Document:

EX-10.11

 Exhibit 10.11 
  

 
  

 
 July 18, 2011 

Han Cao 
 2001 Hamilton St,
#2009 
 Philadelphia, PA 19104 

Dear Han: 
 We
are pleased to confirm the terms of your employment with BioNanomatrix, Inc. (the “Company”) as our Chief Scientific Officer. The following terms apply and will constitute your employment agreement with the Company (the
“Agreement”). 
  

	 	 1.
	 EMPLOYMENT. 

1.1 Term. The term of this Agreement shall begin on the date hereof (the “Commencement Date”)
and shall continue until the termination of your employment with the Company in accordance with Section 4 herein. 

1.2 Title. You shall have the title of Chief Scientific Officer and shall report to the Chief Executive
Officer of the Company (the “CEO”). You shall serve in such other capacity or capacities as the CEO or the Board of Directors of the Company (the “Board”) may from time to time prescribe. 

1.3 Duties. You shall do and perform all services, acts or things necessary or advisable to manage and conduct
the business of the Company and which are normally associated with the position of Chief Scientific Officer, consistent with the Bylaws of the Company and as required by the Board. 

1.4 Location. Unless otherwise agreed in writing by you and the Company, you shall perform services pursuant to
this Agreement primarily at the Company’s headquarters, which are currently located in San Diego, California. In addition, the Company may from time to time require you to travel temporarily to other locations in connection with the
Company’s business. It is anticipated that you will seek to establish your permanent residence in Southern 

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 

 
California as soon as practicable following the date of this Agreement and prior to August 31, 2011. 
  

	 	 2.
	 LOYAL AND CONSCIENTIOUS PERFORMANCE;
NONCOMPETITION. 

 2.1 Loyalty. During your employment by the Company you
shall devote your full business energies, interest, abilities and productive time to the proper and efficient performance of your duties under this Agreement. 

2.2 Covenant not to Compete. Except with the express prior written consent of the Company, you will not, during
the term of this Agreement or during any period during which you are receiving Severance Benefits (as defined below) from the Company, engage in competition with the Company and/or any of its affiliates, subsidiaries or joint ventures currently
existing or which shall be established during your employment by the Company (collectively, “Affiliates”) either directly or indirectly, in any manner or capacity, as adviser, principal, agent, affiliate, promoter, partner, officer,
director, employee, stockholder, owner, co-owner, consultant, or member of any association or otherwise, in any phase of the business of developing, manufacturing and marketing of products or services which
are in the same field of use or which otherwise compete with the products or services or proposed products or services of the Company and/or any of its Affiliates. 

2.3 Agreement not to Maintain Conflicts of Interest. During your employment by the Company, you agree not to
acquire, assume or participate in, directly or indirectly, any position, investment or interest known by you to be adverse or antagonistic to the Company, its business or prospects, financial or otherwise or in any company, person or entity
that is, directly or indirectly, in competition with the business of the Company or any of its Affiliates. Ownership by you, as a passive investment, of less than two percent (2%) of the outstanding shares of capital stock of any corporation
with one or more classes of its capital stock listed on a national securities exchange, including, but not limited to, any market of the NASDAQ Stock Market, or publicly traded in the over-the-counter market shall not constitute a breach of the foregoing Section 2.2 or this Section 2.3. 
  

	 	 3.
	 COMPENSATION. 

3.1 Base Salary. The Company shall pay you a base salary of two hundred fifty thousand dollars ($250,000) per
year, payable in regular periodic payments in accordance with Company policy. Such base salary shall be prorated for any partial year of employment on the basis of a 365-day fiscal year. 

3.2 Signing Bonus. The Company will pay you a one-time signing bonus of
$40,000 in cash (the “Signing Bonus”) as soon as reasonably practicable following the Commencement Date, less payroll deductions and all required withholdings. It is anticipated that you will apply this Signing Bonus
towards the costs associated with storage of your household belongings and approximately six months of temporary housing following your relocation to Southern California. 

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 2 of 17 

 3.3 Annual Performance Bonus. In addition to your base salary and
Signing Bonus, you will be eligible to be considered for an annual discretionary bonus of twenty percent (20%) of your base salary based upon the Company’s performance (25% weighting) and your personal performance (75% weighting), at the sole
discretion of the Board, against specific milestones to be defined by the Board and agreed to by you. 
 3.4 Equity
Participation. 
 3.4.1 As soon as practicable following the Commencement Date, you will be granted an
option to purchase a number of shares of the Company’s common stock that, together with shares and/or options currently owned by you and the shares of Series B Preferred Stock of the Company to be issued to you pursuant to Section 3.4.3,
represents no less than 7.5% of the total outstanding shares of the common stock of the Company (on a fully diluted and as converted to common stock basis) pursuant to the Company’s Amended and Restated 2006 Equity Compensation Plan (the
“Plan”). The exercise price per share of such shares shall be the fair market value of such shares as determined in good faith by the Board and is anticipated to be $0.10 per share. 

3.4.2 The option granted pursuant to Section 3.4.1 will vest over a period of four (4) years commencing
upon the Commencement Date, with 1/48th of such shares vesting on a monthly basis until all the shares are vested, so long as you remain continuously employed by the Company and subject to (i) the establishment of your permanent residence in
Southern California by not later than August 31, 2011 and (ii) the provisions of Sections 4.1.2 and 4.3. Your option will be an incentive stock option to the extent permitted by applicable tax laws and will be governed by a separate
Stock Option Agreement (that shall be substantially in the form annexed hereto as Exhibit A) that you and the Company agree to use reasonable efforts to enter into by not later than August 31, 2011 and the Plan. 

3.4.3 As soon as practicable following the Commencement Date, you will be granted a bonus consisting of 240,800 shares
of Series B Preferred Stock of the Company (the “Series B Bonus Shares”) pursuant to the terms of a restricted stock purchase agreement in a form reasonably acceptable to you and the Company that you and Company agree to use
reasonable efforts to enter into by not later than August 31, 2011. The Series B Bonus Shares will have a right of repurchase in favor of the Company (for no consideration) (the “Repurchase Right”) that lapses and may
not be exercised with respect to 1/48th of such shares per month over a period of four (4) years commencing upon the Commencement Date, so long as you remain continuously employed by the Company through each applicable lapse date and subject to
the establishment of your permanent residence in Southern California by not later than August 31, 2011. If the provisions of Sections 4.1.2 or 4.3 are triggered and become applicable and in effect, the Repurchase Right shall lapse and may not
be exercised with respect to an additional number of shares that would have lapsed and become unexercisable if you had been employed for an additional (i) twelve (12) months as of the date of termination if the termination of your employment is
on or before the date that is two years following the Commencement Date or (ii) six (6) months as of the date of termination if the 

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 3 of 17 

 
termination of your employment is after the date that is two years following the Commencement Date. In addition to any other limitation on transfer created by applicable securities laws, you will
be prohibited from assigning, hypothecating, donating, encumbering or otherwise disposing of any interest in any portion of the Series B Bonus Shares while such portion of the shares are subject to the Repurchase Right. The Series B Bonus Shares
will be subject to standard market stand-off provisions. Subject to your timely filing an election under Section 83(b) of the Internal Revenue Code with respect to all the Series B Bonus Shares, the
Company will provide you no less than $150,908 in the form of a forgivable loan (the “Loan”) pursuant to the terms of a promissory note in a form reasonably acceptable to you and the Company (the “Promissory Note”) that you and
the Company shall use reasonable efforts to execute by not later than August 31, 2011, which amount will be retained by the Company and applied towards covering the Company’s federal, state and local tax withholding obligations that arise
during 2011 (i) in connection with the issuance of the Series B Bonus Shares, and (ii) as a result of the Loan. The Company intends to treat the entire amount of the Loan as taxable income to you during 2011. The Promissory Note will provide
(i) that the interest rate is equal to the applicable federal rate in effect as of the date of such Promissory Note and (ii) that the Company will forgive 1/48th of the principal, along with the accrued interest associated therewith, under
the Loan per month during the term of the Loan, so long as you remain continuously employed by the Company through each applicable Loan forgiveness date and subject to the establishment of your permanent residence in Southern California by not later
than August 31, 2011. If the provisions of Sections 4.1.2 or 4.3 are triggered and become applicable and in effect, the Company shall immediately forgive an additional portion of the principal, along with the accrued interest associated
therewith, under the Loan that would have been forgiven if you had been employed for an additional (i) twelve (12) months as of the date of termination if the termination of your employment is on or before the date that is two years following
the Commencement Date or (ii) six (6) months as of the date of termination if the termination of your employment is after the date that is two years following the Commencement Date. The Loan forgiveness will be fully accelerated on the first to
occur of (a) the closing of a Change of Control (as defined in the Plan) (“Change of Control”), (b) the date on which the securities of the Company become registered under Section 12 of the Securities Exchange Act
of 1934, as amended (the “Exchange Act”), (c) the date on which the Company becomes subject to the reporting requirements under Section 15(d) of the Exchange Act, or (d) immediately prior to the filing by the
Company of a registration statement under the Securities Act of 1933, as amended (the “Securities Act”). Any unforgiven principal and accrued interest under the Loan will be due and payable in full 60 days following the
termination of your employment with the Company. Upon maturity of the Loan, you will have the election to satisfy payment of any unforgiven principal and accrued interest that is due thereunder and subject to the provisions of this Agreement by
delivery of any combination of cash or shares of common stock or Series B Preferred Stock of the Company held by you that are not at such time subject to a contractual right of repurchase by the Company, valued at fair market value as reasonably
determined by the Company’s board of directors. 
 3.5 Relocation Allowance. In addition to the
provisions of Sections 3.1 through 3.4 above, the Company shall provide you with relocation assistance benefits as follows. In order for any relocation expenses to be eligible for reimbursement, such expenses must be

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 4 of 17 

 
incurred by you no later than December 31, 2011 (except as to the expenses referenced in Sections 3.5.2 and 3.5.3, as to which such expenses must be incurred no later than
December 31, 2012), and you must provide receipts or other satisfactory documentation of such expenses to the Company no later than sixty (60) days following the date such expenses are incurred. All verified eligible expenses will be
reimbursed be the Company no later than sixty (60) days following submission of such documentation. To the extent such amounts are taxable income, such payments shall be subject to applicable payroll deduction and withholding. 

3.5.1 The Company shall reimburse you for the following relocation expenses not to exceed $20,000 in the aggregate,
subject to your delivery to the Company of reasonably satisfactory evidence of such expenses: (i) moving costs with respect to your primary household belongings; (ii) airfare for up to two round-trip flights for you and each of your
immediate family members from the region of your current residence to the region of the Company’s headquarters; and (iii) airfare for one one-way flight for you and each of your immediate family
members from the region of your current residence to the region of the Company’s headquarters. 
 3.5.2 The
Company shall reimburse you $10,000 for mortgage points and related loan origination and closing expenses incurred with respect to the purchase of a residential property in Southern California to serve as your permanent residence. 

3.5.3 The Company shall reimburse you seven percent (7%) of the sales price of your permanent residence in
Philadelphia, Pennsylvania (“Philadelphia Residence”), subject to the completion of such sale, to cover the costs associated therewith including, but not limited to, real estate sales commissions and other closing costs (the
“Residence Sale Costs Reimbursal”). Prior to the sale or your Philadelphia Residence, the Company shall reimburse you on a monthly basis for your carrying costs with respect to your Philadelphia Residence at a rate of
$2,000 per month commencing on the Commencement Date and not to exceed twelve (12) months (the “Carrying Cost Reimbursal”), subject to your delivery of a signed affidavit stating that you have not sold such
permanent residence or been given approval by the applicable homeowners’ association to rent out such permanent residence prior to or during the period of such reimbursement. The amount of any Carrying Cost Reimbursal actually paid by the
Company shall be applied against and reduce the amount of the Residence Sale Costs Reimbursal to be paid by the Company. 

3.6 Employment Taxes and Withholdings. All of your compensation shall be subject to payroll deductions and
withholdings required to be collected or withheld by the Company. 
 3.7 Vacation; Benefits. You shall, in
accordance with Company policy and the terms of any applicable plan documents, be eligible for paid time off (at a rate of no less than four weeks per year with respect to vacation days) and benefits under any executive benefit plan or arrangement,
such as group health insurance coverage and other fringe benefits, which may be in effect from time to time and made available to the Company’s executives or key management employees. 

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 5 of 17 

	 	 4.
	 TERMINATION. 

4.1 Termination Without Cause or for Good Reason. If your employment with the Company is terminated by the
Company without Cause or you terminate your employment for Good Reason, then subject to your delivery to the Company of a Release and Waiver in the form attached hereto as Exhibit B within the applicable time period set forth therein, but in
no event later than forty-five (45) days following termination of your employment, and permitting such Release and Waiver to become fully effective in accordance with its terms, the Company shall provide you with the following: 

4.1.1 Severance pay in the form of salary continuation at your then-current salary over a period of six
(6) months, to be paid on the Company’s normal pay days commencing with the first regular payroll date of the Company following the effective date of the Release and Waiver; and 

4.1.2 You shall vest immediately such number of unvested stock options that would have vested in accordance with the
applicable vesting schedule as if you had been employed for an additional (i) twelve (12) months as of the date of termination if the termination of your employment is on or before the date that is two years following the Commencement Date or
(ii) six (6) months as of the date of termination if the termination of your employment is after the date that is two years following the Commencement Date. 

4.2 For purposes of this Agreement: 

“Cause” shall mean your: 

(i) gross negligence or willful misconduct in the performance of your duties to the Company as an employee of the
Company (other than a failure resulting your complete or partial incapacity due to physical or mental illness or impairment); provided, however, that no act, or failure to act, by you shall be considered “willful” unless committed without
good faith and without a reasonable belief that the act or omission was in the Company’s best interest; 
 (ii)
material and willful violation of any federal or state law or regulation applicable to the business of the Company; 

(iii) significant or material refusal or failure to act in accordance with any lawful specific direction or order of
the Board; 
 (iv) commission of any act of fraud with respect to the Company; 

(v) breach of any material provision of your Proprietary Information and Inventions Agreement, including without
limitation, theft or other misappropriation by you of the Company’s proprietary information or trade secrets; 

(vi) conviction of, or entry of plea of nolo contendere to, a felony or a crime involving moral turpitude; or 

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 6 of 17 

 (vii) failure to establish your permanent residence in Southern
California on or prior to August 31, 2011. 
 “Good Reason” means the occurrence of any of the
following events without your consent; provided however, that any resignation by you due to any of the following conditions shall only be deemed for Good Reason if: (i) you give the Company written notice of your intent to terminate
for Good Reason within sixty (60) days following the first occurrence of the condition(s) that you believe constitute Good Reason, which notice shall describe such condition(s); (ii) the Company fails to remedy, if remediable, such condition(s)
within thirty (30) days following receipt of the written notice (the “Cure Period”) of such condition(s) from you; and (iii) you actually resign your employment within the first fifteen (15) days after expiration of
the Cure Period: 
 (i) a material reduction in your authority or job responsibilities as an employee of the Company
or successor to the Company, where such material reduction in authority or job responsibilities is accompanied by a change in title; 

(ii) a material reduction in your base compensation, other than pursuant to a Company-wide reduction of base
compensation for employees of the Company generally; 
 (iii) the relocation of the Company’s executive offices
by a distance of fifty (50) miles or more, which relocation requires an increase in your one-way driving distance by more than twenty-five (25) miles; or 

(iv) breach by the Company of any material term of this Agreement. 

Whether or not the actions or omissions of Executive constitute “Cause” within the meaning of this Section 4 shall be decided
by the Board based upon a reasonable good faith investigation and determination. 
 4.3 Termination for Death or
Disability. Your employment with the Company shall terminate effective upon the date of your death or Complete Disability. “Complete Disability” shall mean your inability to perform your duties under this Agreement by reason of
any medically determinable physical or mental impairment which could reasonably be expected to result in death or which has lasted or could reasonably be expected to last for a continuous period of not less than six (6) months. If your
employment shall be terminated by death or Complete Disability, (a) the Company shall pay to you, and/or your heirs, your base salary and accrued and unused vacation benefits earned through the date of termination at the rate in
effect at the time of termination as well as unreimbursed amounts that are due and any amounts not yet paid under Section 3.5 hereof, less standard deductions and withholdings as applicable, (b) you shall vest immediately such number of
unvested stock options that would have vested in accordance with the applicable vesting schedule as if you had been employed for an additional (i) twelve (12) months as of the date of termination if the termination of your employment is on or
before the date that is two years following the Commencement Date or (ii) 

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 7 of 17 

 
six (6) months as of the date of termination if the termination of your employment is after the date that is two years following the Commencement Date and (c) the Company shall
thereafter have no further obligations to you and/or your heirs under this Agreement. 
 4.4 Termination by You
Without Good Reason. You may resign your employment without Good Reason upon thirty (30) days written notice to the Company. Upon such resignation, the Company shall pay you your base salary and accrued and unused vacation earned through
the date upon which the Company accepts such resignation, and you shall not be entitled to any other benefit or compensation and the Company shall have no further obligations to you under this Agreement. 

4.5 Termination by Mutual Agreement of the Parties. Your employment pursuant to this Agreement may be terminated
at any time upon mutual agreement, in writing. Any such termination of employment shall have the consequences specified in such writing. 

4.6 Survival of Certain Provisions. Sections 2.2 and 5 shall survive the termination of this Agreement. 

4.7 LIMITATION ON PAYMENTS. 

4.7.1 Reductions. If any payment or benefit you would receive from the Company (a “Payment”) would
(i) constitute a “parachute payment” within the meaning of Section 280G of the Internal Revenue Code of 1986, as amended (the “Code”), and (ii) but for this sentence, be subject to the excise tax
imposed by Section 4999 of the Code (the “Excise Tax”), then such Payment shall be equal to the Reduced Amount (as defined below). The “Reduced Amount” shall be either (x) the largest portion of the
Payment that would result in no portion of the Payment being subject to the Excise Tax or (y) the largest portion of the Payment, up to and including the total Payment, whichever amount, after taking into account all applicable federal, state
and local employment taxes, income taxes, and the Excise Tax (all computed at the highest applicable marginal rate), results in your receipt, on an after-tax basis, of the greater amount of the Payment
notwithstanding that all or some portion of the Payment may be subject to the Excise Tax. If a reduction in payments or benefits constituting “parachute payments” is necessary so that the Payment equals the Reduced Amount, reduction shall
occur in the following order unless you elect in writing a different order: reduction of cash payments; cancellation of accelerated vesting of stock awards; reduction of employee benefits. If acceleration of vesting of stock award compensation is to
be reduced, such acceleration of vesting shall be cancelled in the reverse order of the date of grant of your stock awards. 

4.7.2 Accounting Firm. The accounting firm engaged by the Company for general audit purposes as of the time of
the Payment shall perform the foregoing calculations, subject to the necessary authorizations of the Audit Committee of the Company’s Board (the “Audit Committee”). Alternatively, the Audit Committee may engage a consulting firm with
expertise in calculations under Section 280G of the Code to perform such calculations. The 

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 8 of 17 

 
Company shall bear all expenses with respect to the determinations by such accounting or consulting firm required to be made hereunder. 

4.7.3 Determinations. The accounting or consulting firm engaged to make the determinations hereunder shall
provide its calculations, together with detailed supporting documentation, to the Company and you within ten (10) calendar days after the date on which your right to a Payment is triggered (if requested at that time by the Company or
you) or such other time as requested by the Company or you. If the accounting or consulting firm determines that no Excise Tax is payable with respect to a Payment, either before or after the application of the Reduced Amount, it shall furnish
the Company and you with an opinion reasonably acceptable to you that no Excise Tax will be imposed with respect to such Payment. Any good faith determinations of the accounting firm made hereunder shall be final, binding and conclusive upon the
Company and you. 
  

	 	 5.
	 CONFIDENTIAL AND PROPRIETARY
INFORMATION;NONSOLICITATION. 

 5.1 As a condition of employment
pursuant to this Agreement you agree to abide by the Company’s standard Proprietary Information and Inventions Agreement which you have executed prior to the date hereof, attached hereto as EXHIBIT C. 

5.2 While employed by the Company and for one (1) year thereafter, you agree that in order to protect the
Company’s trade secrets and confidential and proprietary information from unauthorized use, you will not, either directly or through others, solicit or attempt to solicit any employee, consultant or independent contractor of the Company to
terminate his or her relationship with the Company in order to become an employee, consultant or independent contractor to or for any other person or business entity. 
  

	 	 6.
	 ASSIGNMENT AND BINDING EFFECT.

 This Agreement shall be binding upon and inure to the benefit of you and your heirs, executors,
personal representatives, assigns, administrators and legal representatives. Because of the unique and personal nature of your duties under this Agreement, neither this Agreement nor any rights or obligations under this Agreement shall be assignable
by you. This Agreement shall be binding upon and inure to the benefit of the Company and its successors, assigns and legal representatives. 
  

	 	 7.
	 CHOICE OF LAW. 

This Agreement shall be construed and interpreted in accordance with the internal laws of the State of California without
regard to conflict of laws principles. 
  

	 	 8.
	 INTEGRATION. 

This Agreement, including Exhibits A, B and C, and the other agreements referenced herein as being entered into in connection
herewith contain the complete, final and exclusive agreement of the Parties relating to the terms and conditions of your employment and the 

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 9 of 17 

 
termination of your employment, and supersedes all prior and contemporaneous oral and written employment agreements or arrangements between you and the Company. To the extent this Agreement
conflicts with the Proprietary Information and Inventions Agreement attached as Exhibit B hereto, the Proprietary Information and Inventions Agreement controls. 
  

	 	 9.
	 AMENDMENT. 

This Agreement cannot be amended or modified except by a written agreement signed by you and the Company. 

 

	 	 10.
	 WAIVER. 

No term, covenant or condition of this Agreement or any breach thereof shall be deemed waived, except with the written consent
of the party against whom the wavier is claimed, and any waiver or any such term, covenant, condition or breach shall not be deemed to be a waiver of any preceding or succeeding breach of the same or any other term, covenant, condition or breach.

  

	 	 11.
	 SEVERABILITY. 

The finding by a court of competent jurisdiction of the unenforceability, invalidity or illegality of any provision of this
Agreement shall not render any other provision of this Agreement unenforceable, invalid or illegal. Such court shall have the authority to modify or replace the invalid or unenforceable term or provision with a valid and enforceable term or
provision which most accurately represents the parties’ intention with respect to the invalid or unenforceable term or provision. 
  

	 	 12.
	 INTERPRETATION; CONSTRUCTION. 

The headings set forth in this Agreement are for convenience of reference only and shall not be used in interpreting this
Agreement. This Agreement has been drafted by legal counsel representing the Company, but you have been encouraged to consult with, and have consulted with, your own independent counsel and tax advisors with respect to the terms of this Agreement.
The parties hereto acknowledge that each party and its counsel has reviewed and revised, or had an opportunity to review and revise, this Agreement, and any rule of construction to the effect that any ambiguities are to be resolved against the
drafting party shall not be employed in the interpretation of this Agreement. 
  

	 	 13.
	 REPRESENTATIONS AND WARRANTIES. 

You represent and warrant that you are not restricted or prohibited, contractually or otherwise, from entering into and
performing each of the terms and covenants contained in this Agreement, and that your execution and performance of this Agreement will not violate or breach any other agreements between you and any other person or entity. 

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 10 of 17 

	 	 14.
	 COUNTERPARTS; FACSIMILE. 

This Agreement may be executed in two counterparts, each of which shall be deemed an original, and all of which together shall
contribute one and the same instrument. Facsimile or other electronically transmitted signatures shall be as effective as original signatures. 
  

	 	 15.
	 LITIGATION COSTS. 

Should any claim be commenced between the parties hereto or their personal representatives concerning any provision of this
Agreement or the rights and duties of any person in relation to this Agreement, the party prevailing in such action shall be entitled, in addition to such other relief as may be granted to a reasonable sum as and for that party’s
attorney’s fees in such action. 
  

	 	 16.
	 APPLICATION OF INTERNAL REVENUE
CODE SECTION 409A. 

 Notwithstanding anything to the contrary set
forth herein, any payments and benefits provided under this Agreement {the “Severance Benefits”) that constitute “deferred compensation” within the meaning of Section 409A of the Code and the regulations and other
guidance thereunder and any state law of similar effect (collectively “Section 409A”) shall not commence in connection with your termination of employment unless and until you have also incurred a “separation
from service” (as such term is defined in Treasury Regulation Section 1.409A-1(h)) (the “Separation From Service”), unless the Company reasonably determines that such amounts may be
provided to you without causing you to incur adverse taxation under Section 409A. For the avoidance of doubt, it is intended that payments of the Severance Benefits set forth in this Agreement satisfy, to the greatest extent possible, the
exemptions from the application of Section 409A provided under Treasury Regulation Sections 1.409A-1(b)(4), 1.409A-1(b)(5)
and 1.409A-1(b)(9) and this Agreement will be construed to the greatest extent possible as consistent with those provisions, and to the extent no so exempt, this Agreement (and any definitions hereunder)
will be construed in a manner that complies with Section 409A. However, if the Company (or, if applicable, the successor entity thereto) determines that the Severance Benefits constitute “deferred compensation” under Section 409A
and you are, on the termination of your service, a “specified employee” of the Company or any successor entity thereto, as such term is defined in Section 409A(a)(2)(B)(i) of the Code, then, to the extent delayed commencement of
any portion of such payments is required in order to avoid a prohibited distribution under Code Section 409A(a)(2)(B)(i) and the related adverse taxation under Section 409A, the timing of the Severance Benefit payments shall be
delayed until the earlier to occur of (i) the date that is six months and one day after your Separation From Service, (ii) the date of your death or (iii) such earlier date as permitted under Section 409A without the
imposition of adverse taxation (such applicable date, the “Specified Executive Initial Payment Date”). Upon the first business day following the Specified Executive Initial Payment Date, and subject to the effectiveness of the
Release and Waiver, the Company {or the successor entity thereto, as applicable) shall pay to you a lump sum amount equal to the sum of the Severance Benefit payments that you would otherwise have received through the Specified Executive Initial

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 11 of 17 

 
Payment Date if the commencement of the payment of the Severance Benefits had not been so delayed pursuant to this paragraph and any remaining payments due shall be paid as otherwise provided
herein. No interest shall be due on any amounts so deferred. 
 Notwithstanding the foregoing provisions of this Agreement,
you shall receive Severance Benefits only if you execute and return to the Company, within the applicable time period set forth therein but in no event more than forty-five (45) days following the date of your termination of
employment, the Release and Waiver in the form attached hereto as Exhibit B, and permit such release to become effective in accordance with its terms (such latest permitted date, the “Release Deadline”). If the Severance
Benefits are not covered by one or more exemptions from the application of Section 409A and the Release and Waiver could become effective in the calendar year following the calendar year in which your termination of employment occurs, the
Release and Waiver will not be deemed effective any earlier than the Release Deadline. None of the Severance Benefits will be paid or otherwise delivered prior to the effective date of the Release and Waiver. Except to the minimum extent that
payments must be delayed until the Specified Executive Initial Payout Date because you are a “specified employee” or until the effectiveness of the Release and Waiver, the Company will pay you the Severance Benefits as soon as practicable
in accordance with the Company’s normal payroll practices. All amounts payable under the Agreement will be subject to standard payroll taxes and deductions. 
  

	 	 17.
	 ELIGIBILITY. 

As required by law, this offer and Agreement is subject to satisfactory proof of your right to work in the United States. 

[REMAINDER OF THIS PAGE INTENTIONALLY LEFT
BLANK] 

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 12 of 17 

 If you accept employment on the terms described above, please sign and date this letter in the
space provided below and return it to me. 
 We look forward to your favorable reply and to a productive and enjoyable
working relationship. 
  

	
	 Sincerely,

	
	 BioNanomatrix, Inc.

	
	 /s/ Erik Holmlin

	 Erik Holmlin

	 President and Chief Executive Officer

	
	 Agreed and Accepted:

	
	 /s/ Han Cao

	 Han Cao

	
	 Dated: 7/18/2011

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 

 EXHIBIT A 

STOCK OPTION AGREEMENT 

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 

 EXHIBIT B 

RELEASE AND WAIVER OF CLAIMS 

In consideration of the payments and other benefits set forth in Section 4.1 of the Employment Agreement dated July
    , 2011 (the “Employment Agreement”) to which this form is attached as Exhibit B, I, Han Cao, hereby furnish BioNanomatrix, Inc. (the “Company”), with the following release and waiver
(“Release and Waiver”). 
 In exchange for the consideration provided to me by the Employment Agreement that I am
not otherwise entitled to receive, I hereby generally and completely release the Company and its directors, officers, employees, shareholders, partners, agents, attorneys, predecessors, successors, parent and subsidiary entities, insurers,
Affiliates (as defined in the Employment Agreement), and assigns from any and all claims, liabilities and obligations, both known and unknown, that arise out of or are in any way related to events, acts, conduct, or omissions occurring prior to my
signing this Release and Waiver. This general release includes, but is not limited to: (1) all claims arising out of or in any way related to my employment with the Company or the termination of that employment; (2) all claims related to
my compensation or benefits from the Company, including salary, bonuses, commissions, vacation pay, expense reimbursements, severance pay, fringe benefits, stock, stock options, or any other ownership interests in the Company; (3) all claims
for breach of contract, wrongful termination, and breach of the implied covenant of good faith and fair dealing; (4) all tort claims, including claims for fraud, defamation, emotional distress, and discharge in violation of public policy; and
(5) all federal, state, and local statutory claims, including claims for discrimination, harassment, retaliation, attorneys’ fees, or other claims arising under the federal Civil Rights Act of 1964 (as amended), the federal Americans with
Disabilities Act of 1990, the federal Age Discrimination in Employment Act of 1967 (as amended) (“ADEA”), and the California Fair Employment and Housing Act (as amended); provided, however, that nothing in this Release and Waiver of
Claims shall release the Company from its obligations pursuant to the Employment Agreement or any other contract with the Company to which I am a party or under which I am an intended beneficiary, including without limitation my rights to exercise
vested stock options following termination of employment pursuant to the terms of those stock options, to indemnification pursuant to the Company’s Bylaws or any contracts to which I am a party providing for indemnification or to benefits which
have vested as of the termination of my employment with the Company pursuant to the terms of applicable Company benefit plans. 

I also acknowledge that I have read and understand Section 1542 of the California Civil Code which reads as follows:
“A general release does not extend to claims which the creditor does not know or suspect to exist in his favor at the time of executing the release, which if known by him must have materially affected his settlement with the
debtor.” I hereby expressly waive and relinquish all rights and benefits under that section and any law of any jurisdiction of similar effect with respect to any claims I may have against the Company. 

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 

 I acknowledge that, among other rights, I am waiving and releasing any rights I
may have under ADEA, that this Release and Waiver is knowing and voluntary, and that the consideration given for this Release and Waiver is in addition to anything of value to which I was already entitled as an executive of the Company. I further
acknowledge that I have been advised, as required by the Older Workers Benefit Protection Act, that: (a) the release and waiver granted herein does not relate to claims under the ADEA which may arise after this Release and Waiver is executed;
(b) I have the right to consult with an attorney prior to executing this Release and Waiver (although I may choose voluntarily not to do so); and (c) I have twenty-one (21) days from the date of
termination of my employment with the Company in which to consider this Release and Waiver (although I may choose voluntarily to execute this Release and Waiver earlier); (d) I have seven (7) days following the execution of this Release and
Waiver to revoke my consent to this Release and Waiver; and (e) this Release and Waiver shall not be effective until the seven (7) day revocation period has expired. 

I acknowledge that I have the right to consult with an attorney prior to executing this Release and Waiver (although I may
choose voluntarily not to do so); and (c) I have five (5) days from the date of termination of my employment with the Company in which to consider this Release and Waiver (although I may choose voluntarily to execute this Release and
Waiver earlier). 
 I acknowledge my continuing obligations under my Proprietary Information and Inventions Agreement, a
copy of which is attached to the Employment Agreement as Exhibit C. Pursuant to the Proprietary Information and Inventions Agreement I understand that among other things, I must not use or disclose any confidential or proprietary information of the
Company and I must immediately return all Company property and documents (including all embodiments of proprietary information) and all copies thereof in my possession or control. I understand and agree that my right to the severance pay I am
receiving in exchange for my agreement to the terms of this Release and Waiver is contingent upon my continued compliance with my Proprietary Information & Inventions Agreement. 

This Release and Waiver, including Exhibits A and C to the Employment Agreement, constitutes the complete, final and exclusive
embodiment of the entire agreement between the Company and me with regard to the subject matter hereof. I am not relying on any promise or representation by the Company that is not expressly stated herein. This Release and Waiver may only be
modified by a writing signed by both me and a duly authorized officer of the Company. 
  

							
	 Date: 7/18/2011
	 		  	 By:
	 	 /s/ Han Cao

		 		  		 	 Han Cao

  

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 
 Page 16 of 17 

 EXHIBIT C 

PROPRIETARY INFORMATION AND INVENTIONS AGREEMENT 

  
 3545 John Hopkins Court
Ste 160 | San Diego, CA 92121 | 858.888.7600 tel | 858.888.7601 fax | www.bionanomatrix.com 

 AMENDMENT NO. 1 TO 

EMPLOYMENT AGREEMENT 

This AMENDMENT NO. 1 TO EMPLOYMENT AGREEMENT (this “Amendment”) is made and entered into as of
November 7, 2017 (the “Effective Date”) by and between Bionano Genomics, Inc., a Delaware corporation (the “Company”), formerly known as BioNanoMatrix, Inc., and Han Cao, an individual resident in the State of
California (the “Employee”) (the Company and the Employee are hereinafter sometimes individually referred to as a “Party” and together referred to as the “Parties”). 

WHEREAS, the Employee and the Company have entered into that certain Employment Agreement dated July 18, 2011 (the
“Agreement”); 
 WHEREAS, the Parties now wish to amend the Agreement as specified herein; 

NOW, THEREFORE, as an inducement to the Investors to consummate the Financing and in consideration of the mutual
covenants and agreements of the Parties hereinafter set forth, and for other good and valuable consideration, the receipt and sufficient of which is hereby acknowledged, the Parties hereto, intending to be legally bound, hereby agree as follows:

 1. Amendment. A new clause, (4.1.3), is added to Section 4: Termination of the
Agreement, as follows: 
 “provided that the Employee timely elects COBRA insurance continuation coverage, the Company
will pay one hundred percent of the premium cost of such coverage for a period of six (6) months following the Termination Date, or until such time as the Employee is no longer eligible for COBRA continuation coverage, whichever comes first.
Notwithstanding the foregoing, if at any time the Company determines, in its sole discretion, that its payment of COBRA premiums on the Employee’s behalf would result in a violation of applicable law (including, without limitation,
Section 2716 of the Public Health Service Act), then in lieu of paying COBRA premiums on the Employee’s behalf, the Company will pay the Employee a fully taxable cash payment equal to the COBRA premium for that month, subject to applicable
tax withholding such amount, the “Special Severance Payment”), such Special Severance Payment to be made without regard to the Employee’s payment of COBRA premiums. 

2. Miscellaneous. Except as expressly amended hereby, the Agreement, shall continue in full force and effect in
accordance with its terms. This Amendment shall be governed by and interpreted according to the internal laws of the State of California, without regard to any choice of law rules that may direct the application of the laws of 

  
 1 

 
another jurisdiction. 
 IN WITNESS WHEREOF, each of the
Parties has executed this Amendment as of the date first above written. 
  

			
	 COMPANY:

	
	 BIONANO GENOMICS, INC.

			
		
	 By:
	 	 /s/ R. Erik Holmlin

			
	 Name:
	 	 R. Erik Holmlin

 
			
	 Title:
	 	 President and CEO

	
	 EMPLOYEE:

	
	 /s/ Han Cao

	 Han Cao

  
 2EX-10.12

 Exhibit 10.12 

BIONANO GENOMICS, INC. 

EMPLOYMENT AGREEMENT 

This EMPLOYMENT AGREEMENT (this “Agreement”) is
made and entered into effective as of July 1, 2016 (the “Effective Date”) by and among BIONANO GENOMICS, INC. (the
“Company”) and Michael Ward (the “Executive”). The Company and Executive are hereinafter collectively referred to as the “Parties”, and individually referred to as a
“Party”. 
 RECITALS 

A. The Company desires assurance of the association and services of Executive in order to retain Executive’s experience, skills,
abilities, background and knowledge, and is willing to continue the engagement of Executive’s services on the terms and conditions set forth in this Agreement. 

B. Executive desires to be in the employ of the Company, and is willing to accept employment on the terms and conditions set forth in
this Agreement. 
 AGREEMENT 

In consideration of the foregoing Recitals and the mutual promises and covenants herein contained, and for other good and
valuable consideration, the Parties, intending to be legally bound, agree as follows: 
  

	 	 1.
	 EMPLOYMENT. 

1.1 Title. Executive’s position shall be Chief Business Officer of the Company, subject to the terms and
conditions set forth in this Agreement. 
 1.2 Term. The term of this Agreement shall begin on the Effective
Date and shall continue until it is terminated pursuant to Section 4 herein (the “Term”). 

1.3 Duties. Executive shall do and perform all services, acts or things necessary or advisable to manage and
conduct the business of the Company and that are normally associated with the position of Chief Business Officer, and such other duties as may from time to time be assigned to Executive. Executive shall report to the Chief Executive Officer of the
Company. 
 1.4 Policies and Practices. The employment relationship between the Parties shall be governed by
this Agreement and by the policies and practices established by the Company and/or the Company’s Board of Directors (the “Board”), or any designated committee thereof. In the event that the terms of this
Agreement differ from or are in conflict with the Company’s policies or practices or the Company’s Employee Handbook, this Agreement shall control. 

 1.5 Location. Unless the Parties otherwise agree in writing, during
the Term Executive shall perform the services Executive is required to perform pursuant to this Agreement at the Company’s offices in San Diego, California, provided, however, that the Company may from time to time require
Executive to travel temporarily to other locations in connection with the Company’s business. 
  

	 	 2.
	 LOYALTY; NONCOMPETITION; NONSOLICITATION.

 2.1 Loyalty. During Executive’s employment with the Company, Executive shall
devote Executive’s full business energies, interest, abilities and productive time to the proper and efficient performance of Executive’s duties under this Agreement. 

2.2 Agreement not to Participate in Company’s Competitors. During
Executive’s employment with the Company, Executive agrees not to acquire, assume or participate in, directly or indirectly, any position, investment or interest known by Executive to be adverse or antagonistic to the Company, its business, or
prospects, financial or otherwise, or in any company, person, or entity that is, directly or indirectly, in competition with the business of the Company or any of its Affiliates (as defined below). Ownership by Executive, in professionally managed
funds over which the Executive does not have control or discretion in investment decisions, or as a passive investment, of less than two percent (2%) of the outstanding shares of capital stock of any corporation with one or more classes of its
capital stock listed on a national securities exchange or publicly traded on a national securities exchange or in the over-the-counter market shall not constitute a
breach of this Section. For purposes of this Agreement, “Affiliate,” means, with respect to any specific entity, any other entity that, directly or indirectly, through one or more intermediaries,
controls, is controlled by or is under common control with such specified entity. 
 2.3 Covenant not to
Compete. During Executive’s employment with the Company, the Executive shall not engage in competition with the Company and/or any of its Affiliates, either directly or indirectly, in any manner or capacity, as adviser,
principal, agent, affiliate, promoter, partner, officer, director, employee, stockholder, owner, co-owner, consultant, or member of any association or otherwise, in any phase of the business of developing,
manufacturing and marketing of products or services that are in the same field of use or which otherwise compete with the products or services of the Company, except with the prior written consent of the Company. 

 

	 	 3.
	 COMPENSATION OF THE EXECUTIVE.

 3.1 Base Salary. The Company shall pay Executive a base salary at the annualized rate
of $278,250 (the “Base Salary”), less payroll deductions and all required withholdings, payable in regular periodic installments in accordance with the Company’s normal payroll practices. The Base Salary shall be
prorated for any partial year of employment on the basis of a 365-day fiscal year. 

3.2 Discretionary Bonus. At the sole discretion of the Company, following each calendar year of employment
Executive shall be eligible to receive a discretionary cash 

  
 2 

 
bonus with a target amount of up to thirty percent (30%) of Executive’s then-current base salary (the “Bonus”), based on Executive’s achievement relative to
certain performance goals (“Performance Goals”) to be established by the Company. The determination of whether Executive has met the Performance Goals for any given year, and if so, the amount of any Bonus that will be paid
for such year (if any), shall be determined by the Company in its sole and absolute discretion. In order to be eligible to earn or receive any Bonus, Executive must remain employed by the Company through and including the end of the year with
respect to which such Bonus is earned. 
 3.3 Expense Reimbursements. The Company will reimburse Executive for
all reasonable business expenses Executive incurs in conducting his duties hereunder, pursuant to the Company’s usual expense reimbursement policies; provided that Executive supplies the appropriate substantiation for such expenses no later
than the end of the calendar month following the month in which such expenses were incurred by Executive. For the avoidance of doubt, to the extent that any expense reimbursements payable to Executive under Section 3.3 above or this
Section 3.4 are taxable income and subject to the provisions of Section 409A of the Internal Revenue Code of 1986, as amended (the “Code”) and the regulations and other guidance thereunder and any state law of
similar effect (collectively “Section 409A”): (i) to be eligible to obtain reimbursement for such expenses Executive must supply the appropriate documentation substantiating such expenses no
later than the end of the calendar month following the month in which such expenses were incurred by Executive, (ii) any such reimbursements will be paid by the Company as soon as administratively practicable after submission of such
documentation, but in no event later than December 31 of the year following the year in which the expense was incurred, (iii) the amount of expenses reimbursed in one year will not affect the amount eligible for reimbursement in any
subsequent year, and (iv) the right to expense reimbursement under this Agreement will not be subject to liquidation or exchange for another benefit. 

3.4 Changes to Compensation. Executive’s compensation will be reviewed annually and may be increased from
time to time in the Company’s sole discretion. 
 3.5 Employment Taxes. All of Executive’s
compensation shall be subject to customary withholding taxes and any other employment taxes as are commonly required to be collected or withheld by the Company. 

3.6 Benefits. Executive shall, in accordance with Company policy and the terms of the applicable plan documents,
be eligible to participate in benefits under any benefit plan or arrangement that may be in effect from time to time and made available to the Company’s senior management employees. 

3.7 Holidays and Vacation. Executive shall be eligible for paid holiday and vacation time in accordance with
Company policy as in effect from time to time. 
  

	 	 4.
	 TERMINATION. 

4.1 Termination by the Company. Executive’s employment with the Company is at will and may be terminated by
the Company at any time and for any reason, or for 

  
 3 

 
no reason, including, but not limited to, under the following conditions: 

4.1.1 Termination by the Company for Cause. The Company may terminate Executive’s employment under this
Agreement for Cause by delivery of written notice to Executive. Any notice of termination given pursuant to this Section shall effect termination as of the date of the notice, or as of such other date specified in the notice. 

4.1.2 Termination by the Company without Cause. The Company may terminate Executive’s employment under
this Agreement without Cause at any time and for any reason, or for no reason. Such termination shall be effective on the date Executive is so informed by the Company. 

4.2 Termination By Executive. Executive may terminate his employment with the Company at any time
and for any reason, or for no reason, upon thirty (30) days written notice to the Company. 
 4.3 Termination
for Death or Complete Disability. Executive’s employment with the Company shall automatically terminate effective upon the date of Executive’s death or Complete Disability (as defined below). 

4.4 Termination by Mutual Agreement of the Parties. Executive’s employment with the Company may be
terminated at any time upon a mutual agreement in writing of the Parties. Any such termination of employment shall have the consequences specified in such agreement. 

4.5 Compensation Upon Termination. 

4.5.1 Death or Complete Disability. If Executive’s employment is terminated by death or due to Complete
Disability, the Company shall pay to Executive, or to Executive’s heirs, Executive’s base salary and accrued and unused vacation benefits earned through the date of termination at the rate in effect at the time of termination, less
standard deductions and withholdings. The Company shall thereafter have no further obligations to Executive and/or Executive’s heirs under this Agreement, except as otherwise provided by law (and except as provided otherwise in Executive’s
stock option agreements with the Company). 
 4.5.2 Termination For Cause If the Company terminates
Executive’s employment for Cause, then the Company shall pay Executive’s base salary and accrued and unused vacation benefits earned through the date of termination, at the rate in effect at the time of termination, less standard
deductions and withholdings. The Company shall thereafter have no further obligations to Executive under this Agreement, except as otherwise provided by law (and except as provided otherwise in Executive’s stock option agreements with the
Company). 
 4.5.3 Termination Without Cause. If the Company terminates Executive’s employment without
Cause, the Company shall pay Executive’s base salary and accrued and unused vacation benefits earned through the date of termination, at the rate in effect at the time of termination, less standard deductions and withholdings. In addition, if
Executive 

  
 4 

 
furnishes to the Company an executed waiver and release of claims in the form attached hereto as Exhibit A (the “Release”) within the time period
specified therein, but in no event later than forty-five (45) days following Executive’s termination, and if Executive allows such Release to become effective in accordance with its terms, then Executive shall be entitled to receive the
following severance benefits: 
 4.5.3.1 cash payments in the form of continuation of Executive’s base salary
at the rate in effect at the time of termination for a period of six (6) months following the termination date, and 

4.5.3.2 provided that Executive is eligible for and timely elects continued group health plan coverage under the
Consolidated Omnibus Budget Reconciliation Act of 1985 (“COBRA”) following the Executive’s termination date, the Company shall pay directly to the insurance provider the premium for COBRA continuation coverage for the
Executive and the Executive’s family for a period that will expire upon the earliest of (i) six (6) months following the termination date (the “COBRA Payment Period”), (ii) the effective date that Executive becomes
eligible for new healthcare coverage eligibility available through new employment, or (iii) the date Executive is no longer eligible for COBRA coverage, whichever comes first. 

4.5.4 General Severance Benefit Terms. 

4.5.4.1 The provisions in this Section 4.5.5.1 shall control and supersede anything to the contrary set forth in
this Agreement. For all purposes of this Agreement, references to COBRA premiums shall not include any amounts payable by Executive under a Section 125 health care reimbursement plan under the Code. If at any time the Company determines, in its
sole discretion, that it cannot pay the COBRA premiums without potentially incurring financial costs or penalties under applicable law (including, without limitation, Section 2716 of the Public Health Service Act), then regardless of whether
Executive elects continued health coverage under COBRA, and in lieu of providing the COBRA premiums, the Company will instead pay Executive on the last day of each remaining month of the COBRA Payment Period a fully taxable cash payment equal to the
COBRA premiums for that month, subject to applicable tax withholdings, which payments shall continue until the earlier of expiration of the COBRA Payment Period or the date when Executive becomes eligible for health insurance coverage in connection
with new employment. If Executive becomes eligible for coverage under another employer’s group health plan, Executive must immediately notify the Company of such event, and all COBRA severance benefit payments and obligations under this
Agreement shall cease effective as of such date of the Executive’s eligibility. 
 4.5.4.2 All severance
payments made under this Agreement will be subject to standard payroll deductions and withholdings and will be made on the Company’s regular payroll cycle, provided, however, that any severance payments otherwise scheduled to be made prior to
the effective date of the Release shall instead accrue and be paid in the first payroll period that follows such effective date. Following provision of any severance benefits to which the Executive may be entitled under Section 4.5.3, the
Company shall thereafter have no further 

  
 5 

 
obligations to Executive under this Agreement, except as otherwise provided by law (and except as provided otherwise in Executive’s stock option agreements with the Company). 

4.6 Additional Definitions. For purposes of this Agreement, the following terms shall have the following
meanings: 
 4.6.1 “Complete Disability” shall mean the inability of Executive to
perform Executive’s duties under this Agreement, whether with or without reasonable accommodation, because Executive has become permanently disabled within the meaning of any policy of disability income insurance covering employees of the
Company then in force. In the event the Company has no policy of disability income insurance covering employees of the Company in force when Executive becomes disabled, the term “Complete Disability” shall mean the
inability of Executive to perform Executive’s duties under this Agreement, whether with or without reasonable accommodation, by reason of any incapacity, physical or mental, which the Company, based upon medical advice or an opinion provided by
a licensed physician acceptable to the Company, determines to have incapacitated Executive from satisfactorily performing all of Executive’s usual services for the Company, with or without reasonable accommodation, for a period of at least one
hundred twenty (120) days during any twelve (12) month period (whether or not consecutive). Based upon such medical advice or opinion, the determination of the Company shall be final and binding and the date such determination is made
shall be the date of such Complete Disability for purposes of this Agreement. 
 4.6.2
“Cause” shall mean the occurrence of any of the following: (i) Executive’s conviction of any felony or any crime involving fraud or dishonesty that has a material adverse effect on the Company;
(ii) Executive’s active participation (whether by affirmative act or material omission) in a fraud, act of dishonesty or other act of misconduct against the Company and/or its affiliates; (iii) conduct by Executive which, based upon a
good faith and reasonable factual investigation by the Company, demonstrates Executive’s gross unfitness to serve; (iv) Executive’s material violation of any statutory or fiduciary duty, or duty of loyalty, owed to the Company;
(v) Executive’s breach of any material term of any material contract between such Executive and the Company and the failure to cure such breach within 30 days of written notice; and (vi) Executive’s repeated violation of any
material Company policy. Executive’s Complete Disability shall not constitute Cause as set forth herein. The determination that a termination is for Cause shall be by the Company in its sole and exclusive judgment and discretion. 

4.7 Survival of Certain Sections. Sections 2, 3.5 and 4 through 18 of this Agreement will survive the
termination of this Agreement. 
 4.8 Parachute Payment. If any payment or benefit the Executive would receive
pursuant to this Agreement (“Payment”) would (i) constitute a “Parachute Payment” within the meaning of Section 280G of the Code, and (ii) but for this sentence, be subject to the excise
tax imposed by Section 4999 of the Code (the “Excise Tax”), then such Payment shall be equal to the Reduced Amount. The “Reduced Amount” shall be either (x) the largest portion of the Payment
that would result in no portion of the Payment being subject to the Excise Tax or (y) the largest portion, up to and including the total of the Payment, whichever amount, after taking 

  
 6 

 
into account all applicable federal, state and local employment taxes, income taxes, and the Excise Tax (all computed at the highest applicable marginal rate), results in the Executive’s
receipt, on an after-tax basis, of the greatest economic benefit notwithstanding that all or some portion of the Payment may be subject to the Excise Tax. If a reduction in payments or benefits constituting
Parachute Payments is necessary so that the Payment equals the Reduced Amount, reduction shall occur in the manner that results in the greatest economic benefit for the Executive. If more than one method of reduction will result in the same
economic benefit, the items so reduced will be reduced pro rata. 
 In the event it is subsequently determined by the
Internal Revenue Service that some portion of the Reduced Amount (as determined pursuant to clause (x) in the preceding paragraph) is subject to the Excise Tax, Executive agrees to promptly return to the Company a sufficient amount of the
Payment so that no portion of the Reduced Amount is subject to the Excise Tax. For the avoidance of doubt, if the Reduced Amount is determined in accordance with clause (y) in the preceding paragraph, Executive will have no obligation to return
any portion of the Payment pursuant to the preceding sentence. 
 Unless Executive and the Company agree on an alternative
accounting or law firm, the accounting firm then engaged by the Company for general tax compliance purposes shall perform the foregoing calculations. If the accounting firm so engaged by the Company is serving as accountant or auditor for the
individual, entity or group effecting the Change in Control, the Company shall appoint a nationally recognized accounting, law or consulting firm to make the determinations required hereunder. The Company shall bear all expenses with respect to the
determinations by such accounting, law or consulting firm required to be made hereunder. 
 The Company shall use
commercially reasonable efforts such that the accounting, law or consulting firm engaged to make the determinations hereunder shall provide its calculations, together with detailed supporting documentation, to Executive and the Company within
fifteen (15) calendar days after the date on which Executive’s right to a Payment is triggered (if requested at that time by the Executive or the Company) or such other time as requested by the Executive or the Company. 

In the event the payment of any amounts pursuant to this letter agreement would result in Executive being subject to an Excise
Tax (without giving effect to any reduction in such payments to the Reduced Amount), at Executive’s request in Executive’s sole discretion, the Company will use its commercially reasonable best efforts to obtain a vote of the stockholders
of the Company approving such payments in the manner set forth in Section 280G(b)(5)(B) of the Code and the Treasury Regulations issued thereunder such that the payments would not be subject to the Excise Tax if the required stockholder
approval is obtained. In the event Executive so requests that such a vote be taken, Executive agrees to execute a waiver and enter into such additional agreements as may be reasonably requested by the Company in relation thereto, including, without
limitation, agreeing that the portion of such payments that would otherwise, if made, result in Executive becoming liable for the Excise Tax will not be made if the required stockholder approval is not obtained. 

  
 7 

 4.9 Application of Internal Revenue Code Section 409A.
Notwithstanding anything to the contrary set forth herein, any payments and benefits provided under this Agreement (the “Severance Benefits”) that constitute “deferred compensation” within the meaning of
Section 409A shall not commence in connection with Executive’s termination of employment unless and until Executive has also incurred a “separation from service” (as such term is defined in Treasury Regulation Section 1.409A-1(h) (“Separation From Service”), unless the Company reasonably determines that such amounts may be provided to Executive without causing Executive to incur the additional
20% tax under Section 409A. 
 It is intended that each installment of the Severance Benefits payments provided for in
this Agreement is a separate “payment” for purposes of Treasury Regulation Section 1.409A-2(b)(2)(i). For the avoidance of doubt, it is intended that payments of the Severance Benefits set forth
in this Agreement satisfy, to the greatest extent possible, the exemptions from the application of Section 409A provided under Treasury Regulation Sections 1.409A-1(b)(4),
1.409A-1(b)(5) and 1.409A-1(b)(9). However, if the Company (or, if applicable, the successor entity thereto) determines that the Severance Benefits constitute
“deferred compensation” under Section 409A and Executive is, on the termination of service, a “specified employee” of the Company or any successor entity thereto, as such term is defined in Section 409A(a)(2)(B)(i) of
the Code, then, solely to the extent necessary to avoid the incurrence of the adverse personal tax consequences under Section 409A, the timing of the Severance Benefit payments shall be delayed until the earlier to occur of: (i) the date
that is six months and one day after Executive’s Separation From Service, or (ii) the date of Executive’s death (such applicable date, the “Specified Employee Initial Payment Date”), the Company (or the
successor entity thereto, as applicable) shall (A) pay to Executive a lump sum amount equal to the sum of the Severance Benefit payments that Executive would otherwise have received through the Specified Employee Initial Payment Date if the
commencement of the payment of the Severance Benefits had not been so delayed pursuant to this Section and (B) commence paying the balance of the Severance Benefits in accordance with the applicable payment schedules set forth in this
Agreement. 
 Notwithstanding anything to the contrary set forth herein, Executive shall receive the Severance Benefits
described above, if and only if Executive duly executes and returns to the Company within the applicable time period set forth therein, but in no event more than forty-five days following Separation From Service, the Release and permits the Release
to become effective in accordance with its terms. Notwithstanding any other payment schedule set forth in this Agreement, none of the Severance Benefits will be paid or otherwise delivered prior to the effective date of the Release. Except to the
extent that payments may be delayed until the Specified Employee Initial Payment Date pursuant to the preceding paragraph, on the first regular payroll pay day following the effective date of the Release, the Company will pay Executive the Severance
Benefits Executive would otherwise have received under the Agreement on or prior to such date but for the delay in payment related to the effectiveness of the Release, with the balance of the Severance Benefits being paid as originally scheduled.
All amounts payable under the Agreement will be subject to standard payroll taxes and deductions. 
 The severance benefits
are intended to qualify for an exemption from application of Section 409A or comply with its requirements to the extent necessary to avoid adverse personal 

  
 8 

 
tax consequences under Section 409A, and any ambiguities herein shall be interpreted accordingly. 
  

	 	 5.
	 CONFIDENTIAL AND PROPRIETARY INFORMATION.

 As a condition of continued employment, Executive agrees to execute and continue to abide by the
Company’s standard form of Proprietary Information and Inventions Agreement (“PIIA”). 
  

	 	 6.
	 ASSIGNMENT AND BINDING EFFECT.

 This Agreement shall be binding upon and inure to the benefit of Executive and Executive’s
heirs, executors, personal representatives, assigns, administrators and legal representatives. Because of the unique and personal nature of Executive’s duties under this Agreement, neither this Agreement nor any rights or obligations under this
Agreement shall be assignable by Executive. This Agreement shall be binding upon and inure to the benefit of the Company and its successors, assigns and legal representatives. Any such successor of the Company will be deemed substituted for the
Company under the terms of this Agreement for all purposes. For this purpose, “successor” means any person, firm, corporation or other business entity which at any tie, whether by purchase, merger or otherwise, directly or indirectly
acquires all or substantially all of the assets or business of the Company. 
  

	 	 7.
	 NOTICES. 

All notices or demands of any kind required or permitted to be given by the Company or Executive under this Agreement shall be
given in writing and shall be personally delivered (and receipted for) or faxed during normal business hours or mailed by certified mail, return receipt requested, postage prepaid, addressed as follows: 

If to the Company: 

BioNano Genomics, Inc. 

9640 Towne Centre Drive, Ste. 100 

San Diego, CA 92121 

Attention: Chief Executive Officer 

If to Executive: 

Michael Ward 

2221 Forestview Road 

Evanston, IL 60201 

Any such written notice shall be deemed given on the earlier of the date on which such notice is personally delivered or three (3) days
after its deposit in the United States mail as specified 

  
 9 

 
above. Either Party may change its address for notices by giving notice to the other Party in the manner specified in this Section. 

 

	 	 8.
	 CHOICE OF LAW. 

This Agreement shall be construed and interpreted in accordance with the internal laws of the State of California without
regard to its conflict of laws principles. 
  

	 	 9.
	 INTEGRATION. 

This Agreement, including Exhibit A, and the PIIA contain the complete, final and exclusive agreement of the Parties relating
to the terms and conditions of Executive’s employment and the termination of Executive’s employment, and supersedes any and all prior and/or contemporaneous oral and written employment agreements or arrangements between the Parties
regarding Executive’s service with the Company, including, without limitation, that certain offer letter dated April 16, 2014. 
  

	 	 10.
	 AMENDMENT. 

This Agreement cannot be amended or modified except by a written agreement signed by Executive and the Company. 

 

	 	 11.
	 WAIVER. 

No term, covenant or condition of this Agreement or any breach thereof shall be deemed waived, except with the written consent
of the Party against whom the wavier is claimed, and any waiver or any such term, covenant, condition or breach shall not be deemed to be a waiver of any preceding or succeeding breach of the same or any other term, covenant, condition or breach.

  

	 	 12.
	 SEVERABILITY. 

The finding by a court of competent jurisdiction of the unenforceability, invalidity or illegality of any provision of this
Agreement shall not render any other provision of this Agreement unenforceable, invalid or illegal. Such court shall have the authority to modify or replace the invalid or unenforceable term or provision with a valid and enforceable term or
provision, which most accurately represents the Parties’ intention with respect to the invalid or unenforceable term, or provision. 
  

	 	 13.
	 INTERPRETATION; CONSTRUCTION. 

The headings set forth in this Agreement are for convenience of reference only and shall not be used in interpreting this
Agreement. This Agreement has been drafted by legal counsel representing the Company, but the Executive has been encouraged to consult with, and has consulted with, Executive’s own independent counsel and tax advisors with respect to the terms
of this Agreement. The Parties acknowledge that each Party and its counsel has reviewed and revised, or had an opportunity to review and revise, this Agreement, and any rule of 

  
 10 

 
construction to the effect that any ambiguities are to be resolved against the drafting party shall not be employed in the interpretation of this Agreement. 

 

	 	 14.
	 REPRESENTATIONS AND WARRANTIES. 

Executive represents and warrants that Executive is not restricted or prohibited, contractually or otherwise, from entering
into and performing each of the terms and covenants contained in this Agreement, and that Executive’s execution and performance of this Agreement will not violate or breach any other agreements between the Executive and any other person or
entity. 
  

	 	 15.
	 COUNTERPARTS. 

This Agreement may be executed in two counterparts, each of which shall be deemed an original, all of which together shall
contribute one and the same instrument. 
  

	 	 16.
	 ARBITRATION. 

To ensure the rapid and economical resolution of disputes that may arise in connection with the Executive’s employment
with the Company, Executive and the Company agree that any and all disputes, claims, or causes of action, in law or equity, arising from or relating to Executive’s employment, or the termination of that employment, will be resolved, to the
fullest extent permitted by law, by final, binding and confidential arbitration pursuant to both the substantive and procedural provisions of the Federal Arbitration Act in San Diego, California conducted by the Judicial Arbitration and Mediation
Services/Endispute, Inc. (“JAMS”), or its successors, under the then current rules of JAMS for employment disputes; provided that the arbitrator shall: (a) have the authority to compel adequate discovery for the
resolution of the dispute and to award such relief as would otherwise be permitted by law; and (b) issue a written arbitration decision including the arbitrator’s essential findings and conclusions and a statement of the award.
Accordingly, Executive and the Company hereby waive any right to a jury trial. Both Executive and the Company shall be entitled to all rights and remedies that either Executive or the Company would be entitled to pursue in a court of law. The
Company shall pay any JAMS filing fee and shall pay the arbitrator’s fee. Nothing in this Agreement is intended to prevent either Executive or the Company from obtaining injunctive relief in court to prevent irreparable harm pending the
conclusion of any such arbitration. Notwithstanding the foregoing, Executive and the Company each have the right to resolve any issue or dispute involving confidential, proprietary or trade secret information, or intellectual property rights, by
Court action instead of arbitration. 
  

	 	 17.
	 TRADE SECRETS OF OTHERS.

 It is the understanding of both the Company and Executive that Executive shall not divulge to the
Company and/or its subsidiaries any confidential information or trade secrets belonging to others, including Executive’s former employers, nor shall the Company and/or its Affiliates seek to elicit from Executive any such information.
Consistent with the foregoing, 

  
 11 

 
Executive shall not provide to the Company and/or its Affiliates, and the Company and/or its Affiliates shall not request, any documents or copies of documents containing such information. 

 

	 	 18.
	 ADVERTISING WAIVER. 

Executive agrees to permit the Company, and persons or other organizations authorized by the Company, to use, publish and
distribute advertising or sales promotional literature concerning the products and/or services of the Company, or the machinery and equipment used in the provision thereof, in which Executive’s name and/or pictures of Executive taken in the
course of Executive’s provision of services to the Company appear. Executive hereby waives and releases any claim or right Executive may otherwise have arising out of such use, publication or distribution. 

[REMAINDER OF THIS PAGE INTENTIONALLY LEFT
BLANK] 

  
 12 

 IN WITNESS
WHEREOF, the Parties have executed this Agreement as of the date first above written. 
  

			
	 BIONANO GENOMICS, INC.

		
	 By:
	 	 /s/ Erik Holmlin

	 Its:
	 	 CEO

			
		
	 Dated:
	 	 Jul 7 2016

			
	
	 EXECUTIVE:

	
	 /s/ Michael Ward

	 MICHAEL
WARD

			
		
	 Dated:
	 	 07/06/16

  
 13 

 EXHIBIT A 

RELEASE AND WAIVER OF CLAIMS 

TO BE SIGNED ON OR FOLLOWING THE SEPARATION DATE ONLY 

In consideration of the payments and other benefits set forth in the Employment Agreement dated July 1, 2016, to which
this form is attached (the “Employment Agreement”), I, Michael Ward, hereby furnish BIONANO GENOMICS, INC. (the
“Company”), with the following release and waiver (“Release and Waiver”). 

In exchange for the consideration provided to me by the Employment Agreement that I am not otherwise entitled to receive, I
hereby generally and completely release the Company and its current and former directors, officers, employees, stockholders, partners, agents, attorneys, predecessors, successors, parent and subsidiary entities, insurers, affiliates, and assigns
(collectively, the “Released Parties”) from any and all claims, liabilities and obligations, both known and unknown, that arise out of or are in any way related to events, acts, conduct, or omissions occurring prior to or on
the date that I sign this Agreement (collectively, the “Released Claims”). The Released Claims include, but are not limited to: (a) all claims arising out of or in any way related to my employment with the Company, or
the termination of that employment; (b) all claims related to my compensation or benefits from the Company including salary, bonuses, commissions, vacation pay, expense reimbursements, severance pay, fringe benefits, stock, stock options, or
any other ownership interests in the Company; (c) all claims for breach of contract, wrongful termination, and breach of the implied covenant of good faith and fair dealing; (d) all tort claims, including claims for fraud, defamation,
emotional distress, and discharge in violation of public policy; and (e) all federal, state, and local statutory claims, including claims for discrimination, harassment, retaliation, misclassification, attorneys’ fees, or other claims
arising under the federal Civil Rights Act of 1964 (as amended), the federal Americans with Disabilities Act of 1990, the federal Age Discrimination in Employment Act of 1967 (as amended) (the “ADEA”), the California Labor
Code, and the California Fair Employment and Housing Act (as amended). Notwithstanding the foregoing, the following are not included in the Released Claims (the “Excluded Claims”): (a) any rights or claims for
indemnification I may have pursuant to any written indemnification agreement with the Company to which I am a party, the charter, bylaws, or operating agreements of the Company, or under applicable law; (b) any rights or claims to unemployment
compensation, funds accrued in my 401k account, or any vested equity incentives; (c) any rights that are not waivable as a matter of law; or (d) any claims arising from the breach of this Agreement. I hereby represent and warrant that,
other than the Excluded Claims, I am not aware of any claims I have or might have against any of the Released Parties that are not included in the Released Claims. 

I also acknowledge that I have read and understand Section 1542 of the California Civil Code which reads as follows:
“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.” I hereby expressly waive and relinquish all rights and benefits under that 

 
Section and any law of any jurisdiction of similar effect with respect to any claims I may have against the Company. 

I acknowledge that, among other rights, I am waiving and releasing any rights I may have under ADEA, that this Release and
Waiver is knowing and voluntary, and that the consideration given for this Release and Waiver is in addition to anything of value to which I was already entitled as an executive of the Company. If I am 40 years of age or older upon execution of this
Release and Waiver, I further acknowledge that I have been advised, as required by the Older Workers Benefit Protection Act, that: (a) the release and waiver granted herein does not relate to claims under the ADEA which may arise after this
Release and Waiver is executed; (b) I should consult with an attorney prior to executing this Release and Waiver; and (c) I have twenty-one (21) days from the date of termination of my
employment with the Company in which to consider this Release and Waiver (although I may choose voluntarily to execute this Release and Waiver earlier); (d) I have seven (7) days following the execution of this Release and Waiver to revoke my
consent to this Release and Waiver; and (e) this Release and Waiver shall not be effective until the seven (7) day revocation period has expired without my having previously revoked this Release and Waiver. 

I acknowledge my continuing obligations under my Proprietary Information and Inventions Agreement. Pursuant to the Proprietary
Information and Inventions Agreement I understand that among other things, I must not use or disclose any confidential or proprietary information of the Company and I must immediately return all Company property and documents (including all
embodiments of proprietary information) and all copies thereof in my possession or control. I understand and agree that my right to the severance pay I am receiving in exchange for my agreement to the terms of this Release and Waiver is contingent
upon my continued compliance with my Proprietary Information and Inventions Agreement. 
 This Release and Waiver
constitutes the complete, final and exclusive embodiment of the entire agreement between the Company and me with regard to the subject matter hereof. I am not relying on any promise or representation by the Company that is not expressly stated
herein. This Release and Waiver may only be modified by a writing signed by both me and a duly authorized officer of the Company. 
  

							
	 Date:
	 		  	 By:
	 	  

	 	 	 	  	 	 	 Michael Ward

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