EX-4.4



 Exhibit 4.4 

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 THE OPINION OF LEGAL COUNSEL IN FORM AND
SUBSTANCE SATISFACTORY TO THE COMPANY, SUCH OFFER, SALE, PLEDGE OR OTHER TRANSFER IS EXEMPT FROM SUCH REGISTRATION. 
 WARRANT TO PURCHASE
STOCK 
  

			
	Company:	  	Ignyta, Inc., a Delaware corporation
	Number of Shares:	  	5,882
	Type/Series of Stock:	  	Common Stock (“Common Stock”)
	Warrant Price:	  	$5.10 per share
	Issue Date:	  	June 30, 2016
	Expiration Date:	  	June 30, 2023 See also Section 5.1(b).
	Credit Facility:	  	This Warrant to Purchase Stock (“Warrant”) is issued in connection with that certain Loan and Security Agreement of even date herewith among Silicon Valley Bank, as Collateral Agent, Oxford Finance LLC, as
Lender, the Lenders from time to time party thereto, including Silicon Valley Bank and the Company (as modified, amended and/or restated from time to time, the “Loan Agreement”).

 THIS WARRANT CERTIFIES THAT, for good and valuable consideration, OXFORD FINANCE LLC
(“Oxford” and, 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 Common Stock as stated above 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. 

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);


  
 1 









			
	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, lease, 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, if such Company stockholders beneficially own a
majority of the outstanding voting power of the surviving or successor entity as of immediately after such merger, consolidation or reorganization, such surviving or successor entity is not the Company); 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”), either (i) Holder shall exercise this Warrant pursuant to Section 1.1
and/or 1.2 and such exercise will be deemed effective immediately prior to and contingent upon the consummation of such Acquisition or (ii) if Holder elects not to exercise the Warrant, this Warrant will expire immediately prior to the
consummation of such Acquisition. 
 (c) The Company shall provide Holder with written notice of its request relating to the Cash/Public
Acquisition (together with such reasonable information as Holder may reasonably require regarding the treatment of this Warrant in connection with such contemplated Cash/Public Acquisition giving rise to such notice), which is to be delivered to
Holder not less than seven (7) Business Days prior to the closing of the proposed Cash/Public Acquisition. In the event the Company does not provide such notice, then if, immediately prior to the Cash/Public Acquisition, the fair market value
of one Share (or other security issuable upon the exercise hereof) as determined in accordance with Section 1.3 above would be 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 promptly notify the Holder of the number of Shares (or such other
securities) issued upon such exercise to the 

  
 2 








 
Holder and Holder shall be deemed to have restated each of the representations and warranties in Section 4 of the Warrant as the date thereof. 

(d) 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. 

(e) 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 any 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. 

  
 3 








 2.6 Notice/Certificate as to Adjustments. Upon each adjustment of the Warrant Price, class
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 thereof at the same time and in the same manner as the Company notifies the holders of
the outstanding shares of the class thereof: 
 Reference is made to Section 1.6(c) whereby this Warrant will be deemed to be exercised pursuant to
Section 1.2 hereof if the Company does not give written notice to Holder of a Cash/Public Acquisition as required by the terms hereof. 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 securities 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 








 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; Automatic Cashless Exercise 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, Eastern 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. Each certificate evidencing Shares (and each certificate evidencing the securities issued upon conversion of any 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 STOCK ISSUED BY THE ISSUER TO
OXFORD FINANCE LLC DATED JUNE 30, 2016, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR, IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE SATISFACTORY TO THE ISSUER, SUCH OFFER,
SALE, PLEDGE OR OTHER TRANSFER IS EXEMPT FROM SUCH REGISTRATION. 

  
 5 








 5.3 Compliance with Securities Laws on Transfer. This Warrant and the Shares issued 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 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 Oxford of the executed Warrant, Oxford may transfer all or part of this Warrant to one or more of Oxford’s affiliates (each, an “Oxford Affiliate”), by execution of an Assignment
substantially in the form of Appendix 2. Subject to the provisions of Article 5.3 and upon providing the Company with written notice, Oxford, any such Oxford Affiliate 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 other transferee, provided, however, in connection with any such transfer, the Oxford Affiliate(s) 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). 
 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: 
 Oxford Finance LLC 

133 N. Fairfax Street 

Alexandria, VA 22314 
 Attn:
Legal Department 
 Telephone: (703) 519-4900 

Facsimile: (703) 519-5225 

Email: LegalDepartment@oxfordfinance.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 
 11111 Flintkote Avenue 

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 

  
 6 








 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 Attorneys’ 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] 

  
 7 








 IN WITNESS WHEREOF, the parties have caused this Warrant to Purchase 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”
	
	OXFORD FINANCE LLC
		
	By:	 	 /s/ Mark Davis

	Name:	 	Mark Davis
		 	(Print)
	Title:	 	Vice President – Finance, Secretary & Treasurer


  

[Signature Page to Warrant to Purchase Stock]  








 APPENDIX 1 

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

	 	 ̈	Check in the amount of $         payable to the 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 Stock as of the date hereof. 
  

			
	HOLDER:
	
	  

		
	By:	 	  

	Name:	 	  

	Title:	 	  

		
	Date:	 	  




  
 Appendix 1 








 APPENDIX 2 

ASSIGNMENT 
 For
value received, Oxford Finance LLC hereby sells, assigns and transfers unto 
  

					
	Name:	 	[OXFORD TRANSFEREE]	  	
			
	Address:	 	  
	  	
			
	Tax ID:	 	  
	  	

 that certain Warrant to Purchase Stock issued by IGNYTA, INC. (the “Company”), on
June 30, 2016 (the “Warrant”) together with all rights, title and interest therein. 
  

			
	OXFORD FINANCE LLC
		
	By:	 	  

	Name:	 	  

	Title:	 	  



 Date:
                                         
                    
 By its execution below, and for the
benefit of the Company, [OXFORD TRANSFEREE] makes each of the representations and warranties set forth in Article 4 of the Warrant and agrees to all other provisions of the Warrant as of the date hereof. 

 

			
	[OXFORD TRANSFEREE]
		
	By:	 	  

	Name:	 	  

	Title:	 	  




  
 Appendix 2