Ignyta, Inc. (Form: 8-K, Received: 09/30/2015 17:11:27)

Dated: September 30, 2015

IGNYTA, INC.

/s/ Jonathan E. Lim, M.D.

Jonathan E. Lim, M.D.

President and Chief Executive Officer

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d)

of the Securities Exchange Act of 1934

Date of Report (Date of earliest event reported): September 27, 2015

IGNYTA, INC.

(Exact Name of Registrant as Specified in its Charter)


Delaware	001-36344	45-3174872
(State of Incorporation)	(Commission File Number)	(IRS Employer Identification No.)

11111 Flintkote Avenue

San Diego, California 92121

(Address of principal executive offices, including zip code)

Registrant’s telephone number, including area code: (858) 255-5959

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

¨	Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

¨	Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

¨	Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

¨	Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

Item 2.03

Creation of a Direct Financial Obligation or an Obligation under an Off-Balance Sheet Arrangement of a Registrant.

As previously reported in the Company’s Current Report on Form 8-K filed with the Securities and Exchange Commission (the “SEC”) on October 1, 2014 (the “October 2014 8-K”), Ignyta, Inc. (the “Company”) entered into a Second Amended and Restated Loan and Security Agreement (the “Loan and Security Agreement”) with Silicon Valley Bank (“SVB”). Upon the signing of the Loan and Security Agreement, the Company borrowed $21.0 million from SVB and had the conditional option to borrow an additional $10.0 million at any time prior to September 30, 2015, subject to certain conditions. The description of the Loan and Security Agreement contained in Item 2.03 of the October 2014 8-K is incorporated herein by reference and is qualified in its entirety by reference to the Loan and Security Agreement, which was filed as Exhibit 10.1 to the October 2014 8-K.

On September 30, 2015, the Company drew down the second tranche of $10.0 million under the Loan and Security Agreement. The Company now has total indebtedness of approximately $31.0 million under the loan facility.

Pursuant to the Loan and Security Agreement, in connection with the draw down the Company issued to SVB and its affiliate, Life Science Loans, LLC, warrants to purchase an aggregate of 15,432 shares of the Company’s common stock (the “Warrants”). The Warrants are exercisable immediately, have a per-share exercise price of $8.78 and have a term of seven years. The foregoing is only a brief description of the Warrants, does not purport to be a complete description of the rights and obligations of the parties thereunder and is qualified in its entirety by reference to the Warrants, which are filed as Exhibits 4.1 and 4.2 to this Current Report on Form 8-K and are incorporated herein by reference.

Item 3.02.

Unregistered Sales of Equity Securities

The Company relied on the exemption from registration contained in Section 4(a)(2) of the Securities Act of 1933, as amended (the “Securities Act”), and Rule 506 of Regulation D, in connection with the issuance of the Warrants. The Warrants and the shares of common stock issuable under the Warrants have not been registered under the Securities Act, or state securities laws, and may not be offered or sold in the United States without being registered with the SEC or through an applicable exemption from SEC registration requirements.

The other information called for by this item is contained in Item 2.03, which is incorporated herein by reference.

Item 7.01

Regulation FD Disclosure

On September 27, 2015, Salvatore Siena, M.D., Director, Niguarda Hospital Cancer Center, Milan, Italy, presented updated results from the Phase 1 clinical trials of entrectinib, the Company’s proprietary oral tyrosine kinase inhibitor targeting solid tumors that harbor activating alterations to NTRK1, NTRK2, NTRK3, ROS1 or ALK , in an oral presentation session at the 2015 European Cancer Congress (ECC) in Vienna, Austria. The slide presentation used by Dr. Siena is attached hereto as Exhibit 99.1.

The information contained in this Item 7.01 and in Exhibit 99.1 of this Current Report on Form 8-K shall not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), or incorporated by reference in any filing under the Securities Act or the Exchange Act, except as expressly set forth by specific reference in such a filing.

Item 8.01

Other Events.

The clinical trials included the ALKA-372-001 study and the STARTRK-1 study, which is the first of the Company’s “ S tudies T argeting A lterations R esponsive to T argeted R eceptor K inase” inhibition. Both trials were designed to determine the maximum tolerated dose and/or recommended Phase 2 dose (“RP2D”), as well as preliminary anti-cancer activity, of single agent entrectinib in patients with solid tumors with the relevant molecular alterations: NTRK1 (encoding TrkA), ROS1 or ALK for ALKA-372-001 and NTRK1/2/3 (encoding TrkA/TrkB/TrkC), ROS1 or ALK for STARTRK-1.

As of the August 15, 2015 data cut-off for the presentation, the findings showed:

•

A total of 92 patients with a range of solid tumors had been dosed across both clinical trials, with nine patients treated at or above the RP2D beyond six months and one patient beyond one year.

•

Entrectinib was well tolerated to date:

•

Across both studies, the most frequent (>10% incidence) treatment-related adverse events were fatigue, dysgeusia, paresthesia, nausea, and myalgia. Seven of these were Grade 3 in severity, consisting of fatigue (4 patients), cognitive impairment (2 patients), and diarrhea (1 patient). No Grade 4 treatment-related adverse events were observed; and

•

Across both studies, there were three treatment-related serious adverse events: Grade 3 cognitive impairment and Grade 3 myocarditis, both of which occurred above the RP2D, and Grade 2 fatigue. All events were reversible and resolved upon dose modification.

•

Pharmacokinetic measurements showed dose-proportional increases across the daily dosing regimens evaluated, with a half-life compatible with once-daily dosing.

•

The fixed daily dose RP2D was determined to be 600 mg, taken orally once per day (QD).

•

18 patients across both clinical trials met the company’s expected Phase 2 eligibility criteria, which include:

•

Presence of NTRK1/2/3, ROS1 or ALK fusions, as opposed to other types of molecular alterations (e.g., SNPs, amplifications, deletions);

•

ALK inhibitor and/or ROS1 inhibitor naïve; and

•

Treatment at or above the RP2D.

•

The response rate in the 18 patients who met these criteria across both studies was 72% (13 responses out of 18 treated patients, as assessed by the clinical sites). Nine of these responders remain on study treatment with durable responses of up to 21 treatment cycles. An additional 3 patients remain on study with stable disease. The responses included:

•

3 responses out of 4 patients with NTRK1/2/3 gene rearrangements, including patients with non-small cell lung cancer (“NSCLC”), colorectal cancer and salivary gland cancer, with one of the responding patients remaining on treatment at 6 months; a fourth patient with an astrocytoma remains on treatment after two months with stable disease;

•

6 responses, including one complete response, out of 8 patients with ROS1 gene rearrangements, all of which were in NSCLC. All of the patients who responded remain on treatment, the longest at 21 months; and

•

4 responses out of 6 patients with ALK gene rearrangements, including two NSCLC patients and two patients with other solid tumors; two of the 4 responders subsequently progressed.

•

Entrectinib has demonstrated objective tumor response in the central nervous system, a frequent site of metastases and progression of advanced solid tumors.

On September 30, 2015, the Company announced the initiation of its Phase 2 clinical trial of entrectinib. This clinical trial is called STARTRK-2, the second of the “ S tudies of T umor A lterations R esponsive to T argeting R eceptor K inases.” It is a global, multicenter, open label, potentially registration-enabling Phase 2 clinical trial of entrectinib that utilizes a basket design with screening of patient tumor samples for the relevant targets.

Item 9.01.

Financial Statements and Exhibits

(d) Exhibits .


Exhibit No.		Description

4.1		Warrant dated September 30, 2015, issued to Silicon Valley Bank.

4.2		Warrant dated September 30, 2015, issued to Life Science Loans, LLC.

99.1		Slide Presentation, dated September 27, 2015.

SIGNATURE

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 hereunto duly authorized.

EXHIBIT INDEX


Exhibit No.		Description

4.1		Warrant dated September 30, 2015, issued to Silicon Valley Bank.

4.2		Warrant dated September 30, 2015, issued to Life Science Loans, LLC.

99.1		Slide Presentation, dated September 27, 2015.

Exhibit 4.1

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ ACT ”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY, SUCH OFFER, SALE, PLEDGE OR OTHER TRANSFER IS EXEMPT FROM SUCH REGISTRATION.

WARRANT TO PURCHASE COMMON STOCK

Company: Ignyta, Inc., a Delaware corporation

Number of Shares of Common Stock: 7,716

Warrant Price: $8.78

Issue Date: September 30, 2015

Expiration Date: September 30, 2022 See also Section 5.1(b).


Credit Facility:		This Warrant to Purchase Common Stock (“ Warrant ”) is issued in connection with that certain Second Amended and Restated Loan and Security Agreement dated as of September 30, 2014 between Silicon Valley Bank and the Company (the “ Loan Agreement ”).

THIS WARRANT CERTIFIES THAT, for good and valuable consideration, SILICON VALLEY BANK (together with any successor or permitted assignee or transferee of this Warrant or of any shares issued upon exercise hereof, “ Holder ”) is entitled to purchase the number of fully paid and non-assessable shares (the “ Shares ”) of the above-stated common stock (the “ Common Stock ”) of the above-named company (the “ Company ”) at the above-stated Warrant Price, all as set forth above and as adjusted pursuant to Section 2 of this Warrant, subject to the provisions and upon the terms and conditions set forth in this Warrant. Reference is made to Section 5.4 of this Warrant whereby Silicon Valley Bank shall transfer this Warrant to its parent company, SVB Financial Group.

SECTION 1. EXERCISE .

1.1 Method of Exercise . Holder may at any time and from time to time exercise this Warrant, in whole or in part, by delivering to the Company the original of this Warrant together with a duly executed Notice of Exercise in substantially the form attached hereto as Appendix 1 and, unless Holder is exercising this Warrant pursuant to a cashless exercise set forth in Section 1.2, a check, wire transfer of same-day funds (to an account designated by the Company), or other form of payment acceptable to the Company for the aggregate Warrant Price for the Shares being purchased.

1.2 Cashless Exercise . On any exercise of this Warrant, in lieu of payment of the aggregate Warrant Price in the manner as specified in Section 1.1 above, but otherwise in accordance with the requirements of Section 1.1, Holder may elect to receive Shares equal to the value of this Warrant, or portion hereof as to which this Warrant is being exercised. Thereupon, the Company shall issue to the Holder such number of fully paid and non-assessable Shares as are computed using the following formula:

X = Y(A-B)/A

where:

X =

the number of Shares to be issued to the Holder;

Y =

the number of Shares with respect to which this Warrant is being exercised (inclusive of the Shares surrendered to the Company in payment of the aggregate Warrant Price);

A =

the Fair Market Value (as determined pursuant to Section 1.3 below) of one Share; and

B =

the Warrant Price.

1.3 Fair Market Value . If the Company’s Common Stock is then traded or quoted on a nationally recognized securities exchange, inter-dealer quotation system or over-the-counter market (a “ Trading Market ”), the fair market value of a Share shall be the closing price or last sale price of a share of Common Stock reported for the Business Day immediately before the date on which Holder delivers this Warrant together with its Notice of Exercise to the Company. If the Company’s Common Stock is not traded in a Trading Market, the Board of Directors of the Company shall determine the fair market value of a Share in its reasonable good faith judgment.

1.4 Delivery of Certificate and New Warrant . Within a reasonable time after Holder exercises this Warrant in the manner set forth in Section 1.1 or 1.2 above, the Company shall deliver to Holder a certificate representing the Shares issued to Holder upon such exercise and, if this Warrant has not been fully exercised and has not expired, a new warrant of like tenor representing the Shares not so acquired.

1.5 Replacement of Warrant . On receipt of evidence reasonably satisfactory to the Company of the loss, theft, destruction or mutilation of this Warrant and, in the case of loss, theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form, substance and amount to the Company or, in the case of mutilation, on surrender of this Warrant to the Company for cancellation, the Company shall, within a reasonable time, execute and deliver to Holder, in lieu of this Warrant, a new warrant of like tenor and amount.

1.6 Treatment of Warrant Upon Acquisition of Company .

(a) Acquisition . For the purpose of this Warrant, “ Acquisition ” means any transaction or series of related transactions involving: (i) the sale, exclusive license, or other disposition of all or substantially all of the assets of the Company (ii) any merger or consolidation of the Company into or with another person or entity (other than a merger or consolidation effected exclusively to change the Company’s domicile), or any other corporate reorganization, in each case which the stockholders of the Company in their capacity as such immediately prior to such merger, consolidation or reorganization, own less than a majority of the Company’s (or the surviving or successor entity’s) outstanding voting power immediately after such merger, consolidation or reorganization; or (iii) any sale or other transfer by the stockholders of the Company of shares representing at least a majority of the Company’s then-total outstanding combined voting power in one or a series of related transactions.

(b) Treatment of Warrant at Acquisition . In the event of an Acquisition in which the consideration to be received by the Company’s stockholders consists solely of cash, solely of Marketable Securities or a combination of cash and Marketable Securities (a “ Cash/Public Acquisition ”), and the fair market value of one Share as determined in accordance with Section 1.3 above would be greater than the Warrant Price in effect on such date immediately prior to such Cash/Public Acquisition, and Holder has not exercised this Warrant pursuant to Section 1.1 or Section 1.2 above as to all Shares that have not been previously exercised, then this Warrant shall automatically be deemed to be Cashless Exercised pursuant to Section 1.2 above as to all Shares effective immediately prior to and contingent upon the consummation of a Cash/Public Acquisition. In connection with such Cashless Exercise, Holder shall be deemed to have restated each of the representations and warranties in Section 4 of the Warrant as the date thereof and the Company shall promptly notify the Holder of the number of Shares (or such other securities) issued upon exercise. In the event of a Cash/Public Acquisition where the fair market value of one Share as determined in accordance with Section 1.3 above would be less than the Warrant Price in effect immediately prior to such Cash/Public Acquisition, then this Warrant will expire immediately prior to the consummation of such Cash/Public Acquisition.

(c) Upon the closing of any Acquisition other than a Cash/Public Acquisition defined above, the acquiring, surviving or successor entity shall assume the obligations of this Warrant, and this Warrant shall thereafter be exercisable for the same securities and/or other property as would have been paid for the Shares issuable upon exercise of the unexercised portion of this Warrant as if such Shares were outstanding on and as of the closing of such Acquisition, subject to further adjustment from time to time in accordance with the provisions of this Warrant.

(d) As used in this Warrant, “ Marketable Securities ” means securities meeting all of the following requirements: (i) the issuer thereof is then subject to the reporting requirements of Section 13 or Section 15(d) of the Securities Exchange Act of 1934, as amended (the “ Exchange Act ”), and is then current in its filing of all required reports and other information under the Act and the Exchange Act; (ii) the class and series of shares or other security of the issuer that would be received by Holder in connection with the Acquisition were Holder to exercise this Warrant on or prior to the closing thereof is then traded in a Trading Market, and (iii) following the closing of such Acquisition, Holder would not be restricted from publicly re-selling all of the issuer’s shares and/or other securities that would be received by Holder in such Acquisition to the same extent had Holder exercised or converted this Warrant in full on or prior to the closing of such Acquisition, except to the extent that any such restriction (x) arises solely under federal or state securities laws, rules or regulations, and (y) does not extend beyond six (6) months from the closing of such Acquisition.

SECTION 2. ADJUSTMENTS TO THE SHARES AND WARRANT PRICE .

2.1 Stock Dividends, Splits, Etc . If the Company declares or pays a dividend or distribution on the outstanding shares of the Common Stock payable in securities or property (other than cash), then upon exercise of this Warrant, for each Share acquired, Holder shall receive, without additional cost to Holder, the total number and kind of securities and property which Holder would have received had Holder owned the Shares of record as of the date the dividend or distribution occurred. If the Company subdivides the outstanding shares of the Common Stock by reclassification or otherwise into a greater number of shares, the number of Shares purchasable hereunder shall be proportionately increased and the Warrant Price shall be proportionately decreased. If the outstanding shares of the Common Stock are combined or consolidated, by reclassification or otherwise, into a lesser number of shares, the Warrant Price shall be proportionately increased and the number of Shares shall be proportionately decreased.

2.2 Reclassification, Exchange, Combinations or Substitution . Upon any event whereby all of the outstanding shares of the Common Stock are reclassified, exchanged, combined, substituted, or replaced for, into, with or by Company securities of a different class and/or series, then from and after the consummation of such event, this Warrant will be exercisable for the number, class and series of Company securities that Holder would have received had the Shares been outstanding on and as of the consummation of such event, and subject to further adjustment thereafter from time to time in accordance with the provisions of this Warrant. The provisions of this Section 2.2 shall similarly apply to successive reclassifications, exchanges, combinations substitutions, replacements or other similar events.

2.3 Intentionally Omitted.

2.4 Intentionally Omitted.

2.5 No Fractional Share . No fractional Share shall be issuable upon exercise of this Warrant and the number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional Share interest arises upon any exercise of the Warrant, the Company shall eliminate such fractional Share interest by paying Holder in cash the amount computed by multiplying the fractional interest by (i) the fair market value (as determined in accordance with Section 1.3 above) of a full Share, less (ii) the then-effective Warrant Price.

2.6 Notice/Certificate as to Adjustments . Upon each adjustment of the Warrant Price, Common Stock and/or number of Shares, the Company, at the Company’s expense, shall notify Holder in writing within a reasonable time setting forth the adjustments to the Warrant Price, class and/or number of Shares and facts upon which such adjustment is based. The Company shall, upon written request from Holder, furnish Holder with a certificate of its Chief Financial Officer, including computations of such adjustment and the Warrant Price, class and number of Shares in effect upon the date of such adjustment.

SECTION 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY .

3.1 Representations and Warranties . The Company represents and warrants to, and agrees with, the Holder as follows: All Shares which may be issued upon the exercise of this Warrant, shall, upon issuance, be duly authorized, validly issued, fully paid and non-assessable, and free of any liens and encumbrances except for restrictions on transfer provided for herein or under applicable federal and state securities laws. The Company covenants that it shall at all times cause to be reserved and kept available out of its authorized and unissued capital stock such number of securities as will be sufficient to permit the exercise in full of this Warrant.

3.2 Notice of Certain Events . If the Company proposes at any time to:

(a) declare any dividend or distribution upon the outstanding shares of the Company’s stock, whether in cash, property, stock, or other securities and whether or not a regular cash dividend;

(b) offer for subscription or sale pro rata to the holders of the outstanding shares any additional shares of any class or series of the Company’s stock (other than pursuant to contractual pre-emptive rights);

(c) effect any reclassification, exchange, combination, substitution, reorganization or recapitalization of the outstanding shares of the Common Stock; or

(d) effect an Acquisition or to liquidate, dissolve or wind up.

then, in connection with each such event, the Company shall give Holder notice thereof at the same time and in the same manner as the Company notifies the holders of the outstanding shares of the Class thereof.

Company will also provide information requested by Holder that is reasonably necessary to enable Holder to comply with Holder’s accounting or reporting requirements.

SECTION 4. REPRESENTATIONS, WARRANTIES OF THE HOLDER .

The Holder represents and warrants to the Company as follows:

4.1 Purchase for Own Account . This Warrant and the Shares to be acquired upon exercise of this Warrant by Holder are being acquired for investment for Holder’s account, not as a nominee or agent, and not with a view to the public resale or distribution within the meaning of the Act. Holder also represents that it has not been formed for the specific purpose of acquiring this Warrant or the Shares.

4.2 Disclosure of Information . Holder is aware of the Company’s business affairs and financial condition and has received or has had full access to all the information it considers necessary or appropriate to make an informed investment decision with respect to the acquisition of this Warrant and its underlying securities. Holder further has had an opportunity to ask questions and receive answers from the Company regarding the terms and conditions of the offering of this Warrant and its underlying securities and to obtain additional information (to the extent the Company possessed such information or could acquire it without unreasonable effort or expense) necessary to verify any information furnished to Holder or to which Holder has access.

4.3 Investment Experience . Holder understands that the purchase of this Warrant and its underlying securities involves substantial risk. Holder has experience as an investor in securities of companies in the development stage and acknowledges that Holder can bear the economic risk of such Holder’s investment in this Warrant and its underlying securities and has such knowledge and experience in financial or business matters that Holder is capable of evaluating the merits and risks of its investment in this Warrant and its underlying securities and/or has a preexisting personal or business relationship with the Company and certain of its officers, directors or controlling persons of a nature and duration that enables Holder to be aware of the character, business acumen and financial circumstances of such persons.

4.4 Accredited Investor Status . Holder is an “accredited investor” within the meaning of Regulation D promulgated under the Act.

4.5 The Act . Holder understands that this Warrant and the Shares issuable upon exercise hereof have not been registered under the Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of the Holder’s investment intent as expressed herein. Holder understands that this Warrant and the Shares issued upon any exercise hereof must be held indefinitely unless subsequently registered under the Act and qualified

under applicable state securities laws, or unless exemption from such registration and qualification are otherwise available. Holder is aware of the provisions of Rule 144 promulgated under the Act.

4.6 No Voting Rights . Holder, as a Holder of this Warrant, will not have any voting rights until the exercise of this Warrant.

SECTION 5. MISCELLANEOUS .

5.1 Term and Automatic Conversion Upon Expiration .

(a) Term . Subject to the provisions of Section 1.6 above, this Warrant is exercisable in whole or in part at any time and from time to time on or before 6:00 PM, Pacific time, on the Expiration Date and shall be void thereafter.

(b) Automatic Cashless Exercise upon Expiration . In the event that, upon the Expiration Date, the fair market value of one Share (or other security issuable upon the exercise hereof) as determined in accordance with Section 1.3 above is greater than the Warrant Price in effect on such date, then this Warrant shall automatically be deemed on and as of such date to be exercised pursuant to Section 1.2 above as to all Shares (or such other securities) for which it shall not previously have been exercised, and the Company shall, within a reasonable time, deliver a certificate representing the Shares (or such other securities) issued upon such exercise to Holder.

5.2 Legends . The Shares (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) shall be imprinted with a legend in substantially the following form:

THE SHARES EVIDENCED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ ACT ”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN THAT CERTAIN WARRANT TO PURCHASE COMMON STOCK ISSUED BY THE ISSUER TO SILICON VALLEY BANK DATED SEPTEMBER 30, 2015, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER, SUCH OFFER, SALE, PLEDGE OR OTHER TRANSFER IS EXEMPT FROM SUCH REGISTRATION.

5.3 Compliance with Securities Laws on Transfer . This Warrant and the Shares issuable upon exercise of this Warrant (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) may not be transferred or assigned in whole or in part except in compliance with applicable federal and state securities laws by the transferor and the transferee (including, without limitation, the delivery of investment representation letters and legal opinions reasonably satisfactory to the Company, as reasonably requested by the Company). The Company shall not require Holder to provide an opinion of counsel if the transfer is to SVB Financial Group (Silicon Valley Bank’s parent company) or any other affiliate of Holder, provided that any such transferee is an “accredited investor” as defined in Regulation D promulgated under the Act. Additionally, the Company shall also not require an opinion of counsel if there is no material question as to the availability of Rule 144 promulgated under the Act.

5.4 Transfer Procedure . After receipt by Silicon Valley Bank of the executed Warrant, Silicon Valley Bank will transfer all of this Warrant to its parent company, SVB Financial

Group. By its acceptance of this Warrant, SVB Financial Group hereby makes to the Company each of the representations and warranties set forth in Section 4 hereof and agrees to be bound by all of the terms and conditions of this Warrant as if the original Holder hereof. Subject to the provisions of Section 5.3 and upon providing the Company with written notice, SVB Financial Group and any subsequent Holder may transfer all or part of this Warrant or the Shares issuable upon exercise of this Warrant (or the securities issuable directly or indirectly, upon conversion of the Shares, if any) to any transferee, provided, however, in connection with any such transfer, SVB Financial Group or any subsequent Holder will give the Company notice of the portion of the Warrant being transferred with the name, address and taxpayer identification number of the transferee and Holder will surrender this Warrant to the Company for reissuance to the transferee(s) (and Holder if applicable); and provided further, that any subsequent transferee other than SVB Financial Group shall agree in writing with the Company to be bound by all of the terms and conditions of this Warrant.

5.5 Notices . All notices and other communications hereunder from the Company to the Holder, or vice versa, shall be deemed delivered and effective (i) when given personally, (ii) on the third (3rd) Business Day after being mailed by first-class registered or certified mail, postage prepaid, (iii) upon actual receipt if given by facsimile or electronic mail and such receipt is confirmed in writing by the recipient, or (iv) on the first Business Day following delivery to a reliable overnight courier service, courier fee prepaid, in any case at such address as may have been furnished to the Company or Holder, as the case may be, in writing by the Company or such Holder from time to time in accordance with the provisions of this Section 5.5. All notices to Holder shall be addressed as follows until the Company receives notice of a change of address in connection with a transfer or otherwise:

SVB Financial Group

Attn: Treasury Department

3003 Tasman Drive, HC 215

Santa Clara, CA 95054

Telephone: (408) 654-7400

Facsimile: (408) 988-8317

Email address: derivatives@svb.com

Notice to the Company shall be addressed as follows until Holder receives notice of a change in address:

Ignyta, Inc.

Attn: Chief Financial Officer

11095 Flintkote Avenue, Suite D

San Diego, CA 92121

Telephone: (858) 255-5959

Facsimile: (858) 255-5960

Email: jc@ignyta.com

With a copy (which shall not constitute notice) to:

Latham & Watkins LLP

Attn: Cheston Larson

12670 High Bluff Drive

San Diego, CA 92130

Telephone: (858) 523-5435

Facsimile: (858) 523-5450

Email: cheston.larson@lw.com

5.6 Waiver . This Warrant and any term hereof may be changed, waived, discharged or terminated (either generally or in a particular instance and either retroactively or prospectively) only by an instrument in writing signed by the party against which enforcement of such change, waiver, discharge or termination is sought.

5.7 Attorney’s Fees . In the event of any dispute between the parties concerning the terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable attorneys’ fees.

5.8 Counterparts; Facsimile/Electronic Signatures . This Warrant may be executed in counterparts, all of which together shall constitute one and the same agreement. Any signature page delivered electronically or by facsimile shall be binding to the same extent as an original signature page with regards to any agreement subject to the terms hereof or any amendment thereto.

5.9 Governing Law . This Warrant shall be governed by and construed in accordance with the laws of the State of California, without giving effect to its principles regarding conflicts of law.

5.10 Headings . The headings in this Warrant are for purposes of reference only and shall not limit or otherwise affect the meaning of any provision of this Warrant.

5.11 Business Days . “ Business Day ” is any day that is not a Saturday, Sunday or a day on which Silicon Valley Bank is closed.

[Remainder of page left blank intentionally]

[Signature page follows]

IN WITNESS WHEREOF, the parties have caused this Warrant to Purchase Common Stock to be executed by their duly authorized representatives effective as of the Issue Date written above.


“COMPANY”

IGNYTA, INC.

By:		/s/ Jacob Chacko

Name:		Jacob Chacko
		(Print)
Title:		CFO

“HOLDER”

SILICON VALLEY BANK

By:		/s/ Anthony Flores

Name:		Anthony Flores
		(Print)
Title:		Vice President

APPENDIX 1

NOTICE OF EXERCISE

1. The undersigned Holder hereby exercises its right purchase shares of the Common Stock of IGNYTA, INC. (the “ Company ”) in accordance with the attached Warrant To Purchase Common Stock, and tenders payment of the aggregate Warrant Price for such shares as follows:

check in the amount of $ payable to order of the Company enclosed herewith

Wire transfer of immediately available funds to the Company’s account

Cashless Exercise pursuant to Section 1.2 of the Warrant

Other [Describe]

2. Please issue a certificate or certificates representing the Shares in the name specified below:



		Holder’s Name




		(Address)

3. By its execution below and for the benefit of the Company, Holder hereby restates each of the representations and warranties in Section 4 of the Warrant to Purchase Common Stock as of the date hereof.


HOLDER:



By:

Name:

Title:

(Date):

Appendix 1

Exhibit 4.2

WARRANT TO PURCHASE COMMON STOCK

Company: Ignyta, Inc., a Delaware corporation

Number of Shares of Common Stock: 7,716

Warrant Price: $8.78

Issue Date: September 30, 2015

Expiration Date: September 30, 2022 See also Section 5.1(b).


Credit Facility:		This Warrant to Purchase Common Stock (“ Warrant ”) is issued in connection with that certain Second Amended and Restated Loan and Security Agreement dated as of September 30, 2014 between Silicon Valley Bank and the Company (the “ Loan Agreement ”).

THIS WARRANT CERTIFIES THAT, for good and valuable consideration, LIFE SCIENCE LOANS, LLC (together with any successor or permitted assignee or transferee of this Warrant or of any shares issued upon exercise hereof, “ Holder ”) is entitled to purchase the number of fully paid and non-assessable shares (the “ Shares ”) of the above-stated common stock (the “ Common Stock ”) of the above-named company (the “ Company ”) at the above-stated Warrant Price, all as set forth above and as adjusted pursuant to Section 2 of this Warrant, subject to the provisions and upon the terms and conditions set forth in this Warrant.

SECTION 1. EXERCISE .

X = Y(A-B)/A

where:

X =

the number of Shares to be issued to the Holder;

Y =

the number of Shares with respect to which this Warrant is being exercised (inclusive of the Shares surrendered to the Company in payment of the aggregate Warrant Price);

A =

the Fair Market Value (as determined pursuant to Section 1.3 below) of one Share; and

B =

the Warrant Price.

1.6 Treatment of Warrant Upon Acquisition of Company .

SECTION 2. ADJUSTMENTS TO THE SHARES AND WARRANT PRICE .

2.3 Intentionally Omitted.

2.4 Intentionally Omitted.

SECTION 3. REPRESENTATIONS AND COVENANTS OF THE COMPANY .

3.2 Notice of Certain Events . If the Company proposes at any time to:

(a) declare any dividend or distribution upon the outstanding shares of the Company’s stock, whether in cash, property, stock, or other securities and whether or not a regular cash dividend;

(c) effect any reclassification, exchange, combination, substitution, reorganization or recapitalization of the outstanding shares of the Common Stock; or

(d) effect an Acquisition or to liquidate, dissolve or wind up.

Company will also provide information requested by Holder that is reasonably necessary to enable Holder to comply with Holder’s accounting or reporting requirements.

SECTION 4. REPRESENTATIONS, WARRANTIES OF THE HOLDER .

The Holder represents and warrants to the Company as follows:

4.4 Accredited Investor Status . Holder is an “accredited investor” within the meaning of Regulation D promulgated under the Act.

under applicable state securities laws, or unless exemption from such registration and qualification are otherwise available. Holder is aware of the provisions of Rule 144 promulgated under the Act.

4.6 No Voting Rights . Holder, as a Holder of this Warrant, will not have any voting rights until the exercise of this Warrant.

SECTION 5. MISCELLANEOUS .

5.1 Term and Automatic Conversion Upon Expiration .

5.2 Legends . The Shares (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) shall be imprinted with a legend in substantially the following form:

THE SHARES EVIDENCED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ ACT ”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN THAT CERTAIN WARRANT TO PURCHASE COMMON STOCK ISSUED BY THE ISSUER TO LIFE SCIENCE LOANS, LLC DATED SEPTEMBER 30, 2015, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER, SUCH OFFER, SALE, PLEDGE OR OTHER TRANSFER IS EXEMPT FROM SUCH REGISTRATION.

5.3 Compliance with Securities Laws on Transfer . This Warrant and the Shares issuable upon exercise of this Warrant (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) may not be transferred or assigned in whole or in part except in compliance with applicable federal and state securities laws by the transferor and the transferee (including, without limitation, the delivery of investment representation letters and legal opinions reasonably satisfactory to the Company, as reasonably requested by the Company). Additionally, the Company shall also not require an opinion of counsel if there is no material question as to the availability of Rule 144 promulgated under the Act.

5.4 Transfer Procedure . Subject to the provisions of Section 5.3 and upon providing the Company with written notice, Life Science Loans, LLC and any subsequent Holder may transfer all or part of this Warrant or the Shares issuable upon exercise of this Warrant (or the securities issuable directly or indirectly, upon conversion of the Shares, if any) to any transferee, provided, however, in connection with any such transfer, Life Science Loans, LLC or any subsequent Holder will give the

Company notice of the portion of the Warrant being transferred with the name, address and taxpayer identification number of the transferee and Holder will surrender this Warrant to the Company for reissuance to the transferee(s) (and Holder if applicable); and provided further, that any subsequent transferee other than SVB Financial Group shall agree in writing with the Company to be bound by all of the terms and conditions of this Warrant.

Life Science Loans, LLC

c/o Chief Financial Officer

Attn: Trent Dawson

3720 Carillon Point

Kirkland, WA 98033

Telephone: 425-952-3951

Email address: tdawson@wrg.vc

Notice to the Company shall be addressed as follows until Holder receives notice of a change in address:

Ignyta, Inc.

Attn: Chief Financial Officer

11095 Flintkote Avenue, Suite D

San Diego, CA 92121

Telephone: (858) 255-5959

Facsimile: (858) 255-5960

Email: jc@ignyta.com

With a copy (which shall not constitute notice) to:

Latham & Watkins LLP

Attn: Cheston Larson

12670 High Bluff Drive

San Diego, CA 92130

Telephone: (858) 523-5435

Facsimile: (858) 523-5450

Email: cheston.larson@lw.com

5.9 Governing Law . This Warrant shall be governed by and construed in accordance with the laws of the State of California, without giving effect to its principles regarding conflicts of law.

5.10 Headings . The headings in this Warrant are for purposes of reference only and shall not limit or otherwise affect the meaning of any provision of this Warrant.

5.11 Business Days . “ Business Day ” is any day that is not a Saturday, Sunday or a day on which Silicon Valley Bank is closed.

[Remainder of page left blank intentionally]

[Signature page follows]

IN WITNESS WHEREOF, the parties have caused this Warrant to Purchase Common Stock to be executed by their duly authorized representatives effective as of the Issue Date written above.


“COMPANY”

IGNYTA, INC.

By:		/s/ Jacob Chacko

Name:		Jacob Chacko
		(Print)
Title:		CFO

“HOLDER”

LIFE SCIENCE LOANS, LLC

By:		/s/ Trent Dawson

Name:		Trent Dawson
		(Print)
Title:		CFO

APPENDIX 1

NOTICE OF EXERCISE

check in the amount of $ payable to order of the Company enclosed herewith

Wire transfer of immediately available funds to the Company’s account

Cashless Exercise pursuant to Section 1.2 of the Warrant

Other [Describe]

2. Please issue a certificate or certificates representing the Shares in the name specified below:



		Holder’s Name




		(Address)


HOLDER:



By:

Name:

Title:

(Date):

Appendix 1

Entrectinib (RXDX-101), an oral pan-Trk, ROS1, and ALK

inhibitor in patients with advanced solid tumors

harboring gene rearrangements

Salvatore

Siena,

Alexander

Drilon,

Sai-Hong

Ou,

Anna

Farago,

Manish Patel,

Todd M. Bauer,

David Hong,

Stephen V. Liu,

JeeYun Lee,

Rupal Patel,

Lisa Schechet,

David Luo,

Edna Chow Maneval,

Pratik S. Multani, and

Filippo G. De Braud

Niguarda Cancer Center, Ospedale Niguarda Ca' Granda, and Università degli Studi di Milano, Milan, Italy;

Memorial

Sloan

Kettering

Cancer

Center,

New

York,

NY;

Chao

Family

Comprehensive

Cancer

Center,

University

California,

Irvine,

CA;

Massachusetts

General

Hospital,

Boston,

MA;

Sarah

Cannon

Research

Institute/Florida

Cancer

Specialists,

Sarasota,

FL;

Sarah

Cannon

Research

Institute/Tennessee

Oncology,

PLLC,

Nashville,

TN;

The

University

Texas

Anderson

Cancer

Center,

Houston,

TX;

Georgetown

Lombardi

Comprehensive

Cancer

Center,

Washington,

D.C.;

Samsung

Medical

Center,

Seoul,

Korea;

Ignyta,

Inc.,

San

Diego,

CA;

Fondazione

IRCCS

Istituto

Nazionale

dei

Tumori,

Milan,

Italy

27 September 2015

Exhibit 99.1

Disclosures

Advisory board member for Amgen, Bayer, Eli Lilly,

Ignyta, Merck, Merrimack, Merus, Novartis, Roche, and

Sanofi

Entrectinib (RXDX-101)

A First-in-Class Trk Inhibitor

In vitro, entrectinib demonstrates

inhibition of targets and

downstream effectors in the PLC

MAPK and PI3K/AKT pathways

Target

TrkA

TrkB

TrkC

ROS1

ALK

IC50* (nM)

1.7

0.1

0.2

1.6

* Biochemical kinase assay

Potent, selective, orally available ATP-competitive inhibitor of 5 oncogenic drivers

In vivo, entrectinib demonstrates complete

tumor growth inhibition and regression in

multiple xenograft models

Granted FDA orphan drug designation for NSCLC,

CRC and neuroblastoma, and rare pediatric disease

designation for neuroblastoma

Gene Rearrangements Targeted by Entrectinib

Are Present in a Large Number of Tumors

NTRK1

NTRK2

NTRK3

ROS1

ALK

NSCLC

1-3%

<1%

1-2%

3-7%

CRC

1-2%

Salivary gland

–

mammary analog

secretory carcinoma [MASC]

90-100%

Salivary gland –

NOS

Sarcomas (soft tissue fibrosarcoma,

neurosarcoma, uterus sarcoma,

small intestine sarcoma, breast

sarcoma)

1-9%

2-11%

2-3%

1-5%

Astrocytoma

Glioblastoma

1-3%

Melanoma

Spitz

16%

17%

10%

Cholangiocarcinoma

Papillary thyroid carcinoma

5-13%

2-14%

Breast

–

secretory carcinoma

92%

Breast

–

NOS

NOS: not otherwise specified

Entrectinib Clinical Program

STARTRK-1

Phase 1/2 dose escalation study of

daily continuous

dosing schedule in

patients with NTRK1/2/3 , ROS1

or ALK

molecular alterations in US, EU and

Asia

Phase 1 initiated in July 2014

RP2D

Recommended

Phase

Dose

ALKA-372-001

Phase 1 dose escalation study of

intermittent and continuous

dosing

schedule in patients with TrkA, ROS1,

or ALK alterations in Italy

First-in-human study initiated by

Nerviano Medical Sciences in

October 2012

Ignyta assumed responsibility in

November 2013

49 patients enrolled

43 patients enrolled

•

Total experience: 92 patients enrolled as of 15 August 2015

•

RP2D*: 600 mg/day on a fed continuous daily dosing regimen

Patient Disposition

Patients, n (%)

ALKA-372-001

Study

STARTRK-1

Study

TOTAL

Enrolled

Ongoing

16 (33)

15 (35)

31 (34)

Discontinued

33 (67)

28 (65)

61 (66)

Disease Progression

30 (61)

19 (44)

49 (53)

Adverse Event

1 (2)

2 (5)

3 (3)

Patient withdrew consent

4 (9)

4 (4)

Other (e.g., Investigator’s decision)

2 (4)

3 (7)

5 (5)

Baseline Characteristics

ALKA-372-001

Study

(n=49)

STARTRK-1

Study

(n=43)

TOTAL

(n=92)

Age, years,

median (range)

53 (22-77)

55 (18-80)

54 (18-80)

Sex,

male/female (%)

47/53

ECOG performance

status, n

(%)

26 (53)

15 (35)

41 (45)

22 (45)

26 (60)

48 (52)

1 (2)

2 (5)

3 (3)

Tumor type,

n (%)

NSCLC

32 (65)

20 (47)

52 (57)

Gastrointestinal tract (CRC)

5 (10)

5 (12)

10 (11)

Gastrointestinal tract (cholangiocarcinoma, liver,

pancreas)

3 (6)

4 (9)

7 (8)

Neoplasms of the CNS (astrocytoma, GBM)

3 (6)

1 (2)

4 (4)

Head and neck

1 (2)

2 (5)

3 (3)

Breast

1 (2)

2 (5)

3 (3)

Other (e.g., endometrial,

leiomyosarcoma,

melanoma, neuroblastoma, ovarian, prostate, RCC,

squamous

cell carcinoma)

4 (8)

(21)

13 (14)

Treatment-Related Adverse Events

(>10% incidence; grades according to NCI CTCAE 4.0)

Adverse Event Term

ALKA-372-001

Study

(n=49)

STARTRK-1

Study

(n=43)

TOTAL

(n=92)

G1-G2

Fatigue/Asthenia

16 (33)

1 (2)

19 (44)

3 (7)

35 (38)

4 (4)

Dysgeusia

16 (33)

(47)

36 (39)

Paresthesia

20 (41)

(26)

31 (34)

Nausea

17 (35)

(12)

22 (24)

Myalgia

16 (33)

(12)

21 (23)

Diarrhea

10 (21)

7 (16)

1 (2)

17 (18)

1 (1)

Dizziness

6 (12)

(19)

14 (15)

Cognitive

Disorder

3 (6)

(12)

2 (5)

8 (9)

2 (2)

Vomiting

9 (18)

9 (10)

•

There were no Grade 4 treatment-related events

•

All adverse events reversible with dose modifications

Treatment-Related

Serious Adverse Events

No SAEs were reported on Study ALKA-372-001

Three SAEs were reported on Study STARTRK-1

•

All resolved with study drug interruption and/or dose modifications

•

At 800 mg/day (dose exceeded the maximum tolerated dose):

Grade 3 cognitive impairment

Grade 3 eosinophilic myocarditis

•

At 600 mg/day (RP2D):

Grade 2 intolerable fatigue and fall

Clinical response to entrectinib in a 46 year-old

male patient with NTRK1 - rearranged NSCLC

Images courtesy of A. Shaw, MD, PhD and A. Farago, MD, PhD (MGH)

Day 1 Baseline

Day 26: -

47% response

Day 155: -

77% response

Baseline

Day 26

Day 155

Complete response of all brain metastases

Images courtesy of A. Shaw, MD, PhD and A. Farago, MD, PhD (MGH)

Antitumor Activity in ALK and ROS1 Inhibitor-Naïve Patients

with NTRK1/2/3 , ROS1 , or ALK

Gene Rearrangements

Overall Response Rate: 13/18 (72%)

•

NTRK

Patients: 3/4 (75%)

•

ROS1

Patients: 6/8 (75%)

•

ALK

Patients: 4/6 (67%)

3 patients have stable disease after 8 weeks on study

Disease Control Rate: 16/18 (89%)

Antitumor Activity in ALK and ROS1 Inhibitor-Naïve Patients

with

NTRK1/2/3 ,

ROS1 ,

ALK

Gene

Rearrangements

Treatment Duration

( arrows represent duration of response )

Conclusions

Entrectinib was well tolerated in patients with relapsed or refractory

metastatic cancers harboring NTRK1/2/3 , ROS1 , or ALK

molecular

alterations

To date, 9 patients have been treated at or above the RP2D beyond

6 months and 1 patient beyond 1 year

Among patients with NTRK1/2/3 , ROS1 , or ALK gene rearrangements

who were ALK-inhibitor or ROS1-inhibitor-naïve, 13/18 (72%) patients

treated at or above the RP2D exhibited objective responses as early as

4 weeks of treatment with durable responses for up to 21 months

Entrectinib has demonstrated objective tumor response also in the CNS

Based on these promising data, STARTRK-2, a global potentially

registration-enabling Phase 2 basket study, will investigate the activity

of entrectinib in multiple tumor histologies

STARTRK-2 Basket Study of Entrectinib

Acknowledgements

Thank you to all the patients and their

families who participated in these studies