Fifth Amendment to Collaboration Agreement, by and among the Company, F. Hoffmann-La Roche Ltd and Hoffman-La Roche Inc., dated September 8, 2017

Exhibit 10.1

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

Confidential Treatment Requested Under

17 C.F.R. Sections 200.80(b)(4) and 240.24b-2

FIFTH AMENDMENT TO

COLLABORATION AGREEMENT

This Fifth Amendment (“Fifth Amendment”) to the Collaboration Agreement (the “Agreement”) by and between F. Hoffmann-La Roche Ltd, with an office and place of business at Grenzacherstrasse 124, 4070, Basel, Switzerland, and Hoffmann-La Roche Inc., with an office and place of business at 150 Clove Road, Suite 8, Little Falls, New Jersey 07424, U.S.A. (together, “Roche”), on the one hand, and Foundation Medicine, Inc., with an office and place of business at 150 Second Street, Cambridge, MA 02141, U.S.A. (“FMI”), on the other hand (each a “Party,” and collectively, the “Parties”), as such Agreement has been amended from time to time, is entered into by and between the Parties and shall be considered effective as of the 8^th of September, 2017 (the “Fifth Amendment Effective Date”). Capitalized terms used in this Fifth Amendment and not otherwise defined herein are used with the meanings ascribed to them in the Agreement.

“1.27 Excepted Activities

The term “Excepted Activities” shall mean […***…].

[Signature page follows.]

IN WITNESS WHEREOF, the Parties hereto have caused this Fifth Amendment to be executed and effective as of the Fifth Amendment Effective Date. All other terms and conditions of the Agreement remain in force and effect.

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