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Exhibit 4.10    
    

GENOPTIX, INC.  

FIRST AMENDMENT TO

AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT  

        This FIRST AMENDMENT TO AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT (this  "Amendment") by and among GENOPTIX, INC., a Delaware corporation (the  "Company") and the investors listed on the signature pages hereof (each, an
"Investor", and together,
the "Investors") dated as of May 9, 2005 (the "Investor Rights Agreement") is entered into as of
August 3, 2005 by and among the Company and the Investors. Capitalized terms used herein which are not defined herein shall have the definition ascribed to them in the Investor Rights
Agreement. 

RECITALS  

        WHEREAS, the Company and the Investors have previously entered into the Investor Rights Agreement, pursuant to
which the Investors possess certain registration, right of first refusal, information and other investor rights; 

        WHEREAS, the Company is entering into a Follow-On Series 1-D Preferred Stock Purchase Agreement with the
purchasers named therein (the "Purchasers" and each individually, a "Purchaser") of even date herewith
(the "Follow-On Purchase Agreement"), pursuant to which the Purchasers will purchase up to an aggregate of 12,618,296 shares of the
Company's
Series 1-D Preferred Stock at the Closing (as defined in the Follow-On Purchase Agreement); 

        WHEREAS, in connection with the Follow-On Purchase Agreement, the Company and Investors desire to amend the Investor Rights
Agreement so to include the Purchasers as "Investors" therein and to make the other changes described herein; 

        WHEREAS, the Purchasers desire to become parties to the Investor Rights Agreement as amended by this Amendment; 

        WHEREAS, Section 5.6 of the Investor Rights Agreement provides that the Investor Rights Agreement may be amended with the written
consent of the Company and the holders of a majority of the Registrable Securities (as defined in the Investor Rights Agreement); and 

        WHEREAS, the undersigned Investors are the holders of at least a majority of all of the Registrable Securities. 

AGREEMENT  

        NOW, THEREFORE, in consideration of the foregoing and the promises and covenants contained herein and in the
Investor Rights Agreement, and for other good and valuable consideration, the receipt of which is hereby acknowledged, the parties hereto agree as follows: 

        1.    Amendments.    

        (a)   Section 2.11 of the Investor Rights Agreement is hereby deleted and replaced and superseded in its entirety with
the following: 

        "2.11    Amendment of Registration Rights.    Any provision of this
Section 2 may be amended and the observance thereof may be waived (either generally or in a particular instance and either retroactively or prospectively), only with the written consent of the
Company and the Holders of at least fifty-five percent (55%) of the Registrable Securities then outstanding. Any amendment or waiver effected in accordance with this Section 2.11 

1

 

shall
be binding upon each Holder and the Company. By acceptance of any benefits under this Section 2, Holders of Registrable Securities hereby agree to be bound by the provisions hereunder." 

        (b)   Section 2.12 of the Investor Rights Agreement is hereby deleted and replaced and superseded in its entirety with
the following: 

        "2.12    Limitation on Subsequent Registration Rights.    Other than
as provided in Section 5.11, after the date of this Agreement, the Company shall not, without the prior written consent of the Holders of at least fifty-five percent (55%) of the
Registrable Securities then outstanding, enter into any agreement with any holder or prospective holder of any securities of the Company that would grant such holder registration rights pari pasu with
or senior to those granted to the Holders hereunder, other than the right to a Special Registration Statement." 

        (c)   Section 5.6 of the Investor Rights Agreement is hereby deleted and replaced and superseded in its entirety with
the following: 

        "5.6    Amendment and Waiver.    

        (a)   Except as otherwise expressly provided, this Agreement may be amended or modified only upon the written consent of the
Company and the holders of at least fifty-five percent (55%) of the Registrable Securities. 

        (b)   Except as otherwise expressly provided, the obligations of the Company and the rights of the Holders under this Agreement
may be waived only with the written consent of the holders of at least fifty-five percent (55%) of the Registrable Securities. 

        (c)   For the purposes of determining the number of Holder or Investors entitled to vote or exercise any rights hereunder, the
Company shall be entitled to rely solely on the list of record holders of its stock as maintained by or on behalf of the Company." 

        (d)   Section 5.11 of the Investor Rights Agreement is hereby deleted and replaced and superseded in its entirety with
the following: 

        "5.11    Additional Investors.    Notwithstanding anything to the
contrary contained herein, if the Company shall issue Equity Securities in accordance with Section 4.5(c), (f), (h) or (i) of this Agreement, any purchaser of such Equity
Securities may become a party to this Agreement by executing and delivering an additional counterpart signature page to this Agreement and shall be deemed an
"Investor," a "Holder" and a party hereunder." 

        (e)   Exhibit A of the Investor Rights Agreement is hereby deleted and replaced and superseded in its entirety with  Exhibit A attached hereto.

        2.    Waiver of Rights of First Refusal.    The rights set forth in Section 4.1 of the Investor Rights
Agreement to purchase shares of Equity Securities (as defined in the Investor Rights Agreement) of the Company are hereby waived, for and on behalf of all Major Investors (as defined in the Investor
Rights Agreement) with respect to the issuance of 12,618,296 shares of Series 1-D Preferred at the Closing pursuant to the Follow-On Purchase Agreement. 

        3.    Counterpart Signature Page.    By executing this Amendment, each of the Purchasers agrees to be bound by the
provisions of the Investor Rights Agreement, as amended by this Amendment, and to be deemed "Investors," "Holders" and parties hereunder and thereunder. 

        4.    Effect of Amendment.    Except as expressly modified by this Amendment, the Investor Rights Agreement shall
remain unmodified and in full force and effect. 

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        5.    Governing Law.    This Amendment shall be governed by and construed in accordance with the laws of the State of
Delaware as applied to agreements among Delaware residents entered into and to be performed entirely within the State of Delaware. 

        6.    Counterparts.    This Amendment may be executed in any number of counterparts and signatures delivered by
facsimile, each of which shall be deemed an original, but all of which together shall constitute one instrument. 

[REMAINDER OF THIS PAGE INTENTIONALLY LEFT BLANK]  

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        IN WITNESS WHEREOF, the parties have executed this FIRST AMENDMENT TO AMENDED AND RESTATED INVESTOR RIGHTS
AGREEMENT as of the date set forth above. 

	COMPANY:	INVESTORS:
	
 GENOPTIX, INC.	

CHICAGO GROWTH PARTNERS VIII, L.P.
	

By:	

/s/ TINA S. NOVA
 Tina S. Nova, Ph.D.	

By:

Its:	

Chicago Growth Management VIII, L.P.

General Partner
	 	President, Chief Executive Officer &	By:	Chicago Growth Management, L.L.C.
	 	Co-Founder	Its:	General Partner
	

Address:	

3398 Carmel Mountain Road
	

By:	

/s/ ARDA M. MINOCHERHOMJEE

	 	San Diego, CA 92121
	Title:	Managing Director
	

 	

 	
WILLIAM BLAIR CAPITAL PARTNERS VII QP, L.P.
	

 	

 	

By:	

William Blair Capital Management VII, L.P.
	 	 	Its:	General Partner
	

 	

 	

By:	

William Blair Capital Management VII, L.L.C.
	 	 	Its:	General Partner
	

 	

 	

By:	

/s/ ARDA M. MINOCHERHOMJEE

	 	 	Title:	Managing Director
	

 	

 	
WILLIAM BLAIR CAPITAL PARTNERS VII, L.P.
	

 	

 	

By:	

William Blair Capital Management VII, L.P.
	 	 	Its:	General Partner
	

 	

 	

By:	

William Blair Capital Management VII, L.L.C.
	 	 	Its:	General Partner
	

 	

 	

By:	

/s/ ARDA M. MINOCHERHOMJEE

	 	 	Title:	Managing Director
	

 	

 	
ALLIANCE TECHNOLOGY VENTURES III, L.P.
	

 	

 	

By:	

ATV III Partners, LLC
	 	 	Its:	General Partner
	

 	

 	

By:	

/s/ MICHAEL A. HENOS

	

 	

 	

Name:	

Michael A. Henos

	

 	

 	

Title:	

General Partner

[SIGNATURE PAGE TO FIRST AMENDMENT TO

AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT] 

4

 

	 	 	ATV III AFFILIATES FUND, L.P.
	

 	

 	

 	

By:	

ATV III Partners, LLC
	 	 	 	Its:	General Partner
	

 	

 	

By:	

/s/ MICHAEL A. HENOS

	

 	

 	

Name:	

Michael A. Henos

	

 	

 	

Title:	

General Partner

	

 	

 	
ENTERPRISE PARTNERS V, L.P.
	

 	

 	

 	

By:	

Enterprise Management Partners V, LLC
	 	 	 	Its:	General Partner
	

 	

 	

By:	

/s/ ANDREW E. SENYEI

	

 	

 	

Name:	

Andrew E. Senyei, M.D.

	

 	

 	

Title:	

Managing Director

	

 	

 	
TULLIS-DICKERSON CAPITAL FOCUS II, L.P.
	

 	

 	

 	

By:	

Tullis-Dickerson Partners II, L.L.C.
	 	 	 	Its:	General Partner
	

 	

 	

By:	

/s/ TIMOTHY M. BUONO

	 	 	 	Timothy M. Buono, Principal
	

 	

 	
TD JAVELIN CAPITAL FUND II, L.P.
	

 	

 	

 	

By:	

TD II Regional Partners, Inc.
	 	 	 	Its:	General Partner
	

 	

 	

By:	

/s/ TIMOTHY M. BUONO

	 	 	 	Timothy M. Buono, Vice President
	

 	

 	
TD LIGHTHOUSE CAPITAL FUND, L.P.
	

 	

 	

 	

By:	

TD II Regional Partners, Inc.
	 	 	 	Its:	General Partner
	

 	

 	

By:	

/s/ TIMOTHY M. BUONO

	 	 	 	Timothy M. Buono, Vice President

[SIGNATURE PAGE TO FIRST AMENDMENT TO

AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT] 

5

 

	 	 	EXCELSIOR VENTURE PARTNERS III, LLC
	

 	

 	

By:	

/s/ LEE A. GARDELLA

	

 	

 	

Name:	

Lee A. Gardella

	

 	

 	

Title:	

Vice President

	

 	

 	
LOTUS BIOSCIENCE INVESTMENT HOLDINGS, LTD.
	

 	

 	

By:	

/s/ MONG CHEUK WAI    /s/ WONG KEN LUM

	

 	

 	

Name:	

Mong Cheuk Wai                  Wong Ken Lum

	

 	

 	

Title:	

Directors

	

 	

 	
GC&H INVESTMENTS
	

 	

 	

By:	

/s/ JOHN L. CARDOZA

	

 	

 	

Name:	

John L. Cardoza

	

 	

 	

Title:	

Managing Member

	

 	

 	
PETE HRONIS
	

 	

 	

/s/ PETE HRONIS

	

 	

 	
ALLEN FAMILY TRUST DATED 10/12/81
	

 	

 	

By:	

/s/ DICK ALLEN
 Dick Allen

Trustee
	

 	

 	
THOMAS & NELL WALTZ FAMILY L.P.
	

 	

 	

By:	

/s/ THOMAS A. WALTZ
 Thomas A. Waltz

General Partner

[SIGNATURE PAGE TO FIRST AMENDMENT TO

AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT] 

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	 	 	GREENE FAMILY TRUST
	

 	

 	

By:	

/s/ HOWARD E. GREENE, JR.

	

 	

 	

Name:	

Howard E. Greene, Jr.

	

 	

 	

Title:	

Trustee

	

 	

 	

 	

 
	

 	

 	
ALLISON M. GREGORY
	

 	

 	

/s/ ALLISON M. GREGORY

	

 	

 	

 	

 
	

 	

 	
HARBOUR VENTURES
	

 	

 	

By:	

 
	 	 	 	

	

 	

 	

Name:	

 
	 	 	 	

	

 	

 	

Title:	

 
	 	 	 	

	

 	

 	
COMERICA INCORPORATED
	

 	

 	

By:	

/s/ ANN M. SCHEUER

	

 	

 	

Name:	

Ann M. Scheuer

	

 	

 	

Title:	

Vice President

[SIGNATURE PAGE TO FIRST AMENDMENT TO

AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT] 

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EXHIBIT A    
    
    SCHEDULE OF INVESTORS    
    

	NAME AND ADDRESS
 
	 	SERIES 1-A

PREFERRED
	 	SERIES 1-B

PREFERRED
	 	SERIES 1-C

PREFERRED
	 	SERIES 1-D

PREFERRED

	1.	 	ENTERPRISE PARTNERS V, L.P.
 2223 Avenida de la Playa, Suite 300

La Jolla, California 92037

Attn: Andrew E. Senyei, M.D.	 	3,759,398	 	6,737,746	 	2,796,072	 	3,281,923
	

2.	
 	

ALLIANCE TECHNOLOGY VENTURES III, L.P.
 8995 Westside Parkway, Suite 200

Alpharetta, Georgia 30004

Attn: Michael Henos	
 	

3,684,211	
 	

3,851,743	
 	

2,025,750	
 	

2,377,748
	

3.	
 	

ATV III AFFILIATES FUND, L.P.
 8995 Westside Parkway, Suite 200

Alpharetta, Georgia 30004

Attn: Michael Henos	
 	

75,188	
 	

78,606	
 	

22,531	
 	

26,446
	

4.	
 	

TULLIS-DICKERSON CAPITAL FOCUS II, L.P.
 c/o Tullis-Dickerson & Co., Inc.

Two Greenwich Plaza, Fourth Floor

Greenwich, Connecticut 06830

Attn: Timothy M. Buono	
 	

563,910	
 	

336,886	
 	

239,942	
 	

281,635
	

5.	
 	

TD JAVELIN CAPITAL FUND II, L.P.
 c/o Tullis-Dickerson & Co., Inc.

Two Greenwich Plaza, Fourth Floor

Greenwich, Connecticut 06830

Attn: Timothy M. Buono	
 	

563,910	
 	

561,478	
 	

299,766	
 	

351,854
	

6.	
 	

TD LIGHTHOUSE CAPITAL FUND, L.P.
 c/o Tullis-Dickerson & Co., Inc.

Two Greenwich Plaza, Fourth Floor

Greenwich, Connecticut 06830

Attn: Timothy M. Buono	
 	

563,910	
 	

870,290	
 	

382,021	
 	

448,402
	

7.	
 	

LOTUS BIOSCIENCE INVESTMENT HOLDINGS, LTD.
 9th floor, Central Building

3 Pedder Street, Hong Kong

Attn: Tiffany Hung/Eric Chung	
 	

375,940	
 	

393,033	
 	

203,400	
 	

238,743
	

8.	
 	

EXCELSIOR VENTURE PARTNERS III, LLC
 c/o U.S. Trust of CT

225 High Ridge Road, East Building

Stamford, CT 06905

Attn: David I. Fann	
 	

942,481	
 	

1,403,696	
 	

620,580	
 	

728,413
	

9.	
 	

ALLEN FAMILY TRUST DATED 10/12/81
 4199 Campus Drive, Suite 830

Irvine, CA 92612

Attn: Dick Allen	
 	

24,000	
 	

47,000	
 	

20,000	
 	

23,475
	

10.	
 	

THOMAS AND NELL WALTZ FAMILY LP
 6075 La Jolla Scenic Drive

La Jolla, CA 92037

Attn: Thomas A. Waltz	
 	

37,532	
 	

39,130	
 	

20,278	
 	

23,802

A-1

 

	

11.	
 	

GREENE FAMILY TRUST
 PO Box 8984

Rancho Santa Fe, CA 92067

Attn: Howard E. Greene Jr.	
 	

18,797	
 	

29,741	
 	

27,995	
 	

32,859	
 
	

12.	
 	

GC&H INVESTMENTS LLC
 One Maritime Plaza

San Francisco, CA 94111

Attn: John Cardoza	
 	

75,188	
 	

78,388	
 	

40,622	
 	

47,681	
 
	

13.	
 	

PETE HRONIS
 10417 Hronis Avenue

Delano, CA 93215	
 	

16,918	
 	

25,196	
 	

11,140	
 	

13,076	
 
	

14.	
 	

COMERICA INCORPORATED
 Attn: Warrant Administrator

500 Woodward Avenue, 32nd Floor, MC 3379

Detroit, MI 48226	
 	

12,000	
(1)	

16,798	
(2)	

0	
 	

276,025	
(3)
	

15.	
 	

ALLISON M. GREGORY
 17549 Oak Meadow Lane

Lake Oswego, Oregon 97034	
 	

0	
 	

12,262	
 	

3,244	
 	

3,808	
 
	

16.	
 	

HARBOUR VENTURES
 7946 Sitio Nispero

Carlsbad, California 92009

Attn: David Blackburn	
 	

0	
 	

11,199	
 	

5,599	
 	

6,572	
 
	

17.	
 	

CHICAGO GROWTH PARTNERS VIII, L.P.
 303 West Madison Street, Suite 2500

Chicago, IL 60606

Attn: Arda Minocherhomjee	
 	

0	
 	

0	
 	

0	
 	

6,309,148	
 
	

18.	
 	

WILLIAM BLAIR CAPITAL PARTNERS VII QP, L.P.
 303 West Madison Street, Suite 2500

Chicago, IL 60606

Attn: Arda Minocherhomjee	
 	

0	
 	

0	
 	

0	
 	

6,075,018	
 
	

19.	
 	

WILLIAM BLAIR CAPITAL PARTNERS VII, L.P.
 303 West Madison Street, Suite 2500

Chicago, IL 60606

Attn: Arda Minocherhomjee	
 	

0	
 	

0	
 	

0	
 	

234,130	
 
	

TOTALS:	
 	

10,701,383	
 	

14,476,394	
 	

6,718,940	
 	

20,504,733	
 

	(1)
	Represents
shares issuable upon exercise of that certain Warrant dated November 26, 2002, originally issued to purchase 12,000 shares of Series B Preferred Stock that
was amended in connection with the Series B-2 Preferred Stock financing to become a warrant to purchase 12,000 shares of Series B-1 Preferred, and further amended
in connection with the Series 1-C Preferred financing to become a warrant to purchase 12,000 shares of Series 1-A Preferred. Such shares are not included in the
"Totals" set forth below.

	(2)
	Represents
shares issuable upon exercise of that certain Warrant dated November 26, 2002 to purchase 16,798 shares of Series B-2 Preferred that was amended
in connection with the Series 1-C Preferred financing to become a warrant exercisable for 16,798 shares of Series 1-B Preferred. Such shares are not included in
the "Totals" set forth below.

	(3)
	Represents
shares issuable upon exercise of that certain Warrant to purchase 276,025 shares of Series 1-D Preferred issued to Comerica Bank in connection with the
Debt Financing. Such shares are not included in the "Totals" set forth below. 

A-2

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Exhibit 4.10

EXHIBIT A SCHEDULE OF INVESTORSQuickLinks
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Exhibit 10.1    
    

GENOPTIX, INC.  

INDEMNITY AGREEMENT  

        THIS INDEMNITY AGREEMENT (this "Agreement") dated as of
                             , 20    , is made by and between GENOPTIX, INC., a Delaware corporation (the
"Company"), and                        ("Indemnitee"). 

 
 

RECITALS    
    

        A.    The Company desires to attract and retain the services of highly qualified individuals as directors, officers, employees
and agents. 

        B.    The Company's Amended and Restated Bylaws (the "Bylaws") require that the
Company indemnify its directors, and empowers the Company to indemnify its officers, employees and agents, as authorized by the Delaware General Corporation Law, as amended (the
"Code"), under which the Company is organized and such Bylaws expressly provide that the indemnification provided therein is not exclusive and
contemplates that the Company may enter into separate agreements with its directors, officers and other persons to set forth specific indemnification provisions. 

        C.    Indemnitee does not regard the protection currently provided by applicable law, the Company's governing documents and
available insurance as adequate under the present circumstances, and the Company has determined that Indemnitee and other directors, officers, employees and agents of the Company may not be willing to
serve or continue to serve in such capacities without additional protection. 

        D.    The Company desires and has requested Indemnitee to serve or continue to serve as a director, officer, employee or agent
of the Company, as the case may be, and has proferred this Agreement to Indemnitee as an additional inducement to serve in such capacity. 

        E.    Indemnitee is willing to serve, or to continue to serve, as a director, officer, employee or agent of the Company, as the
case may be, if Indemnitee is furnished the indemnity provided for herein by the Company. 

 
 

AGREEMENT    
    

        NOW THEREFORE, in consideration of the mutual covenants and agreements set forth herein, the parties hereto,
intending to be legally bound, hereby agree as follows: 

        1.    Definitions.    

         (a)    Agent.    For purposes of this Agreement, the term "agent" of the Company means any person who: (i) is or
was a director,
officer, employee or other fiduciary of the Company, a subsidiary of the Company or an employee benefit plan of the Company or a subsidiary of the Company; or (ii) is or was serving at the
request or for the convenience of, or representing the interests of, the Company or a subsidiary of the Company, as a director, officer, employee or other fiduciary of a foreign or domestic
corporation, partnership, joint venture, trust or other enterprise. 

         (b)    Expenses.    For purposes of this Agreement, the term "expenses" shall be broadly construed and shall include,
without limitation, all
direct and indirect costs of any type or nature whatsoever (including, without limitation, all attorneys', witness, or other professional fees and related disbursements, premiums, security for and
other costs relating to any bonds and other out-of-pocket costs of whatever nature), actually and reasonably incurred by Indemnitee in connection with the investigation,
defense or appeal of a proceeding or establishing or enforcing a 

1

 

right
to indemnification under this Agreement, the Code or otherwise, and amounts paid in settlement by or on behalf of Indemnitee, but shall not include any judgments, fines or penalties actually
levied against Indemnitee for such individual's violations of law. The term "expenses" shall also include reasonable compensation for time spent by Indemnitee for which he is not compensated by the
Company or any subsidiary or third party (i) for any period during which Indemnitee is not an agent, in the employment of, or providing services for compensation to, the Company or any
subsidiary; and (ii) if the rate of compensation and estimated time involved is approved by the directors of the Company who are not parties to any action with respect to which expenses are
incurred, for Indemnitee while an agent of, employed by, or providing services for compensation to, the Company or any subsidiary. 

         (c)    Proceeding.    For purposes of this Agreement, the term "proceeding" shall be broadly construed and shall
include, without limitation,
any threatened, pending, or completed action, suit, arbitration, alternate dispute resolution mechanism, investigation, inquiry, administrative hearing or any other actual, threatened or completed
proceeding, whether brought in the right of the Company or otherwise and whether of a civil, criminal, administrative or investigative nature, and whether formal or informal in any case, in which
Indemnitee was, is or will be involved as a party or otherwise by reason of: (i) the fact that Indemnitee is or was a director or officer of the Company; (ii) the fact that any action
taken by Indemnitee or of any action on Indemnitee's part while acting as director, officer, employee or agent of the Company; or (iii) the fact that Indemnitee is or was serving at the request
of the Company as a director, officer, employee or agent of another corporation, partnership, joint venture, trust, employee benefit plan or other enterprise, and in any such case described above,
whether or not serving in any such capacity at the time any liability or expense is incurred for which indemnification, reimbursement, or advancement of expenses may be provided under this Agreement. 

         (d)    Subsidiary.    For purposes of this Agreement, the term "subsidiary" means any corporation or limited liability
company of which more
than 20% of the outstanding voting securities or equity interests are owned, directly or indirectly, by the Company and one or more of its subsidiaries, and any other corporation, limited liability
company, partnership, joint venture, trust, employee benefit plan or other enterprise of which Indemnitee is or was serving at the request of the Company as a director, officer, employee, agent or
fiduciary. 

        (e)    Independent Counsel.    For purposes of this Agreement, the term "independent counsel" means a law firm, or a
partner (or, if
applicable, member) of such a law firm, that is experienced in matters of corporation law and neither presently is, nor in the past five (5) years has been, retained to represent:
(i) the Company or Indemnitee in any matter material to either such party, or (ii) any other party to the proceeding giving rise to a claim for indemnification hereunder. Notwithstanding
the foregoing, the term "independent counsel" shall not include any person who, under the applicable standards of professional conduct then prevailing, would have a conflict of interest in
representing either the Company or Indemnitee in an action to determine Indemnitee's rights under this Agreement. 

        2.    Consideration.    The Company acknowledges that it has entered into this Agreement and assumes the obligations
imposed on it hereby, in addition to and separate from its obligations to Indemnitee under the Bylaws, to induce Indemnitee to serve, or continue to serve, as a director, officer, employee or agent of
the Company, and the Company acknowledges that Indemnitee is relying upon this Agreement in serving as a director, officer, employee or agent of the Company. 

        3.    Indemnification.    

         (a)    Indemnification in Third Party Proceedings.    Subject to Section 10 below, the Company shall indemnify
Indemnitee, if
Indemnitee is a party to or threatened to be made a party to or 

2

 

otherwise
involved in any proceeding, for any and all expenses, actually and reasonably incurred by Indemnitee in connection with the investigation, defense, settlement or appeal of such proceeding. 

         (b)    Indemnification in Derivative Actions and Direct Actions by the Company.    Subject to Section 10 below,
the Company shall
indemnify Indemnitee, if Indemnitee is a party to or threatened to be made a party to or otherwise involved in any proceeding by or in the right of the Company to procure a judgment in its favor,
against any and all expenses actually and reasonably incurred by Indemnitee in connection with the investigation, defense, settlement, or appeal of such proceedings. 

        4.    Indemnification of Expenses of Successful Party.    Notwithstanding any other provision of this Agreement, to
the extent that Indemnitee has been successful on the merits or otherwise in defense of any proceeding or in defense of any claim, issue or matter therein, including the dismissal of any action
without prejudice, the Company shall indemnify Indemnitee against all expenses actually and reasonably incurred in connection with the investigation, defense or appeal of such proceeding. 

        5.    Partial Indemnification.    If Indemnitee is entitled under any provision of this Agreement to indemnification
by the Company for some or a portion of any expenses actually and reasonably incurred by Indemnitee in the investigation, defense, settlement or appeal of a proceeding, but is precluded by applicable
law or the specific terms of this Agreement to indemnification for the total amount thereof, the Company shall nevertheless indemnify Indemnitee for the portion thereof to which Indemnitee is
entitled. 

        6.    Advancement of Expenses.    To the extent not prohibited by law, the Company shall advance the expenses incurred
by Indemnitee in connection with any proceeding, and such advancement shall be made within twenty (20) days after the receipt by the Company of a statement or statements requesting such
advances (which shall include invoices received by Indemnitee in connection with such expenses but, in the case of invoices in connection with legal services, any references to legal work performed or
to expenditures made that would cause Indemnitee to waive any privilege accorded by applicable law shall not be included with the invoice) and upon request of the Company, an undertaking to repay the
advancement of expenses if and to the extent that it is ultimately determined by a court of competent jurisdiction in a final judgment, not subject to appeal, that Indemnitee is not entitled to be
indemnified by the Company. Advances shall be unsecured, interest free and without regard to Indemnitee's ability to repay the expenses. Advances shall include any and all expenses actually and
reasonably incurred by Indemnitee pursuing an action to enforce Indemnitee's right to indemnification under this Agreement, or otherwise and this right of advancement, including expenses incurred
preparing and forwarding statements to the Company to support the advances claimed. Indemnitee acknowledges that the execution and delivery of this Agreement shall constitute an undertaking providing
that Indemnitee shall, to the fullest extent required by law, repay the advance if and to the extent that it is ultimately determined by a court of competent jurisdiction in a final judgment, not
subject to appeal, that Indemnitee is not entitled to be indemnified by the Company. The right to advances under this Section shall continue until final disposition of any proceeding, including any
appeal therein. This Section 6 shall not apply to any claim made by Indemnitee for which indemnity is excluded pursuant to Section 10(b). 

        7.    Notice and Other Indemnification Procedures.    

         (a)    Notification of Proceeding.    Indemnitee will notify the Company in writing promptly upon being served with
any summons, citation,
subpoena, complaint, indictment, information or other document relating to any proceeding or matter which may be subject to indemnification or advancement of expenses covered hereunder. The failure of
Indemnitee to so notify the Company shall not relieve the Company of any obligation which it may have to Indemnitee under this Agreement or otherwise. 

3

 

         (b)    Request for Indemnification and Indemnification Payments.    Indemnitee shall notify the Company promptly in
writing upon receiving
notice of any demand, judgment or other requirement for payment that Indemnitee reasonably believes to be subject to indemnification under the terms of this
Agreement, and shall request payment thereof by the Company. Indemnification payments requested by Indemnitee under Section 3 hereof shall be made by the Company no later than sixty
(60) days after receipt of the written request of Indemnitee. Claims for advancement of expenses shall be made under the provisions of Section 6 herein. 

         (c)    Application for Enforcement.    In the event the Company fails to make timely payments as set forth in Sections
6 or 7(b) above,
Indemnitee shall have the right to apply to any court of competent jurisdiction for the purpose of enforcing Indemnitee's right to indemnification or advancement of expenses pursuant to this
Agreement. In such an enforcement hearing or proceeding, the burden of proof shall be on the Company to prove that indemnification or advancement of expenses to Indemnitee is not required under this
Agreement or permitted by applicable law. Any determination by the Company (including its Board of Directors, stockholders or independent counsel) that Indemnitee is not entitled to indemnification
hereunder, shall not be a defense by the Company to the action nor create any presumption that Indemnitee is not entitled to indemnification or advancement of expenses hereunder. 

         (d)    Indemnification of Certain Expenses.    The Company shall indemnify Indemnitee against all expenses incurred in
connection with any
hearing or proceeding under this Section 7 unless the Company prevails in such hearing or proceeding on the merits in all material respects. 

        8.    Assumption of Defense.    In the event the Company shall be requested by Indemnitee to pay the expenses of any
proceeding, the Company, if appropriate, shall be entitled to assume the defense of such proceeding, or to participate to the extent permissible in such proceeding, with counsel reasonably acceptable
to Indemnitee. Upon assumption of the defense by the Company and the retention of such counsel by the Company, the Company shall not be liable to Indemnitee under this Agreement for any fees of
counsel subsequently incurred by Indemnitee with respect to the same proceeding, provided that Indemnitee shall have the right to employ separate counsel in such proceeding at Indemnitee's sole cost
and expense. Notwithstanding the foregoing, if Indemnitee's counsel delivers a written notice to the Company stating that such counsel has reasonably concluded that there is an actual or potential
conflict of interest between the Company and Indemnitee in the conduct of any such defense or the Company shall not, in fact, have employed counsel or otherwise actively pursued the defense of such
proceeding within a reasonable time, then in any such event the fees and expenses of Indemnitee's counsel to defend such proceeding shall be subject to the indemnification and advancement of expenses
provisions of this Agreement. 

        9.    Insurance.    To the extent that the Company maintains an insurance policy or policies providing liability
insurance for directors, officers, employees, or agents of the Company or of any subsidiary ("D&O Insurance"), Indemnitee 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 such director, officer, employee or agent under such policy or policies. If, at the time of the receipt of a notice of a claim pursuant to
the terms hereof, the Company has D&O Insurance in effect, the Company shall give prompt notice of the commencement of such proceeding to the insurers in accordance with the procedures set forth in
the respective policies. The Company shall thereafter take all necessary or desirable action to cause such
insurers to pay, on behalf of Indemnitee, all amounts payable as a result of such proceeding in accordance with the terms of such policies. 

        10.    Exceptions.    

         (a)    Certain Matters.    Any provision herein to the contrary notwithstanding, the Company shall not be obligated
pursuant to the terms of
this Agreement to indemnify Indemnitee on account of any proceeding with respect to (i) remuneration paid to Indemnitee if it is determined 

4

 

by
final judgment or other final adjudication that such remuneration was in violation of law (and, in this respect, both the Company and Indemnitee have been advised that the Securities and Exchange
Commission believes that indemnification for liabilities arising under the federal securities laws is against public policy and is, therefore, unenforceable and that claims for indemnification should
be submitted to appropriate courts for adjudication, as indicated in Section 10(d) below); (ii) a final judgment rendered against Indemnitee for an accounting, disgorgement or repayment
of profits made from the purchase or sale by Indemnitee of securities of the Company against Indemnitee or in connection with a settlement by or on behalf of Indemnitee to the extent it is
acknowledged by Indemnitee and the Company that such amount paid in settlement resulted from Indemnitee's conduct from which Indemnitee received monetary personal profit, pursuant to the provisions of
Section 16(b) of the Securities Exchange Act of 1934, as amended, or other provisions of any federal, state or local statute or rules and regulations thereunder; (iii) a final judgment
or other final adjudication that Indemnitee's conduct was in bad faith, knowingly fraudulent or deliberately dishonest or constituted willful misconduct (but only to the extent of such specific
determination); or (iv) on account of conduct that is established by a final judgment as constituting a breach of Indemnitee's duty of loyalty to the Company or resulting in any personal profit
or advantage to which Indemnitee is not legally entitled. For purposes of the foregoing sentence, a final judgment or other adjudication may be reached in either the underlying proceeding or action in
connection with which indemnification is sought or a separate proceeding or action to establish rights and liabilities under this Agreement. 

         (b)    Claims Initiated by Indemnitee.    Any provision herein to the contrary notwithstanding, the Company shall not
be obligated to
indemnify or advance expenses to Indemnitee with respect to proceedings or claims initiated or brought by Indemnitee against the Company or its directors, officers, employees or other agents and not
by way of defense, except (i) with respect to proceedings brought to establish or enforce a right to indemnification under this Agreement or under any other agreement, provision in the Bylaws
or Amended and Restated Certificate of Incorporation (the "Certificate of Incorporation") or applicable law, or (ii) with respect to any other
proceeding initiated by Indemnitee that is either approved by the Board of Directors or Indemnitee's participation is required by applicable law. However, indemnification or advancement of expenses
may be provided by the Company in specific cases if the Board of Directors determines it to be appropriate. 

         (c)    Unauthorized Settlements.    Any provision herein to the contrary notwithstanding, the Company shall not be
obligated pursuant to the
terms of this Agreement to indemnify Indemnitee under this Agreement for any amounts paid in settlement of a proceeding effected without the Company's written consent. Neither the Company nor
Indemnitee shall unreasonably withhold consent to any proposed settlement; provided, however, that the Company may in any event decline to consent to (or to otherwise admit or agree to any liability
for indemnification hereunder in respect of) any proposed settlement if the Company is also a party in such proceeding and determines in good faith that such settlement is not in the best interests of
the Company and its stockholders. 

         (d)    Securities Act Liabilities.    Any provision herein to the contrary notwithstanding, the Company shall not be
obligated pursuant to the
terms of this Agreement to indemnify Indemnitee or otherwise act in violation of any undertaking appearing in and required by the rules and regulations promulgated under the Securities Act of 1933, as
amended (the "Act"), or in any registration statement filed with the SEC under the Act. Indemnitee acknowledges that paragraph (h) of Item 512 of
Regulation S-K currently generally requires the Company to undertake in connection with any registration statement filed under the Act to submit the issue of the enforceability of
Indemnitee's rights under this Agreement in connection with any liability under the Act on public policy grounds to a court of appropriate jurisdiction and to be governed 

5

 

by
any final adjudication of such issue. Indemnitee specifically agrees that any such undertaking shall supersede the provisions of this Agreement and to be bound by any such undertaking. 

        11.    Nonexclusivity and Survival of Rights.    The provisions for indemnification and advancement of expenses set
forth in this Agreement shall not be deemed exclusive of any other rights which Indemnitee may at any time be entitled under any provision of applicable law, the Company's Certificate of
Incorporation, Bylaws or other agreements, both as to action in Indemnitee's official capacity and Indemnitee's action as an agent of the Company, in any court in which a proceeding is brought, and
Indemnitee's rights hereunder shall continue after Indemnitee has ceased acting as an agent of the Company and shall inure to the benefit of the heirs, executors, administrators and assigns of
Indemnitee. The obligations and duties of the Company to Indemnitee under this Agreement shall be binding on the Company and its successors and assigns until terminated in accordance with its terms.
The Company shall require any successor (whether direct or indirect, by purchase, merger, consolidation or otherwise) to all or substantially all of the business or assets of the Company, expressly to
assume and agree in writing to perform this Agreement in the same manner and to the same extent that the Company would be required to perform if no such succession had taken place. 

        No
amendment, alteration or repeal of this Agreement or of any provision hereof shall limit or restrict any right of Indemnitee under this Agreement in respect of any action taken or
omitted by such Indemnitee in his or her corporate status prior to such amendment, alteration or repeal. To the extent that a change in the Code, whether by statute or judicial decision, permits
greater indemnification or advancement of expenses than would be afforded currently under the Company's Certificate of Incorporation, Bylaws and this Agreement, it is the intent of the parties hereto
that Indemnitee shall
enjoy by this Agreement the greater benefits so afforded by such change. No right or remedy herein conferred is intended to be exclusive of any other right or remedy, and every other right and remedy
shall be cumulative and in addition to every other right and remedy given hereunder or now or hereafter existing at law or in equity or otherwise. The assertion or employment of any right or remedy
hereunder, or otherwise, by Indemnitee shall not prevent the concurrent assertion or employment of any other right or remedy by Indemnitee. 

        12.    Subrogation.    In the event of payment under this Agreement, the Company shall be subrogated to the extent of
such payment to all of the rights of recovery of Indemnitee, who, at the request and expense of the Company, shall execute all papers required and shall do everything that may be reasonably necessary
to secure such rights, including the execution of such documents necessary to enable the Company effectively to bring suit to enforce such rights. 

        13.    Interpretation of Agreement.    It is understood that the parties hereto intend this Agreement to be
interpreted and enforced so as to provide indemnification to Indemnitee to the fullest extent now or hereafter permitted by law. 

        14.    Severability.    If any provision of this Agreement shall be held to be invalid, illegal or unenforceable for
any reason whatsoever, (a) the validity, legality and enforceability of the remaining provisions of the Agreement (including without limitation, all portions of any paragraphs of this Agreement
containing any such provision held to be invalid, illegal or unenforceable, that are not themselves invalid, illegal or unenforceable) shall not in any way be affected or impaired thereby; and
(b) to the fullest extent possible, the provisions of this Agreement (including, without limitation, all portions of any paragraph of this Agreement containing any such provision held to be
invalid, illegal or unenforceable, that are not themselves invalid, illegal or unenforceable) shall be construed so as to give effect to the intent manifested by the provision held invalid, illegal or
unenforceable and to give effect to Section 13 hereof. 

        15.    Amendment and Waiver.    No supplement, modification, amendment, termination, or cancellation of this Agreement
shall be binding unless executed in writing by the parties hereto. No 

6

 

waiver
of any of the provisions of this Agreement shall be deemed or shall constitute a waiver of any other provision hereof (whether or not similar) nor shall such waiver constitute a continuing
waiver. 

        16.    Notice.    Except as otherwise provided herein, any notice or demand which, by the provisions hereof, is
required or which may be given to or served upon the parties hereto shall be in writing and, if by telegram, telecopy or telex, shall be deemed to have been validly served, given or delivered when
sent, if by overnight delivery, courier or personal delivery, shall be deemed to have been validly served, given or delivered upon actual delivery and, if mailed, shall be deemed to have been validly
served, given or delivered three (3) business days after deposit in the United States mail, as registered or certified mail, with proper postage prepaid and addressed to the party or parties to
be notified at the addresses set
forth on the signature page of this Agreement (or such other address(es) as a party may designate for itself by like notice). If to the Company, notices and demands shall be delivered to the attention
of the Secretary of the Company. 

        17.    Governing Law.    This Agreement shall be governed exclusively by and construed according to the laws of the
State of California, as applied to contracts between California residents entered into and to be performed entirely within California. 

        18.    Counterparts.    This Agreement may be executed in one or more counterparts, each of which shall for all
purposes be deemed to be an original but all of which together shall constitute but one and the same Agreement. Only one such counterpart need be produced to evidence the existence of this Agreement. 

        19.    Headings.    The headings of the sections of this Agreement are inserted for convenience only and shall not be
deemed to constitute part of this Agreement or to affect the construction hereof. 

        20.    Entire Agreement.    This Agreement constitutes the entire agreement between the parties with respect to the
subject matter hereof and supersedes all prior agreements, understandings and negotiations, written and oral, between the parties with respect to the subject matter of this Agreement; provided,
however, that this Agreement is a supplement to and in furtherance of the Company's Certificate of Incorporation, Bylaws, the Code and any other applicable law, and shall not be deemed a substitute
therefor, and does not diminish or abrogate any rights of Indemnitee thereunder. 

7

        IN WITNESS WHEREOF, the parties hereto have entered into this Agreement effective as of the date first above written. 

	 	 	GENOPTIX, INC.
	

 	
 	
By:	
 	

	 	 	 	 	Name:	

	 	 	 	 	Title:	

	

 	
 	
INDEMNITEE
	

 	
 	

 Signature of Indemnitee
	

 	
 	

 Print or Type Name of Indemnitee

QuickLinks

Exhibit 10.1

RECITALS

AGREEMENT

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