Document:

EX-10.1

 Exhibit 10.1 
  

 
 February 5, 2014 

Dr. Patrick O’Connor 
 3586 Torrey View Court 

San Diego, CA 92130 
 Dear Patrick: 

To confirm our discussion, we understand that you have decided to resign your employment with Ignyta, Inc. and each of its subsidiaries
(collectively, the “Company” or “Ignyta”). As a result of this decision, your last day of employment with the Company will be February 5, 2014 (the “Separation Date”). We would also like to offer you the separation
package described below. 
 On your last day of employment, you will be paid all outstanding salary amounts and any accrued, but unused,
vacation time. You also will be eligible to convert your health insurance coverage under COBRA, and will receive information from our plan administrator describing this conversion election. If you seek reimbursement of any business expenses, your
final expense reimbursement statement must be submitted within two weeks after the Separation Date, along with receipts or other supporting documentation. The Company will reimburse valid business expenses in accordance with its standard expense
reimbursement policies. 
 As you know, you currently hold the following two outstanding equity awards: (i) 500,000 shares of
restricted common stock (as adjusted pursuant to a reverse stock split at a ratio of three-to-one) under the Restricted Stock Purchase Agreement originally entered into between you and Actagene Oncology, Inc. in February 2013, as amended by you and
Ignyta Operating, Inc. in connection with Ignyta Operating, Inc.’s acquisition of Actagene Oncology, Inc., as further amended in September 2013 to suspend the vesting of such shares, and as further amended by you and the Company in October 2013
in connection with the Company’s reverse merger transaction with Ignyta Operating, Inc. (the “Restricted Stock”, and the Restricted Stock Purchase Agreement, as amended, the “RSPA”)); and (ii) an incentive stock option
granted on August 7, 2013 to purchase 20,000 shares of Ignyta Operating, Inc.’s common stock (as adjusted pursuant to a reverse stock split at a ratio of three-to-one) and the Stock Option Award Agreement entered into by you and Ignyta
Operating, Inc. in connection with such grant, which option and award agreement were assumed by the Company in October 2013 in connection with the Company’s reverse merger transaction with Ignyta Operating, Inc. and are subject to the terms and
conditions of the Company’s 2011 Amended and Restated Stock Incentive Plan (the “Option”). Pursuant to the terms and conditions applicable to the Restricted Stock and Option, both equity awards are currently unvested in their
entirety. Although it is under no legal 

  
 1 

 
obligation to do so, the Company will provide you with accelerated vesting with respect to 100,000 shares of the Restricted Stock (the “Accelerated Shares”), in exchange for the general
release of claims and other agreements contained in this letter agreement (the “Agreement”). The Accelerated Shares shall be deemed vested as of the date this Agreement becomes effective (i.e., the 8th day after you have signed this Agreement, provided that the Agreement has not been revoked by either you or the Company before that date). You hereby acknowledge and agree that: (i) except with
respect to the Accelerated Shares, you have not and will not vest in any shares of Restricted Stock and the remaining 400,000 shares of Restricted Stock will continue to be subject to the Repurchase Option (as defined in the RSPA); and (ii) you
have not and will not vest in any portion of the Option, the Option shall terminate immediately upon your Separation Date and you shall have no further rights or interest in the Option. All shares of Restricted Stock, including the Accelerated
Shares, shall continue to be subject to the terms and conditions set forth in the RSPA, except that the Accelerated Shares shall not be subject to the Repurchase Option. This Agreement hereby serves as notice to you of the Company’s decision to
exercise the Repurchase Option with respect to the 400,000 shares of Restricted Stock and, in accordance with the RSPA, the Company is hereby delivering a check in the amount of the Purchase Price (as defined in the RSPA, as amended) multiplied by
the number of shares of Restricted Stock repurchased hereunder. If this Agreement does not become effective, nothing herein shall preclude the Company from exercising its Repurchase Option with respect to the shares intended to be Accelerated
Shares. 
 In exchange for the separation benefits described above, you completely release the Company, its affiliated, related, parent or
subsidiary entities, and its and their present and former directors, officers, and employees (the “Released Parties”) from any and all claims of any kind, known and unknown, which you may now have or have ever had against them. This
release includes all claims arising from your employment with the Company and its termination, including claims under the California Fair Employment and Housing Act, Title VII of the Civil Rights Act of 1964, the Age Discrimination in Employment Act
(“ADEA”), or any other claims for violation of any federal, state, or municipal statutes, and any and all claims for attorneys’ fees and costs.1 You agree not to file, cause to be
filed, or otherwise pursue any claims released by this paragraph. Notwithstanding the foregoing, you acknowledge and understand that you are not waiving and are not being required to waive any right that cannot be waived by law, including the right
to file a charge or participate in an administrative investigation or proceeding; provided, however, that you hereby disclaim and waive any right to share or participate in any monetary award resulting from the prosecution of such charge or
investigation. 
 You acknowledge that the payments described above exceed the amount to which you otherwise are entitled. You understand
and agree that you will maintain this Agreement in strict confidence, and that you shall not disclose any of its terms to another person, except legal counsel, unless required by law. You and the Company hereby agree that any public disclosure
regarding 
  

	1 	Because this release specifically covers known and unknown claims, you are waiving your rights under Section 1542 of the California Civil Code or any comparable law of any other jurisdiction. Section 1542
states: “A general release does not extend to claims which the creditor does not know or suspect to exist in his or her favor at the time of executing the release, which if known by him or her must have materially affected his or her settlement
with the debtor.” 

  
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the circumstances of your separation from employment with the Company shall be made only by the Company and shall be substantially consistent with the following: “Dr. Patrick O’Connor
has resigned as Chief Scientific Officer and SVP, Head of Research of the Company as of February 5, 2014, ending his previously announced medical leave of absence, and has elected to focus on his health.” Except as required by law or court
order (including without limitation any requirement to publicly file this Agreement or a description of the material terms hereof with the SEC), neither you nor the Company shall make any additional or inconsistent public statements regarding your
separation from employment. 
 Please return all the Company materials in your possession, including company credit cards,
confidential/restricted documentation, computer equipment, keys, cell phone etc., by the Separation Date. Also, remember that even after your employment with the Company ends, you must comply with your continuing obligations under the Employee
Proprietary Information and Inventions Assignment Agreement (the “Proprietary Information Agreement”), including but not limited to such obligations relating to confidentiality and use of the Company’s confidential information. 

You and the Company further agree that any and all disputes arising out of the terms, interpretation, application, or alleged breach of this
Agreement (“Arbitrable Claims”) shall be subject to binding arbitration, which shall be conducted in San Diego County, California in accordance with the Commercial Arbitration Rules of the American Arbitration Association, as amended.
Either party may bring an action in court to compel arbitration under this Agreement or to enforce an arbitration award. Otherwise, neither party shall initiate or prosecute any lawsuit or administrative action in any way related to any Arbitrable
Claim. Notwithstanding the foregoing, either party shall have the right to obtain provisional remedies or interim relief from a court of competent jurisdiction for any claim or controversy arising out of or related to the Company’s confidential
and proprietary information or violations of the Proprietary Information Agreement. The costs of the arbitrator shall be shared equally between the parties, but the prevailing party shall be entitled to recover its reasonable attorneys’ fees
and costs. 
 You acknowledge that you have twenty-one (21) days to consider this Agreement (but may sign it at any time beforehand if
you so desire), and that you can consult an attorney in doing so. You also acknowledge that you can revoke this Agreement within seven (7) days of signing it by sending a certified letter to that effect at the following address: 

Jonathan Lim 
 Ignyta, Inc. 

11095 Flintkote Avenue 
 Suite D

 San Diego, CA 92121 
 You understand and
agree that this Agreement shall not become effective or enforceable and no payments or benefits will be provided until the seven (7) day revocation period has expired. 

This Agreement contains all of our agreements and understandings and fully supersedes any prior agreements or understandings that we may have
had regarding your employment with the Company or its termination, except for the Proprietary Information Agreement. This Agreement 

  
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shall be governed by California law and may be amended only in a written document signed by you and Jonathan Lim, Chief Executive Officer. If any term in this Agreement is unenforceable, the
remainder of the Agreement will remain enforceable. 
 If you wish to accept the terms of this Agreement, please sign below and return a
copy of this Agreement to me by February 26, 2014. (You may also sign this Agreement at any time prior to such date, if you prefer.) 

  
 4 

 If you have any questions, please feel free to call me. We appreciate your service to Ignyta,
Inc. and wish you all the best. 
  

	
	Very truly yours,
	
	/s/ Jonathan Lim
	 Jonathan Lim
 Chief Executive Officer

Ignyta, Inc.

  

					
	AGREED AND ACCEPTED:	  	
			
	Dated:	 	January 31, 2014	  	 /s/ Patrick O’Connor

		 		  	     Patrick O’Connor

  
 5Exhibit 4.1

 EXHIBIT 4.1 

THIS SECURITY IS A GLOBAL SECURITY WITHIN THE MEANING OF THE INDENTURE HEREINAFTER REFERRED TO AND IS REGISTERED IN THE NAME OF A DEPOSITARY
OR A NOMINEE THEREOF. THIS SECURITY MAY NOT BE TRANSFERRED TO, OR REGISTERED OR EXCHANGED FOR SECURITIES REGISTERED IN THE NAME OF, ANY PERSON OTHER THAN THE DEPOSITARY OR A NOMINEE THEREOF, AND NO SUCH TRANSFER MAY BE REGISTERED, EXCEPT IN THE
LIMITED CIRCUMSTANCES DESCRIBED IN THE INDENTURE. EVERY SECURITY AUTHENTICATED AND DELIVERED UPON REGISTRATION OF TRANSFER OF, OR IN EXCHANGE FOR, OR IN LIEU OF, THIS SECURITY WILL BE A GLOBAL SECURITY SUBJECT TO THE FOREGOING, EXCEPT IN SUCH
LIMITED CIRCUMSTANCES. 
 ORANGE 

2.750% Notes due 2019 
 CUSIP
No. 685218AA7 
 ISIN No. US685218AA79 
  

			
	No. R-[    ]	  	$[            ]

 Orange, a société anonyme duly organized and existing under the laws of France (formerly
France Telecom, hereinafter called the “Company,” which term includes any successor Person under the Indenture hereinafter referred to), for value received, hereby promises to pay to Cede & Co., or registered assigns, the
principal sum of [        ] dollars ($[        ]) on February 6, 2019, and to pay interest thereon from February 6, 2014 or from the most recent Interest
Payment Date to which interest has been paid or duly provided for, on February 6 and August 6 in each year, commencing on August 6, 2014, at the rate of 2.750% per annum, until the principal hereof is paid or made available for
payment. The interest so payable, and punctually paid or duly provided for, on any Interest Payment Date will, as provided in such Indenture, be paid to the Person in whose name this Security (or one or more Predecessor Securities) is registered at
the close of business on the Regular Record Date for such interest, which will be January 22 or July 22 (whether or not a Business Day), as the case may be, next preceding such Interest Payment Date. Any such interest not so punctually
paid or duly provided for will forthwith cease to be payable to the Holder on such Regular Record Date and may either be paid to the Person in whose name this Security (or one or more Predecessor Securities) is registered at the close of business on
a Special Record Date for the payment of such Defaulted Interest to be fixed by the Trustee, notice whereof will be given to Holders of Securities of this series not less than 10 calendar days prior to such Special Record Date, or be paid at any
time in any other lawful manner not inconsistent with the requirements of any securities exchange on which the Securities of this series may be listed, and upon such notice as may be required by such exchange, all as more fully provided in said
Indenture. 
 Payment of the principal of (and premium, if any) and any such interest on this Security will be made at the office of the
Trustee, in such coin or currency of the United States of America as at the time of payment is legal tender for payment of public and private debts provided, however, that at the option of the Company payment of interest may be made by
check mailed to the Depository or its nominee, which will distribute payments to beneficial holders in accordance with customary procedures. 

 REFERENCE IS HEREBY MADE TO THE FURTHER PROVISIONS SET FORTH ON THE REVERSE HEREOF. SUCH
PROVISIONS WILL FOR ALL PURPOSES HAVE THE SAME EFFECT AS THOUGH FULLY SET FORTH IN THIS PLACE. 
 This Security will not be valid or become
obligatory for any purpose until the certificate of authentication herein has been signed manually by the Trustee under the Indenture referred to on the reverse side hereof. 

IN WITNESS WHEREOF, this instrument has been duly executed in accordance with the Indenture. 

 

			
	ORANGE
		
	By:	 	  

	Name:	 	
	Title:	 	
		
	Dated:	 	February 6, 2014

 Trustee’s Certificate of Authentication 

This is one of the Securities of the series designated therein referred to in the within-mentioned Indenture. 

 

							
		 		 	 The Bank of New York Mellon,
 as
Trustee

				
	Dated: February 6, 2014	 		 	By:	 	  

		 		 		 	Authorized Signatory

 Reverse of Security 
  

 
 This Security is one of a duly
authorized issue of securities of the Company (herein called the “Securities”) and is to be issued outside of France in one or more series under an Indenture, dated as of January 13, 2012 as supplemented and amended by that certain
First Supplemental Indenture, dated as of January 30, 2014, (as so amended, the “Indenture”), between the Company and The Bank of New York Mellon, as Trustee (herein called the “Trustee,” which term includes any successor
trustee under the Indenture), to which Indenture and all indentures supplemental thereto reference is hereby made for a statement of the respective rights, limitations of rights, duties, and immunities thereunder of the Company, the Trustee, and the
Holders of the Securities and of the terms upon which the Securities are, and are to be, authenticated and delivered. Capitalized terms used but not defined herein shall have the respective meanings ascribed to them in the Indenture. This Security
is one of the series designated on the face hereof. 
 The Securities of this series are subject to redemption upon not less than 30
calendar days’ notice by mail: 
 (i) If the Securities are redeemed at the Company’s option, the redemption price shall be equal
to the greater of (a) 100% of the principal amount of the Securities to be redeemed, and (b) the sum of the present values of the remaining scheduled payments of principal and interest thereon (excluding interest accrued to the date of
redemption) discounted to the redemption date on a semi-annual basis (assuming a 360-day year consisting of twelve 30-day months) at a rate equal to the Treasury Rate plus 0.200% for the Securities to be
redeemed. The Company will also pay the Holder accrued interest on the principal amount of the Securities that are redeemed up to, but not including, the date of redemption. “Treasury Rate” means, with respect to any redemption date, the
rate per annum equal to the semi-annual equivalent yield to maturity or, if such equivalent is not available, the interpolated maturity (on a day count basis) of the Comparable Treasury Issue, assuming a price for the Comparable Treasury Issue
(expressed as a percentage of its principal amount) equal to the Comparable Treasury Price for such redemption date. “Comparable Treasury Issue” means the United States Treasury security or securities selected by an Independent Investment
Bank as having an actual or interpolated maturity comparable to the remaining term of the Securities to be redeemed that would be utilized, at the time of selection and in accordance with customary financial practice, in pricing new issues of
corporate debt securities of a comparable maturity to the remaining term of such Securities. “Comparable Treasury Price” means, with respect to any redemption date (1) the average of the Reference Treasury Dealer Quotations for such
redemption date, after excluding the highest and the lowest such Reference Treasury Dealer Quotations for such redemption date, or (2) if the Trustee obtains fewer than four such Reference Treasury Dealer Quotations, the average of all such
quotations. “Independent Investment Bank” means one of the Reference Treasury Dealers appointed by the Company. “Reference Treasury Dealer” means each of Deutsche Bank Securities Inc., J.P. Morgan Securities LLC, Merrill Lynch,
Pierce, Fenner & Smith Incorporated, RBS Securities Inc. or their affiliates which are primary U.S. government securities dealers, and their respective successors, and one other leading primary U.S. government securities dealer in New York
City (each, a “Primary Treasury 

 
Dealer”) designated by the Company. If any of the foregoing shall cease to be a Primary Treasury Dealer, the Company will substitute another Primary Treasury Dealer. “Reference Treasury
Dealer Quotation” means with respect to each Reference Treasury Dealer and any redemption date, the average, as determined by the Trustee in consultation with the Company, of the bid and ask prices for the Comparable Treasury Issue (expressed
in each case as a percentage of its principal amount) quoted in writing or by email to the Trustee by such Reference Treasury Dealer at 3:30 p.m. local time in The City of New York, on the third business day preceding such redemption date. 

(ii) In addition, this Security is redeemable by the Company as permitted under Section 3.02 (“Optional Tax Redemption”) of the
Indenture. 
 In the event of redemption of this Security in part only, a new Security or Securities of this series and of like tenor for
the unredeemed portion hereof will be issued in the name of the Holder hereof upon the cancellation hereof. 
 The Indenture contains
provisions for defeasance at any time of (a) the entire indebtedness evidenced by this Security or (b) certain covenants and Events of Default with respect to this Security, in each case upon compliance with certain conditions set forth in
the Indenture. 
 If an Event of Default with respect to Securities of this series shall occur and be continuing, the principal of the
Securities of this series may be declared due and payable in the manner and with the effect provided in the Indenture. 
 The Indenture
permits, with certain exceptions as therein provided, the amendment thereof and the modification of the rights and obligations of the Company and the rights of the Holders of the Securities of each series to be affected under the Indenture at any
time by the Company and the Trustee with the consent of the Holders of a majority in principal amount of the Securities at the time Outstanding of each series to be affected. The Indenture also contains provisions permitting the Holders of specified
percentages in principal amount of the Securities of each series at the time Outstanding, on behalf of the Holders of all Securities of such series, to waive compliance by the Company with certain provisions of the Indenture and certain past
defaults under the Indenture and their consequences. Any such consent or waiver by the Holder of this Security will be conclusive and binding upon such Holder and upon all future Holders of this Security and of any Security issued upon the
registration of transfer hereof or in exchange herefor or in lieu hereof, whether or not notation of such consent or waiver is made upon this Security. 

As provided in and subject to the provisions of the Indenture, the Holder of this Security will not have the right to institute any proceeding
with respect to the Indenture or for the appointment of a receiver or trustee or for any other remedy thereunder, unless such Holder shall have previously given the Trustee written notice of a continuing Event of Default with respect to the
Securities of this series, the Holders of not less than 25% in principal amount of the Securities of this series at the time Outstanding shall have made written request to the Trustee to institute proceedings in respect of such Event of Default as
Trustee and offered the Trustee indemnity reasonably satisfactory to it, and the Trustee shall not have received from the Holders of a majority in principal amount 

 
of Securities of this series at the time Outstanding a direction inconsistent with such request and shall have failed to institute such proceeding for 60 calendar days after receipt of such
notice, request, and offer of indemnity. The foregoing will apply to any suit instituted by the Holder of this Security for the enforcement of any payment of principal hereof or any premium or interest hereon on or after the respective due dates
expressed herein. 
 No reference herein to the Indenture and no provision of this Security or of the Indenture will alter or impair the
obligation of the Company, which is absolute and unconditional, to pay the principal of and any premium and interest on this Security at the times, place, and rate, and in the coin or currency, herein prescribed. 

As provided in the Indenture and subject to certain limitations therein set forth, the transfer of this Security is registerable in the
Security Register, upon surrender of this Security for registration of transfer at the office or agency of the Company in any place where the principal of and any premium and interest on this Security are payable, duly endorsed by, or accompanied by
a written instrument of transfer in form satisfactory to the Company and the Security Registrar duly executed by, the Holder hereof or his attorney duly authorized in writing, and thereupon one or more new Securities of this series and of like
tenor, of authorized denominations and for the same aggregate principal amount, will be issued to the designated transferee or transferees. 

The Securities of this series are issuable only in registered form without coupons in minimum denominations of $2,000 and integral multiples
of $1,000 in excess thereof. As provided in the Indenture and subject to certain limitations therein set forth, Securities of this series are exchangeable for a like aggregate principal amount of Securities of this series and of like tenor of a
different authorized denomination, as requested by the Holder surrendering the same. 
 No service charge will be made for any such
registration of transfer or exchange, but the Company may require payment of a sum sufficient to cover any tax or other governmental charge payable in connection therewith. 

Prior to due presentment of this Security for registration of transfer, the Company, the Trustee, and any agent of the Company or the Trustee
may treat the Person in whose name this Security is registered as the owner hereof for all purposes (subject to Section 2.10 of the Indenture), whether or not this Security shall be overdue, and neither the Company, the Trustee, nor any such
agent will be affected by notice to the contrary. 
 The Indenture provides that the Company, at the Company’s option, (a) will be
discharged from any and all obligations in respect of the Securities (except for certain obligations to register the transfer or exchange of Securities, replace stolen, lost or mutilated Securities, maintain paying agencies and hold moneys for
payment in trust and certain other obligations in respect of the Trustee, the Paying Agent, Authenticating Agent and Securities Registrar) or (b) need not comply with certain covenants of the Indenture, in each case if the Company deposits, in
trust, with the Trustee money or U.S. Government Obligations which, through the payment of interest thereon and principal thereof in accordance with their terms, will provide money, in an amount sufficient to pay all the principal of, and premium,
if any, and interest on, the Securities on the dates such payments are due in accordance with the terms of such Securities, and certain other conditions are satisfied. 

 All terms used in this Security that are defined in the Indenture will have the respective
meanings assigned to them in the Indenture. 
 This Security shall be governed by, and construed in accordance with, the laws of the State
of New York, without regard to conflicts of laws principles thereof. 

 SCHEDULE OF INCREASES OR DECREASES IN GLOBAL SECURITY 

 

									
	 The following increases or decreases in this Global Security have been made 

	Date of
Exchange	 	Amount of decrease
in principal amount
of this Global
Security	 	Amount of increase
in principal amount
of this Global
Security	 	Principal amount of
this Global Security
following such
increase or decrease	 	Signature of
authorized signatory
of Trustee or
custodian

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