Document:

Exhibit 10.51

 

EXHIBIT 10.51

ILLUMINA, INC.

NEW HIRE STOCK AND INCENTIVE PLAN

     1. Purposes of the Plan. The purposes of this New Hire Stock and Incentive Plan are to
attract and retain the best available personnel for positions of substantial responsibility and
to promote the success of the Company’s business. Options and Stock Awards may be granted under
the Plan.

     This New Hire Stock and Incentive Plan is patterned after the Amended and Restated 2005
Stock and Incentive Plan but is to be used only for grants to Newly Hired Employees in
connection with their hiring by the Company. The Plan is, therefore, exempt from the rule of the
NASDAQ National Market that requires stockholder approval of issuances of securities to existing
directors and employees and, accordingly, the Plan has not been submitted for approval by the
stockholders of the Company.

     2. Definitions. As used herein, the following definitions shall apply:

	 	(a)	 	“Administrator” means the Board or any of its Committees as shall be
administering the Plan, in accordance with Section 4 hereof.
	 
	 	(b)	 	“Applicable Laws” means the requirements relating to the administration of
stock option and restricted stock plans, the grant of options and the issuance of
shares under U.S. state corporate laws, U.S. federal and state securities laws, the
Code, any Nasdaq National Market, stock exchange or quotation system on which the
Common Stock is listed or quoted and the applicable laws of any other country or
jurisdiction where Options or Awards are granted under the Plan, as such laws, rules,
regulations and requirements shall be in place from time to time.
	 
	 	(c)	 	“Award” means an Option or a Stock Award granted in accordance with the terms
of the Plan.
	 
	 	(d)	 	“Award Agreement” means a Stock Award Agreement and/or Option Agreement,
which may be in written or electronic format, in such form and with such terms and
conditions as may be specified by the Administrator, evidencing the terms and
conditions of an individual Award. Each Award Agreement is subject to the terms and
conditions of the Plan.

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	 	(e)	 	“Board” means the Board of Directors of the Company.
	 
	 	(f)	 	[Omitted]
	 
	 	(g)	 	“Code” means the Internal Revenue Code of 1986, as amended.
	 
	 	(h)	 	“Committee” means a committee of Directors appointed by the Board in
accordance with Section 4 hereof.
	 
	 	(i)	 	“Common Stock” means the common stock of the Company.
	 
	 	(j)	 	“Company” means Illumina, Inc., a Delaware corporation.
	 
	 	(k)	 	[Omitted]
	 
	 	(l)	 	“Corporate Transaction” means any of the following, unless the Administrator
provides otherwise:

	 	(i)	 	any merger or consolidation in which the Company shall not be
the surviving entity (or survives only as a subsidiary of another entity whose
stockholders did not own all or substantially all of the Common Stock in
substantially the same proportions as immediately prior to such transaction),
	 
	 	(ii)	 	the sale of all or substantially all of the Company’s assets
to any other person or entity (other than a wholly-owned subsidiary),
	 
	 	(iii)	 	the acquisition of beneficial ownership of a controlling
interest (including, without limitation, power to vote) the outstanding shares
of Common Stock by any person or entity (including a “group” as defined by or
under Section 13(d)(3) of the Exchange Act),
	 
	 	(iv)	 	a contested election of Directors, as a result of which or in
connection with which the persons who were Directors before such election or
their nominees (the “Incumbent Directors”) cease to constitute a majority of
the Board; provided however that if the election, or nomination for election
by the Company’s

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	 	 	 	stockholders, of any new director was approved by a vote of at least fifty
percent (50%) of the Incumbent Directors, such new Director shall be
considered as an Incumbent Director, or
	 
	 	(v)	 	any other event specified by the Board or a Committee,
regardless of whether at the time an Award is granted or thereafter.

	 	(m)	 	[Omitted]
	 
	 	(n)	 	“Disability” means total and permanent disability as defined in Section 21
(e)(3) of the Code.
	 
	 	(o)	 	“Effective Date” means the date on which the Board approves the Plan.
	 
	 	(p)	 	[Omitted]
	 
	 	(q)	 	“Exchange Act” means the Securities Exchange Act of 1934, as amended.
	 
	 	(r)	 	“Fair Market Value” means, as of any date, the value of a Share determined as
follows:

	 	(i)	 	If the Common Stock is listed on any established stock
exchange or traded on a national market system, including without limitation
the Nasdaq National Market or the Nasdaq SmallCap Market of The Nasdaq Stock
Market, the Fair Market Value of a Share shall be the closing selling price
for such Common Stock (or the closing bid, if no sales were reported) as
quoted on such exchange or system on the day of determination, as reported in
The Wall Street Journal or such other source as the Administrator deems
reliable;
	 
	 	(ii)	 	If the Common Stock is regularly quoted by a recognized
securities dealer but selling prices are not reported, the Fair Market Value
of a Share shall be the mean between the high bid and low asked prices for the
Common Stock on the day of determination, as reported in The Wall Street
Journal or such other source as the Administrator deems reliable; or

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	 	(iii)	 	In the absence of an established market for the Common
Stock, the Fair Market Value shall be determined in good faith by the
Administrator.

	 	(s)	 	[Omitted]
	 
	 	(t)	 	[Omitted]
	 
	 	(u)	 	[Omitted]
	 
	 	(v)	 	“Newly Hired Employee” means any person, including Officers, recently
employed by the Company or any Subsidiary of the Company at the time of the Award.
	 
	 	(w)	 	“Notice of Grant” means a written or electronic notice evidencing certain
terms and conditions of an individual Option grant. The Notice of Grant is part of
the Option Agreement.
	 
	 	(x)	 	“Officer” means a person who is an executive officer of the Company within
the meaning of Section 16 of the Exchange Act and the rules and regulations
promulgated thereunder.
	 
	 	(y)	 	“Option” means a stock option granted pursuant to the Plan that is not
intended to qualify as an incentive stock option (as defined in the Code) and as
designated in the applicable Option Agreement.
	 
	 	(z)	 	“Option Agreement” means an agreement between the Company and an Optionee
evidencing the terms and conditions of an individual Option grant. The Option
Agreement is subject to the terms and conditions of the Plan.
	 
	 	(aa)	 	“Optioned Shares” means the Shares subject to an Option.
	 
	 	(bb)	 	“Optionee” means the holder of an outstanding Option granted under the Plan.
	 
	 	(cc)	 	[Omitted]

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	 	(dd)	 	[Omitted]
	 
	 	(ee)	 	“Participant” means any holder of one or more Options, Stock Awards, or the
Shares issuable or issued upon exercise of such Awards, under the Plan.
	 
	 	(ff)	 	“Plan” means this New Hire Stock and Incentive Plan.
	 
	 	(gg)	 	“[Omitted]
	 
	 	(hh)	 	“Qualifying Performance Criteria” means any one or more of the following
performance criteria, either individually, alternatively or in any combination,
applied to either the Company as a whole or to a business unit, Subsidiary or business
segment, either individually, alternatively or in any combination, and measured either
annually or cumulatively over a period of years, on an absolute basis or relative to a
pre-established target, to previous years’ results or to a designated comparison
group, in each case as specified by the Committee in the Award: (i) cash flow; (ii)
earnings (including gross margin, earnings before interest and taxes, earnings before
taxes, and net earnings); (iii) earnings per share; (iv) growth in earnings or
earnings per share; (v) stock price; (vi) return on equity or average stockholders’
equity; (vii) total stockholder return; (viii) return on capital; (ix) return on
assets or net assets; (x) return on investment; (xi) revenue; (xii) income or net
income; (xiii) operating income or net operating income; (xiv) operating profit or net
operating profit; (xv) operating margin; (xvi) return on operating revenue; (xvii)
market share; (xviii) contract awards or backlog; (xix) overhead or other expense
reduction; (xx) growth in stockholder value relative to the moving average of the S&P
500 Index or a peer group index; (xxi) credit rating; (xxii) strategic plan
development and implementation (including individual performance objectives that
relate to achievement of the Company’s or any business unit’s strategic plan); (xxiii)
improvement in workforce diversity, and (xxiv) any other similar criteria as may be
determined by the Administrator. The Committee may appropriately adjust any
evaluation of performance under a Qualifying Performance Criteria to exclude any of
the following events that occurs during a performance period: (A) asset write-downs;
(B) litigation or claim judgments or settlements; (C) the effect of changes in tax
law, accounting principles or other such laws or provisions affecting reported
results; (D) accruals for reorganization and restructuring programs; and (E) any gains
or losses classified as extraordinary or as discontinued operations in the Company’s
financial statements.

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	 	(ii)	 	“Rule 16b-3” means Rule 16b-3 of the Exchange Act, as the same may be amended
from time to time, or any successor to Rule 16b-3, as in effect when discretion is
being exercised with respect to the Plan.
	 
	 	(jj)	 	[Omitted]
	 
	 	(kk)	 	“Share” means a share of the Common Stock, as adjusted in accordance with
Section 17 hereof.
	 
	 	(ll)	 	[Omitted]
	 
	 	(mm)	 	“Stock Award” means a Stock Grant granted under Section 13 below or other
similar awards granted under the Plan (including phantom stock rights).
	 
	 	(nn)	 	“Stock Award Agreement” means a written agreement, the form(s) of which shall
be approved from time to time by the Administrator, between the Company and a holder
of a Stock Award evidencing the terms and conditions of an individual Stock Award
grant. Each Stock Award Agreement shall be subject to the terms and conditions of the
Plan.
	 
	 	(oo)	 	“Stock Grant” means the award of a certain number of Shares granted under
Section 13 below.
	 
	 	(pp)	 	[Omitted]
	 
	 	(qq)	 	“Subsidiary” means a “subsidiary corporation,” whether now or hereafter
existing, as defined in Section 424(f) of the Code, or any successor provision.
	 
	 	(rr)	 	“Withholding Taxes” means the federal, state and local income and employment
withholding taxes, or any other taxes required to be withheld, to which the holder of
an Award may be subject in connection with the grant, exercise, or vesting of an Award
or the issuance or transfer of Shares issued or issuable pursuant to an Award.
	 
	 	3.	 	[Omitted]

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	 	4.	 	Administration of the Plan.
	 
	 	(a)	 	Procedure.

	 	(i)	 	Multiple Administrative Bodies. Different Committees with
respect to different groups of Newly Hired Employees may administer the Plan.
	 
	 	(ii)	 	Section 162(m). To the extent that the Administrator
determines it to be desirable to qualify Awards granted hereunder as
“performance-based compensation” within the meaning of Section 162(m) of the
Code, the Plan shall be administered by a Committee of two or more “outside
directors” within the meaning of Section 162(m) of the Code.
	 
	 	(iii)	 	Rule 16b-3. To the extent desirable to qualify transactions
hereunder as exempt under Rule 16b-3, the transactions contemplated hereunder
shall be structured to satisfy the requirements for exemption under Rule
16b-3.
	 
	 	(iv)	 	Other Administration. Other than as provided above, the Plan
shall be administered by (A) the Board, (B) a Committee, which committee shall
be constituted to satisfy Applicable Laws or (C) subject to the Applicable
Laws, one or more officers of the Company to whom the Board or Committee has
delegated the power to grant Awards to persons eligible to receive Awards
under the Plan provided such grantees may not be officers.

	 	(b)	 	Powers of the Administrator. Subject to the provisions of the Plan, and in
the case of a Committee, subject to the specific duties delegated by the Board to such
Committee, the Administrator shall have the authority, in its discretion:

     (A) to determine the Fair Market Value of the Common Stock in
accordance with Section 2(r) of the Plan;

     (B) to select the Newly Hired Employees to whom Awards may be granted
hereunder;

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     (C) to determine the number of Shares or amount of cash to be covered
by each Award granted hereunder;

     (D) to approve forms of Award Agreements for use under the Plan;

     (E) to determine the terms and conditions, not inconsistent with the
terms of the Plan, of any Award granted hereunder, which terms and
conditions include, but are not limited to, the exercise price and/or
purchase price (if applicable), the time or times when Awards may be
exercised (which may be based on performance criteria), the vesting
schedule, any vesting and/or exercisability acceleration or waiver of
forfeiture restrictions, the acceptable forms of consideration, the term
and any restriction or limitation regarding any Award or the Shares
relating thereto, based in each case on such factors as the Administrator,
in its sole discretion, shall determine and may be established at the time
an Award is granted or thereafter;

     (F) to construe and interpret the terms of the Plan and Awards
granted pursuant to the Plan;

     (G) to prescribe, amend and rescind rules and regulations relating to
the Plan, including rules and regulations relating to sub-plans
established for the purpose of satisfying applicable foreign laws;

     (H) to modify or amend each Award (subject to Section 19 hereof),
including the discretionary authority to extend the post-termination
exercisability or purchase period of Awards longer than is originally
provided for in the Award Agreement;

     (I) to allow Participants to satisfy Withholding Tax obligations by
electing to have the Company withhold from the Shares to be issued upon
exercise or settlement of an Award that number of Shares having a Fair
Market Value equal to the minimum amount required to be withheld. The
Fair Market Value of the Shares to be withheld shall be determined on the
date that the amount of Withholding Tax is to be determined. All
elections by a Participant to have Shares withheld for this purpose shall
be made in such form and under such conditions as the Administrator may
deem necessary or advisable;

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     (J) to authorize any person to execute on behalf of the Company any
instrument required to effect the grant of an Award previously granted by
the Administrator;

     (K) to make all other determinations deemed necessary or advisable
for administering the Plan.

	 	(c)	 	Effect of Administrator’s Decision. The Administrator’s decisions,
determinations and interpretations shall be final and binding on all Participants and
any other holders of Options, Stock Awards, or Shares issued under the Plan.

     5. Eligibility. Options and Stock Awards may be granted to Newly Hired Employees.

     6. Limitations.

	 	(a)	 	[Omitted]
	 
	 	(b)	 	Neither the Plan nor any Award shall confer upon a Participant any right with
respect to continuing the Participant’s employment relationship with the Company, nor
shall they interfere in any way with the Participant’s right or the Company’s right to
terminate such relationship at any time, with or without cause.
	 
	 	(c)	 	[Omitted]

     7. Term of Plan. The Plan shall become effective on the Effective Date. Unless the Plan is
terminated earlier pursuant to Section 19 hereof, the Plan shall terminate upon the earliest to
occur of (a) December 31, 2017 or (b) the termination of all outstanding Awards in connection
with a dissolution or liquidation pursuant to Section 17(b) hereof or a Corporate Transaction
pursuant to Section 17(c) hereof. Should the Plan terminate on December 31, 2017, then all
Awards outstanding at that time shall continue to have force and effect in accordance with the
provisions of the applicable Award Agreement.

     8. Term of Option. The term of each Option shall be stated in the Option Agreement;
provided, however that the term shall be no more than ten (10) years from the date of grant or
such shorter term as may be provided in the Option Agreement.

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     9. Option Exercise Price and Consideration.

	 	(a)	 	Exercise Price. The per Share exercise price for the Shares to be issued
pursuant to exercise of an Option shall be no less than 100% of the Fair Market Value
per share on the date of grant.
	 
	 	(b)	 	Waiting Period and Exercise Dates. At the time an Option is granted, the
Administrator shall fix the period within which the Option may be exercised and shall
determine any conditions (including any vesting conditions) that must be satisfied
before the Option may be exercised.
	 
	 	(c)	 	Form of Consideration. The Administrator shall determine the acceptable form
of consideration for exercising an Option, including the method of payment. Such
consideration may consist entirely of:

	 	(i)	 	cash;
	 
	 	(ii)	 	check;
	 
	 	(iii)	 	other Shares which, in the case of Shares acquired directly
or indirectly from the Company, (A) have been owned by the Optionee for more
than six (6) months on the date of surrender (if it is required to eliminate
or reduce accounting charges incurred by the Company in connection with the
Option, or such other period (if any) required to so eliminate or reduce such
charges), and (B) have a Fair Market Value on the date of surrender equal to
the aggregate exercise price of the Shares as to which said Option shall be
exercised;
	 
	 	(iv)	 	consideration received through a special sale and remittance
procedure pursuant to which the Optionee shall concurrently provide
irrevocable instructions to (A) a Company-designated brokerage firm to effect
the immediate sale of the purchased Shares and remit to the Company, out of
the sale proceeds available on the settlement date, sufficient funds to cover
the aggregate exercise price payable for the purchased Shares plus all
Withholding Taxes required to be withheld by the Company by reason of such
exercise and (B) the Company to deliver the certificates for the purchased
Shares directly to such brokerage firm in order to complete the sale;

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	 	(v)	 	a reduction in the amount of any Company liability to the
Optionee, including any liability attributable to the Optionee’s participation
in any Company-sponsored deferred compensation program or arrangement;
	 
	 	(vi)	 	any combination of the foregoing methods of payment; or
	 
	 	(vii)	 	such other consideration and method of payment for the
issuance of Optioned Shares as determined by the Administrator and to the
extent permitted by Applicable Laws.

	 	(d)	 	No Option Repricings. Other than in connection with a change in the
Company’s capitalization (as described in Section 17(a) of the Plan), the exercise
price of an Option may not be reduced.

     10. Exercise of Option.

	 	(a)	 	Procedure for Exercise; Rights as a Stockholder.

	 	(i)	 	Any Option granted hereunder shall be exercisable according
to the terms of the Plan and at such times and under such conditions as
determined by the Administrator and set forth in the Option Agreement. Unless
the Administrator provides otherwise, vesting of Options granted hereunder
shall be suspended during any unpaid leave of absence. An Option may not be
exercised for a fraction of a Share.
	 
	 	(ii)	 	An Option shall be deemed exercised when the Company
receives: (A) written or electronic notice of exercise (in accordance with the
Option Agreement) from the person entitled to exercise the Option, and (B)
full payment for the Optioned Shares with respect to which the Option is
exercised and (C) satisfaction of any Withholding Taxes. Full payment may
consist of any consideration and method of payment authorized by the
Administrator and permitted by the Plan and shall be set forth in the Option
Agreement. Shares issued upon exercise of an Option shall be issued in the
name of the Optionee or, if requested by the Optionee, in the name of the
Optionee and his or her spouse. Until the Shares are issued (as evidenced by
the appropriate entry on the books of the Company or of a duly authorized
transfer agent of the Company), no right to vote or receive dividends or any
other rights as a stockholder shall

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	 	 	 	exist with respect to the Optioned Shares, notwithstanding the exercise of
the Option. The Company shall issue (or cause to be issued) such Shares
promptly after the Option is exercised. No adjustment will be made for a
dividend or other right for which the record date is prior to the date the
Shares are issued, except as provided in Section 17 hereof.
	 
	 	(iii)	 	Exercising an Option in any manner shall decrease the number
of Optioned Shares thereafter available for sale under the Option, by the
number of Shares as to which the Option is exercised.

	 	(b)	 	Termination of Employment Relationship. Unless otherwise provided by the
Administrator in the Option Agreement, if an Optionee ceases to be employed by the
Company, other than upon the Optionee’s death or Disability, such Optionee may
exercise his or her Option for a period of three (3) months measured from the date of
termination, or such longer period of time as specified in the Option Agreement, to
the extent that the Option is vested on the date of termination (but in no event later
than the expiration of the term of the Option as set forth in the Option Agreement).
If, on the date of termination, the Optionee is not vested as to his or her entire
Option, the Option shall immediately terminate as to all the Optioned Shares covered
by the unvested portion of the Option, and those Optioned Shares shall revert
immediately to the Plan. To the extent the Optionee does not, within the
post-termination time period specified in the Option Agreement, exercise the Option
for the Optioned Shares in which Optionee is vested at the time of such termination of
the Newly Hired Employee, the Option shall terminate with respect to those vested
Optioned Shares at the end of such period, and those Optioned Shares shall revert to
the Plan.
	 
	 	(c)	 	Disability of Optionee. Unless otherwise provided by the Administrator in
the Option Agreement, if an Optionee ceases to be employed by the Company as a result
of the Optionee’s Disability, the Optionee may exercise his or her Option within
twelve (12) months of termination, or such longer period of time as specified in the
Option Agreement, to the extent the Option is vested on the date of termination (but
in no event later than the expiration of the term of such Option as set forth in the
Option Agreement). If, on the date of termination, the Optionee is not vested as to
his or her entire Option, the Option shall immediately terminate as to the Optioned
Shares covered by the unvested portion of the Option, and those Optioned Shares shall
revert immediately to the Plan. To the extent the Optionee does not, within the
post-termination time period specified in the Option Agreement, exercise the Option
for the Optioned Shares in which Optionee is vested at the time of such termination of
the Newly

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	 	 	 	Hired Employee, the Option shall terminate with respect to those vested Optioned
Shares at the end of such period, and those Optioned Shares shall revert to the
Plan.
	 
	 	(d)	 	Death of Optionee. Unless otherwise provided by the Administrator in the
Option Agreement, if an Optionee dies while employed, the Option may be exercised
within twelve (12) months following Optionee’s death, or such longer period of time as
specified in the Option Agreement, to the extent that the Option is vested on the date
of death (but in no event later than the expiration of the term of such Option as set
forth in the Option Agreement) by the Optionee’s designated beneficiary, provided such
beneficiary has been designated prior to Optionee’s death in a form acceptable to the
Administrator. If no such beneficiary has been designated by the Optionee, then such
Option may be exercised by the personal representative of the Optionee’s estate or by
the person(s) to whom the Option is transferred pursuant to the Optionee’s will or in
accordance with the laws of descent and distribution. If, at the time of death, the
Optionee is not vested as to his or her entire Option, the Option shall immediately
terminate as to the Optioned Shares covered by the unvested portion of the Option, and
those Optioned Shares shall immediately revert to the Plan. To the extent the Option
is not, within the post-termination time period specified in the Option Agreement,
exercised for the Optioned Shares in which Optionee is vested at the time of such
termination of the Newly Hired Employee, the Option shall terminate with respect to
those vested Optioned Shares, and those Optioned Shares shall revert to the Plan.

     11. [Omitted]

     12. Limited Transferability of Options. An Option generally may not be sold, pledged,
assigned, hypothecated, transferred, or disposed of in any manner other than by will or by the
laws of descent or distribution and may be exercised, during the lifetime of the Optionee, only
by the Optionee; provided however that Options may be transferred by instrument to an inter vivos
or testamentary trust in which the Options are to be passed to beneficiaries upon the death of
the trustor (settlor) or by gift or pursuant to domestic relations orders to “Immediate Family
Members” (as defined below) of the Optionee. “Immediate Family” means any child, stepchild,
grandchild, parent, stepparent, grandparent, spouse, former spouse, sibling, niece, nephew,
mother-in-law, father-in-law, son-in-law, daughter-in-law, brother-in-law, or sister-in-law
(including adoptive relationships), a trust in which these persons have more than fifty percent
of the beneficial interest, a foundation in which these persons (or the Optionee) control the
management of assets, and any other entity in which these persons (or the Optionee) own more than
fifty percent of the voting interests. The Optionee may designate one or more persons as the
beneficiary or beneficiaries of his or her

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outstanding Options, and those Options shall, in accordance with such designation,
automatically be transferred to such beneficiary or beneficiaries upon the Optionee’s death while
holding those Options. Such beneficiary or beneficiaries shall take the transferred Options
subject to all the terms and conditions of the applicable agreement evidencing each such
transferred Option, including (without limitation) the limited time period during which the
Option may be exercised following the Optionee’s death.

     13. Stock Awards. Each Stock Award Agreement shall be in such form and shall contain such
terms and conditions as the Administrator shall deem appropriate. The terms and conditions of
such agreements may change from time to time, and the terms and conditions of separate agreements
need not be identical, but each such agreement shall include (through incorporation of provisions
hereof by reference in the agreement or otherwise) the substance of each of the following
provisions:

	 	(a)	 	Consideration. A Stock Grant may be awarded in consideration for such
property or services as is permitted under Applicable Law.
	 
	 	(b)	 	Vesting. Shares of Common Stock awarded under an agreement reflecting a
Stock Grant may, but need not, be subject to a share repurchase option, forfeiture
restriction or other conditions in favor of the Company in accordance with a vesting
or lapse schedule to be determined by the Administrator.
	 
	 	(c)	 	Termination of Participant’s Employment Relationship. In the event a
Participant’s employment terminates, the Company may reacquire any or all of the
Shares held by the Participant which have not vested or which are otherwise subject to
forfeiture or other conditions as of the date of termination under the terms of the
agreement.
	 
	 	(d)	 	Transferability. Except as determined by the Board, no rights to acquire
Shares under a Stock Grant shall be assignable or otherwise transferable by the
Participant except by will or by the laws of descent and distribution.

     14. [Omitted]

     15. [Omitted]

     16. Section 162(m) Compliance. Any Stock Award (other than an Option or any other Stock
Award having a purchase price equal to 100% of the Fair Market Value on the date such award is
made) that is intended as “qualified performance-based compensation” within the meaning of
Section 162(m) of the Code must vest or become

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exercisable or payable contingent on the achievement of one or more Qualifying Performance
Criteria. Notwithstanding anything to the contrary herein, the Committee shall have the
discretion to determine the time and manner of compliance with Section 162 (m) of the Code as
required under applicable regulations and to conform the procedures related to the Award to the
requirements of Section 162(m) and may in its discretion reduce the number of Shares granted or
amount of cash or other property to which a Participant may otherwise have been entitled with
respect to an Award designed to qualify as performance-based compensation under Section 162(m).

     17. Adjustments Upon Changes in Capitalization, Dissolution or Corporate Transaction.

	 	(a)	 	Changes in Capitalization. The number of Shares as well as the price per
Share subject to each outstanding Award, shall be proportionately adjusted for any
increase or decrease in the number of issued Shares resulting from a stock split,
reverse stock split, stock dividend, combination or reclassification of the Common
Stock, or any other increase or decrease in the number of issued Shares effected
without receipt of consideration by the Company; provided, however, that conversion of
any convertible securities of the Company shall not be deemed to have been “effected
without receipt of consideration.” Such adjustment shall be made by the Administrator,
whose determination in that respect shall be final, binding and conclusive. Except as
expressly provided herein, no issuance by the Company of shares of stock of any class,
or securities convertible into shares of stock of any class, shall affect, and no
adjustment by reason thereof shall be made with respect to, the number or price of
Shares. Notwithstanding the foregoing, any such adjustment shall not (i) cause an
Award which is exempt from Code Section 409A to become subject to Code Section 409A or
(ii) cause an Award subject to Code Section 409A not to comply with the requirements
of Code Section 409A.
	 
	 	(b)	 	Dissolution or Liquidation. In the event of the proposed dissolution or
liquidation of the Company, the Administrator shall notify each Participant as soon as
practicable prior to the effective date of such proposed transaction. The
Administrator in its discretion may (but need not) provide for a Participant to have
the right to exercise his or her Option or Stock Award until ten (10) days prior to
such transaction as to all of the Shares covered thereby, including Shares as to which
the Option or Stock Award would not otherwise be exercisable. In addition, the
Administrator may (but need not) provide that any Company repurchase option applicable
to any unvested Shares purchased upon exercise of an Option or issued under a Stock
Award shall lapse as to all such Shares, provided the proposed dissolution or
liquidation takes place at the time and in the manner contemplated. To the extent it
has not been previously exercised,

15

 

	 	 	 	an Award will terminate immediately prior to the consummation of such proposed
action.
	 
	 	(c)	 	Corporate Transaction.

	 	(i)	 	In the event of a Corporate Transaction, as determined by the
Board or a Committee, the Board or Committee may, in its discretion, (i)
provide for the assumption or substitution of, or adjustment to, each
outstanding Award; (ii) accelerate the vesting of Options and terminate any
restrictions on Stock Awards; and/or (iii) provide for termination of Awards
as a result of the Corporate Transaction on such terms and conditions as it
deems appropriate, including providing for the cancellation of Awards for a
cash payment to the Participant. For the purposes of this paragraph, the
Award shall be considered assumed if, following the Corporate Transaction, the
Award confers the right to purchase or receive, for each Share or amount of
cash covered by the Award immediately prior to the Corporate Transaction, the
consideration (whether stock, cash, or other securities or property) received
in the Corporate Transaction by holders of Common Stock for each Share held on
the effective date of the Corporate Transaction (and if holders were offered a
choice of consideration, the type of consideration chosen by the holders of a
majority of the outstanding Shares); provided, however, that if such
consideration received in the Corporate Transaction is not solely common stock
of the successor corporation, the Administrator may, with the consent of the
successor corporation, provide for the consideration to be received upon the
exercise of the Award, for each Share covered by the Award, to be solely
common stock of the successor corporation equal in fair market value to the
per share consideration received by holders of Shares in the Corporate
Transaction.
	 
	 	(ii)	 	Each Option or Stock Award which is assumed pursuant to this
Section 17(c) shall be appropriately adjusted, immediately after such
Corporate Transaction, to apply to the number and class of securities which
would have been issuable to the Participant in consummation of such Corporate
Transaction had the Option or Stock Award been exercised immediately prior to
such Corporate Transaction. Appropriate adjustments to reflect such Corporate
Transaction shall also be made to the exercise or purchase price payable per
share under each outstanding Option or Stock Award, provided the aggregate
exercise or purchase price payable for such securities shall remain the same.
Notwithstanding the foregoing,

16

 

	 	 	 	any such adjustment shall not (i) cause an Award which is exempt from Code
Section 409A to become subject to Code Section 409A or (ii) cause an Award
subject to Code Section 409A not to comply with the requirements of Code
Section 409A.

     18. Date of Grant. The date of grant of any Award shall be, for all purposes, the date on
which the Administrator grants such Award. Notice of the grant shall be provided to each
Participant within a reasonable time after the date of such grant.

     19. Amendment and Termination of the Plan. The Board may at any time amend, alter, suspend
or terminate the Plan. No amendment, alteration, suspension or termination of the Plan shall
impair the rights of any Participant under any grant theretofore made, unless mutually agreed
otherwise between the Participant and the Administrator, which agreement must be in writing and
signed by the Participant and the Company. Termination of the Plan shall not affect the
Administrator’s ability to exercise the powers granted to it hereunder with respect to Awards
granted under the Plan prior to the date of such termination.

     20. Conditions Upon Issuance of Shares.

	 	(a)	 	Awards shall not be granted and Shares shall not be issued pursuant to the
exercise of an Award unless the grant of the Award, the exercise or settlement of such
Award and the issuance and delivery of such Shares shall comply with Applicable Laws
and shall be further subject to the approval of counsel for the Company with respect
to such compliance.
	 
	 	(b)	 	No Shares or other assets shall be issued or delivered under the Plan unless
and until there shall have been compliance with all applicable requirements of Federal
and state securities laws, including the filing and effectiveness of the Form S-8
registration statement for the Shares, and all applicable listing requirements of any
stock exchange (or the Nasdaq National Market, if applicable) on which Common Stock is
then listed for trading.

     21. Inability to Obtain Authority. The inability of the Company to obtain authority from
any regulatory body having jurisdiction (including under Section 20), which authority is deemed
by the Company’s counsel to be necessary to the lawful grant of Awards and issuance and sale of
any Shares hereunder, shall relieve the Company of any liability in respect of the failure to
grant such Awards or issue or sell such Shares as to which such requisite authority shall not
have been obtained.

17

 

     22. Reservation of Shares. The Company, during the term of this Plan, will at all times
reserve and keep available such number of Shares as shall be sufficient to satisfy the
requirements of the Plan.

     23. [Omitted]

     24. Code Section 409A. Notwithstanding any provision of this Plan to the contrary, no
deferral election, payment election, time or form of payment, modification or other action with
respect to the Plan shall be permitted to the extent that such election, time or form of payment,
modification or other action would violate any requirement of Code Section 409A of the Code or
the regulations thereunder, as determined in the sole discretion of the Administrator.

18Exhibit 10.52

 

EXHIBIT 10.52

Confidential Executive Transition Agreement

     This Confidential Executive Transition Agreement (“Agreement”) is entered into by and between
ILLUMINA, INC. (“the Company”) and JOHN R. STUELPNAGEL (“Executive”) (collectively “the Parties”),
as of the date of the last Party to sign it below, with respect to the following:

     A. Executive shall work in his current role with the Company through March 31, 2008. In doing
so Executive will continue through March 31, 2008 (i) to act in the same Executive Officer capacity
as Executive has been holding to date, driving the operating goals and results of the Array
Business Unit; (ii) to serve as a Director in the Company; and (iii) to be compensated at his
current level.

     B. Effective April 1, 2008 at 12 a.m. Pacific Time, Executive shall resign his position (i) as
the Company’s Senior Vice President, Chief Operating Officer and General Manager Micro Arrays, and
(ii) from the Company’s Board of Directors.

     C. Effective April 1, 2008 at 12 a.m. Pacific Time, Executive’s Change in Control Severance
Agreement made as of August 21, 2006 shall terminate without any additional notice or other action
on the part of the Company.

     D. With the first bi-weekly pay cycle after April 1, 2008, Executive shall be paid in full his
unused paid time off accrued through March 31, 2008.

     E. Commencing on April 1, 2008 and through March 30, 2009, Executive shall become an Illumina
Fellow that is defined as a part-time Company employee acting in an advisory capacity to the
Company’s CEO and Management.

     F. The specifics of Executive’s part-time employment with the Company shall be as follows:

	 	1.	 	“Part-time” is defined as up to 25% of a
standard work week with additional time as mutually agreed between
Executive and the Company CEO.
	 
	 	2.	 	Unless otherwise mutually agreed between
Executive and Company CEO, Executive will work on the development of
the Infinium HD and follow-on products and their manufacturing.
Executive may undertake other assignments by mutual verbal agreement
between Executive and Company CEO.
	 
	 	3.	 	Executive will work up to 25% of a standard
work week on average if requested and shall be paid on an hourly basis
for the time worked at an equivalent hourly rate to Executive’s current
salary. Executive shall be compensated at a minimum of 5 hours worked
each week, even if the actual hours worked fall below this level.

1

 

	 	4.	 	From April 1, 2008 to March 31, 2009 (12 full
months), Executive shall continue vesting his existing stock options as
if Executive was working as a full-time Company employee.
	 
	 	5.	 	From April 1, 2008 to March 31, 2009 (12 full
months), irrespective of time worked in any period, Executive will
continue to receive Company health and welfare benefits under
conditions then applicable to part-time Illumina employees,
unless such benefit is prohibited by Company policy or by the
Company’s group insurance policies in effect at that time.
Notwithstanding the above, Executive will retain his access to the
Company’s exercise facility.
	 
	 	6.	 	From April 1, 2008 onward, Executive will
neither accrue paid time off nor will Executive earn or be eligible to
receive any bonus, stock option or restricted stock unit grants.
	 
	 	7.	 	During his Part-time employment, Executive
shall fully comply with all Company rules and policies related the
Company’s stock, including, but not limited to the Company’s Insider
Trading Policy.

     G. Executive may terminate his Part-time arrangement with the Company at any time and for any
reason by prior written notice to the Company CEO. Executive acknowledges that upon such
termination all continued vesting of Executive’s options as provided in Paragraph F.4 above shall
cease immediately. The Company may terminate this Agreement for material breach or for violations
of the Executive’s obligations as an employee as determined by a majority of the independent
members of the Company’s Board of Directors and if Executive fails to remedy any such breach, or
fails to act reasonably to remedy breach, within thirty (30) days after receipt of written notice
thereof by Company’s Board of Directors.

     H. As partial consideration for the continued vesting of Executive’s options during the period
from April 1, 2008 to March 31, 2009 as provided in Paragraph F.4 above, Executive agrees to sign a
release of the form attached as Exhibit A contemporaneously with the execution of this Agreement.

     I. The terms and conditions of this Agreement are strictly confidential. Accordingly, except
and only to the extent required by law and in such event after notice has been timely provided to
the Company, such terms and conditions shall not be disclosed, discussed or revealed by Executive
(directly or indirectly) to any current or former Company employee, or to any other person or
entity. Notwithstanding the preceding sentence, Executive may disclose in strict confidence such
terms and conditions to members of his direct family, tax advisors, attorneys, but only after such
persons have been made aware of the strict confidential nature of that information and have agreed
to maintain that information in confidence.

     J. This Agreement, including Exhibit A attached hereto, contains the entire agreement between
Executive and the Company and supersedes any prior agreement or understanding between the Parties
(whether oral or written) regarding the subject matter herein. Executive acknowledges that no
promise has been made to Executive that is not contained in this Agreement. The provisions of this
Agreement are severable, and if any one or more provisions may be determined to be judicially
unenforceable, in whole or in part, the remaining provisions

2

 

shall nevertheless be binding and enforceable. This Agreement may be amended only by a
written agreement executed by the Parties. The validity, interpretation and performance of this
Agreement shall be construed and interpreted according to the laws of the State of California.

	 	 	 	 	 	 	 	 	 	 	 
	/s/
John R. Stuelpnagel 

	 	 	 	Dated:	 	March 21, 2008 	 	 
	 	 	 	 	 	 	 	 	 
	John R. Stuelpnagel	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	ILLUMINA, INC.	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Jay T. Flatley 	 	 	 	Dated:	 	March 21, 2008	 	 
	 

	 	 
	 	 	 	 	 	 	 	 
	Jay T. Flatley, President & CEO	 	 	 	 	 	 	 	 

3

 

Exhibit A

Executive and Company, for themselves, their successors, heirs and assigns (as applicable)
hereby fully, irrevocably, unconditionally and forever release, acquit and discharge each
other and Company’s past and present directors, officers, employees, attorneys and agents,
in each and every case from any and all rights, claims, demands, causes of action,
obligations, suits, liens, damages, losses, or liabilities of any kind and character
whatsoever, whether in law or in equity, whether known or unknown, claimed, suspected or
unsuspected, that either Party does, can, shall or may have or ever had, directly or
indirectly, against the other arising out of, or connected in any way to, the Executive’s
employment with Company or to the Executive’s resignation and change of status as
contemplated by this Agreement. This release is intended by the Parties to have the
broadest possible scope.  Consistent with that intention, the Parties agree that it includes
a release of any act, cause, matter or thing, known or unknown, that is or could have been
alleged by either Party in any action (in tort, contract, or under any other legal theory
including for violation of state or federal labor laws) against the other Party as of the
date of this Agreement.  In addition, both Parties assume the risk of any mistake of fact in
connection with this release and with respect to any fact that is now unknown to the Parties
or to their officers, directors, employees, attorneys, agents or representatives.  
Accordingly, the Parties expressly waive all rights under Section 1542 of the Civil Code of
California which reads as follows:  “A general release does not extend to claims which the
creditor does not know or suspect to exist in his favor at the time of executing the
release, which if known by him must have materially affected his settlement with the
debtor”.

	 	 	 	 	 	 	 	 	 	 	 
	/s/
John R. Stuelpnagel 

	 	 	 	Dated:	 	March 21, 2008	 	 
	 	 	 	 	 	 	 	 	 
	John R. Stuelpnagel	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	ILLUMINA, INC.	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By:

	 	/s/ Jay T. Flatley 	 	 	 	Dated:	 	March 21, 2008	 	 
	 

	 	 
	 	 	 	 	 	 	 	 
	Jay T. Flatley, President & CEO	 	 	 	 	 	 	 	 

4

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