SECOND AMENDMENT TO LABORATORY MASTER SERVICES AGREEMENT

Exhibit 10.1

***Text Omitted and Filed Separately with the Securities and Exchange Commission

Confidential Treatment Request Under

Rule 24b-2 of the Securities Exchange Act of 1934

SECOND AMENDMENT TO

LABORATORY MASTER SERVICES AGREEMENT

This Second Amendment (“Second Amendment”), which shall be considered effective as of the 1^st of October, 2013 (the “Second Amendment Effective Date”), is entered into by and between Novartis Pharmaceuticals Corporation (“Novartis”), with an office at 59 Route 10, East Hanover, New Jersey 07936, and Foundation Medicine, Inc. (“Institution”), with an office at 150 Second Street, Cambridge, MA 02141, and amends the Laboratory Master Services Agreement dated November 21, 2011 (referred to herein as the “Master Agreement”) as amended by the First Amendment to Laboratory Master Services Agreement dated May 29, 2012 (referred to together herein as the “First Amended Master Agreement”). The First Amended Master Agreement as amended by this Second Amendment shall be referred to herein as the “Agreement” or the “Second Amended Master Agreement.” Capitalized terms used in this Second Amendment and not otherwise defined herein are used with the meanings ascribed to them in the First Amended Master Agreement.

“A. Institution hereby agrees to perform genomic testing and analysis, molecular information, and related technology services, as set forth in any Statement of Work issued in the sample form attached hereto as Attachment 1 (the “Services”), after the Second Amendment Effective Date hereof, to Institution by Novartis and accepted by Institution, with respect to laboratory samples identified therein (the “Samples”). Institution shall not provide any Services hereunder beyond the scope of the Statement of Work without the prior written approval of Novartis. References to Task Orders in other provisions of this Agreement shall be deemed to refer to the Statement of Work attached hereto as Attachment 1.”

“2. TERM OF AGREEMENT

Unless sooner terminated pursuant to the terms of this Agreement, this Agreement shall be deemed effective from as of the Second Amendment Effective Date and shall continue in force until September 30, 2016 (the “Term”), subject to Novartis’ right to extend the Term as described herein. Each one-year period under this Second Amended Master Agreement shall be deemed a “Contract Year,” and, in consideration of work performed under the Master Agreement and First Amended Master Agreement dating back to November 21, 2011, the first Contract Year under this Second Amended Master Agreement (beginning October 1, 2013) shall be deemed the “Third Contract Year,” the second Contract Year under this Second Amended Master Agreement (beginning

October 1, 2014) shall be deemed the “Fourth Contract Year,” and the third Contract Year under this Second Master Agreement (beginning October 1, 2015) shall be deemed the “Fifth Contract Year.” Notwithstanding the foregoing, (a) any payment obligations accrued under the First Amended Master Agreement prior to the Second Amendment Effective Date shall be paid in full to Institution by Novartis pursuant to the terms of the First Amended Master Agreement; and (b) should any Statement of Work entered into during the term of this Second Amended Master Agreement require Services to be performed beyond the termination date of this Second Amended Master Agreement, then the terms of this Second Amended Master Agreement shall remain in effect with respect to such Statement of Work until the termination of the Statement of Work. Novartis shall have the option to extend the Term for two additional years (“Sixth and Seventh Contract Years”) by providing written notice to Institution no later than ninety (90) days prior to the expiration of the Term. If Novartis exercises this option, the provisions of this Second Amended Master Agreement shall remain in full force and effect for the Sixth and Seventh Contract Years, except to the extent the parties mutually agree to any changes to the Agreement, in which case they shall be incorporated pursuant to an amendment hereto.”

“A. During the Third through Fifth Contract Years (in the period running from October 1, 2013 through September 30, 2016), and, in the event Novartis exercises its option to extend the Term under Section 2, in the Sixth and Seventh Contract Years (in the period running from October 1, 2016 through September 30, 2018), in consideration of Institution reserving capacity to perform the genomic testing and analysis aspects of the Services (“Reserved Capacity”) and of satisfactory performance of the Services generally, Novartis shall pay Institution as described in detail below, […***…] beginning on the Second Amendment Effective Date. Institution shall invoice Novartis for the first quarterly payment due hereunder in accordance with the terms specified below on December 9, 2013. Thereafter, Institution shall invoice Novartis on or around (but not before) the first day of each calendar quarter during the Term of this Agreement. Unless Novartis reasonably objects to all or a portion of any new invoice submitted to it by Institution, Novartis shall make payments against each invoice within sixty (60) days of its receipt.

i. Genomic Testing and Analysis of Samples.

x. Third through Fifth Contract Years. During each of the Third, Fourth, and Fifth Contract Years, in consideration of Institution reserving capacity to perform the genomic testing and analysis aspects of the Services and of Institution’s satisfactory performance of the Services generally, Novartis shall pay Institution a minimum of […***…] per Contract Year (“Reserved Capacity Fee”), payable in advance of each quarter in non-refundable, non-creditable, equal installments of […***…], based on a per Sample price of […***…] for Institution’s solid

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tumor genomic testing and analysis platform (“Solid Tumor Platform”) and a per Sample price of […***…] for Institution’s hematological malignancy genomic testing and analysis platform (“Heme Platform”). Fees for Services performed on Samples exceeding Reserved Capacity shall be governed by Section 3.A.i.b. Notwithstanding the above, payments may be refunded, as appropriate, pursuant to Section 10 of this Agreement.

y. Sixth and Seventh Contract Years. If Novartis exercises its option under Section 2 to extend the Term for the Sixth and Seventh Contract Years (beginning October 1^st in 2016 and 2017, respectively), Novartis shall pay Institution a per sample rate that is the lesser of the pricing shown on Attachment 4 or Institution’s then current standard pricing, and Reserved Capacity for the Sixth and Seventh Contract Years shall be agreed upon between the Parties. For clarity, the amounts shown in Figure 1 for the Sixth and Seventh Contract Years are examples only. They are not binding on Novartis. Both pricing and Reserved Capacity for the Sixth and Seventh Contract Years reflected in Figure 1 may change pursuant to this provision. Fees for Services performed on Samples exceeding Reserved Capacity shall be governed by Section 3.A.i.b.

b. Fees for Samples Exceeding Reserved Capacity. In the event Novartis chooses to seek genomic testing and analysis for Samples under this Second Amended Master Agreement in a given Contract Year in excess of annual Reserved Capacity (“Excess Samples”), the following pricing shall apply:

x. Tier Two Excess Samples. For the Third through Fifth Contract Years, after the Reserved Capacity Fee has been reached, Excess Samples shall initially be billed monthly on a per Sample basis at a per Sample rate for the Solid Tumor Platform of […***…] and a per Sample rate for the Heme Platform of […***…] until additional fees for Services performed of […***…] (“Tier Two Value Threshold”) have been reached. If Novartis exercises its option under Section 2 to extend the Term for the Sixth and Seventh Contract Years (beginning October 1^st in 2016 and 2017, respectively), after the Reserved Capacity fee for the Sixth and Seventh Contract Years (to be determined pursuant to Section 3.A.i.a.y) has been reached, Excess Samples shall initially be billed at a rate to be agreed upon between the Parties until additional fees for Services performed in an amount to be agreed by the Parties (“Tier Two Year Six and Seven Value Threshold”) have been reached. See Figure 1. For clarity, the amounts shown in Figure 1 for the Sixth and Seventh Contract Years are examples only. They are not binding on Novartis. Both pricing and volume for the Sixth and Seventh Contract Years reflected in Figure 1 may change pursuant to this provision.

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y. Tier Three Excess Samples. For the Third through Fifth Contract Years, after the Tier Two Value Threshold has been reached during a given Contract Year, additional Excess Samples shall be billed monthly on a per Sample basis at a per Sample rate for the Solid Tumor Platform of […***…] and a per Sample rate for the Heme Platform of […***…] (“Tier Three Pricing”). If Novartis exercises its option under Section 2 to extend the Term for the Sixth and Seventh Contract Years (beginning October 1^st in 2016 and 2017, respectively), after the Tier Two Year Six and Seven Value Threshold (which amount is to be determined pursuant to Section 3.A.i.b.x) has been reached, Excess Samples shall be billed at a rate to be agreed upon between the Parties. See Figure 1. For clarity, the amounts shown in Figure 1 for the Sixth and Seventh Contract Years are examples only. They are not binding on Novartis. Both pricing and volume for the Sixth and Seventh Contract Years reflected in Figure 1 may change pursuant to this provision.

Figure 1

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ii. Alliance Management and Technology Support. During each Contract Year, Novartis shall pay Institution an Alliance Management and Technology Support Service Fee for services to support the continued collaboration between the Parties and ongoing enhancement to Sample management and reporting tools for Novartis studies. The Service Fee payable by Novartis under this Section 3.A.ii shall be […***…] per year, which shall be payable in advance of each quarter in non-refundable, non-creditable equal installments of […***…] per quarter. Institution bears the sole responsibility for compensation (including overtime to hourly employees, if applicable) of Institution’s employees who provide the services set forth in this Section 3.A.ii. Notwithstanding the above, payments may be refunded, as appropriate, pursuant to Section 10 of the Master Agreement.

iii. Molecular Information and Analysis Services. During each Contract Year, Novartis shall pay Institution […***…] (“Molecular Information Service Fee”), payable in advance of each quarter in non-refundable, non-creditable equal installments of […***…] per quarter, to develop and conduct queries of Institution’s database of aggregated genomic alteration information on behalf of Novartis and provide results to Novartis as more fully described in Section 4.J. The work required of Institution to perform the molecular information services hereunder shall not, in aggregate across all Statements of Work in any Contract Year, exceed performance of […***…]. Institution bears the sole responsibility for compensation (including overtime to hourly employees, if applicable) of Institution’s employees for the services set forth in this Section 3.A.iii. Notwithstanding the above, Novartis may, at its own discretion, discontinue requests for services under this Section 3.A.iii by notifying Institution in writing no less than ninety (90) days before the start of the next Contract Year. Novartis

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shall not be required to pay the Molecular Information Service Fee for any Contract Year for which it requests discontinuation of the services set forth hereunder. Notwithstanding the above, payments may be refunded, as appropriate, pursuant to Section 10 of the Master Agreement.”

4. Section 4. Section 4.D is amended and Section 4.J is newly added as follows:

Following the last sentence of Section 4.D of the First Amended Master Agreement, the following sentence is added: “In addition, Novartis grants Institution a non-exclusive, royalty-free, sublicensable to Affiliates, worldwide, transferable (but only in connection with the sale of all or substantially all of Institution’s business to which this Agreement relates) and perpetual license to include the data derived from the Samples resulting from the Services (“Results”) into Institution’s databases for use with its products and services relating to genomic testing and analysis in the field of oncology.”

“J. Novartis acknowledges that Institution possesses and owns genomic information pertaining to the nature and prevalence of known and likely somatic alterations, including base substitutions, insertions and deletions, focal amplifications, homozygous deletions, and rearrangements contained in Institutions proprietary database of de-identified clinical patient data (“Molecular Information”), which may be interrogated by one or more queries of Molecular Information performed by Institution at Novartis’s request as part of the Services hereunder (“Database Queries”) to generate certain results (“Database Query Results”). Institution shall exclusively own all Database Query Results, but Institution hereby grants to Novartis and its Affiliates a non-exclusive, royalty-free, non-sublicensable, worldwide and perpetual license to use the Database Query Results for its internal business and development purposes and for patent filings and regulatory submissions. For clarity, the Database Query Results shall NOT be considered works for hire under copyright law or any other applicable law or doctrine. Ownership of any patentable inventions arising directly from the Database Query Results shall follow inventorship in accordance with United States patent law. For any patentable inventions arising directly from the Database Query Results and owned by Institution (“Institution Database Query Inventions”), Institution grants Novartis and its Affiliates a non-exclusive, royalty-free, sublicensable, worldwide and perpetual license to such patentable inventions to research, develop, make, have made, use, offer for sale, sell and import Novartis products. Furthermore, Institution agrees to promptly notify Novartis of any Institution Database Query Inventions and grants Novartis the option to negotiate an exclusive license under reasonable commercial terms for any Institution Database Query Inventions or Institution’s interest in any inventions arising directly from the Database Query Results that are jointly invented between Novartis and Institution. Novartis shall notify Institution of its intent to exercise such option to negotiate within ninety (90) days after Institution’s disclosure to Novartis of the applicable Institution Database Query Invention. If Novartis exercises such option, the Parties shall thereafter work in good faith to negotiate the terms of such license within a period of ninety (90) days after exercise of such option, or within such other period of time as is mutually agreed upon by the Parties. Prior to notifying Novartis of an Institution Database Query Invention, during the period following notification but prior to Novartis’s exercise of the option, and during the ninety (90) days prescribed for license negotiations if Novartis exercises its option, Institution shall not […***…].”

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5. New Section 5.A.iii. Section 5.A.iii of the First Amended Master Agreement is added as follows:

“Notwithstanding the above, with regard to Third Party Samples, Novartis represents that the Third Party has made a representation, warranty and covenant with regard to the facts and obligations set forth in 5.A.i and 5.A.ii.”

6. New Section 5.F. Section 5.F of the First Amended Master Agreement is added as follows:

“From time to time, and subject to the provisions below, a third party (“Third Party Provider”) may, on behalf of Novartis, provide to Institution samples (“Third Party Samples”) for services under this Agreement. Third Party Samples for which Institution performs Services shall be counted as part of the total number of Samples provided to Institution in the applicable Contract Year, and Section 3.A shall apply to Third Party Samples. Institution’s obligations with regard to Services and Samples as set forth throughout this Agreement shall apply to Third Party Samples. Services to be performed with regard to Third Party Samples will be specified in a Statement of Work to be completed by the party supplying Third Party Samples. Any license and use rights granted by Novartis to Institution under Section 4 shall not be applied as they relate to Third Party Samples but instead such grant rights by Novartis to Institution relating to Third Party Samples are specified below. Novartis agrees […***…] Prior to the provision of Third Party Samples to Institution for performance of Services under this Agreement, Novartis also agrees […***…] Prior to initiation of Services for Third Party Samples, Novartis shall […***…] For clarity, it is understood between Novartis and Institution that […***…]”

7. Section 7. Section 7 of the of the First Amended Master Agreement is hereby replaced with the following:

“The Institution shall not disclose that Novartis has retained the Institution for professional services, and neither party shall use, or authorize others to use, the name, symbols, or marks of the other party hereto in any advertising or publicity material, press release, or other public statement, without prior written permission of the other Party (which consent will not be unreasonably withheld or delayed), except to the extent such disclosure is required to be disclosed pursuant to (a) judicial process, court order or administrative request, or (b) applicable legal requirements or governmental regulations, including any securities laws or regulations, or the regulations or requirements of any stock exchange or stock listing entity. Notwithstanding the above, Institution shall provide Novartis with prompt notice of any requirement to disclose such information so as to permit Novartis to seek a protective order or other appropriate remedy and will disclose only that information which Institution’s counsel has concluded is legally required to be disclosed.”

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8. Section 10.A. The first sentence of Section 10.A of the First Amended Master Agreement is hereby amended as follows:

“A. This Agreement and any Task Orders issued hereunder may be terminated by Novartis for any reason or for no reason at all after September 30, 2016 upon ninety (90) days written notice to Institution.”

9. Section 12. The first sentence of Section 12 of the of the First Amended Master Agreement is hereby amended as follows:

“Institution shall not subcontract any of this Master Agreement without the prior written approval of Novartis, except that Institution may engage non-employee contractors to perform aspects of the Services under this Master Agreement on Institution’s premises and under the supervision of appropriate Institution personnel, provided such non-employee contractors are bound by obligations applicable to Institution’s employees no less stringent than those contained in this Master Agreement. In the event that Novartis approves the use of non-employee contractors, Institution shall remain fully liable for the performance of its obligations under this Master Agreement.”

10. New Section 23. A new Section 23 is hereby added as follows:

“23. Anti-Bribery

In consideration of the mutual covenants, terms and conditions set forth below, the parties agree as follows:

A. In exercising its rights and performing its obligations under the Master Agreement, the Institution will comply with all applicable federal, state and local anti-corruption and anti-bribery laws, statutes, rules, regulations and orders, applicable industry standards, and the Novartis Global Anti-Bribery Policy, as amended from time to time, and attached hereto as Attachment 5.

B. The Institution shall train any individual who is involved with the activities set forth in the Master Agreement on anti-corruption and anti-bribery at its own expense using training materials provided by Novartis and the attached Novartis Global Anti-Bribery Policy.

C. The Institution warrants that should Novartis require Institution to complete a “Questionnaire for Third Parties”, the information provided by Institution with such Questionnaire shall be accurate and complete. The Institution agrees to inform Novartis promptly of any significant change to the information provided with such Questionnaire.

D. Novartis shall have the right, at its cost, at any time upon reasonable prior written notice, to audit the Institution’s records to ensure compliance with this provision. Novartis may appoint a third party auditor to perform such audit and if so, the appointed auditor will be subject to reasonable confidentiality obligations in relation to its review of the Institution’s records. The Institution will provide full cooperation and grant access to all relevant documents and materials as reasonably necessary during normal business hours.

E. The Institution’s breach of any obligation or warranty set forth in this provision shall be considered a material breach of the Master Agreement, and Novartis shall have the right to immediately terminate the Master Agreement.”

11. New Section 24. A new section 24 is added as follows:

“24. Healthcare Professionals and Healthcare Institutions

“Healthcare Professional” or “HCP” shall mean any person possessing a relevant healthcare degree and any pharmacy & therapeutics (P&T) committee member including but not limited to any person licensed to prescribe, administer, dispense, or purchase prescription drugs/medicines for resale or distribution for human and animal use.

“Healthcare Institution” or “HCI” shall mean any institution that provides healthcare to patients, purchases or dispenses prescription medication, conducts clinical research, recommends or advocates treatment options, or whose entire members, entire shareholders, or all employees include healthcare professionals.

In consideration of the mutual covenants, terms and conditions set forth herein, the parties agree as follows:

A. HCI/HCP shall perform the services under the Master Agreement: (i) in a professional manner, consistent with applicable industry standards and practices; (ii) in conformance with that level of care and skill ordinarily exercised in similar circumstances by providers of the same or similar services; (iii) in compliance with all applicable federal, state and local laws, statutes, rules, regulations and orders, including, but not limited to, the applicable requirements of the Federal Food, Drug, and Cosmetic Act (21 U.S.C. § 301 et seq.) and the Federal Healthcare Programs Antikickback Statute (42 U.S.C. § 1320a-7b(b)); and (iv) in compliance with all Novartis policies and procedures communicated to HCI/HCP and applicable to the Services or to HCI/HCP. HCI/HCP shall ensure that each person assigned to perform the Services has the appropriate level of expertise, training, experience and, where applicable, licenses, necessary to perform such Services. Upon Novartis’ reasonable request, HCI/HCP shall reassign and replace any of its employees and subcontractors assigned to perform the Services. Novartis reserves the right to deny access to its facilities or remove from its premises, any individual who does not comply with Novartis’ rules, regulations and policies.

B. If HCI/HCP is a United States (“US”) based healthcare professional or an entity by or in which any US based healthcare professional receiving payments under the Master Agreement or in connection with the Services is (1) employed; (2) a principal; (3) an owner; or (4) a contractor, Novartis will have the right (i) to make public on its web site information relating to the Services or the Master Agreement, including without limitation, the relevant name, city, and state of residence or business (as applicable), the nature of the services performed pursuant to the Agreement, and any and all payments, reimbursements for expenses, or other transfers of value made in other than dollar form relating to the Master Agreement and (ii) to otherwise disclose as Novartis determines or as may be required under applicable state or federal law or any Corporate Integrity Agreement, such information or any other information relating to the Master Agreement. Furthermore, if a payment or other transfer of value is made under the Master Agreement, (1) on behalf of, at the request of, for the benefit or use of, or under the name of a US based healthcare professional for whom Novartis would otherwise report payments if made directly to the US based healthcare professional; or (2) at the request

of, or designated on behalf of, a US based healthcare professional, then Novartis shall have the right to post and/or disclose the information referenced in the preceding sentence under the name of the HCI/HCP and/or the healthcare professional, as Novartis shall determine. Novartis shall also have the right to disclose this information to such healthcare professional’s employer, or affiliated hospitals or institutions.

C. If any HCI/HCP or any employee, subcontractor or agent of the HCI/HCP involved with the performance of the Services is currently or during the term of the Master Agreement becomes a member of a committee that sets formularies of covered medicines (e.g., formulary committee or Pharmacy & Therapeutics committee) or develops clinical practice guidelines or treatment protocols or standards, HCI/HCP shall or shall ensure that such person shall comply with the disclosure requirements of the respective committee(s) and, at a minimum, shall follow the procedures of such committee and disclose to such committee that (i) such person(s) provide services to Novartis and (ii) the nature of such services, for example, services related to the current or potential marketing and/or sales of a Novartis product; clinical research activities relating to a Novartis product; and/or non-promotional activities relating to a therapeutic area in which Novartis researches, develops, markets or sells pharmaceutical products.

The obligation to disclose to such committee as contemplated above shall extend for two (2) years beyond the termination or expiration of the Master Agreement, or a longer period of time as required by such committee. If and to the extent that the procedures or disclosure requirements of any committee(s) referenced above of which such person is a member require disclosure of confidential information of Novartis and/or work product produced under the Master Agreement to such committee(s), HCI/HCP will notify Novartis of such procedure or requirement reasonably in advance of making such disclosure, to the extent not prohibited by the policies of such committee(s).

D. If HCI/HCP, or any employee, subcontractor or agent of HCI/HCP involved with the performance of Services is or during the term of the Master Agreement subsequently becomes, a member of, affiliated with, or an employee of an educational or not-for-profit institution, health care institution, medical committee, or other medical or scientific organization and is required by such institution, committee, or organization to disclose any proposed or current agreements for Services as contemplated herein, HCI/HCP will or will ensure that said employee, subcontractor or agent will, make such disclosure(s) in accordance with the policies and procedures of such institution, committee, or organization, and will obtain prior written approval of the Master Agreement by such institution, committee, or organization, if required. The obligation to make the disclosures and obtain the approvals contemplated above shall extend beyond the termination or expiration of the Master Agreement for such period of time as required by such institution, committee, or organization. If and to the extent that the procedures or disclosure requirements of any institution, committee, or organization referenced above require disclosure of confidential information of Novartis and/or work product produced under the Master Agreement to such institution, committee, or organization, HCI/HCP will notify Novartis of such procedure or requirement reasonably in advance of making such disclosure, to the extent not prohibited by the policies of such institution, committee, or organization.

E. If the Services include authoring or production of articles or other publications, HCI/HCP shall, and shall ensure that its employees, subcontractors and agents shall (1) comply with the International Committee of Medical Journal Editors (“ICMJE”) criteria concerning authorship and disclosure of relationships with industry; and (2) disclose in any manuscript, journal submission, and elsewhere as appropriate or required, any potential conflict of interest, including any financial or personal relationships with Novartis, the names of any individuals who have provided editorial support for any manuscripts or other publications, and all funding sources for the study or publication.

F. Neither HCI/HCP nor any person currently employed by or under contract to HCI/HCP now or in the future in connection with any work to be performed for or on behalf of Novartis, including without limitation, any Services performed under the Master Agreement (i) has been convicted of an offense related to any Federal or State healthcare program, including (but not limited to) those within the scope of 42 U.S.C. § 1320a-7(a); (ii) has been excluded, suspended or is otherwise ineligible for Federal or State healthcare program participation, including (but not limited to) persons identified on the General Services Administration’s List of Parties Excluded from Federal Programs or the HHS/OIG List of Excluded Individuals/Entities; (iii) has been debarred from or under any Federal or State healthcare program (including, but not limited to debarment under Section 306 of the Federal Food, Drug and Cosmetic Act (21 USC 335a); or (iv) is on any of the FDA Clinical Investigator enforcement lists, including, but not limited to, the (1) Disqualified/Totally Restricted List, (2) Restricted List and (3) Adequate Assurances List. HCI/HCP further agrees that if, at any time after execution of this Amendment, HCI/HCP becomes aware that it has or any person who participated, or is participating, in the performance of any Service or any other work for Novartis has become or is in the process of being charged, convicted, debarred, excluded, proposed to be excluded, suspended or otherwise rendered ineligible or is on an enforcement list, HCI/HCP will immediately notify Novartis in writing at: Novartis Pharmaceuticals Corporation, Attn: Ethics and Compliance, 59 Route 10, East Hanover, NJ ###-###-####.”

12. New Section 25. A new Section 25 is hereby added as follows:

“25. Spend Information. During the term of this Agreement, Institution shall retain and provide to Novartis certain spend information reasonably requested by Novartis to enable Novartis to comply with federal and/or state law requirements and meet other Novartis information needs (e.g., aggregate spend). Novartis shall request only that information reasonably necessary to fulfill its obligations and will request such information in a common or easily accessible format (e.g., by Excel file). Such spend information shall be provided or transmitted to Novartis on a calendar monthly basis no later than the fifteenth (15th) business day of each month. After the fifteenth (15th) business day, Institution shall have another five (5) business days to correct any errors or omissions to the Spend Report identified by Novartis.”

13. Press Release. Upon execution of this Second Amendment, Institution shall issue a press release in a form mutually agreed to by the Parties in writing announcing the full collaboration established by the Second Amended Master Agreement. Institution shall provide Novartis a press release in draft form five (5) business days prior to its publication in order to provide Novartis sufficient time to review and comment.

14. Entire Agreement. Except as provided herein, the First Amended Master Agreement shall remain in full force and effect without amendment or modification and is hereby ratified. The First Amended Master Agreement, as amended by this Second Amendment, supersedes any prior understandings or written or oral agreements between the parties respecting the subject matter hereof and contains the entire understanding of the parties with respect thereto. This Second Amendment shall not have any force or effect until executed by all parties. The headings of this Second Amendment are for informational purposes only and shall not be used to interpret this Second Amendment.

15. Counterparts. This Second Amendment may be executed in multiple counterparts, each of which shall be deemed to be an original and all of which taken together shall constitute one agreement. This Second Amendment may also be executed by facsimile counterparts.

[Remainder of this page intentionally left blank. Signature page follows.]

IN WITNESS WHEREOF, the parties hereto have caused this Second Amendment to be executed as of the date of last signature below. All other terms and conditions of the Master Agreement, as amended, remain in effect.

NOVARTIS PHARMACEUTICALS CORPORATION

FOUNDATION MEDICINE, INC.

Attachment 1

Statement of Work Template

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 1 of 11

A STUDY TO USE THE FOUNDATION MEDICINE COMPREHENSIVE GENOMIC PROFILING ASSAY TO ANALYZE <INSERT ADDITIONAL STUDY INFORMATION HERE or STUDY TITLE FROM PROTOCOL>

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 2 of 11

A STUDY TO USE THE FOUNDATION MEDICINE COMPREHENSIVE GENOMIC PROFILING ASSAY

TO ANALYZE <INSERT ADDITIONAL STUDY INFORMATION HERE>

I. APPROVAL SIGNATURES

Signature of Agreement for Protocol

I have read this protocol and agree to the Statement of Work as outlined herein:

CONFIDENTIALITY

The information contained in this document is the confidential and proprietary information of Foundation

Medicine. Except as may be required by Federal, State, or local laws or regulations, this document may not be

disclosed to others without written permission of Foundation Medicine.

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 3 of 11

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 4 of 11

Table of Contents

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 5 of 11

<Please provide a short background paragraph on study here><Short background paragraph on disease studied, if relevant.>

The samples used for this study come from COMPANY NAME protocol number XXXXXXX, a <TRIAL DESCRIBED HERE>.

The purpose of this study is to use the Foundation Medicine comprehensive genomic assay to profile tumor specimens on a selection of tumors from the <XXXX study/research project.>

Primary Objective:

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 6 of 11

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 7 of 11

Quality control checks are critical to every step of the FMI assay. These steps are:

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 8 of 11

Refer to the SOW appendices for the list of genes in each assay.

If remaining tissue is to be returned, the following table must be completed including destination, address, and recipient contact info, timelines, shipping conditions (e.g. ambient, cold pack, frozen), labeling, and manifest requirements (electronic and hard copies)

FM should notify partner contact when a shipment is scheduled with tracking numbers and expected delivery dates. Return shipments should only be scheduled on a Monday, Tuesday, or Wednesday, unless partner explicitly requests otherwise.

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 9 of 11

If remaining tissue is to be destroyed, FM must receive a written request with a listing of exactly which samples are to be destroyed. FM will provide documentation of destruction upon completion of the process.

The success of this work will be facilitated by timely sample receipt and associated data transfer and regular communication between the relevant scientific and operational contacts at Foundation and Novartis. IF RELEVANT: NGS data from this study is required at PARTNER by XX date. The achievability of this date is dependent upon receiving samples and sample information in a timely manner (by XXXX, 2013 at the latest).

All data types/formats in the table below will provide information regarding:

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 10 of 11

Foundation Medicine will provide tracking and sample progress reports either in a centralized tracking sheet delivered to Novartis, the BioTrack sample annotation file, or a web-based tracking platform maintained by Foundation Medicine.

Add or remove contact information as needed

		Foundation Medicine Statement of Work
Doc. ID Number: RES-RSP-13-XXX		Partner Trial: XXX		Effective Date: <DATE>		Page: 11 of 11

Attachment 4

***Confidential Treatment Requested***

Attachment 5

Anti-Bribery Policy

Novartis Global Policy