Ignyta POS AM Prospectus update (post-effective amendment)

Exhibit 5.1

	12670 High Bluff Drive
	San Diego, California 92130
	Tel: +1.858.523.5400 Fax: +1.858.523.5450
	www.lw.com
	FIRM / AFFILIATE OFFICES
	Abu Dhabi	Milan
	Barcelona	Moscow
	Beijing	Munich
	Boston	New Jersey
	Brussels	New York
June 16, 2014	Chicago	Orange County
	Doha	Paris
	Dubai	Riyadh
	Düsseldorf	Rome
	Frankfurt	San Diego
	Hamburg	San Francisco
	Hong Kong	Shanghai
	Houston	Silicon Valley
Ignyta, Inc.	London	Singapore
11095 Flintkote Ave., Suite D	Los Angeles	Tokyo
San Diego, CA 92121	Madrid	Washington, D.C.

Re: Registration Statement on Form S-1 with respect to 9,010,238 Shares of Common Stock, par value $0.0001 per share

Ladies and Gentlemen:

We have acted as special counsel to Ignyta, Inc., a Delaware corporation (the “Company”), in connection with its filing on June 16, 2014, with the Securities and Exchange Commission (the “Commission”) of a Post-Effective Amendment No. 2 to the Registration Statement on Form S-1 (Registration No. 333-192956) (the “Registration Statement”) under the Securities Act of 1933, as amended (the “Act”), relating to the resale from time to time of an aggregate of 9,010,238 shares of common stock, $0.0001 par value per share (the “Shares”) by the selling stockholders identified in the Registration Statement. This opinion is being furnished in connection with the requirements of Item 601(b)(5) of Regulation S-K under the Act, and no opinion is expressed herein as to any matter pertaining to the contents of the Registration Statement, other than as expressly stated herein with respect to the issue of the Shares.

As such counsel, we have examined such matters of fact and questions of law as we have considered appropriate for purposes of this letter. With your consent, we have relied upon certificates and other assurances of officers of the Company and others as to factual matters without having independently verified such factual matters. We are opining herein only as to the General Corporation Law of the State of Delaware, as amended (the “DGCL”), and we express no opinion with respect to any other laws.

Subject to the foregoing and the other matters set forth herein, it is our opinion that, as of the date hereof, the Shares have been duly authorized by all necessary corporate action of the Company, and the Shares are validly issued, fully paid and nonassessable. In rendering the foregoing opinion, we have assumed that the Company will comply with all applicable notice requirements regarding uncertificated shares provided in the DGCL.

June 16, 2014

Page 2

This opinion is for your benefit in connection with the Registration Statement and may be relied upon by you and by persons entitled to rely upon it pursuant to the applicable provisions of the Act. We consent to your filing this opinion as an exhibit to the Registration Statement. In giving such consent, we do not thereby admit that we are in the category of persons whose consent is required under Section 7 of the Act or the rules and regulations of the Commission thereunder.

Very truly yours,

/s/ Latham & Watkins LLP