UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549





FORM 10-K/A

Amendment No. 1





(Mark One)

|☒ | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ------------------------------------------------------------------------------------

For the fiscal year ended December 31, 2016

OR



|☐ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ----------------------------------------------------------------------------------------

For the transition period from
 to

Commission file number: 001-36086





FOUNDATION MEDICINE, INC.

(Exact name of registrant as specified in its charter)







|                                                               |  |                                     
|-------------------------------------------------------------- |  | ------------------------------------
|DELAWARE                                                       |  | 27-1316416                          
|(State or other jurisdiction of
incorporation or organization) |  | (I.R.S. Employer
Identification No.)

150 Second Street

Cambridge MA, 02141

(Address of principal executive offices, including zip code)

Registrants Telephone Number, Including Area Code:

(617) 418-2200

Securities registered pursuant to Section 12(b) of the Act:



|                                |  |                                            
|------------------------------- |  | -------------------------------------------
|Common Stock, $0.0001 Par Value |  | The NASDAQ Global Select
Market            
|(Title of each class)           |  | (Name of each exchange on which registered)

Securities registered pursuant to Section 12(g) of the Act: NONE





Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities
Act.    Yes  ☐    No  ☒

Indicate by check mark if the registrant
is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.    Yes  ☐    No  ☒

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the
Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90
days.    Yes  ☐    No  ☒

Indicate by check mark whether the
registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of
this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    ☒  Yes    ☐  No

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K
is not contained herein, and will not be contained, to the best of registrants knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any
amendment to this Form 10-K.  ☒

Indicate by check mark whether the registrant is
a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller reporting company. See definitions of large accelerated filer, accelerated filer and smaller
reporting company in 12b-2 of the Exchange Act.



|                        |  |   |  |                           |  |  
|----------------------- |  | - |  | ------------------------- |  | -
|Large accelerated filer |  | ☐ |  | Accelerated filer         |  | ☒
|                        |  |   | 
|Non-accelerated filer   |  | ☐ |  | Smaller reporting company |  | ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).    Yes  ☐    No  ☒

As of June 30, 2016, the last business day of the registrants most recently completed second fiscal quarter, the aggregate market
value of common stock held by non-affiliates of the registrant computed by reference to the last reported sale price of the registrants common stock on the Nasdaq Global Select Market as of such date was
approximately $252.7 million. As of February 24, 2017 there were 35,418,498 shares of the registrants common stock, $0.0001 par value per share, outstanding.

DOCUMENTS INCORPORATED BY REFERENCE

The registrant intends to file a definitive proxy statement pursuant to Regulation 14A within 120 days of the end of the fiscal year ended
December 31, 2016. Portions of such definitive proxy statement are incorporated by reference into Part III of this Annual Report on Form 10-K.









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EXPLANATORY NOTE  EXHIBIT FILING ONLY

Foundation Medicine, Inc. (the Company) is filing this Amendment No. 1 (this Amendment) to its Annual Report on Form 10-K for the year ended December 31, 2016 (the Form 10-K), originally filed on March 3, 2017. This Amendment is an exhibit-only filing in response to
comments received from the Securities and Exchange Commission (the Commission) regarding a request for confidential treatment of certain portions of Exhibit 10.11 originally filed with the Form
10-K. This Amendment is being filed solely to re-file Exhibit 10.11 based on Commission comments in order to restore certain redacted information in the agreement on
such exhibit that was subject to a confidential treatment request. In addition, as required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, new certifications by our principal executive
officer and principal financial officer are filed as exhibits to this Amendment.

This Amendment is limited in scope to the items identified above and
should be read in conjunction with the Form 10-K. This Amendment does not reflect events occurring after the filing of the Form 10-K and no revisions are being made to
the Companys financial statements pursuant to this Amendment. Other than the filing of the information identified above, this Amendment does not modify or update the disclosure in the Form 10-K in any
way.



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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf on
the date set forth below by the undersigned thereunto duly authorized.



|                     |  |                           |  |                                             
|-------------------- |  | ------------------------- |  | --------------------------------------------
|                     |  | FOUNDATION MEDICINE, INC.
|                     |  |                          
|Date: March 30, 2017 |  | By:                       |  | /s/ Troy Cox                                
|                     |  |                           |  | Troy Cox                                    
|                     |  |                           |  | Chief Executive Officer                     
|                     |  |                           |  | (Principal Executive Officer)               
|                     |  |                          
|Date: March 30, 2017 |  | By:                       |  | /s/ Jason Ryan                              
|                     |  |                           |  | Jason Ryan                                  
|                     |  |                           |  | Chief Financial Officer                     
|                     |  |                           |  | (Principal Financial and Accounting Officer)



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|            |  |                                                                                                                                                                                                                                      
|----------- |  | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|Exhibit
No. |  | Exhibit Index                                                                                                                                                                                                                        
|            | 
|10.11*#     |  | First Amendment to Supply and Support Agreement, by and between the Company and Illumina, Inc., dated as of October 1, 2016.                                                                                                         
|            | 
|31.1*       |  | Certification of Principal Executive Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted
pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.                              
|            | 
|31.2*       |  | Certification of Principal Financial Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted
pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.                              
|            | 
|32.1**      |  | Certification of Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley
Act of 2002.



|* | Filed herewith.
|- | ---------------

|** | Furnished herewith.
|-- | -------------------

|# | Confidential treatment has been requested for certain information contained in this exhibit. Such information has been omitted and filed separately with the Securities and Exchange Commission.
|- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



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