Document:

EX-10.1

 Exhibit 10.1 
  

 
 150 Second Street, 1st Floor 

Cambridge Massachusetts 02141 

TEL 617.418.2200 

FAX 617.418.2201 

January 5, 2017     
 Troy Cox 

464 Tehama Street 
 San Francisco, CA 94103 

 

	Re:	Employment with Foundation Medicine, Inc. 

 Dear Troy: 

On behalf of Foundation Medicine, Inc. (“Foundation Medicine” or “the Company”), I am very pleased to offer
you the position of Chief Executive Officer. 
 The terms of your position with the Company are as set forth below in this letter agreement
(“Agreement”): 
 1.    Position and Start Date. Your position at the Company will be as Chief
Executive Officer (“CEO”). As CEO, you shall have supervision and control over and responsibility for the day-to-day business and affairs of the Company
and shall have such other powers and duties as may from time to time be prescribed by the Board of Directors of the Company (the “Board”). For so long as you serve as CEO, the Company shall nominate you for election to the Board by
the Company’s shareholders. Upon the ending of your employment as CEO, you shall immediately resign from the Board as well as from any other position(s) to which you were elected or appointed in connection with your position as CEO. You will
begin your employment with the Company no later than February 6, 2017. For purposes of this Agreement, the actual first date of your employment shall be the “Start Date”. 

 

	 	2.	Compensation and Related Matters. 

 a.    Base
Salary. You will be paid on a salary basis at a rate of $21,153.85 per bi-weekly pay period, representing payment for all hours worked by you for Foundation Medicine, equivalent to an annualized base
salary of approximately $550,000 (“Base Salary”). The Base Salary will be paid in accordance with Foundation Medicine’s standard payroll practices and subject to customary deductions and withholdings as required by law. You
will be eligible to participate in annual merit salary increases, in the discretion of the Board or the Compensation Committee of the Board (the “Compensation Committee”), in accordance with the Company’s compensation
practices. To be eligible for a merit increase, you must be employed by September 30 of the previous year. 

 Troy Cox 

January 5, 2017 
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	 	a.	Performance Incentives. 

  

	 	i.	Annual Bonus. You will be eligible to participate in the Company’s annual performance incentive program, subject to its terms and conditions and at the discretion of the Company’s Board, with the potential to
earn incentive compensation equivalent to a target of 70% of your then annual Base Salary (“Annual Performance Incentive Target”). The performance incentive is based upon the achievement of Company performance, department
performance, and individual performance objectives. The Company may also increase the Annual Performance Incentive Target in connection with a promotion and otherwise in its discretion. Except in connection with the payment to you of a Severance
Payment, you must be employed by the Company at the time a performance incentive is paid to earn any part of an incentive. 

  

	 	ii.	Annual Equity Incentive. You will be eligible for annual equity awards under the Company’s equity compensation plan. The CEO’s annual award is currently in the range of an aggregate value of $1,000,000-$2,000,000 subject to vesting, provided and notwithstanding the foregoing, the equity award(s) shall be determined at the complete and total discretion of the Compensation Committee. 

 

	 	b.	Expenses. The Company will reimburse your expenses related to your work in accordance with the Company’s expense reimbursement policy. 

 

	 	c.	Restricted Stock Units. Subject to approval by the Board of Directors or a committee thereof, as may be required by the Company’s applicable governance rules, you will be granted an equity award of
Restricted Stock Units (“RSUs”) with an aggregate value of $4,750,000 (“Equity Award”). The number of RSUs to be granted as part of the Equity Award will be calculated based on the
30-day average closing price of Foundation Medicine common stock preceding the Start Date. The effective date for the grant will be the Start Date (“Equity Grant Date”). The Equity Award will
vest over a four-year period as follows: 25% will vest on the first anniversary of the Equity Grant Date, and an additional 6.25% will vest on the first day of each subsequent quarter thereafter until 100% of the RSUs have vested. As a
condition to receiving each portion of the Equity Award, you must be an employee of Foundation Medicine as of the relevant vesting date and without any prior interruption of service. The Equity Award will be governed by a restricted stock unit
award agreement that will not conflict with this Agreement but will be in the standard form approved by Foundation Medicine’s Board of Directors and shareholders, and will be subject to the provisions of Foundation Medicine’s then-current
stock incentive plan (together with any other incentive equity plan(s), as may be amended from time to time, any associated award agreements, the “Equity Documents”).

 Troy Cox 

January 5, 2017 
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	 	d.	Other Benefits. As a regular, full-time employee, you will be eligible to participate in the employee benefit program that Foundation Medicine offers to its employees in
comparable positions, which currently include Health, Dental, Life and Disability Insurance, matching 401(k) Plan, and Sick Time, subject to plan terms and generally applicable Foundation Medicine policies. You will be also be entitled to accrue up
to fifteen (15) days of vacation each calendar year and to such other holidays as Foundation Medicine recognizes for employees having comparable responsibilities and duties. For any calendar year in which you are employed with the Company for
only a portion of such year, the vacation time will be pro-rated. Notwithstanding the foregoing, however, you will be entitled to take a one week sabbatical in 2017 which will be in addition to your regular
vacation days. Descriptions of the Company’s benefits will be available upon request. The Company retains the right to amend, modify, or cancel any benefits program. Where a particular benefit is subject to a formal plan (for example, medical
insurance or 401(k)), eligibility to participate in and receive any particular benefit is governed solely by the applicable plan document. 

  

	 	e.	Sign-on bonus. You will receive a one-time payment of $324,000 (less required withholdings) within 30 days of the Start Date
(“Payment Date”). If you resign from Foundation Medicine other than for Good Reason (defined below) within one (1) year of the Payment Date, or you are terminated by Foundation Medicine for Cause (defined below) within
one (1) year of the Payment Date, you are required to repay Foundation Medicine for the total amount of the sign-on bonus within one week of your termination date, and to the maximum extent permitted by
applicable law, you hereby authorize Foundation Medicine to deduct as a valid set-off of wages, any sign-on bonus owed to Foundation Medicine from your final wages and
any accrued and unused vacation pay, any performance bonus/incentive compensation, outstanding expense report, and/or any other payments or compensation otherwise owed to you by Foundation Medicine. 

3.    Living Assistance Allowance and Relocation Assistance. As a material condition of your employment, you are
required to relocate to the greater Boston area within three months of the Start Date, unless a later date is expressly authorized by the Board. For purposes of this Agreement, the actual date of your relocation shall be the “Relocation
Date”. During the period between the Start Date and the Relocation Date (the “Pre-Relocation Period”), (i) you shall spend at least 85% of your working time at the Company’s
office in Cambridge, Massachusetts (exclusive of Foundation Medicine business travel) and (ii) the Company will reimburse you, in accordance with the Company’s expense reimbursement policy, for apartment or hotel payments and

 Troy Cox 

January 5, 2017 
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associated utilities (“Living Assistance Allowance”) of up to $5,000 per month. In addition to the Living Assistance Allowance, during the
Pre-Relocation Period the Company shall reimburse you, in accordance with the Company’s reimbursement policy, for travel between Boston and San Francisco. If the Relocation Date occurs within three months
of the Start Date, the Company shall reimburse you for actual relocation expenses incurred and substantiated up to a maximum of $100,000 (“Relocation Assistance”). The Relocation Assistance shall be paid in a lump sum payment within
ten days of the Company’s receipt of final documented expenses (which you agree to submit promptly but in no later than November 30, 2017). If you resign from Foundation Medicine other than for Good Reason (defined below) within eighteen
(18) months of receiving Relocation Assistance (“Relocation Payment Date”), or you are terminated by Foundation Medicine for Cause (defined below) within eighteen (18) months of the Relocation Payment Date, you are
required to repay Foundation Medicine for the total amount of the Relocation Assistance within one week of your termination date, and to the maximum extent permitted by applicable law, you hereby authorize Foundation Medicine to deduct as a valid set-off of wages, any Relocation Assistance owed to Foundation Medicine from your final wages and any accrued and unused vacation pay, any performance bonus/incentive compensation, outstanding expense report, and/or
any other payments or compensation otherwise owed to you by Foundation Medicine. The Company will determine in its reasonable, good faith judgment what, if any, of your reimbursed amounts pursuant to this Section 3 are for nondeductible
expenses in accordance with applicable law and will comply with associated withholding and tax reporting obligations. 

4.    At-Will Employment. Your employment at all times shall remain “at
will,” meaning that either you or the Company may terminate the employment relationship at any time, for any lawful reason, with or without cause. 

5.    Non-Competition, Non-Solicitation,
Confidentiality and Assignment Agreement. As part of your employment with Foundation Medicine, you will be exposed to, and provided with, valuable confidential and/or trade secret information concerning Foundation Medicine and its present and
future business plans and operations. As a result, in order to protect Foundation Medicine’s substantial investment of time and money in the creation and maintaining of its confidential information and good-will with its customers, clients, and
collaborators, your offer of employment is contingent upon your signing the Company’s Employee Non-Competition, Non-Solicitation, Confidentiality and Assignment
Agreement (the “Restrictive Covenant Agreement”), a copy of which is attached to this Agreement as Exhibit A and your continued willingness to abide by its terms. 

By the same token, Foundation Medicine expects you to abide by and honor the terms of any agreements you may have with your present or prior
employers. By signing below, you represent that you are not subject to any agreements which might restrict your conduct at the Company, and that you understand that if you become aware at any time 

 Troy Cox 

January 5, 2017 
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during your employment with the Company that you are subject to any agreements which might restrict your activities at Foundation Medicine, you are required to immediately inform the
Company’s General Counsel of the existence of such agreements. In the event of an irresolvable conflict, your employment by Foundation Medicine could be subject to termination and such termination would be deemed a for “Cause”
termination for purposes of this Agreement and the Equity Documents. 
 Also, just as Foundation Medicine regards the protection of our
confidential information as a matter of great importance, we also respect that you may have an obligation to your present and/or prior employers to safeguard the confidential information of those companies. Foundation Medicine respects these
obligations, and expects you to honor them as well. To that end, we expect that you have not taken any documents or other confidential information from your employer. Further, we want to make it perfectly clear you should not bring with you to
Foundation Medicine, or use in the performance of your duties for our Company, any proprietary business or technical information, materials or documents of a former employer, or otherwise disclose or use any former employer’s confidential
information. 
 6.    Work Authorization. This offer of employment is contingent on you being legally authorized
to work in the United States, and you will need to complete an I-9 Employment Verification Form no later than your first day of work. 

7.    Termination of Employment. 

a.    Severance Payments. Without otherwise limiting the “at will” nature of your
employment if: (i) your employment is terminated by the Company without Cause at any time, or (ii) within eighteen (18) months following a Change in Control you terminate your employment with the Company for Good Reason in accordance
with the Good Reason Process, and, in either event, you enter into, do not revoke, and comply with a Release, the Company shall pay or provide you with: (a) Salary Continuation for eighteen (18) months following your termination date (the
“Salary Continuation Period”); (b) Health Care Continuation during the Salary Continuation Period; and (c) a Performance Incentive Payment equal to your current year Annual Performance Incentive Target, prorated based on the
length of time that you have been employed with the Company during the calendar year in which your employment is terminated (collectively, the “Severance Payments”); provided and notwithstanding the foregoing, if your employment is
terminated in connection with a Change in Control and you immediately become reemployed by any direct or indirect successor to the business or assets of the Company, the termination of your employment upon the Change in Control shall not be
considered a Termination without Cause for purposes of this Agreement. 
 b.    Equity
Acceleration. In the event that you become entitled to Severance Payments at any time within eighteen (18) months following a Change in Control, and you enter into, do not revoke, and comply with a Release, then all outstanding unvested
time-based equity-based compensation awards that have been granted acceleration rights 

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January 5, 2017 
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and were granted to you under the Equity Documents prior to the Change in Control shall become exercisable and vested in full, and all restrictions thereon shall lapse, notwithstanding any
vesting schedule or other provisions to the contrary in the agreements evidencing such awards or in the underlying equity plan, and the Company and you hereby agree that any agreements covering such awards are hereby, and will be deemed to be,
amended to give effect to this provision. 

c.    Non-Eligibility for Severance Payments or Equity Award
Acceleration. For the avoidance of doubt, you and the Company acknowledge that if your employment is terminated: (i) by the Company for Cause, (ii) by you without Good Reason, (iii) by you with Good Reason following a Change
in Control but without complying with the Good Reason Process, or (iv) as a result of your death or disability, then, as a result of such termination, (w) you shall not be entitled to Severance Payments, (x) you shall be entitled to
receive only base salary earned plus accrued but unused vacation pay through the date of termination, (y) the unvested portion of your Equity Awards will not accelerate, and (z) your Equity Awards shall expire or be forfeited in accordance
with the terms of the Equity Documents. 
 8.    Definitions. For purposes of this Agreement, the following
terms shall have the following meanings: 
 “Company” means Foundation Medicine, Inc., and its successors
and assigns. 
 “Cause” means one or more of the following events: (i) your conviction of, or the entry
of a pleading of guilty or nolo contendere to, any crime involving (A) fraud or embezzlement, or (B) any felony; (ii) your willful failure to perform (other than by reason of disability), or gross negligence in the performance of,
your duties and responsibilities as set forth in your job description; (iii) a material breach by you of any provision of this Agreement, the Restrictive Covenant Agreement, or any of the other agreements you have with the Company; or
(iv) material fraudulent conduct by you with respect to the Company. Notwithstanding the foregoing, in no event shall “Cause” be deemed to exist unless you have been given an opportunity to be heard by the Board and a reasonable
opportunity to cure the circumstances that give rise to Cause if doing so is reasonable. 
 “Change in
Control” shall mean: 
 a.    any “person,” as such term is used in Sections 13(d) and
14(d) of the Securities Exchange Act of 1934, as amended (the “Act”) (other than the Company, any of its subsidiaries, or any trustee, fiduciary or other person or entity holding securities under any employee benefit plan or trust
of the Company or any of its subsidiaries), together with all “affiliates” and “associates” (as such terms are defined in Rule 12b-2 under the Act) of such person, shall become the
“beneficial owner” (as such term is defined in Rule 13d-3 under the Act), directly or indirectly, of securities of the Company representing 50 percent or more of the combined voting power of the
Company’s then 

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January 5, 2017 
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outstanding securities having the right to vote in an election of the Board (“Voting Securities”) (in such case other than as a result of an acquisition of securities directly
from the Company); or 
 b.    the date when a majority of the members of the Board of Directors of the
Company is replaced by individuals who, prior to their election, or nomination for election by the Company’s shareholders, were not approved by a majority of the members of the Board of Directors in existence on the date immediately prior to
such election, appointment or nomination (excluding any individuals nominated by any member of the Investor Group (as defined in that certain Investor Rights Agreement, dated as of January 11, 2015 (as amended from time to time), by and among
the Company, Roche Holdings, Inc. and certain other stockholders of the Company named therein (the “Investor Rights Agreement”)) following the occurrence of a Material Breach (as defined in the Investor Rights Agreement)); or 

c.    the consummation of (A) any consolidation or merger of the Company where the stockholders of the
Company, immediately prior to the consolidation or merger, would not, immediately after the consolidation or merger, beneficially own (as such term is defined in Rule 13d-3 under the Act), directly or
indirectly, shares representing in the aggregate more than 50 percent of the voting shares of the Company issuing cash or securities in the consolidation or merger (or of its ultimate parent corporation, if any), or (B) any sale or other
transfer (in one transaction or a series of transactions contemplated or arranged by any party as a single plan) of all or substantially all of the assets of the Company; or 

d.    the consummation by any member of the Investor Group of any tender or exchange offer, merger,
consolidation, business combination or other similar transaction involving the Company that results in the Investor Group collectively owning all of the outstanding Voting Securities of the Company. 

Notwithstanding the foregoing, a “Change in Control” shall not be deemed to have occurred for purposes of the
foregoing clause (a), (i) solely as the result of an acquisition of securities by the Company which, by reducing the number of shares of Voting Securities outstanding, increases the proportionate number of Voting Securities beneficially owned by any
person to 50 percent or more of the combined voting power of all of the then outstanding Voting Securities; provided, however, that if any person referred to in this sentence shall thereafter become the beneficial owner of any additional shares
of Voting Securities (other than pursuant to a stock split, stock dividend, or similar transaction or as a result of an acquisition of securities directly from the Company) and immediately thereafter beneficially owns 50 percent or more of the
combined voting power of all of the then outstanding Voting Securities, then a “Change in Control” shall be deemed to have occurred for purposes of the foregoing clause (a); or (ii) as a result of Roche’s acquisition of Voting
Securities as provided under Section 4.03(a) and/or 4.04(b) of the Investor Rights Agreement. 

 Troy Cox 

January 5, 2017 
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 “Equity Award” means all incentive stock options, non-statutory stock options, shares of restricted stock, restricted stock units or other incentive equity awards in respect of shares of the Company’s equity securities that have been or will be granted to you
by the Company. 
 “Good Reason” means that you have complied with the “Good Reason Process”
(hereinafter defined) following the occurrence of any of the following events in connection with a Change in Control: 

(i)    a material diminution in your responsibilities, authority or duties; 

(ii)    a material diminution in your Base Salary, except for across-the-board salary reductions based on the Company’s financial performance similarly affecting all or substantially all senior management employees of the Company; 

(iii)     your principal work location is moved to a principal work location that is located more than
fifty (50) miles from the work location at which you were principally working as of the effective date of the Change in Control; or 

(iv)    the material breach of this Agreement by the Company. 

“Good Reason Process” means that (i) you reasonably determine that a Good Reason condition has occurred,
(ii) you notify the Company in writing of the first occurrence of the Good Reason condition within sixty (60) days of the first occurrence of such condition, (iii) you cooperate in good faith with the Company’s efforts (if such
efforts are taken) for a period of not less than thirty (30) days following such notice (the “Cure Period”) to remedy the Good Reason condition, (iv) notwithstanding such efforts a material element of at least one Good
Reason condition continues to exist, and (v) you terminate your employment within sixty (60) days after the end of the Cure Period. If the Company claims in a written notice to you to have fully cured the Good Reason condition during the
Cure Period, and you have not contested the cure within sixty (60) days after receiving such notice, Good Reason shall be deemed not to have occurred. The Company’s success at curing a Good Reason condition shall not bar or preclude your
right to notify the Company of the occurrence of another Good Reason condition and to proceed with the Good Reason Process. 

“Health Care Continuation” means that if you are participating in the Company’s group health plan
immediately prior to the date of your termination, then subject to your timely election and eligibility for benefits under the law known as COBRA, and any law that is the successor to COBRA, the Company shall continue to pay the employer portion of
your health benefits until the earlier of the end of the Salary Continuation Period and the date you become re-employed or otherwise ineligible for COBRA. 

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January 5, 2017 
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 “Release” shall mean a separation agreement in a form
prescribed by the Company that includes, without limitation, (i) a general release of claims and non-disparagement covenant, both in favor of the Company and related persons and entities,
(ii) reaffirmation of your obligations under the Employee Agreement, the terms of which will be incorporated by reference into the Release, and (iii) a provision stating that, if you breach any of the material provisions of Release, in
addition to all other rights and remedies, the Company shall have the right to receive reimbursement for, or to terminate or cease payment of, Severance Payments paid or payable to you. 

“Salary Continuation” means that the Company shall continue to pay you your base salary at the rate in effect
on the date of termination during the Salary Continuation Period. The first payment of Salary Continuation shall be paid within sixty (60) days after the date of termination and shall be made on the Company’s regular payroll dates;
provided, however, that if the sixty (60) day period begins in one calendar year and ends in a second calendar year, the first payment of Salary Continuation shall be paid in the second calendar year. In the event you miss one or more
regular payroll periods between the date of termination and the first Salary Continuation payment, the first Salary Continuation payment shall include a “catch up” payment of accrued but unpaid Salary Continuation payments.

9.    Section 409A Compliance. To the extent that any Severance Payments or other benefits to you constitute “non-qualified deferred compensation” under Section 409A of the Internal Revenue Code of 1986 (as amended or replaced) (the “Code”), then such Severance Payments or benefits shall
begin only upon or after the date of your “separation from service” (within the meaning of Section 409A of the Code), which may occur on or after the date of the termination of your employment. Neither the Company nor you shall have the
right to accelerate or defer the delivery of any such payments except to the extent specifically permitted or required by Section 409A. Anything to the contrary notwithstanding, if at the time of your separation from service within the meaning of
Section 409A of the Code, the Company determines that you are a “specified employee” within the meaning of Section 409A(a)(2)(B)(i) of the Code, then to the extent any payment or benefit that you become entitled to under this Agreement on
account of your separation from service would be considered deferred compensation otherwise subject to the twenty percent (20%) additional tax imposed pursuant to Section 409A(a) of the Code as a result of the application of Section 409A(a)(2)(B)(i)
of the Code, such payment shall not be payable and such benefit shall not be provided until the date that is the earlier of (i) six (6) months and one day after your separation from service, or (ii) your death. If any such delayed cash
payment is otherwise payable on an installment basis, the first payment shall include a catch-up payment covering amounts that would otherwise have been paid during the six (6)-month period but for the
application of this provision, and the balance of the installments shall be payable in accordance with their original schedule. The determination of whether and when your “separation from service” from the Company has occurred shall be
made in a manner consistent with, and based on the presumptions set forth in, Treasury Regulation Section 1.409A-l(h). Solely for purposes of this Section, “Company” shall include all persons with
whom the Company would be considered a single employer under Sections 414(b) and 414(c) of the Code. 

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January 5, 2017 
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 All in-kind benefits provided and
expenses eligible for reimbursement under this Agreement shall be provided by the Company or incurred by you during the time periods set forth in this Agreement. All reimbursements shall be paid as soon as administratively practicable, but in no
event shall any reimbursement be paid after the last day of the taxable year following the taxable year in which the expense was incurred. The amount of in-kind benefits provided or reimbursable expenses
incurred in one taxable year shall not affect the in-kind benefits to be provided or the expenses eligible for reimbursement in any other taxable year (except for any lifetime or other aggregate limitation
applicable to medical expenses). Such right to reimbursement or in-kind benefits is not subject to liquidation or exchange for another benefit. 

The parties intend that this Agreement will be administered in accordance with Section 409A. To the extent that any provision
of this Agreement is ambiguous as to its compliance with Section 409A, the provision shall be read in such a manner so that all payments hereunder comply with Section 409A. Each payment pursuant to this Agreement is intended to constitute a separate
payment for purposes of Treasury Regulation Section 1.409A-2(b)(2). The parties agree that this Agreement may be amended, as reasonably requested by either party, and as may be necessary to fully comply with
Section 409A and all related rules and regulations in order to preserve the payments and benefits provided hereunder without additional cost to either party. The Company shall have no liability to you or to any other person if any provisions of this
Agreement that are intended to be exempt from or compliant with Section 409A are not so exempt or compliant. 

10.    Section 280G Limitation. 

(a)    Anything in this Agreement to the contrary notwithstanding, in the event that the amount of the
Severance Payments, and any additional compensation, payment or distribution by the Company to or for the benefit of you, whether paid or payable or distributed or distributable pursuant to the terms of this Agreement or otherwise, calculated in a
manner consistent with Section 280G of the Code and the applicable regulations thereunder (the “Total Severance Payments”), would be subject to the excise tax imposed by Section 4999 of the Code, the following provisions shall
apply: 
 (i)    If the Total Severance Payments, reduced by the sum of (1) the Excise Tax and
(2) the total of the Federal, state, and local income and employment taxes payable by you on the amount of the Total Severance Payments which are in excess of the Threshold Amount, are greater than or equal to the Threshold Amount, you
shall be entitled to the full benefits payable under this Agreement. 
 (ii)    If the Threshold Amount
is less than (x) the Total Severance Payments, but greater than (y) the Total Severance Payments reduced by the sum of (1) the Excise 

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January 5, 2017 
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Tax and (2) the total of the Federal, state, and local income and employment taxes on the amount of the Total Severance Payments which are in excess of the Threshold Amount, then the Total
Severance Payments shall be reduced (but not below zero) to the extent necessary so that the sum of all Total Severance Payments shall not exceed the Threshold Amount. In such event, the Total Severance Payments shall be reduced in the following
order: (1) cash payments not subject to Section 409A of the Code; (2) cash payments subject to Section 409A of the Code; (3) equity-based payments and acceleration; and (4) non-cash forms of benefits.
To the extent any payment is to be made over time (e.g., in installments, etc.), then the payments shall be reduced in reverse chronological order. 

(b)    For the purposes of this Section 10, “Threshold Amount” shall mean three times the
your “base amount” within the meaning of Section 280G(b)(3) of the Code and the regulations promulgated thereunder less one dollar ($1.00); and “Excise Tax” shall mean the excise tax imposed by Section 4999 of the
Code, and any interest or penalties incurred by you with respect to such excise tax. 
 (c)    The
determination as to which of the alternative provisions of Section 10(a) shall apply to you shall be made by a nationally recognized accounting firm selected by the Company (the “Accounting Firm”), which shall provide detailed
supporting calculations both to the Company and you within fifteen (15) business days of the termination date, if applicable, or at such earlier time as is reasonably requested by the Company or you. For purposes of determining which of the
alternative provisions of Section 10(a) shall apply, you shall be deemed to pay federal income taxes at the highest marginal rate of federal income taxation applicable to individuals for the calendar year in which the determination is to be made,
and state and local income taxes at the highest marginal rates of individual taxation in the state and locality of your residence on the date of termination, net of the maximum reduction in federal income taxes which could be obtained from deduction
of such state and local taxes. Any determination by the Accounting Firm shall be binding upon the Company and you. 

11.    Litigation and Regulatory Cooperation. During and after your employment, you agree to cooperate fully with
the Company in the defense or prosecution of any claims or actions now in existence or which may be brought in the future against or on behalf of the Company which relate to events or occurrences that transpired while you were employed by the
Company. Your full cooperation in connection with such claims or actions shall include, but not be limited to, being available to meet with counsel to prepare for discovery or trial and to act as a witness on behalf of the Company at mutually
convenient times. During and after your employment, you also agree to cooperate fully with the Company in connection with any investigation or review of any federal, state or local regulatory authority as any such investigation or review relates to
events or occurrences that transpired while you were employed by the Company. The Company shall reimburse you for any reasonable out-of-pocket expenses incurred in
connection with your performance of obligations pursuant to this Section 11. 

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January 5, 2017 
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 12.    Relief. If you breach, or propose to breach, any portion of
this Agreement, including any of the provisions of the Restrictive Covenant Agreement, or, if applicable, the Release Agreement, the Company shall be entitled, in addition to all other remedies that it may have, to an injunction or other appropriate
equitable relief to restrain any such breach, and, if applicable, the Company shall have the right to suspend or terminate payment of the Severance Payments or any other payments, benefits and or accelerated vesting pursuant to Section 7 of
this Agreement. Such suspension or termination shall not limit the Company’s other options with respect to relief for such breach and shall not relieve you of duties under this Agreement, the Restrictive Covenant Agreement, the Equity Documents
or the Release Agreement. 
 13.    Miscellaneous. 

a.    This Agreement, including the Restrictive Covenant Agreement and the Equity Documents constitute the
entire agreement as to your employment relationship with the Company and will supersede any prior agreements or understandings, whether in writing or oral. 

b.    This Agreement shall remain in effect if you are transferred, promoted, or reassigned to work in
functions other than your current functions at the Company. Your obligations under this Agreement shall survive the termination of your employment with the Company regardless of the manner or the reasons for such termination. 

c.    This Agreement may not be modified or amended unless agreed to in writing by you and an expressly
authorized representative of the Company. 
 d.    No waiver of any provision hereof shall be effective
unless made in writing and signed by the waiving party. The failure of any party to require the performance of any term or obligation of this Agreement, or the waiver by any party of any breach of this Agreement, shall not prevent any subsequent
enforcement of such term or obligation or be deemed a waiver of any subsequent breach. 
 e.    All forms
of compensation referred to in this Agreement are subject to reduction to reflect applicable withholding and payroll taxes and other deductions required by law. 

f.    This Agreement shall inure to the benefit of, and be binding upon, the Company and you, and our
respective heirs, legal representatives, successors and assigns. This Agreement may be assigned by the Company without your consent to any successor entity in the event of a merger, acquisition, change of control, or sale of all or substantially all
of the business or assets of the Company. “Foundation Medicine” and “Company” shall also mean any such successor entity as the context requires. 

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January 5, 2017 
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 g.    The resolution of any disputes as to the meaning,
effect, performance or validity of this Agreement, the Restrictive Covenant Agreement or arising out of, related to, or in any way connected with your employment with the Company or any other relationship between you and the Company will be governed
by the law of the Commonwealth of Massachusetts, excluding laws relating to conflicts or choice of law. Any dispute arising under this Agreement, except those under the Restricted Covenant Agreement, shall be resolved exclusively by arbitration
conducted before a single arbitrator in accordance with the Employment Arbitration Rules of the American Arbitration Association in effect at the time such arbitration is conducted. All hearings shall be held in Boston,
Massachusetts. Judgment upon the award rendered by the arbitrator may be entered in any court having jurisdiction thereof. The parties shall bear equally the costs of arbitration, including the costs of the arbitrator. 

h.    If any portion or provision of this Agreement shall to any extent be declared illegal or
unenforceable by a court of competent jurisdiction, then the remainder of this Agreement, or the application of such portion or provision in circumstances other than those as to which it is so declared illegal or unenforceable, shall not be affected
thereby, and each portion and provision hereof shall be valid and enforceable to the fullest extent permitted by law. 

i.    The Company shall reimburse you for your reasonable and documented attorney’s fees associated
with the negotiation and review of this Agreement up to $15,000. 
 j.    This Agreement may be executed
in two counterparts, each of which shall be an original and all of which together shall constitute one and the same instrument. 
 Troy, I
look forward to you joining the Company. If you have further questions or require additional information, please feel free to contact me. 
  

			
	Sincerely,
	
	FOUNDATION MEDICINE, INC.
	
	 /s/ Alexis Borisy

	By:	 	Alexis Borisy
	Title:	 	Chairman, Board of Directors

 Please confirm your acceptance of this offer by signing this letter and emailing the signed letter to Alexis Borisy
(alexis.borisy@thirdrockventures.com) or Robert W. Hesslein (rhesslein@foundationmedicine.com) by close of business on Thursday, January 5, 2017. 

 Troy Cox 

January 5, 2017 
  Page
 14
 
  

 YOU ACKNOWLEDGE THAT YOU HAVE CAREFULLY READ THIS AGREEMENT, INCLUDING EXHIBIT A, AND UNDERSTAND AND AGREE TO
ALL OF THE PROVISIONS IN THIS AGREEMENT AND ITS EXHIBITS. 3 FACIMILE AND PDF SIGNATURES SHALL HAVE THE SAME LEGAL EFFECT AS ORIGINALS.     

Accepted and agreed by: 
  

	
	 /s/ Troy Cox

	Employee Signature
	
	
	  
 Troy Cox

	
	Date: 1/5/2017EX-10.2

 Exhibit 10.2 

January 5, 2017 
 Michael Pellini, M.D. 

33841 Niguel Shores Drive 
 Dana Point, CA 92629 

Dear Dr. Pellini: 
 This letter is intended
to memorialize the understanding regarding the ending of your employment with Foundation Medicine, Inc. (“Foundation Medicine” or the “Company”) and your continuing role as an active member of the Company’s Board of
Directors (the “Board”). 
  

	 	1.	Resignation from CEO Position. The Company accepts your voluntary resignation as Chief Executive Officer effective February 6, 2017 (the “CEO Resignation Date”). Your employment with Foundation
Medicine shall terminate on the CEO Resignation Date. Accordingly, your salary, benefits and other compensation referenced in your Amended and Restated Offer Letter, dated September 9, 2013 (the “Employment Agreement”), shall cease as
of the CEO Resignation Date. Notwithstanding the foregoing, for calendar year 2016, you will be eligible to receive an annual performance bonus up to 60% of your final annual salary rate pursuant to your Employment Agreement. The actual bonus
percentage is discretionary and will be subject to the Board or Compensation Committee’s assessment of your performance, as well as business conditions at the Company (the “2016 Bonus”). The 2016 Bonus shall be paid at the time bonus
payments are made to the Company’s other executives but in no event later than March 15, 2017. You acknowledge and agree that you are not entitled to any severance pay or post-employment benefits in connection with the ending of your
employment with Foundation Medicine pursuant to the Employment Agreement or otherwise. 

  

	 	2.	Continuing Role as Chairman. To facilitate the transition to the Company’s recently hired Chief Executive Officer (the “New CEO”), you have agreed that during the Term of this Agreement (as defined
below), if you are elected by the Board to serve as the Chairman of the Board (“Chairman”), you will agree to serve as an active Chairman. If elected Chairman, subject to Section 3 of this Agreement, you shall commit up to two
(2) days per week in 2017 and up to one (1) day per week in 2018 to Chairman activities and responsibilities, inclusive of ordinary Board activities but excluding service as a member of any committees of the Board. The scope and nature of
your activities as Chairman shall be determined by the Board in its reasonable discretion, with advice from the New CEO, in consultation with you. 

  

	 	3.	Term. This Agreement shall commence on the CEO Resignation Date and shall expire on the second anniversary of the CEO Resignation Date (the “Second Anniversary”), provided this Agreement shall end on an
earlier date if you are no longer serving as a member of the Board (the “Term”). After the Second Anniversary, your service and compensation as Chairman and/or as member of the Board, including any service on committees of the Board, to
the extent applicable, shall be governed by the Company’s then effective standard compensation plan for non-employee directors (the “Director Compensation Policy”). 

 Michael Pellini, M.D. 

January 5, 2017 
  Page
 2
 
  

	 	4.	Base Compensation; Expense Reimbursement. From the CEO Resignation Date to the first anniversary of the CEO Resignation Date (the ‘First Anniversary”), you will be paid base compensation at a rate of
$250,000 per year, and from First Anniversary to the Second Anniversary you will be paid at a rate of $125,000 per year (the “Base Compensation”), prorated as necessary for any partial month, provided and notwithstanding anything to the
contrary in this Agreement, if you are removed from the Board without cause pursuant to applicable law and the Company’s charter prior to the Second Anniversary (a “Without Cause Board Removal”), the Company shall continue to pay your
Base Compensation through the Second Anniversary. You may eligible for additional compensation for your service, if any, as a member of any committees of the Board in accordance with Director Compensation Policy. The Base Compensation will be paid
in monthly installments and reported to taxing authorities on Form 1099. Payment for service on committees of the Board, if any, shall be paid in accordance with the schedule set forth in the Director Compensation Policy. You will be entitled to
expense reimbursement consistent with the Company’s then effective standard compensation plan for non-employee directors and in connection with your other service as Chairman in accordance with the
Company’s expense reimbursement policy. 

  

	 	5.	COBRA. Due to the resignation of your employment, you will no longer qualify for continued participation in employee benefit plans. However, to the extent that you are eligible to continue to participate in the
Company’s medical and dental plans under COBRA and you elect to continue such benefits, the Company will continue to contribute toward such benefits at the employer rate in effect as of the CEO Resignation Date in accordance with the benefit
plans until the earlier of (i) the end of the Term or, in the event of a Without Cause Board Removal, the Second Anniversary, in either event to the extent permissible under the Company’s health and dental plans, (ii) your eligibility
for group medical care coverage through other employment, or (iii) the end of your eligibility under COBRA for continuation coverage (the “COBRA Continuation Period”). You will be responsible for paying the employee portion of the
COBRA premiums. 

  

	 	6.	Equity. The plans and agreements governing your awards of stock options, restricted stock units subject to time-based vesting criteria and restricted stock units subject to performance-based vesting
criteria are collectively referred to as the “Equity Documents.” 

 a) Stock Options. Pursuant to the
Foundation Medicine Amended and Restated 2010 Stock Incentive Plan (the “2010 Plan”), you were granted nonstatutory stock options of: (i) 550,000 shares of Company Common Stock on February 9, 2011, (ii) 148,158 shares of Company
Common Stock on January 10, 2012, (iii) 97,748 shares of Company Common Stock on March 27, 2012, (iv) 87,500 shares of Company Common Stock on March 7, 2013, and (v) 87,500 shares of Company Common Stock on May 21, 2013

 Michael Pellini, M.D. 

January 5, 2017 
  Page
 3
 
  

 
(collectively, the “Stock Options”). All of the Stock Options are fully vested as of the CEO Resignation Date. You and the Company acknowledge and agree that your continued service as a
member of the Board shall constitute service as a director and an advisor to the Company and, therefore, you will continue to be an Eligible Participant as defined in the 2010 Plan. Further, (subject to Sections 3(d) and (e) of the Stock Option
Agreements) your right to exercise the Stock Options shall continue until the later of (A) the third anniversary of the CEO Resignation Date and (B) one year after your cession of service as a director, but in no event later than the Final
Exercise Date, as those terms defined in the Equity Documents. In furtherance of the foregoing, Section 3(c) of each respective Stock Option Agreement is, effective as of the CEO Resignation Date, hereby amended so that, “the right to exercise
shall terminate three months after such cessation (but in no event after the Final Exercise Date)” is deleted and replaced with “the right to exercise shall terminate on the later of (A) February 6, 2020 and (B) one year
after such cession (but in no event after the Final Exercise Date).” 
 b) RSUs. Pursuant to the Foundation Medicine 2013
Stock Option and Incentive Plan (the “2013 Plan”), you were granted awards of: (i) 59,365 Restricted Stock Units (“RSUs”) on July 15, 2015; and (ii) 90,000 RSUs on April 1, 2016 (collectively, the “RSU
Grants”). As of the CEO Resignation Date, 61,680 RSUs have vested and 87,685 are unvested. Notwithstanding Section 3 of the respective RSU award agreements, upon the effectiveness of this Agreement, you and the Company acknowledge and
agree that the termination of your employment shall not cause the RSUs to be terminated and forfeited and that your continued service as a member of the Board shall constitute sufficient service in lieu of employment to prevent such termination and
forfeiture of the unvested RSUs, provided in no event shall vesting of the RSUs continue beyond December 31, 2017. In furtherance of the foregoing, Section 3 of the RSU award agreements is, effective as of the CEO Resignation Date, hereby
amended so that, “employment with Company and Subsidiaries” is deleted and replaced with, “service as a director of the Company” and “any Restricted Stock Units that have not vested as of such date” is deleted and
replaced with “any Restricted Stock Units that have not vested as such date or December, 31, 2017, whichever is earlier, provided if the Grantee is removed from the Board without cause pursuant to applicable law and the Company’s charter
prior to December 31, 2017 (a “Without Cause Board Removal”), the Restricted Stock Units that would have vested had the Grantee remained on the Board through December 31, 2017 shall accelerate and become vested as of the
effective date of the Without Cause Board Removal”. All other terms of the RSU award agreements and the RSUs are governed by the Equity Documents. 
  

	 	c)	 PSUs. Pursuant to the 2013 Plan, you were granted 86,034 Restricted Stock Units on December 15, 2015
that were subject to performance-based vesting (the “PSUs”). Notwithstanding Section 3 of the PSU award agreement, upon the effectiveness of this Agreement, you and the Company acknowledge and agree that the termination of your
employment shall not cause the PSUs to be terminated and forfeited and that your continued service as a member of the Board shall constitute sufficient service in lieu of 

 Michael Pellini, M.D. 

January 5, 2017 
  Page
 4
 
  

	 	
employment to prevent such termination and forfeiture of the unvested PSUs. In furtherance of the foregoing, Section 3 of the PSU award agreement is, effective as of the CEO Resignation
Date, hereby amended so that, “employment with Company and Subsidiaries” is deleted and replaced with, “service as a director of the Company”. Except as may hereafter be expressly amended in writing (including potential
amendments to Section 2 thereof), all other terms of the PSU award agreement and the PSUs are governed by the Equity Documents. 

d) Board-Level Equity Grants. Commencing as of the Company’s 2018 annual stockholders meeting, you will be eligible receive
annual equity awards for Board members pursuant to the Director Compensation Policy. For the sake of clarity, you will not receive the “Initial Equity Grant” under the Director Compensation Policy. 

 

	 	7.	Restrictive Covenants. On the CEO Resignation Date, your employment with the Company shall terminate, and all provisions of the Employee Non-Competition, Nonsolicitation,
Confidentiality and Assignment Agreement attached to the Employment Agreement as Exhibit C (the “Restrictive Covenants”) that are intended to survive and to apply to you following your termination shall continue to be in full force and
effect. You reaffirm the Restrictive Covenants are not modified, rescinded or waived in any respect by this Agreement, and are incorporated by reference into this Agreement. 

 

	 	8.	Taxes. You shall perform all services contemplated herein as an “independent contractor” and not as an employee or agent of the Company. Other than as set forth in Section 5 above, you acknowledge
and agree that you have no right to participate in any of the Company’s employee benefit plans or perquisites. Nothing herein shall create, expressly or by implication, a partnership, joint venture or other association between you and the
Company. You acknowledge that you have not relied on any statements or representations by the Company or its attorneys with respect to the tax treatment of any compensation due under this Agreement. You understand that the Company will not be
responsible for withholding or paying any federal or state income, social security or other taxes in connection with Base Compensation paid under this Agreement, and you agree that you are solely responsible for any such tax payments that are his
responsibility under applicable law. The Company shall undertake to make deductions, withholdings and tax reports with respect to payments and benefits under this Agreement to the extent that it reasonably and in good faith determines that it is
required to make such deductions, withholdings and tax reports. Nothing in this Agreement shall be construed to require the Company to make any payments to compensate you for any adverse tax effect associated with any payments or benefits or for any
deduction or withholding from any payment or benefit. 

  

	 	9.	 Entire Agreement. For the avoidance of any doubt, this Agreement, the Restrictive Covenants, the Equity
Agreements, as amended in this Agreement, the Director Compensation Policy, the Company’s Statement of Company Policy on Insider Trading and Disclosure, and Code of Business Conduct and Ethics constitute the entire agreement

 Michael Pellini, M.D. 

January 5, 2017 
  Page
 5
 
  

	 	
as to your role with the Company and will supersede any prior agreements or understandings, whether in writing or oral with respect to the subject matter herein. This Agreement may not be
amended, varied, modified or changed (in whole or in part), except by a formal, definitive written agreement expressly referring to this Agreement, which agreement is executed by both of the parties to this Agreement. 

 

	 	10.	Miscellaneous. Neither the failure nor any delay on the part of a party to exercise any right, remedy, power or privilege under this Agreement shall operate as a waiver thereof, nor shall any single or partial
exercise of any right, remedy, power or privilege preclude any other or further exercise of the same or of any right, remedy, power or privilege, nor shall any waiver of any right, remedy, power or privilege with respect to any occurrence be
construed as a waiver of such right, remedy, power or privilege with respect to any other occurrence. No waiver shall be effective unless it is in writing and is signed by the party asserted to have granted such waiver. Each party recognizes that
this Agreement is a legally binding contract and acknowledges that such party has had the opportunity to consult with his legal counsel of choice. In any construction of the terms of this Agreement, the same shall not be construed against either
party on the basis of that party being the drafter of such terms. 

  

	 	11.	Counterparts. This Agreement may be executed in any number of counterparts, each of which shall be deemed an original as against any Party whose signature appears thereon, and all of which together shall
constitute one and the same instrument. This Agreement shall become binding when one or more counterparts hereof, individually or taken together, shall bear the signatures of all of the parties reflected hereon as the signatories. 

 

	 	12.	Governing Law. The interpretation of this Agreement will be governed by the laws of Massachusetts, without regard to the conflicts of laws principles thereof. 

 Michael Pellini, M.D. 

January 5, 2017 
  Page
 6
 
  

 Please acknowledge, by signing below, that you agree and accept the terms of this Agreement.

  

			
	Very truly yours,
	
	FOUNDATION MEDICINE, INC.
		
	By:	 	 /s/ Alexis Borisy

		 	Alexis Borisy
		 	Chairman of the Board of Directors

  

	
	ACKNOWLEDGED AND AGREED:
	
	 /s/ Michael Pellini

	Michael Pellini, M.D.
	
	 1/5/2017

	Date

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