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** **

**UNITED STATES**

**SECURITIES AND EXCHANGE COMMISSION**

**WASHINGTON, D.C. 20549**

 

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**FORM 10-Q/A**

**(Amendment No. 1)**

 

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**(Mark One)**

 

**x**      **QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934**

 

**For the quarterly period ended March 31, 2015**

 

**OR**

 

**o**         **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 001-36156**

 

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**VERACYTE, INC.**

(Exact name of registrant as specified in its charter)

 

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| **Delaware**                      |   | **20-5455398**      |
|-----------------------------------|--------|---------------------|
| (State or other   jurisdiction of |   | (I.R.S. Employer    |
| incorporation or   organization)  |   | Identification No.) |

 

**7000 Shoreline Court, Suite 250**

**South San Francisco, California 94080**

(Address of principal executive offices, zip code)

 

**(650) 243-6300**

(Registrant’s telephone number, including area code)

 

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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 x No o

 

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 x No o

 

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 the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

 
| Large   accelerated filer o | Accelerated filer x | Non-accelerated filer o                         | Smaller reporting company o |
|-----------------------------|---------------------|-------------------------------------------------|-----------------------------|
|                        |                | (Do not check if a   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 o No x

 

As of May 1, 2015, there were 27,462,532 shares of common stock, par value $0.001 per share, outstanding.

 

 

 

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**EXPLANATORY NOTE**

 

Veracyte, Inc. (“we”, “our” or the “Company”) is filing this Amendment No. 1 to its Quarterly Report on Form 10-Q for the quarterly period ended March 30, 2015 filed with the Securities and Exchange Commission on May 15, 2015 (the “Original Filing”). This Amendment is being filed solely to revise the Company’s filing status on the cover page hereof, to revise the disclosure in Part I, Item 4. Controls and Procedures — (a) Evaluation of Disclosure Controls and Procedures, and to include new certifications of the Chief Executive Officer and Chief Financial Officer, respectively, pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.

 

Except as described above, this Amendment No. 1 does not otherwise amend or update any exhibit to or disclosure set forth in the Original Filing.

 

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**VERACYTE, INC.**

**INDEX**

 
| ** **                                      | **Page   No.** |
|-------------------------------------------------|----------------|
| **PART I. — FINANCIAL   INFORMATION** |           |
| Item 4. Controls and Procedures                 | 1              |
| **PART II. — OTHER   INFORMATION**    |           |
| Item 6. Exhibits                                | 2              |
| SIGNATURES                                      | 3              |
| EXHIBIT INDEX                              | 4              |

 

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**PART I. — FINANCIAL INFORMATION**

 

**Item 4.**         **Controls and Procedures**

 

**(a) Evaluation of Disclosure Controls and Procedures**

 

We maintain “disclosure controls and procedures,” as such term is defined in Rule 13a-15(e) under the Securities Exchange Act of 1934, or Exchange Act, that are designed to ensure that information required to be disclosed by us in reports that we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in Securities and Exchange Commission (“SEC”) rules and forms, and that such information is accumulated and communicated to our management, including our Chief Executive Officer and Chief Financial Officer, as appropriate, to allow timely decisions regarding required disclosure. In designing and evaluating our disclosure controls and procedures, management recognized that disclosure controls and procedures, no matter how well conceived and operated, can provide only reasonable, not absolute, assurance that the objectives of the disclosure controls and procedures are met. Our disclosure controls and procedures have been designed to meet reasonable assurance standards. Additionally, in designing disclosure controls and procedures, our management necessarily was required to apply its judgment in evaluating the cost-benefit relationship of possible disclosure controls and procedures. The design of any disclosure controls and procedures also is based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions.

 

Based on their evaluation as of the end of the period covered by this Quarterly Report on Form 10-Q, our Chief Executive Officer and Chief Financial Officer have concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level. After that evaluation, we subsequently determined that we were an accelerated filer as of December 31, 2014 and that, as a result, our Quarterly Report on Form 10-Q was filed late. Our Chief Executive Officer and Chief Financial Officer have re-evaluated the effectiveness of our disclosure controls and procedures as of the end of the period covered by this report. Based upon that re-evaluation, our Chief Executive Officer and Chief Financial Officer have concluded that our disclosure controls and procedures were not effective to provide reasonable assurance that our Quarterly Report on Form 10-Q would be filed within the period specified in the SEC rules and forms, in particular those relating to our filing status and related deadlines. We have made refinements to the process by which we assess our filing status and the related filing deadlines for our Forms 10-K and 10-Q, and communicate such status and filing deadlines to the persons responsible for preparation of such Forms. Our Chief Executive Officer and Chief Financial Officer have concluded that our disclosure controls and procedures were effective at the reasonable assurance level as of the date of this Quarterly Report on Form 10-Q/A.

 

**(b) Changes in Internal Control over Financial Reporting**

 

There were no changes in our internal control over financial reporting (as such term is defined in Rule 13a-15(f) under the Exchange Act) identified in connection with the evaluation identified above that occurred during the quarter ended March 31, 2015 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

 

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**PART II. — OTHER INFORMATION**

 

**Item 6. Exhibits**

 
| **Exhibit   Number** | ** ** | **Description**                                                                                                                                     |
|----------------------|------------|-----------------------------------------------------------------------------------------------------------------------------------------------------|
| 10.1#^               |       | Amended and Restated   Change of Control and Severance Agreement, effective as of May 14, 2015,   between Bonnie Anderson and the Registrant.  |
| 10.2#^               |       | Amended and Restated   Change of Control and Severance Agreement, effective as of May 14, 2015,   between Shelly Guyer and the Registrant.     |
| 10.3#^               |       | Amended and Restated   Change of Control and Severance Agreement, effective as of May 14, 2015,   between Christopher Hall and the Registrant. |
| 10.4#^               |       | Amended and Restated   Change of Control and Severance Agreement, effective as of May 14, 2015,   between Julie Brooks and the Registrant.     |
| 31.1                 |       | Principal Executive   Officer’s Certification Pursuant to Section 302 of the Sarbanes- Oxley   Act of 2002.                               |
| 31.2                 |       | Principal Financial   Officer’s Certification Pursuant to Section 302 of the Sarbanes-Oxley   Act of 2002.                                |
| 32.1^**              |       | Certification Pursuant   to 18 U.S.C. § 1350 (Section 906 of Sarbanes-Oxley Act of 2002).                                                 |
| 32.2^**              |       | Certification Pursuant   to 18 U.S.C. § 1350 (Section 906 of Sarbanes-Oxley Act of 2002).                                                 |
| 101.INS^             |       | XBRL Instance Document                                                                                                                              |
| 101.SCH^             |       | XBRL Taxonomy Extension   Schema                                                                                                                    |
| 101.CAL^             |       | XBRL Taxonomy Extension   Calculation Linkbase                                                                                                      |
| 101.DEF^             |       | XBRL Taxonomy Extension   Definition Linkbase                                                                                                       |
| 101.LAB^             |       | XBRL Taxonomy Extension   Label Linkbase                                                                                                            |
| 101.PRE^             |       | XBRL Taxonomy Extension   Presentation Linkbase                                                                                                     |

 

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# Indicates management contract or compensatory plan or arrangement

 

^ Filed (furnished, with respect to 32.1 and 32.2) with the Original Filing.

 

** In accordance with Item 601(b)(32)(ii) of Regulation S-K and SEC Release No. 34-47986, the certifications furnished in Exhibits 32.1 and 32.2 hereto are deemed to accompany this Form 10-Q and will not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934 (the “Exchange Act”) or deemed to be incorporated by reference into any filing under the Exchange Act or the Securities Act of 1933 except to the extent that the registrant specifically incorporates it by reference.

 

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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 by the undersigned, thereunto duly authorized.

 
| Date:   September 25, 2015 |                |
|---------------------------------|---------------------|
|                            |                |
|                            | VERACYTE, INC. |
|                            |                |
|                            | By:                 | /s/   Shelly D. Guyer |
|                            |                | Shelly   D. Guyer |
|                            |                | Chief   Financial Officer |
|                            |                | (Principal   Financial and Accounting Officer) |

 

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| **Exhibit   Number** | ** ** | **Description**                                                                                                                                     |
|----------------------|------------|-----------------------------------------------------------------------------------------------------------------------------------------------------|
| 10.1#^               |       | Amended and Restated   Change of Control and Severance Agreement, effective as of May 14, 2015,   between Bonnie Anderson and the Registrant.  |
| 10.2#^               |       | Amended and Restated   Change of Control and Severance Agreement, effective as of May 14, 2015,   between Shelly Guyer and the Registrant.     |
| 10.3#^               |       | Amended and Restated   Change of Control and Severance Agreement, effective as of May 14, 2015,   between Christopher Hall and the Registrant. |
| 10.4#^               |       | Amended and Restated   Change of Control and Severance Agreement, effective as of May 14, 2015,   between Julie Brooks and the Registrant.     |
| 31.1                 |       | Principal Executive   Officer’s Certification Pursuant to Section 302 of the Sarbanes- Oxley   Act of 2002.                               |
| 31.2                 |       | Principal Financial   Officer’s Certification Pursuant to Section 302 of the Sarbanes-Oxley   Act of 2002.                                |
| 32.1^**              |       | Certification Pursuant   to 18 U.S.C. § 1350 (Section 906 of Sarbanes-Oxley Act of 2002).                                                 |
| 32.2^**              |       | Certification Pursuant   to 18 U.S.C. § 1350 (Section 906 of Sarbanes-Oxley Act of 2002).                                                 |
| 101.INS^             |       | XBRL Instance Document                                                                                                                              |
| 101.SCH^             |       | XBRL Taxonomy Extension   Schema                                                                                                                    |
| 101.CAL^             |       | XBRL Taxonomy Extension   Calculation Linkbase                                                                                                      |
| 101.DEF^             |       | XBRL Taxonomy Extension   Definition Linkbase                                                                                                       |
| 101.LAB^             |       | XBRL Taxonomy Extension   Label Linkbase                                                                                                            |
| 101.PRE^             |       | XBRL Taxonomy Extension   Presentation Linkbase                                                                                                     |

 

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# Indicates management contract or compensatory plan or arrangement.

 

^ Filed (furnished, with respect to Exhibits 32.1 and 32.2) with the Original Filing.

 

** In accordance with Item 601(b)(32)(ii) of Regulation S-K and SEC Release No. 34-47986, the certifications furnished in Exhibits 32.1 and 32.2 hereto are deemed to accompany this Form 10-Q and will not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934 (the “Exchange Act”) or deemed to be incorporated by reference into any filing under the Exchange Act or the Securities Act of 1933 except to the extent that the registrant specifically incorporates it by reference.

 

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