EX-4.1



 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: 18,925 

Warrant Price: $7.518 
 Issue Date:
September 30, 2014 
 Expiration Date: September 30, 2021 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. 

  
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 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. 

  
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 (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. 

  
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 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); 

  
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 (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. 

  
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 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, 2014, 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. 

  
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 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 

  
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 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, LP 

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] 

  
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 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:	 	Chief Financial Officer

  

									
	“HOLDER”
	
	SILICON VALLEY BANK
		
	By:	 	 /s/ R. Michael White

	Name:	 	 R. Michael White

		 	(Print)
	Title:	 	Managing Director


  
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 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