegated to Executive from time
to time by the Board, Executive shall be responsible for the general supervision, direction, and
authority over the business, affairs, and officers of Solexa and its Affiliates, and shall perform
all the duties commonly incident to the office of a chief executive. Unless otherwise requested by
the Board, Executive shall continue to serve as a director of Solexa so long as Executive is
elected to the Board by Solexa’s stockholders.

     1.2 Budgetary Authority. So long as Executive is employed as Chief Executive Officer
of Solexa, Executive shall have responsbility over the budgetary and financial affairs of Solexa
subject to procedures and limitations established by the Board from time to time or contained in
the Solexa’s bylaws or certificate of incorporation or subject to the Executive’s general fiduciary
duties.

     1.3 Solexa Employment Policies. The employment relationship between Executive and
Solexa shall be governed by the general employment policies and procedures of Solexa ,

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including those relating to protection of confidential information and assignment of
inventions, except that when the terms of this Agreement differ from or are in conflict with such
general employment policies or procedures, this Agreement shall control. Executive agrees to
execute Solexa ’s standard Proprietary Information and Inventions Agreement (“Inventions
Agreement”) attached hereto as Exhibit A.

     1.4 Board Reporting. Executive shall keep the Board reasonably informed (in writing,
if so requested) of his conduct of the business or affairs of Solexa and provide such explanations
of his conduct as the Board may reasonably require.

     1.5 Prior Employment.  From and after Closing, this Agreement shall govern
Executive’s employment and services provided with regard to Solexa and its Affiliates, including
Solexa UK, and the Executive Employment Agreement dated July 28, 2004, by and among Executive,
Abingworth Management Inc., a California corporation (“Abingworth”) and Solexa UK (the
“Prior Agreement”) will be terminated and shall have no further force or effect except with
respect to obligations that have accrued thereunder upon or prior to Closing or which by their
terms continue to apply in regard to services provided prior to Closing.

2. COMPENSATION AND BENEFITS.

     2.1 Salary; Housing Allowance; Taxes. For services rendered hereunder as Chief
Executive Officer of Solexa , Executive shall receive an annualized base salary of Three Hundred
and Fifty Thousand Dollars ($350,000.00), less required withholdings and deductions, payable in
accordance with Solexa ’s standard payroll procedures. All elements of Executive’s compensation
will be considered for annual changes upon the review and approval by the Board.

     2.2 Performance Bonuses. Executive shall be eligible for the annual and special
bonuses set forth on Exhibit B attached hereto so long as Executive is employed by Solexa.
All bonuses paid to Executive shall be paid out in accordance with Solexa’s standard payroll
policies.

     2.3 Benefits. Executive shall be entitled to all rights and benefits for which he is
eligible under the terms and conditions of the standard benefits and compensation plans which may
be in effect from time to time and provided by Solexa to its executive level employees generally.
In addition, at a minimum, Solexa shall provide the following benefits to Executive:

     (a) US-based company-paid health insurance for Executive and Executive’s dependents which is
substantially the same as that provided to senior executives of Solexa;

     (b) Such monthly contributions, if any to a 401(k) as provided to other senior executives of
Solexa;

     (c) Long-term and short-term disability insurance coverage to the extent of fifty percent
(50%) of Executive’s starting base salary; and

     (d) Executive shall be entitled to twenty (20) paid days of vacation per year, to begin
accruing upon Closing, which unused vacation accruals shall carry over from year to year, up to

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a maximum of twenty (20) days, after which no further vacation shall accrue until Executive
has reduced his vacation accrual balance below twenty (20) days.

     2.4 Issuance of Options to Purchase Solexa Stock.

     As soon as practicable after Closing, Solexa shall issue to Executive an option (“Option”)
under Solexa’s 1992 Stock Option Plan (the “Plan”) to purchase 600,000 shares of common
stock of Solexa at an exercise price equal to the fair market value of Solexa’s common stock on the
last market trading day prior to the effective date of such Option as set forth in the Plan. The
shares underlying the Option shall vest in substantially equal montly installments over the 48
months beginning with effect from August 9, 2004.

     2.5 Business Expense Reimbursement. Solexa shall reimburse Executive for all
reasonable travel (airfare, hotels, meals, fees, etc.), entertainment or other business expenses he
incurs in furtherance of or in connection with the performance of his duties hereunder, in
accordance with Solexa ’s expense reimbursement policies as in effect from time to time. To the
extent reasonably practicable, upon the request of Executive, Solexa shall pay all such expenses
in advance.

     2.6 Liability and Indemnification. Solexa shall indemnify Executive as a corporate
officer of Solexa and its affiliates to the maximum extent extended to the other officers and
directors of each such entity and as required by law (such indemnification is set forth in the
agreement attached as Exhibit C) and for claims relating to Executive’s duties for Solexa
but arising out of his previous employment. In addition, for so long as Executive is employed as
an executive officer or director Solexa or its Affiliates, Solexa shall use commercially reasonable
efforts to maintain an insurance policy or policies providing liability insurance for directors,
officers and employees of Solexa and any other corporation, partnership, joint venture, trust,
employee benefit plan or other enterprise that such person serves at the request of Solexa, and
Executive shall be covered by such policy or policies in accordance with its or their terms to the
maximum extent of the coverage available for any director, officer, employee, agent or fiduciary
under such policy or policies.

3. OUTSIDE ACTIVITIES; NON-COMPETE.

     3.1 Activities. Executive may (a) engage in civic and not-for-profit activities so
long as such activities do not materially interfere with the performance of his duties hereunder
and (b) serve as a member of the board of directors of any entity so long as such service does not,
in the sole discretion of the Board, materially interfere with the performance of his duties
hereunder or violate Section 3.2 hereof. Executive agrees to consult the Board at the first
appropriate opportunity and in any case prior to the commencement of any such board service.

     3.2 Non-Competition During Employment. During his employment by Solexa, Executive
will not directly or indirectly, whether as an officer, director, stockholder, partner, proprietor,
associate, representative, consultant, or in any capacity whatsoever engage in, become financially
interested in, be employed by or have any business connection with any other person, corporation,
firm, partnership or other entity anywhere in the world with major businesses or

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business units making instrument systems for high speed sequencing of DNA (other than
companies making systems primarily for genotyping or gene expression); provided, however, that
anything above to the contrary notwithstanding, Executive may own, as a passive investor,
securities of any competitor corporation, so long as Executive’s direct holdings in any one such
corporation shall not in the aggregate constitute more than five percent (5%) of the voting stock
of such corporation.

     3.3 Non-Competition Post Employment. As the acquisition of goodwill is a key asset
motivating the participation of Solexa in the Acquisition Agreement, for a period of one year
after the termination of the Executive’s employment hereunder howsoever arising, Executive will not
directly, whether as an officer, director, stockholder holding more than 5% of the voting stock of
the relevant corporation, or partner be employed or engaged anywhere in the world in either a
company whose main business is the making of instrument systems for high speed sequencing of DNA,
or be employed in direct operational control of the business unit of a larger company which
business unit has as its main business the making of instrument systems for high speed sequencing
of DNA (other than companies or business units, as applicable, making systems primarily for
genotyping or gene expression).

     3.4 Non-solicitation of staff. During his employment under this Agreement and for a
period of one year after the termination of the Executive’s employment hereunder howsoever arising,
Executive shall not without the prior written consent of the Board directly or indirectly employ,
engage or endeavour to entice away from Solexa any key personnel.

     3.5 Non-solicitation of customers. During his employment under this Agreement and for
a period of one year after the termination of the Executive’s employment hereunder howsoever
arising, Executive shall not induce or seek to induce, by any means involving the disclosure or use
of confidential information, any customer or corporate partner of Solexa to cease dealing with
Solexa or to restrict or vary the terms upon which it deals with Solexa.

     3.6 Enforceability. If any part of this entire Section 3 is found to be unenforceable
by a competent court with jurisdiction over this Agreement, notwithstanding any other provision in
this Agreement to the contrary, nothing shall be paid to Executive under this Agreement and no
other benefits shall accrue under this Agreement except for the payment of wages and benefits
accrued immediately as of Executive’s termination of employment with Solexa.

4. OTHER AGREEMENTS.

     Executive represents and warrants that his employment by Solexa will not conflict with and will
not be constrained by any prior agreement or relationship with any third party which has not been
disclosed to Solexa . During Executive’s employment by Solexa , Executive may use, in the
performance of his duties, all information generally known and used by persons with training and
experience comparable to his own and all information which is common knowledge in the industry or
otherwise legally in the public domain.

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5. TERMINATION OF EMPLOYMENT.

     5.1 At-Will Employment. Executive’s relationship with Solexa is at will. Both
Executive, on the one hand, and Solexa on the other, shall have the right to terminate Executive’s
employment with Solexa at any time with or without Cause (as defined below). In the event of such
termination, Executive agrees to resign from the Board and any committees of the Board on which he
may be serving, effective as of the date of termination. Notwithstanding any other provision of
the Agreement, the Board shall be under no obligation to vest in or assign to Executive any powers
or duties or provide any work for Executive, and the Board may at any time prior to termination and
from time to time suspend the Executive from the performance of his duties or exclude him from any
premises of Solexa and its Affiliates, in which case the other provisions of this Agreement shall
continue to have full force and effect.

     5.2 Termination for Cause. If Solexa terminates Executive’s employment at any time
for Cause (as defined below), Executive’s salary shall cease on the date of termination and
Executive shall not be entitled to severance pay, pay in lieu of notice or any other such
compensation other than payment of accrued salary and vacation and such other benefits as expressly
required in such event by applicable law or the terms of applicable benefit plans.

     (a) Definition of “Cause”. For purposes of this Agreement, “Cause” shall mean
the occurrence of one or more of the following: (i) Executive’s knowing and willful action which
is or is likely to be seriously injurious to Solexa ; (ii) any intentional act by Executive in
connection with his responsibilities as an employee constituting fraud or a felony crime; (iii)
Executive’s consistent failure to report for work; (iv) persistent or repeated material breach of
this Agreement; or (v) Executive becoming disqualified from holding office through his own act or
omission; provided that in any such event, there has been delivered to Executive a written demand
for performance from the Board which describes the basis for the Board’s belief that Executive has
committed one of the acts set forth in clauses (i)-(v) above and provides Executive with thirty
(30) days to take corrective action (which may include any suspension period). Notwithstanding the
foregoing, Cause shall not include Executive’s physical or mental disability or death, poor
operating results of Solexa, litigation filed against Solexa or Executive, or general incompetence.

     5.3 Termination Without Cause. Except as provided in Section 6 below under “Change of
Control” “Change of Control Acceleration Benefit” if Executive’s employment is terminated
at any time without Cause, Executive shall be entitled to the following severance benefits:

     (a) a lump sum payment in an amount equal to twelve (12) months of Executive’s base salary as
of his termination date, less required withholdings and deductions;

     (b) reimbursement of the cost of continued health insurance coverage for Executive and
Executive’s eligible dependents, regardless of whether Executive elects continued coverage under
federal COBRA or any state equivalent or elects to procure reasonably equivalent private coverage,
for a period of twelve (12) months from the termination date; and

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     (c) shares subject to the outstanding options to purchase Solexa stock then held by Executive
which, but for such termination, would have become vested over the succeeding twelve (12) months
following such termination shall immediately vest and become exercisable.

     5.4 Executive’s Voluntary Resignation. Executive may voluntarily terminate his
employment hereunder at any time with a minimum of one month notice, and with or without Good
Reason (as defined below). If Executive voluntarily terminates his employment other than for Good
Reason, he will not be entitled to severance pay, pay in lieu of notice or any other such
compensation other than payment of accrued salary and vacation and such other benefits as expressly
required in such event by applicable law or the terms of applicable benefit plans.

     5.5 Termination for Death or Disability. Executive’s employment will be
terminated in the event of Executive’s death, or, subject to applicable law, any illness,
disability or other incapacity that renders Executive physically or mentally unable to
perform his duties hereunder for a period in excess of ninety (90) consecutive days or more
than one hundred twenty (120) days in any consecutive twelve (12) month period. The
determination regarding whether Executive is physically or mentally unable to perform his
duties shall be based on the opinion of Executive’s physician(s) and/or mental health
professional(s). Executive’s inability to be physically present on Solexa’s premises shall
not constitute a presumption that Executive is unable to perform such duties. If
Executive’s employment is terminated for death or disability as described in this Section,
Executive or Executive’s heirs, successors, and assigns shall not receive any compensation
or benefits other than payment of accrued salary and vacation and such other benefits as
expressly required in such event by applicable law or the terms of applicable benefits
plans.

     5.6 Executive’s Resignation for Good Reason. Executive may resign his employment for
Good Reason so long as Executive tenders his resignation to Solexa within one hundred and twenty
(120) days after Executive learns of the occurrence of the event which forms the basis for his
termination for Good Reason. Except as provided under Section 6.2 of this Agreement, if Executive
terminates his employment for Good Reason, Executive shall be entitled to the same severance
benefits as set forth in Section 5.3 above. In the event of Executive’s termination/resignation
for Good Reason, severance benefits under Section 5.3(a) or Section 6.2(a)(i), shall be based on
Executive’s base salary immediately prior to any reduction that constitutes Good Reason under
Section 5.6(a)(ii).

     (a) Definition of “Good Reason”.

     For purposes of this Agreement, “Good Reason” shall mean any one of the following
events without Executive’s express written consent: (i) a substantial reduction of Executive’s
duties, title, authority, status, or responsibilities; (ii) a reduction of Executive’s then current
base salary; (iii) the relocation of Executive, without Executive’s consent, to a facility or
location more than 50 miles from his current home at the date of this Agreement; (iv) a material
breach by Solexa of any of its obligations under this Agreement.

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6. CHANGE OF CONTROL.

     6.1 Definition. For purposes of this Agreement, a “Change of Control” means the
happening of any of the following events:

     (a) A dissolution or liquidation of Solexa.

     (b) A sale, lease, exchange or other transfer (in one transaction or a series of related
transactions) of all or substantially all of the assets of Solexa.

     (c) A consolidation or merger of Solexa in which Solexa is not the continuing or surviving
corporation or pursuant to which the stock of Solexa would be converted into cash, securities or
other property, other than a merger or consolidation of Solexa in which the holders of such
entity’s stock immediately prior to the merger or consolidation hold more than fifty percent (50%)
of the stock or other forms of equity of the surviving corporation immediately after the merger in
substantially the same proportions of ownership of shares of Solexa immediately prior to the
merger or consolidation.

     (d) A sale or exchange by the shareholders of Solexa, in a single transaction or series of
related transactions, of more than fifty percent (50%) of the voting stock of such entity, after
which the shareholders of such entity immediately before such transaction do not retain immediately
after such transaction, in substantially the same proportions of their ownership of shares of
Solexa immediately before the transaction, direct or indirect beneficial ownership of more than
fifty percent (50%) of the combined voting power of such entity.

     6.2 Change of Control Termination. If, within six (6) months prior to or twelve (12)
months following a Change of Control, Executive’s employment is terminated without Cause or
Executive resigns from employment for Good Reason (a “Change of Control Termination”),
Executive shall be eligible to receive the severance benefits described in Section 6.2(a).

     (a) Severance Benefits. In the event of a Change of Control Termination, Executive
shall receive the following severance benefits in lieu of those set forth in Section 5 above:

      (i) a lump sum payment in an amount equal to twelve (12) months of Executive’s base
salary as of his termination date, less required withholdings and deductions; and

      (ii) reimbursement of the cost of continued health insurance coverage for Executive and
Executive’s eligible dependents, regardless of whether Executive elects continued coverage
under federal COBRA or any state equivalent or elects to procure reasonably equivalent
private coverage, for a period of twelve (12) months from the termination date.

     6.3 Change of Control Acceleration Benefit. If, at any time during Executive’s term
of employment, there is a Change of Control, shares subject to the outstanding options to purchase
Solexa stock then held by Executive which are scheduled to vest over the succeeding twenty-four
(24) months following the Change of Control shall immediately vest and become

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exercisable. In the event Executive becomes entitled to this benefit, he shall no longer be
entitled to any vesting acceleration benefit pursuant to Section 5.3 or 5.6.

     GENERAL PROVISIONS.

     7.1 Notices. Any notices provided hereunder must be in writing and shall be deemed
effective upon the earlier of personal delivery (including, personal delivery by facsimile
transmission or the third day after mailing by first class mail) to each party hereto at his or its
address as listed on the signature page hereto (which address may be changed by written notice).

     7.2 Severability. Whenever possible, each provision of this Agreement will be
interpreted in such manner as to be effective and valid under applicable law, but if any provision
of this Agreement is held to be invalid, illegal or unenforceable in any respect under any
applicable law or rule in any jurisdiction, such invalidity, illegality or unenforceability will
not affect any other provision or any other jurisdiction, but such invalid, illegal or
unenforceable provision will be reformed, construed and enforced in such jurisdiction so as to
render it valid, legal, and enforceable consistent with the intent of the parties insofar as
possible.

     7.3 Waiver. If either party should waive any breach of any provisions of this
Agreement, he or it shall not thereby be deemed to have waived any preceding or succeeding breach
of the same or any other provision of this Agreement.

     7.4 Entire Agreement. This Agreement and its Exhibits together constitute the entire
agreement among Executive and Solexa and supersede any prior agreement, promise, representation,
or statement written or otherwise among such parties with regard to this subject matter. This
Agreement is entered into without reliance on any promise, representation, statement or agreement
other than those expressly contained or incorporated herein, and it cannot be modified or amended
except in a writing signed by Executive and a duly authorized officer of Solexa.

     7.5 Counterparts. This Agreement may be executed in separate counterparts, any one
of which need not contain signatures of more than one party, but all of which taken together will
constitute one and the same Agreement.

     7.6 Headings. The headings of the sections hereof are inserted for convenience only
and shall not be deemed to constitute a part hereof nor to affect the meaning thereof.

     7.7 Successors and Assigns. This Agreement is intended to bind and inure to the
benefit of and be enforceable by Executive, Solexa and their respective successors, assigns,
heirs, executors and administrators, except that Executive may not assign any of his duties
hereunder and he may not assign any of his rights hereunder without the written consent of the
other parties hereto, which shall not be withheld unreasonably.

     7.8 Remedies. Executive’s duties under Section 3 shall survive termination of
Executive’s employment. Executive acknowledges that a remedy at law for any breach or threatened
breach by Executive of the Inventions Agreement would be inadequate, and Executive therefore agrees
that Solexa shall be entitled to injunctive relief in case of any such breach or threatened
breach.

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     7.9 Governing Law. All questions concerning the construction, validity and
interpretation of this Agreement will be governed by the law of the State of California, without
regard to conflicts of laws principles thereof, as applied to contracts made and to be performed
entirely within California.

	 	 	 	 	 
	 	 	IN WITNESS WHEREOF, the parties have
executed this Agreement effective as of the
date first above written.
	 
	 	 	 	 
	 	 	SOLEXA, INC.
	 
	 	 	 	 
	 
	 	 	 	 
	 

	 	By:
	 	/s/ Craig C. Taylor
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Name:
	 	Craig C. Taylor
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Title:
	 	Chairman of the Board
	 

	 	 	 	 
	 
	 	 	 	 
	 

	 	Address:	 	 
	 
	 	 	 	 
	 
	 	 	 	 
	 
	 	 	 	 
	 	 	John S. West
	 
	 	 	 	 
	 	 	/s/ John West
	 	 	 

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EXHIBIT A

PROPRIETARY INFORMATION AND INVENTIONS AGREEMENT

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EXHIBIT B

ANNUAL AND SPECIAL PERFORMANCE BONUSES

In addition to the base compensation payable to Executive as provided in Section 2.1, Solexa shall
pay to Executive, as compensation for his continued services to Solexa, the following:

          (a) In respect of fiscal year 2005, Solexa shall pay to the Executive an aggregate lump sum
bonus of up to forty per cent (40%) of Executive’s annual salary (subject to adjustment pursuant to
good faith negotiations between Executive and Solexa ) proportionately upon achievement of the
milestones set forth in the business plan as approved by the Board.

          (b) Thereafter, Executive shall be paid an annual bonus on a similar basis as (a) above as
determined pursuant to good faith negotiations between Executive and Solexa based on the
achievement of milestones set forth in the annual operating plan developed by Solexa’s management
team and approved by the compensation committee of the Board.

          (c) Until August 9, 2006, upon the initial closing of any collaboration or other strategic
alliance or partnership the terms of which provide for at least Four Million Dollars ($4,000,000)
of committed cash investment in or payment to Solexa other than for goods or services, Solexa
shall, unless such investments or payments fall within Section (d) below, pay to Executive, when
received by Solexa, an aggregate lump sum bonus equal to the greater of: (i) one percent (1%) of
the aggregate committed amount to be paid in such transaction (without regard to any commissions or
other transaction expenses paid by Solexa), such amount to include upfront payments, payments in
respect of intellectual property and the premium for any equity investment above the market price
of Solexa stock; or (ii) One Hundred Thousand Dollars ($100,000).

          (d) In the event of a Change of Control (as defined in Section 6) Solexa shall pay to
Executive an aggregate lump sum bonus equal to the greater of (i) two percent (2%) of the amount by
which the value received by Solexa’s stockholders in connection with the Change of Control exceeds
the sum of Fifty Million Dollars ($50,000,000) plus the aggregate gross proceeds received by Solexa
through sales of equity securities after the Closing; or (ii) One Hundred Thousand Dollars
($100,000).

11

 

EXHIBIT C

INDEMNIFICATION AGREEMENT

12exv10w44

 

Exhibit 10.44

[SOLEXA LETTERHEAD]

May 19, 2006

VIA HAND DELIVERY

Linda M. Rubinstein

Solexa, Inc.

25861 Industrial Boulevard

Hayward, CA 94545

			
	Re:	 	Salary Increase and New Alternative One-Time Bonus Arrangement

Dear Linda:

This letter confirms your recent salary increase and contains the terms and conditions of the new
alternative one-time bonus arrangement that Solexa, Inc. (“Solexa” or the “Company”) is offering
you, subject to the terms and conditions set forth in this letter. This new bonus arrangement will
be a supplemental bonus arrangement and it does not replace or cancel any other current bonus
program of the Company.

A. Salary Increase:

We are pleased to confirm that your annual base salary was increased to $261,700, retroactive to
January 1, 2006.

B. New Bonus Overview:

The two below potential bonuses are alternative one-time bonuses. Accordingly, if the terms and
conditions are met for one of these bonuses at any time, you will not earn or be eligible to
receive any additional such bonus, and you will not earn or be eligible to receive the other
one-time bonus (even if the applicable terms and conditions subsequently are met). In addition,
because the alternative one-time bonuses are intended to incentivize you with respect to your
employment services and your continued employment with the Company, in order to earn and be
eligible to receive either of the below alternative one-time bonuses, you must remain an employee
in good standing of the Company (or a successor entity) as of the date that such bonus is earned.

Additional specific terms and conditions of each alternative one-time bonus are set forth below.

1. One-Time Market Capitalization Bonus:

In the event that the closing price of the Company’s common stock equals or exceeds twenty-seven
dollars and sixty cents ($27.60) per share (as presently constituted) for each of twenty-five (25)
consecutive public trading days (the “Trading Period”), you will be entitled to receive a one-time
bonus of seventy-seven thousand, one hundred fifty-one (77,151) shares of the Company’s common
stock (as adjusted for stock splits, stock dividends or the like) pursuant to the Company’s 2005
Equity Incentive Plan (the “Plan”) (the “Market Capitalization Bonus”). If it is reasonably
determined by the Company that it would be inadvisable or impractical for you to sell or otherwise
dispose of a portion of the common stock constituting the Market Capitalization Bonus for the
purposes of paying applicable taxes, the Company may at its election provide you with cash
compensation in lieu of a portion of the common stock sufficient to pay, valued based on the
average of the per share closing prices during the Trading

 

 

Linda M. Rubinstein

May 19, 2006

Page 2 of 3

Period, the taxes applicable to the Market Capitalization Bonus, with the remaining portion of the
Market Capitalization Bonus to be provided as Company common stock pursuant to the Plan.

If earned, the Market Capitalization Bonus will be provided to you within forty-five (45) days
after the Trading Period. Notwithstanding the preceding sentence, at your written election,
delivery of all or a portion of the Market Capitalization Bonus will be delayed until January 15 of
the tax year following the year in which the bonus is earned, without any interest or additional
consideration being owed to you. The Company shall make all determinations and calculations
regarding whether and when the Market Period Capitalization Bonus has been earned and the amount of
the Market Capitalization Bonus.

2. One-Time Change in Control Bonus:

In the event of a Change in Control (as defined below), you shall be eligible to receive a bonus
equivalent to one quarter of one percent (.25%) of the amount by which the consideration received
by the Company’s stockholders as a direct result of the Change in Control exceeds the sum of One
Hundred Fifty Million Dollars ($150,000,000) plus the aggregate gross proceeds received by the
Company through sales of equity securities occurring after the date of this letter (the “Change in
Control Bonus”).

The Change in Control Bonus will be provided to you in the same form as the consideration received
by the Company’s stockholders as a direct result of the Change in Control. For example, if cash is
the consideration provided to the Company’s stockholders as a direct result of the Change in
Control, you will be provided a cash Change in Control Bonus; and if the consideration provided to
the Company’s stockholders as a direct result of the Change in Control consists of securities or
other non-cash consideration, your Change in Control Bonus (if earned) will be paid in such form
and determined based on the value thereof established in the Change in Control, provided that,
notwithstanding the preceding, the Company may in its sole discretion elect to substitute cash for
all or any portion of the securities or other non-cash consideration that would otherwise be
payable based on the value thereof established in the Change in Control. The Company shall make
all determinations and calculations regarding whether the Change in Control Bonus has been earned
and the amount of the Change in Control Bonus.

For purposes of the Change in Control Bonus, a “Change of Control” means the happening of any of
the following events: (a) a dissolution or liquidation of Solexa; (b) a sale, lease, exchange or
other transfer (in one transaction or a series of related transactions) of all or substantially all
of the assets of Solexa; (c) a consolidation or merger of Solexa in which Solexa is not the
continuing or surviving corporation or pursuant to which the stock of Solexa would be converted
into cash, securities or other property, other than a merger or consolidation of Solexa in which
the holders of such entity’s stock immediately prior to the merger or consolidation hold more than
fifty percent (50%) of the stock or other forms of equity of the surviving corporation immediately
after the merger in substantially the same proportions of ownership of shares of Solexa
immediately prior to the merger or consolidation; or (d) a sale or exchange by the shareholders of
Solexa, in a single transaction or series of related transactions, of more than fifty percent (50%)
of the voting stock of such entity, after which the shareholders of such entity immediately before
such transaction do not retain immediately after such transaction, in substantially the same
proportions of their ownership of shares of Solexa immediately before the transaction, direct or
indirect beneficial ownership of more than fifty percent (50%) of the combined voting power of such
entity.

C. Miscellaneous:

Nothing in this letter is intended to alter the at-will nature of your employment with the Company.
In addition, this letter does not alter any existing agreement between you and the Company
(including but not limited to your offer letter agreement dated March 23, 2005), except to the
extent such other existing

 

 

Linda M. Rubinstein

May 19, 2006

Page 3 of 3

agreement contains any terms inconsistent with this letter, which inconsistent terms are hereby
superseded. This letter constitutes the complete, final and exclusive embodiment of the entire
agreement between the Company and you with regard to this subject matter. It is entered into
without reliance on any promise or representation, written or oral, other than those expressly
contained herein, and it supersedes any other such promises, warranties or representations. This
letter agreement may not be modified or amended except in a writing signed by you and a duly
authorized officer of the Company. This letter agreement will bind the heirs, personal
representatives, successors and assigns of both you and the Company, and inure to the benefit of
both you and the Company, their heirs, successors and assigns. If any provision of this letter
agreement is determined to be invalid or unenforceable, in whole or in part, this determination
shall not affect any other provision of this letter agreement and the provision in question shall
be modified so as to be rendered enforceable in a manner consistent with the intent of the parties
insofar as possible under applicable law. This letter agreement shall be construed and enforced in
accordance with the laws of the State of California without regard to conflicts of law principles.
Any ambiguity in this letter agreement shall not be construed against either party as the drafter.
Any waiver of a breach of this letter agreement, or rights hereunder, shall be in writing and shall
not be deemed to be a waiver of any successive breach or rights hereunder. This letter agreement
may be executed in counterparts which shall be deemed to be part of one original, and facsimile
signatures shall be equivalent to original signatures.

To indicate your understanding and acceptance of your salary increase and new bonus arrangement,
please sign and date this letter below, and return this letter to me within five (5) business days.
You may retain the enclosed additional copy of this letter for your files.

We are very pleased to offer these new employment terms, and look forward to a continued productive
employment relationship.

	 	 	 
	Sincerely,

Solexa, Inc.
	 	 
	 
	 	 
	/s/ John West
	 	 
	 

John West

	 	 
	Chief Executive Officer
	 	 
	 
	 	 
	UNDERSTOOD AND AGREED:
	 	 
	 
	 	 
	/s/ Linda M. Rubsinstein
	 	 
	 

Linda M. Rubinstein

	 	 
	 
	 	 
	5/19/06 

	 	 
	Date

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