Document:

EX-10.2

 Exhibit 10.2 

BIONANO GENOMICS, INC. 

AMENDED AND RESTATED 

2006 EQUITY COMPENSATION PLAN 

  
 1. 

 BIONANO GENOMICS, INC. 

AMENDED AND RESTATED 

2006 EQUITY COMPENSATION PLAN 

MOST RECENTLY AMENDED BY THE BOARD
OF DIRECTORS: MARCH 1, 2016 
 AMENDMENT APPROVED
BY THE STOCKHOLDERS: MARCH 3, 2016 
 TERMINATION
DATE: SEPTEMBER 11, 2018 
 The purpose of the BioNano Genomics, Inc. Amended and
Restated 2006 Equity Compensation Plan (the “Plan”) is to provide (i) designated employees of BioNano Genomics, Inc. (the “Company”) and its subsidiaries, (ii) certain consultants and advisors who perform services for
the Company or its subsidiaries and (iii) non-employee members of the Board of Directors of the Company (the “Board”) with the opportunity to receive grants of incentive stock options,
nonqualified stock options, stock awards, stock units, stock appreciation rights and other equity-based awards. The Company believes that the Plan will encourage the participants to contribute materially to the growth of the Company, thereby
benefiting the Company’s members, and will align the economic interests of the participants with those of the members. 
 SECTION 1
    Administration 
 (a)    Board. The Plan shall be administered and
interpreted by the Board or by a committee consisting of members of the Board, which shall be appointed by the Board. However, the Board shall approve and administer all grants made to non-employee directors.
The committee may delegate authority to one or more subcommittees, as it deems appropriate. To the extent the Board, committee or subcommittee administers the Plan, references in the Plan to the “Board” shall be deemed to refer to such
committee or subcommittee. 
 (b)    Board Authority. The Board shall have the sole authority to
(i) determine the individuals to whom grants shall be made under the Plan, (ii) determine the type, size and terms of the grants to be made to each such individual, (iii) determine the time when the grants will be made and the
duration of any applicable exercise or restriction period, including the criteria for exercisability and the acceleration of exercisability, (iv) amend the terms of any previously issued grant, and (v) deal with any other matters arising
under the Plan. 
 (c)    Board Determinations. The Board shall have full power and authority to
administer and interpret the Plan, to make factual determinations and to adopt or amend such rules, regulations, agreements and instruments for implementing the Plan and for the conduct of its business as it deems necessary or advisable, in its sole
discretion. The Board’s interpretations of the Plan and all determinations made by the Board pursuant to the powers vested in it hereunder shall be conclusive and binding on all persons having any interest in the Plan or in any awards granted
hereunder. All powers of the Board shall be executed in its sole discretion, in the best interest of the Company, not as a fiduciary, and in keeping with the objectives of the Plan and need not be uniform as to similarly situated individuals. 

  
 2. 

 SECTION 2     Grants 

Awards under the Plan may consist of grants of incentive stock options as described in Section 5 (“Incentive Stock
Options”), nonqualified stock options as described in Section 5 (“Nonqualified Stock Options”) (Incentive Stock Options and Nonqualified Stock Options are collectively referred to as “Options”), stock awards as
described in Section 6 (“Stock Awards”), stock units as described in Section 7 (“Stock Units”), stock appreciation rights (“SARs”) as described in Section 8, and other equity-based awards as described in
Section 9 (“Other Equity Awards”) (collectively referred to herein as “Grants”). All Grants shall be subject to the terms and conditions set forth herein and to such other terms and conditions consistent with this Plan as
the Board deems appropriate and as are specified in writing by the Board to the individual in a grant instrument or an amendment to the grant instrument (the “Grant Instrument”). All Grants shall be made conditional upon the Grantee’s
(as defined below) acknowledgement, in writing or by acceptance of the Grant, that all decisions and determinations of the Board shall be final and binding on the Grantee, the Grantee’s beneficiaries and any other person having or claiming an
interest under such Grant. The Board shall approve the form and provisions of each Grant Instrument. Grants under a particular Section of the Plan need not be uniform as among the Grantees. 

SECTION 3     Shares Subject to the Plan 

(a)    Shares Authorized. Subject to adjustment as described below, the aggregate number of shares
of common stock of the Company (“Company Stock”) that may be issued or transferred under the Plan is 218,791,131. 

(b)    Determination of Authorized Shares. The shares may be authorized but unissued shares of
Company Stock or reacquired shares of Company Stock. If and to the extent Options or SARs granted under the Plan terminate, expire, or are canceled, forfeited, exchanged or surrendered without having been exercised or if any Stock Awards, Stock
Units, or Other Equity Awards are forfeited, the shares subject to such Grants shall again be available for purposes of the Plan. 

(c)    Adjustments. If there is any change in the number or kind of shares of Company Stock
outstanding (i) by reason of a stock dividend, spinoff, recapitalization, stock split, or combination or exchange of shares, (ii) by reason of a merger, reorganization or consolidation, (iii) by reason of a reclassification or change
in par value, or (iv) by reason of any other extraordinary or unusual event affecting the outstanding Company Stock as a class without the Company’s receipt of consideration, or if the value of outstanding shares of Company Stock is
substantially reduced as a result of a spinoff or the Company’s payment of an extraordinary dividend or distribution, the maximum number of shares of Company Stock available for issuance under the Plan, the maximum number of shares of Company
Stock for which any individual may receive Grants in any year, the kind and number of shares covered by outstanding Grants, the kind and number of shares issued and to be issued under the Plan, and the price per share or the applicable market value
of such Grants shall be equitably adjusted by the Board to reflect any increase or decrease in the number of, or change in the kind or value of, the issued shares of Company Stock to preclude, to the extent practicable, the enlargement or dilution
of rights and benefits under the Plan and such outstanding Grants; provided, however, that any 

  
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fractional shares resulting from such adjustment shall be eliminated. In addition, in the event of a Change of Control of the Company, the provisions of Section 13 of the Plan shall apply.
Any adjustments to outstanding Grants shall be consistent with section 409A or 424 of the Internal Revenue Code of 1986, as amended (the “Code”), to the extent applicable. Any adjustments determined by the Board shall be final, binding and
conclusive. 
 SECTION 4     Eligibility for Participation 

(a)    Eligible Persons. All employees of the Company and its subsidiaries, including Employees who
are officers or members of the Board (“Employees”), and members of the Board who are not Employees (“Non-Employee Directors”) shall be eligible to participate in the Plan. Consultants and
advisors who perform services for the Company or any of its subsidiaries including managers who provide consulting or advisory services (“Key Advisors”) shall be eligible to participate in the Plan if the Key Advisors render bona fide
services to the Company or its subsidiaries, the services are not in connection with the offer and sale of securities in a capital-raising transaction and the Key Advisors do not directly or indirectly promote or maintain a market for the
Company’s securities. 
 (b)    Selection of Grantees. The Board shall select the Employees,
Non-Employee Directors and Key Advisors to receive Grants and shall determine the number of shares of Company Stock subject to a particular Grant in such manner as the Board determines. Employees, Key Advisors
and Non-Employee Directors who receive Grants under this Plan shall hereinafter be referred to as “Grantees.” 

SECTION 5     Options 

The Board may grant Options to an Employee, Non-Employee Director or Key Advisor, upon
such terms as the Board deems appropriate. The following provisions are applicable to Options: 

(a)    Number of Shares. The Board shall determine the number of shares of Company Stock that will
be subject to each Grant of Options to Employees, Non-Employee Directors and Key Advisors. 

(b)    Type of Option and Price. 

(i)    The Board may grant Incentive Stock Options that are intended to qualify as “incentive stock
options” within the meaning of section 422 of the Code or Nonqualified Stock Options that are not intended so to qualify or any combination of Incentive Stock Options and Nonqualified Stock Options, all in accordance with the terms and
conditions set forth herein. Incentive Stock Options may be granted only to Employees. Nonqualified Stock Options may be granted to Employees, Non-Employee Directors and Key Advisors. 

(ii)    The purchase price (the “Exercise Price”) of Company Stock subject to an Option shall be
determined by the Board and must be equal to or greater than the Fair Market Value (as defined below) of a share of Company Stock on the date the Option is granted. However, an Incentive Stock Option may not be granted to an Employee who, at the
time of grant, owns stock possessing more than 10% of the total combined voting power of all classes of 

  
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stock of the Company or any subsidiary of the Company, unless the Exercise Price per share is not less than 110% of the Fair Market Value of Company Stock on the date of grant. 

(iii)    “Fair Market Value” of Company Stock means, unless the Board determines otherwise with
respect to a particular Grant, (i) if the principal trading market for the Company Stock is a national securities exchange, the last reported sale price of Company Stock on the relevant date or (if there were no trades on that date) the latest
preceding date upon which a sale was reported, (ii) if the Company Stock is not principally traded on such exchange, the mean between the last reported “bid” and “asked” prices of Company Stock on the relevant date, as
reported on the OTC Bulletin Board, or (iii) if the Company Stock is not publicly traded or, if publicly traded, is not so reported, the Fair Market Value per share shall be as determined by the Board through the reasonable application of any
reasonable valuation method authorized under the Code. 
 (c)    Option Term. The Board shall
determine the term of each Option. The term of any Option shall not exceed ten years from the date of grant. However, an Incentive Stock Option that is granted to an Employee who, at the time of grant, owns stock possessing more than 10% of the
total combined voting power of all classes of stock of the Company, or any subsidiary of the Company, may not have a term that exceeds five years from the date of grant. 

(d)    Exercisability of Options. 

(i)    Options shall become exercisable in accordance with such terms and conditions, consistent with the
Plan, as may be determined by the Board and specified in the Grant Instrument. The Board may accelerate the exercisability of any or all outstanding Options at any time for any reason. 

(ii)    The Board may provide in a Grant Instrument that the Grantee may elect to exercise part or all of
an Option before it otherwise has become exercisable. Any shares so purchased shall be restricted shares and shall be subject to a repurchase right in favor of the Company during a specified restriction period, with the repurchase price equal to the
lesser of (A) the Exercise Price or (B) the Fair Market Value of such shares at the time of repurchase, or such other restrictions as the Board deems appropriate. 

(e)    Grants to Non-Exempt Employees. Notwithstanding the
foregoing, Options granted to persons who are non-exempt employees under the Fair Labor Standards Act of 1938, as amended, may not be exercisable for at least six months after the date of grant (except that
such Options may become exercisable, as determined by the Board, upon the Grantee’s death, Disability (as defined below) or retirement, or upon a Change of Control or other circumstances permitted by applicable regulations). 

(f)    Termination of Employment, Disability or Death. 

(i)    Except as provided below, an Option may only be exercised while the Grantee is employed by, or
providing service to, the Employer (as defined below) as an Employee, Key Advisor or member of the Board. 

  
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 (ii)    In the event that a Grantee ceases to be employed by,
or provide service to, the Employer for any reason other than Disability, death, or termination for Cause (as defined below), any Option which is otherwise exercisable by the Grantee shall terminate unless exercised within 90 days after the date on
which the Grantee ceases to be employed by, or provide service to, the Employer (or within such other period of time as may be specified by the Board), but in any event no later than the date of expiration of the Option term. Except as otherwise
provided by the Board, any of the Grantee’s Options that are not otherwise exercisable as of the date on which the Grantee ceases to be employed by, or provide service to, the Employer shall terminate as of such date. 

(iii)    In the event the Grantee ceases to be employed by, or provide service to, the Employer on account
of a termination for Cause by the Employer, any Option held by the Grantee shall terminate as of the date the Grantee ceases to be employed by, or provide service to, the Employer. In addition, notwithstanding any other provisions of this
Section 5, if the Board determines that the Grantee has engaged in conduct that constitutes Cause at any time while the Grantee is employed by, or providing service to, the Employer or after the Grantee’s termination of employment or
service, any Option held by the Grantee shall immediately terminate and the Grantee shall automatically forfeit all shares underlying any exercised portion of an Option for which the Company has not yet delivered the share certificates, upon refund
by the Company of the Exercise Price paid by the Grantee for such shares. Upon any exercise of an Option, the Company may withhold delivery of share certificates pending resolution of an inquiry that could lead to a finding resulting in a
forfeiture. 
 (iv)    In the event the Grantee ceases to be employed by, or provide service to, the
Employer on account of the Grantee’s Disability, any Option which is otherwise exercisable by the Grantee shall terminate unless exercised within one year after the date on which the Grantee ceases to be employed by, or provide service to, the
Employer (or within such other period of time as may be specified by the Board), but in any event no later than the date of expiration of the Option term. Except as otherwise provided by the Board, any of the Grantee’s Options which are not
otherwise exercisable as of the date on which the Grantee ceases to be employed by, or provide service to, the Employer shall terminate as of such date. 

(v)    If the Grantee dies while employed by, or providing service to, the Employer or within 90 days
after the date on which the Grantee ceases to be employed or provide service on account of a termination specified in Section 5(f)(ii) above (or within such other period of time as may be specified by the Board), any Option that is otherwise
exercisable by the Grantee shall terminate unless exercised within one year after the date on which the Grantee ceases to be employed by, or provide service to, the Employer (or within such other period of time as may be specified by the Board or in
the Grantee’s employment agreement, if any), but in any event no later than the date of expiration of the Option term. Except as otherwise provided by the Board, any of the Grantee’s Options that are not otherwise exercisable as of the
date on which the Grantee ceases to be employed by, or provide service to, the Employer shall terminate as of such date. 

(vi)    For purposes of the Plan: 

  
 6. 

 (A)    The term “Employer” shall mean the Company
and its subsidiary companies, as determined by the Board. 
 (B)    “Employed by, or provide
service to, the Employer” shall mean employment or service as an Employee, Key Advisor or member of the Board (so that, for purposes of exercising Options and satisfying conditions with respect to other Grants, a Grantee shall not be considered
to have terminated employment or service until the Grantee ceases to be an Employee, Key Advisor and member of the Board), unless the Board determines otherwise. 

(C)    “Disability” shall mean a Grantee’s becoming disabled within the meaning of section
22(e)(3) of the Code, within the meaning of the Employer’s long-term disability plan applicable to the Grantee, or as otherwise determined by the Board. 

(D)    “Cause” shall mean, except to the extent otherwise specified by the Board, a finding by
the Board that the Grantee (i) has materially breached his or her employment or service contract with the Employer, which breach has not been remedied by the Grantee after written notice has been provided to the Grantee of such breach,
(ii) has engaged in disloyalty to the Employer, including, without limitation, fraud, embezzlement, theft, commission of a felony or proven dishonesty, (iii) has disclosed trade secrets or confidential information of the Employer to
persons not entitled to receive such information, (iv) has breached any written non-competition or non- solicitation agreement between the Grantee and the Employer
or (v) has engaged in such other behavior detrimental to the interests of the Employer as the Board determines. 

(g)    Exercise of Options. A Grantee may exercise an Option that has become exercisable, in whole
or in part, by delivering a notice of exercise to the Company. The Grantee shall pay the Exercise Price for an Option as specified by the Board (i) in cash, (ii) with the approval of the Board, by delivering shares of Company Stock owned
by the Grantee (including Company Stock acquired in connection with the exercise of an Option, subject to such restrictions as the Board deems appropriate) and having a Fair Market Value on the date of exercise equal to the Exercise Price or by
attestation (on a form prescribed by the Board) to ownership of shares of Company Stock having a Fair Market Value on the date of exercise equal to the Exercise Price, (iii) after a Public Offering (as defined in Section 20) of the
Company’s stock, payment through a broker in accordance with procedures permitted by Regulation T of the Federal Reserve Board, or (iv) by such other method as the Board may approve. Shares of Company Stock used to exercise an Option shall
have been held by the Grantee for the requisite period of time to avoid adverse accounting consequences to the Company with respect to the Option. The Grantee shall pay the Exercise Price and the amount of any withholding tax due (pursuant to
Section 10) at such time as may be specified by the Board. 
 (h)    Limits on Incentive Stock
Options. Each Incentive Stock Option shall provide that, if the aggregate Fair Market Value of the stock on the date of the grant with respect to which Incentive Stock Options are exercisable for the first time by a Grantee during any calendar
year, under the Plan or any other stock option plan of the Company or a subsidiary, exceeds $100,000, then the Option, as to the excess, shall be treated as a Nonqualified Stock Option. An Incentive Stock Option shall not be granted to any person
who is not an Employee of the Company. 

  
 7. 

 SECTION 6    Stock Awards 

The Board may issue or transfer shares of Company Stock to an Employee, Non-Employee
Director or Key Advisor under a Stock Award, upon such terms as the Board deems appropriate. The following provisions are applicable to Stock Awards: 

(a)    General Requirements. Shares of Company Stock issued or transferred pursuant to Stock Awards
may be issued or transferred for cash consideration or for no cash consideration, and may be subject to restrictions or no restrictions, as determined by the Board. The Board may, but shall not be required to, establish conditions under which
restrictions on Stock Awards shall lapse over a period of time or according to such other criteria as the Board deems appropriate, including, without limitation, restrictions based upon the achievement of specific performance goals. Any period of
time during which the Stock Awards will remain subject to restrictions will be designated in the Grant Instrument as the “Restriction Period.” 

(b)    Number of Shares. The Board shall determine the number of shares of Company Stock to be
issued or transferred pursuant to a Stock Award and the restrictions applicable to such shares. 

(c)    Requirement of Employment or Service. Unless the Board determines otherwise, if the Grantee
ceases to be employed by, or provide service to, the Employer during a period designated in the Grant Instrument as the Restriction Period, or if other specified conditions are not met, the Stock Award shall terminate and be forfeited as to all
shares covered by the Grant as to which the restrictions have not lapsed, and those shares of Company Stock must be immediately returned to the Company. The Board may, however, provide for complete or partial exceptions to this requirement as it
deems appropriate. 
 (d)    Restrictions on Transfer and Legend on Stock Certificate. During the
Restriction Period, a Grantee may not sell, assign, transfer, pledge or otherwise dispose of the shares of a Stock Award except to a successor under Section 11(a). Each certificate for a share of a Stock Award shall contain a legend giving
appropriate notice of the restrictions in the Grant. The Grantee shall be entitled to have the legend removed from the stock certificate covering the shares subject to restrictions when all restrictions on such shares have lapsed. The Board may
determine that the Company will not issue certificates for Stock Awards until all restrictions on such shares have lapsed, or that the Company will retain possession of certificates for shares of Stock Awards until all restrictions on such shares
have lapsed. 
 (e)    Right to Vote and to Receive Dividends. Unless the Board determines
otherwise, during the Restriction Period, the Grantee shall have the right to vote shares of Stock Awards and to receive any dividends or other distributions paid on such shares, subject to any restrictions deemed appropriate by the Board,
including, without limitation, the achievement of specific performance goals. 
 (f)    Lapse of
Restrictions. All restrictions imposed on Stock Awards shall lapse upon the expiration of the applicable Restriction Period and the satisfaction of all conditions imposed by the Board. The Board may determine, as to any or all Stock Awards, that
the restrictions shall lapse without regard to any Restriction Period. 

  
 8. 

 SECTION 7    Stock Units 

The Board may grant Stock Units representing one or more shares of Company Stock to an Employee,
Non-Employee Director or Key Advisor, upon such terms and conditions as the Board deems appropriate. The following provisions are applicable to Stock Units: 

(a)    Crediting of Units. Each Stock Unit shall represent the right of the Grantee to receive an
amount based on the value of a share of Company Stock, if specified conditions are met. All Stock Units shall be credited to bookkeeping accounts established on the Company’s records for purposes of the Plan. 

(b)    Terms of Stock Units. The Board may grant Stock Units that are payable if specified
performance goals or other conditions are met, or under other circumstances. Stock Units may be paid at the end of a specified performance period or other period, or payment may be deferred to a date authorized by the Board. The Board shall
determine the number of Stock Units to be granted and the requirements applicable to such Stock Units. 

(c)    Requirement of Employment or Service. Unless the Board determines otherwise, if the Grantee
ceases to be employed by, or provide service to, the Employer during a specified period, or if other conditions established by the Board are not met, the Grantee’s Stock Units shall be forfeited. The Board may, however, provide for complete or
partial exceptions to this requirement as it deems appropriate. 
 (d)    Payment With Respect to
Stock Units. Payments with respect to Stock Units may be made in cash, in Company Stock, or in a combination of the two, as determined by the Board. 

SECTION 8    Stock Appreciation Rights 

The Board may grant SARs to an Employee, Non-Employee Director or Key Advisor
separately or in tandem with any Option. The following provisions are applicable to SARs: 

(a)    Base Amount. The Board shall establish the base amount of the SAR at the time the SAR is
granted. The base amount of each SAR shall not be less than the Fair Market Value of a share of Company Stock on the date of Grant of the SAR. 

(b)    Tandem SARs. In the case of tandem SARs, the number of SARs granted to a Grantee that shall
be exercisable during a specified period shall not exceed the number of shares of Company Stock that the Grantee may purchase upon the exercise of the related Option during such period. Upon the exercise of an Option, the SARs relating to the
Company Stock covered by such Option shall terminate. Upon the exercise of SARs, the related Option shall terminate to the extent of an equal number of shares of Company Stock. 

(c)    Exercisability. An SAR shall be exercisable during the period specified by the Board in the
Grant Instrument and shall be subject to such vesting and other restrictions as may be specified in the Grant Instrument. The Board may accelerate the exercisability of any or all outstanding SARs at any time for any reason. SARs may only be
exercised while the Grantee is employed by, or providing service to, the Employer or during the applicable period after 

  
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termination of employment or service as described in Section 5(e) above. A tandem SAR shall be exercisable only during the period when the Option to which it is related is also exercisable.

 (d)    Grants to Non-Exempt Employees. Notwithstanding
the foregoing, SARs granted to persons who are non-exempt employees under the Fair Labor Standards Act of 1938, as amended, may not be exercisable for at least six months after the date of grant (except that
such SARs may become exercisable, as determined by the Board, upon the Grantee’s death, Disability or retirement, or upon a Change of Control or other circumstances permitted by applicable regulations). 

(e)    Value of SARs. When a Grantee exercises SARs, the Grantee shall receive in settlement of
such SARs an amount equal to the value of the stock appreciation for the number of SARs exercised. The stock appreciation for an SAR is the amount by which the Fair Market Value of the underlying Company Stock on the date of exercise of the SAR
exceeds the base amount of the SAR as described in subsection (a). 
 (f)    Form of Payment. The
appreciation in an SAR shall be paid in shares of Company Stock, cash or any combination of the foregoing, as the Board shall determine. For purposes of calculating the number of shares of Company Stock to be received, shares of Company Stock shall
be valued at their Fair Market Value on the date of exercise of the SAR. 
 SECTION 9    Other Equity Awards 

The Board may grant Other Equity Awards, which are awards (other than those described in Sections 5, 6, 7 and 8 of the Plan)
that are based on, measured by or payable in Company Stock, including, without limitation, stock appreciation rights, to any Employee, Non-Employee Director or Key Advisor, on such terms and conditions as the
Board shall determine. Other Equity Awards may be awarded subject to the achievement of performance goals or other conditions and may be payable in cash, Company Stock or any combination of the foregoing, as the Board shall determine. 

SECTION 10    Withholding of Taxes 

(a)    Required Withholding. All Grants under the Plan shall be subject to applicable federal
(including FICA), state and local tax withholding requirements. The Employer may require that the Grantee or other person receiving or exercising Grants pay to the Employer the amount of any federal, state or local taxes that the Employer is
required to withhold with respect to such Grants, or the Employer may deduct from other wages paid by the Employer the amount of any withholding taxes due with respect to such Grants. 

(b)    Election to Withhold Shares. If the Board so permits, a Grantee may elect to satisfy the
Employer’s tax withholding obligation with respect to Grants paid in Company Stock by having shares withheld up to an amount that does not exceed the minimum applicable withholding tax rate for federal (including FICA), state and local tax
liabilities. The election must be in a form and manner prescribed by the Board and may be subject to the prior approval of the Board. 

  
 10. 

 SECTION 11    Transferability of Grants 

(a)    Nontransferability of Grants. Except as provided below, only the Grantee may exercise rights
under a Grant during the Grantee’s lifetime. A Grantee may not transfer those rights except (i) by will or by the laws of descent and distribution or (ii) with respect to Grants other than Incentive Stock Options, if permitted in any
specific case by the Board, pursuant to a domestic relations order or otherwise as permitted by the Board. When a Grantee dies, the personal representative or other person entitled to succeed to the rights of the Grantee may exercise such rights.
Any such successor must furnish proof satisfactory to the Company of his or her right to receive the Grant under the Grantee’s will or under the applicable laws of descent and distribution. 

(b)    Transfer of Nonqualified Stock Options. Notwithstanding the foregoing, the Board may
provide, in a Grant Instrument, that a Grantee may transfer Nonqualified Stock Options to family members, or one or more trusts or other entities for the benefit of or owned by family members, consistent with the applicable securities laws,
according to such terms as the Board may determine; provided that the Grantee receives no consideration for the transfer of an Option and the transferred Option shall continue to be subject to the same terms and conditions as were applicable to the
Option immediately before the transfer. 
 SECTION 12    Right of First Refusal; Repurchase Right 

(a)    Offer. Prior to a Public Offering, if at any time an individual desires to sell, encumber, or
otherwise dispose of shares of Company Stock that were distributed to him or her under this Plan and that are transferable, the individual may do so only pursuant to a bona fide written offer, and the individual shall first offer the shares to the
Company by giving the Company written notice disclosing: (i) the name of the proposed transferee of the Company Stock, (ii) the certificate number and number of shares of Company Stock proposed to be transferred or encumbered,
(iii) the proposed price, (iv) all other terms of the proposed transfer, and (v) a written copy of the proposed offer. Within 60 days after receipt of such notice, the Company shall have the option to purchase all or part of such
Company Stock at the price and on the terms described in the written notice; provided that the Company may pay such price in installments over a period not to exceed four years, at the discretion of the Board. 

(b)    Sale. In the event the Company (or a stockholder, as described below) does not exercise the
option to purchase Company Stock, as provided above, the individual shall have the right to sell, encumber, or otherwise dispose of the shares of Company Stock described in subsection (a) at the price and on the terms of the transfer set forth
in the written notice to the Company, provided such transfer is effected within 15 days after the expiration of the option period. If the transfer is not effected within such period, the Company must again be given an option to purchase, as provided
above. 
 (c)    Assignment of Rights. The Board, in its sole discretion, may waive the
Company’s right of first refusal and repurchase right under this Section 12. If the Company’s right of first refusal or repurchase right is so waived, the Board may, in its sole discretion, assign such right to the remaining
stockholders of the Company in the same proportion that each stockholder’s stock ownership bears to the stock ownership of all the stockholders of the 

  
 11. 

 
Company, as determined by the Board. To the extent that a stockholder has been given such right and does not purchase his or her allotment, the other stockholders shall have the right to purchase
such allotment on the same basis. 
 (d)    Purchase by the Company. Prior to a Public Offering,
if a Grantee ceases to be employed by, or provide service to, the Employer, the Company shall have the right to purchase all or part of any Company Stock distributed to the Grantee under this Plan at its then current Fair Market Value (as defined in
Section 5(b)) or at such other price as may be established in the Grant Instrument; provided, however, that such repurchase shall be made in accordance with applicable accounting rules to avoid adverse accounting treatment. 

(e)    Public Offering. On and after a Public Offering, the Company shall have no further right to
purchase shares of Company Stock under this Section 12. The requirements of this Section 12 shall lapse and cease to be effective upon a Public Offering. 

(f)    Stockholder’s Agreement. Notwithstanding the provisions of this Section 12, if the
Board requires that a Grantee execute a stockholder’s agreement with respect to any Company Stock distributed pursuant to this Plan, which contains a right of first refusal or repurchase right, the provisions of this Section 12 shall not
apply to such Company Stock, unless the Board determines otherwise. 
 SECTION 13    Change of Control of the Company

 (a)    Change of Control. As used herein, a “Change of Control” shall be deemed
to have occurred if: 
 (i)    Any “person,” as such term is used in sections 13(d) and 14(d)
of Securities Exchange Act of 1934, as amended (the “Exchange Act”) (other than a person who is a stockholder of the Company on the effective date of the Plan) becomes a “beneficial owner” (as defined in Rule 13d-3 under the Exchange Act), directly or indirectly, of securities of the Company representing more than 50% of the voting power of the then outstanding securities of the Company; provided that a Change of Control
shall not be deemed to occur as a result of a transaction in which the Company becomes a subsidiary of another corporation and in which the stockholders of the Company, immediately prior to the transaction, will beneficially own, immediately after
the transaction, shares entitling such stockholders to more than 50% of all votes to which all stockholders of the parent corporation would be entitled in the election of directors; or 

(ii)    The consummation of (i) a merger or consolidation of the Company with another corporation
where the stockholders of the Company, immediately prior to the merger or consolidation, will not beneficially own, immediately after the merger or consolidation, shares entitling such stockholders to more than 50% of all votes to which all
stockholders of the surviving corporation would be entitled in the election of directors, (ii) a sale or other disposition of all or substantially all of the assets of the Company, or (iii) a liquidation or dissolution of the Company. 

  
 12. 

 (b)    Other Definition. The Board may modify the
definition of Change of Control for a particular Grant as the Board deems appropriate to comply with section 409A of the Code or otherwise. 

SECTION 14    Consequences of a Change of Control 

(a)    Acceleration. Upon a Change of Control, unless the Board determines otherwise, (i) all
outstanding Options and SARs shall accelerate and become fully exercisable, and (ii) all outstanding Stock Awards, Stock Units and Other Equity Awards shall become fully vested and shall be payable on terms determined by the Board. 

(b)    Other Alternatives. In the event of a Change of Control, the Board may take any of the
following actions with respect to any or all outstanding Grants: the Board may (i) determine that all outstanding Options and SARs that are not exercised shall be assumed by, or replaced with comparable options by the surviving corporation (or
a parent or subsidiary of the surviving corporation), and other outstanding Grants that remain in effect after the Change of Control shall be converted to similar grants of the surviving corporation (or a parent or subsidiary of the surviving
corporation), (ii) require that Grantees surrender their outstanding Options and SARs in exchange for one or more payments, in cash or Company Stock as determined by the Board, in an amount, if any, equal to the amount by which the then Fair Market
Value of the shares of Company Stock subject to the Grantee’s unexercised Options and SARs exceeds the Exercise Price or base amount of the Options and SARs, on such terms as the Board determines, or (iii) after giving Grantees an
opportunity to exercise their outstanding Options and SARs, terminate any or all unexercised Options and SARs at such time as the Board deems appropriate. Such assumption, surrender or termination shall take place as of the date of the Change of
Control or such other date as the Board may specify. 
 SECTION 15    Limitations on Issuance or Transfer of Shares

 (a)    Stockholder’s Agreement. The Board may require that a Grantee execute a
stockholder’s agreement, with such terms as the Board deems appropriate, with respect to any Company Stock issued or distributed pursuant to this Plan. 

(b)    Limitations on Issuance or Transfer of Shares. No Company Stock shall be issued or
transferred in connection with any Grant hereunder unless and until all legal requirements applicable to the issuance or transfer of such Company Stock have been complied with to the satisfaction of the Board. The Board shall have the right to
condition any Grant made to any Grantee hereunder on such Grantee’s undertaking in writing to comply with such restrictions on his or her subsequent disposition of such shares of Company Stock as the Board shall deem necessary or advisable, and
certificates representing such shares may be legended to reflect any such restrictions. Certificates representing shares of Company Stock issued or transferred under the Plan will be subject to such stop-transfer orders and other restrictions as may
be required by applicable laws, regulations and interpretations, including any requirement that a legend be placed thereon. 

(c)    Lock-Up Period. If so requested by the Company or
any representative of the underwriters (the “Managing Underwriter”) in connection with any underwritten offering of 

  
 13. 

 
securities of the Company, a Grantee (including any successor or assigns) shall not sell or otherwise transfer any shares or other securities of the Company during the 30-day period preceding and the 180-day period following the effective date of a registration statement filed by the Company for such underwriting (or such shorter period as
may be requested by the Managing Underwriter and agreed to by the Company) (the “Market Standoff Period”). The Company may impose stop-transfer instructions with respect to securities subject to the foregoing restrictions until the end of
such Market Standoff Period. 
 SECTION 16    Amendment and Termination of the Plan 

(a)    Amendment. The Board may amend or terminate the Plan at any time; provided, however, that the
Board shall not amend the Plan without stockholder approval if such approval is required in order to comply with the Code or to other applicable law. 

(b)    Termination of Plan. The Plan shall terminate on the day immediately preceding the tenth
anniversary of its effective date, unless the Plan is terminated earlier by the Board or is extended by the Board with the approval of the stockholders. 

(c)    Termination and Amendment of Outstanding Grants. A termination or amendment of the Plan that
occurs after a Grant is made shall not materially impair the rights of a Grantee unless the Grantee consents or unless the Board acts under Section 22(b). The termination of the Plan shall not impair the power and authority of the Board with
respect to an outstanding Grant. Whether or not the Plan has terminated, an outstanding Grant may be terminated or amended under Section 22(b) or may be amended by agreement of the Company and the Grantee consistent with the Plan. 

(d)    Governing Document. The Plan shall be the controlling document. No other statements,
representations, explanatory materials or examples, oral or written, may amend the Plan in any manner. The Plan shall be binding upon and enforceable against the Company and its successors and assigns. 

SECTION 17    Funding of the Plan 

This Plan shall be unfunded. The Company shall not be required to establish any special or separate fund or to make any other
segregation of assets to assure the payment of any Grants under this Plan. In no event shall interest be paid or accrued on any Grant, including unpaid installment of Grants. 

SECTION 18    Rights of Participants 

Nothing in this Plan shall entitle any Employee, Non-Employee Director, Key Advisor or
other person to any claim or right to be granted a Grant under this Plan. Neither this Plan nor any action taken hereunder shall be construed as giving any individual any rights to be retained by or in the employ of the Employer or any other
employment rights. 

  
 14. 

 SECTION 19    No Fractional Shares 

No fractional shares of Company Stock shall be issued or delivered pursuant to the Plan or any Grant. The Board shall determine
whether cash, other awards or other property shall be issued or paid in lieu of such fractional shares or whether such fractional shares or any rights thereto shall be forfeited or otherwise eliminated. 

SECTION 20    Effective Date of the Plan 

(a)    Effective Date. The Plan was originally effective as of September 28, 2006 and the
amended and restated Plan is effective as of September 12, 2008. 
 (b)    Public Offering.
The provisions of the Plan that refer to a Public Offering shall be effective, if at all, upon the initial registration of the Company Stock under section 12(g) of the Exchange Act, and shall remain effective thereafter for so long as such stock is
so registered. 
 SECTION 21    Miscellaneous 

(a)    Grants in Connection with Corporate Transactions and Otherwise. Nothing contained in this
Plan shall be construed to (i) limit the right of the Board to make Grants under this Plan in connection with the acquisition, by purchase, lease, merger, consolidation or otherwise, of the business or assets of any corporation, firm or
association, including Grants to employees thereof who become Employees, or for other proper corporate purposes, or (ii) limit the right of the Company to grant stock options or make other awards outside of this Plan. Without limiting the
foregoing, the Board may make a Grant to an employee, director or advisor of another corporation who becomes an Employee, Non-Employee Director or Key Advisor by reason of a corporate merger, consolidation,
acquisition of stock or property, reorganization or liquidation involving the Company, the parent or any of their subsidiaries in substitution for a stock option or stock awards grant made by such corporation. The terms and conditions of the
substitute grants may vary from the terms and conditions required by the Plan and from those of the substituted stock incentives. The Board shall prescribe the provisions of the substitute grants. 

(b)    Compliance with Law. The Plan, the exercise of Options and the obligations of the Company to
issue or transfer shares of Company Stock under Grants shall be subject to all applicable laws and to approvals by any governmental or regulatory agency as may be required. It is the intent of the Company that the Plan and Incentive Stock Options
granted under the Plan comply with the applicable provisions of section 422 of the Code and that, to the extent applicable, Grants made under the Plan comply with the requirements of section 409A of the Code and the regulations thereunder. To the
extent that any legal requirement as set forth in the Plan ceases to be required under applicable law, the Board may determine that such Plan provision shall cease to apply. The Board may revoke any Grant if it is contrary to law or modify a Grant
or the Plan to bring a Grant or the Plan into compliance with any applicable law or regulation. 

(c)    Employees Subject to Taxation Outside the United States. With respect to Grantees who are
subject to taxation in countries other than the United States, the Board may make Grants on such terms and conditions as the Board deems appropriate to comply with the laws of the applicable countries, and the Board may create such procedures,
addenda and 

  
 15. 

 
subplans and make such modifications as may be necessary or advisable to comply with such laws. 

(d)    Governing Law. The validity, construction, interpretation and effect of the Plan and Grant
Instruments issued under the Plan shall be governed and construed by and determined in accordance with the laws of the state of Delaware without giving effect to the conflict of laws provisions thereof. 

  
 16.EX-10.3

 Exhibit 10.3 

BioNano Genomics, Inc. 

Amended and Restated 2006 Equity Compensation Plan 

NOTICE OF STOCK OPTION GRANT     

[Optionholder name and address] 
 You
have been granted an option to purchase COMMON Stock of BioNano Genomics, Inc. (the “Company”) as follows: 
  

			
	 Board Approval Date:
	 	                    
		
	 Grant ID:
	 	                    
		
	 Grant Date:
	 	                    
		
	 Vesting Start Date:
	 	                    
		
	 Total Number of Shares Granted:
	 	                    
		
	 Exercise Price Per Share:
	 	$                  
		
	 Total Exercise Price:
	 	$                  
		
	 Expiration Date:
	 	                    
		
	 Type of Option Grant:
	 	Nonstatutory Stock Option (NSO)
		
	 Vesting Schedule:
	 	                    
		
	 Exercise Schedule:
	 	                    
		
	 Termination Period:
	 	The vested shares of this Option may be exercised after termination of your continuous service as an Employee, Key Advisor or member of the Board (“Continuous Service Status”) except as set out the Option Agreement (but
in no event later than the Expiration Date specified in Section 2 of the Option Agreement). Optionee is responsible for keeping track of these exercise periods following termination for any reason of his or her service relationship with the
Company. The Company will not provide further notice of such periods.
		
	 Exercise Payment Methods
	 	 By one or a combination of the following items (described in the Option Agreement):

By cash or check

Pursuant to a Regulation T Program promulgated by the U.S. Federal Reserve Board if the shares are publicly traded

		
	 Transferability:
	 	This Option may not be transferred.

 By clicking the “ACCEPT” button below, you and the Company agree that this option is granted under
and governed by the terms and conditions of the BioNano Genomics, Inc. Amended and Restated 2006 Equity Compensation Plan (the “Plan”), the Option Agreement and any ancillary documents, all of which you can access through a link from this
Notice of Grant and made a part of this document. Before you may electronically sign this Notice of Grant, you must click on and review the linked Plan, Option Agreement and any ancillary documents. PLEASE BE SURE TO READ THE OPTION AGREEMENT,
WHICH CONTAINS THE SPECIFIC TERMS AND CONDITIONS OF THIS OPTION, INCLUDING INFORMATION CONCERNING CANCELLATION AND TERMINATION OF THIS OPTION. 

PLEASE SEE NEXT PAGE OF THIS 2 PAGE NOTICE 

 Choice # 3 (continued) 

By clicking the “ACCEPT” button below, you agree to the following: 

I acknowledge and agree that: 

(a)    I have been able to access and view the Notice of Grant, the Plan, the Option Agreement and understand that all
rights and obligations with respect to these Shares are set forth in the Notice of Grant, the Plan and the Option Agreement; 

(b)    I agree to all terms and conditions contained in the Notice of Grant, the Plan and the Option Agreement; 

(c)    as of the date hereof, the Notice of Grant, the Plan and the Option Agreement set forth the entire understanding
between the Company and me regarding the acquisition of the Shares and supersedes all prior oral and written agreements with respect thereto; 

(d)    the exercise of this Option shall be conditional on me entering into a Joint Election with my employer in such form
as approved by HM Revenue & Customs for the transfer of any liability to employer’s Class 1 National Insurance contributions which may arise in respect of my Option; 

(e)    my rights to any Shares underlying the Option will be earned only as I provide services to the Company over time,
that the grant of the Option is not as consideration for services I rendered to the Company prior to my Vesting Commencement Date, and that nothing in this Notice or the attached documents confers upon me any right to continue my Continuous Service
Status with the Company for any period of time, nor does it interfere in any way with my right or the Company’s right to terminate that relationship at any time, for any reason, with or without cause; and 

(f)    I consent to receive the Notice of Grant, the Plan, the Option Agreement and any other ancillary documents by
electronic delivery and to participate in the Plan through an on line or electronic system established and maintained by the Company or another third party designated by the Company. 

It is recommended that you print a copy of your Grant Notice and all documents linked to this page for your records. 

 

	
	BioNano Genomics, Inc.
	
	

	
	Chief Financial Officer

  
  

 BIONANO GENOMICS, INC. 

AMENDED AND RESTATED 
 2006 EQUITY
COMPENSATION PLAN 
 OPTION AGREEMENT 

(INCENTIVE STOCK OPTION OR NONQUALIFIED STOCK OPTION GRANT) 

The BioNano Genomics, Inc. Amended and Restated 2006 Equity Compensation Plan (the “Plan”) provides for the grant of stock options
to purchase shares of common stock of BioNano Genomics, Inc. (the “Company”). 
 Pursuant to a Stock Option Grant Notice
(“Grant Notice”) and this Option Agreement (together with the Grant Notice, the “Grant Instrument”), the Company has granted the Grantee (as indicated on the Grant Notice) an option (the “Option”) under its Plan to
purchase the number of shares of the Company’s common stock indicated in the Grant Notice (the “Shares”) at the exercise price indicated in the Grant Notice. The Option is granted as an inducement for the Grantee to promote the best
interests of the Company and its stockholders. 
 Provided the Grantee timely and properly accepts the Grant Notice in accordance with the
terms set forth therein, the Option is effective as of the date of grant set forth in the Grant Notice (the “Date of Grant”). By accepting the Grant Notice, the Grantee agrees to be bound by the terms of the Grant Instrument and the Plan
and further agrees that all the decisions and determinations of the Board pursuant to the Plan shall be final and binding. 
 If there is
any conflict between the terms in the Grant Instrument and the terms of the Plan, the terms of the Plan will control. Capitalized terms not explicitly defined in this Option Agreement or in the Grant Notice but defined in the Plan will have the same
definitions as in the Plan. 
 The details of the Option, in addition to those set forth in the Grant Notice and the Plan, are as follows:

 1.    Vesting and Exercise of Option. 

(a)    The Option shall generally become exercisable pursuant to the vesting schedule set forth on the Grant Notice,
provided that the Grantee continues to be employed by, or providing service to, the Employer (as defined in the Plan) as an Employee, Key Advisor or member of the Board on the applicable vesting date. If the vesting would produce fractional Shares,
the number of Shares for which the Option becomes vested shall be rounded down to the nearest whole Share. 
 (b)    If
permitted in your Grant Notice and subject to the provisions of the Option, Grantee may elect at any time that is both (i) during the period of time Grantee continues to be employed by, or providing service to, the Employer as an Employee, Key
Advisor or member of 

 
the Board and (ii) during the term of the Option, to exercise all or part of the Option, including the unvested portion of the Option; provided, however, that: 

(i)    a partial exercise of the Option will be deemed to cover first vested shares of Common Stock and
then the earliest vesting installment of unvested shares of Common Stock; 
 (ii)    any shares of Common
Stock so purchased from installments that have not vested as of the date of exercise will be subject to the purchase option in favor of the Company as described in the Company’s form of Early Exercise Stock Purchase Agreement and the Plan; 

(iii)    Grantee will enter into the Company’s form of Early Exercise Stock Purchase Agreement with a
vesting schedule that will result in the same vesting as if no early exercise had occurred; and 

(iv)    if the Option is an incentive stock option (an “Incentive Stock Option”) under section
422 of the Internal Revenue Code of 1986, as amended (the “Code”), then, to the extent that the aggregate Fair Market Value (determined at the Date of Grant) of the shares of Common Stock with respect to which the Option plus all other
Incentive Stock Options Grantee holds are exercisable for the first time by Grantee during any calendar year (under all plans of the Company and its affiliates) exceeds one hundred thousand dollars ($100,000), the Option(s) or portions thereof that
exceed such limit (according to the order in which they were granted) will be treated as Nonqualified Stock Options. 
 2.    Term of
Option. 
 (a)    The Option shall have a term of ten years from the Date of Grant and shall terminate at the
expiration of that period, unless it is terminated at an earlier date pursuant to the provisions of this Agreement or the Plan. 

(b)    The Option shall automatically terminate upon the happening of the first of the following events: 

(i)    The expiration of the 90-day period after the Grantee ceases
to be employed by, or provide service to, the Employer, if the termination is for any reason other than Disability (as defined in the Plan), death or Cause (as defined in the Plan). 

(ii)    The expiration of the one-year period after the Grantee
ceases to be employed by, or provide service to, the Employer on account of the Grantee’s Disability. 

(iii)    The expiration of the one-year period after the Grantee
ceases to be employed by, or provide service to, the Employer, if the Grantee dies while employed by, or providing service to, the Employer or within 90 days after the Grantee ceases to be so employed or provide services on account of a termination
described in subparagraph (i) above. 

  
 -2- 

 (iv)    The date on which the Grantee ceases to be employed
by, or provide service to, the Employer for Cause. In addition, notwithstanding the prior provisions of this Paragraph 3, if the Grantee engages in conduct that constitutes Cause after the Grantee’s employment or service terminates, the Option
shall immediately terminate. 
 Notwithstanding the foregoing, in no event may the Option be exercised after the date that is immediately before the tenth
anniversary of the Date of Grant. Any portion of the Option that is not exercisable at the time the Grantee ceases to be employed by, or provide service to, the Employer shall immediately terminate. 

3.    Exercise Procedures. 

(a)    Subject to the provisions of Paragraphs 1 and 2 above, the Grantee may exercise part or all of the exercisable
Option by giving the Company notice of intent to exercise by (i) delivering a notice of exercise in such form designated by the Company (or a third party designated by the Company, if applicable) (the “Exercise Notice”) or completing
such other document and/or procedures designated by the Company for exercise, specifying the number of Shares as to which the Option is to be exercised and the method of payment and (ii) paying the exercise price and any applicable withholding
taxes to the Company’s Secretary, stock plan administrator or such other person as the Company may designate, together with such additional documents as the Company may then require. Payment of the exercise price shall be made in accordance
with procedures established by the Board from time to time based on type of payment being made but, in any event, prior to issuance of the Shares. The Grantee shall pay the exercise price (i) in cash, (ii) with the approval of the Board,
by delivering Shares of the Company, which shall be valued at their Fair Market Value (as defined in the Plan) on the date of delivery, or by attestation (on a form prescribed by the Board) to ownership of Shares having a Fair Market Value on the
date of exercise equal to the exercise price, (iii) after a Public Offering (as defined by the Plan), by payment through a broker in accordance with procedures permitted by Regulation T of the Federal Reserve Board or (iv) by such other
method as the Board may approve. The Board may impose from time to time such limitations as it deems appropriate on the use of Shares to exercise the Option. 

(b)    The obligation of the Company to deliver Shares upon exercise of the Option shall be subject to all applicable
laws, rules, and regulations and such approvals by governmental agencies as may be deemed appropriate by the Board, including such actions as Company counsel shall deem necessary or appropriate to comply with relevant securities laws and
regulations. The Company may require that the Grantee (or other person exercising the Option after the Grantee’s death) represent that the Grantee is purchasing Shares for the Grantee’s own account and not with a view to or for sale in
connection with any distribution of the Shares, or such other representation as the Board deems appropriate. 

(c)    All obligations of the Company under this Agreement shall be subject to the rights of the Company as set forth in
the Plan to withhold amounts required to be withheld for any taxes, if applicable. Subject to Board approval, the Grantee may elect to satisfy any tax withholding obligation of the Employer with respect to the Option by having Shares withheld up

  
 -3- 

 
to an amount that does not exceed the minimum applicable withholding tax rate for federal (including FICA), state and local tax liabilities. 

4.    Designation as Incentive Stock Option. If the Grant Notice indicates this Option is an Incentive Stock Option, the following
provisions shall apply. 
 (a)    If the aggregate fair market value of the stock on the date of the grant with respect
to which Incentive Stock Options are exercisable for the first time by the Grantee during any calendar year, under the Plan or any other stock option plan of the Company or a parent or subsidiary, exceeds $100,000, then the Option, as to the excess,
shall be treated as a nonqualified stock option that does not meet the requirements of section 422. If and to the extent that the Option fails to qualify as an Incentive Stock Option under the Code, the Option shall remain outstanding according to
its terms as a nonqualified stock option. 
 (b)    The Grantee understands that favorable Incentive Stock Option tax
treatment is available only if the Option is exercised while the Grantee is an employee of the Company or a parent or subsidiary of the Company or within a period of time specified in the Code after the Grantee ceases to be an employee. The Grantee
understands that the Grantee is responsible for the income tax consequences of the Option, and, among other tax consequences, the Grantee understands that he or she may be subject to the alternative minimum tax under the Code in the year in which
the Option is exercised. The Grantee will consult with his or her tax adviser regarding the tax consequences of the Option. 

(c)    The Grantee agrees that the Grantee shall immediately notify the Company in writing if the Grantee sells or
otherwise disposes of any Shares acquired upon the exercise of the Option and such sale or other disposition occurs on or before the later of (i) two years after the Date of Grant or (ii) one year after the exercise of the Option. The
Grantee also agrees to provide the Company with any information requested by the Company with respect to such sale or other disposition. 

5.    Change of Control. The provisions of the Plan applicable to a Change of Control shall apply to the Option, and, in the event
of a Change of Control, the Board may take such actions as it deems appropriate pursuant to the Plan. 
 6.    Right of First
Refusal; Repurchase Right; Stockholder’s Agreement. As a condition of receiving this Option, the Grantee hereby agrees that all Shares issued under the Plan shall be subject to a right of first refusal and repurchase right as described in
the Plan, and the Board may require that the Grantee (or other person exercising the Option) execute a stockholder’s agreement, in such form as the Board determines, with respect to all Shares issued upon the exercise of the Option before a
Public Offering. 
 7.    Restrictions on Exercise. Only the Grantee may exercise the Option during the Grantee’s lifetime.
After the Grantee’s death, the Option shall be exercisable (subject to the limitations specified in the Plan) solely by the legal representatives of the Grantee, or by the person who acquires the right to exercise the Option by will or by the
laws of descent and distribution, to the extent that the Option is exercisable pursuant to this Agreement. If the Option is not an Incentive 

  
 -4- 

 
Stock Option, the foregoing provisions of this section shall apply, except as the Board otherwise permits pursuant to the Plan. Notwithstanding the foregoing, if the Option is a nonnqualified
stock option, the foregoing provisions of this section shall apply, except to the extent the Board otherwise permits pursuant to the Plan. 

8.    Grant Subject to Plan Provisions. This grant is made pursuant to the Plan, the terms of which are incorporated herein by
reference, and in all respects shall be interpreted in accordance with the Plan. The grant and exercise of the Option are subject to interpretations, regulations and determinations concerning the Plan established from time to time by the Board in
accordance with the provisions of the Plan, including, but not limited to, provisions pertaining to (a) rights and obligations with respect to withholding taxes, (b) the registration, qualification or listing of the Shares,
(c) changes in capitalization of the Company and (d) other requirements of applicable law. The Board shall have the authority to interpret and construe the Option pursuant to the terms of the Plan, and its decisions shall be conclusive as
to any questions arising hereunder. 
 9.    No Employment or Other Rights. The grant of the Option shall not confer upon the
Grantee any right to be retained by or in the employ or service of the Employer and shall not interfere in any way with the right of the Employer to terminate the Grantee’s employment or service at any time. The right of the Employer to
terminate at will the Grantee’s employment or service at any time for any reason is specifically reserved. 
 10.    No
Stockholder Rights. Neither the Grantee, nor any person entitled to exercise the Grantee’s rights in the event of the Grantee’s death, shall have any of the rights and privileges of a stockholder with respect to the Shares subject to
the Option, until certificates for Shares have been issued upon the exercise of the Option. 
 11.    Assignment and Transfers.
The rights and interests of the Grantee under this Agreement may not be sold, assigned, encumbered or otherwise transferred except, in the event of the death of the Grantee, by will or by the laws of descent and distribution. In the event of any
attempt by the Grantee to alienate, assign, pledge, hypothecate, or otherwise dispose of the Option or any right hereunder, except as provided for in this Agreement, or in the event of the levy or any attachment, execution or similar process upon
the rights or interests hereby conferred, the Company may terminate the Option by notice to the Grantee, and the Option and all rights hereunder shall thereupon become null and void. The rights and protections of the Company hereunder shall extend
to any successors or assigns of the Company and to the Company’s parents, subsidiaries, and affiliates. This Agreement may be assigned by the Company without the Grantee’s consent. Notwithstanding the foregoing, if the Option is a
nonnqualified stock option, the foregoing provisions of this section shall apply, except to the extent the Board otherwise permits pursuant to the Plan. 

12.    Applicable Law. The validity, construction, interpretation and effect of this instrument shall be governed by and construed
in accordance with the laws of the State of Delaware, without giving effect to the conflicts of laws provisions thereof. 

13.    Notice. Any notice to the Company provided for in this instrument shall be addressed to the Company’s corporate
headquarters, and any notice to the Grantee shall be addressed to such 

  
 -5- 

 
Grantee at the current address shown on the payroll of the Company, or to such other address as the Grantee may designate to the Company in writing. Any notice shall be delivered by hand, sent by
telecopy or enclosed in a properly sealed envelope addressed as stated above, registered and deposited, postage prepaid, in a post office regularly maintained by the United States Postal Service. The Company may, in its sole discretion, decide to
deliver any documents related to participation in the Plan and this Option by electronic means or to request Grantee’s consent to participate in the Plan by electronic means. By accepting this Option, Grantee consents to receive such documents
by electronic delivery and to participate in the Plan through an on-line or electronic system established and maintained by the Company or another third party designated by the Company. 

  
 -6- 

 BIONANOMATRIX, INC 

AMENDED AND RESTATED 2006 EQUITY COMPENSATION PLAN 

Notice of Stock Option Exercise 
  

			
	To:	  	 Lorraine LoPresti, VP -
Finance & Administration, CFO

	  
 From:
	  	 Name:
                                         
                               

		  	 Social Security Number:
                                         
  

		  	 Address:
                                         
                           

		  	
                      
                                         
                    

	  
 Date:
	  	        ,     ,          (Original exercise notice is in the form of an email dated,
		  	        ,     ,         , which is attached hereto)

  

	 	1.    Exercise	

 I hereby elect to exercise the following option (the “Option”) under the BioNanomatrix, Inc.
Amended and Restated 2006 Equity Compensation Plan (the “Plan”): 
 Date of Option:
                     
 Exercise Price:
$                     
 The Option is: 

☐    an incentive stock option 

☐    a nonqualified stock option 
  

	 	2.	Payment 

  

							
	 I hereby elect to exercise the Option as set forth below.
	  			
			
	(a)	  	Number of shares being purchased:                     	  			
			
	(b)	  	Total exercise price to be paid	  			

							
		  	(per share exercise price multiplied by the number of shares being purchased):	  	$	                    	 
			
	(c)	  	Payment is made in:	  			
			
		  	Cash:	  	$	                    	 
			
		  	Shares of Company stock equal to the exercise price:	  	 	                    	 

 If shares of Company stock that I currently hold are being used to exercise the Option, a fully executed
Attestation to Ownership is attached. 
  

	 	3.	Tax Withholding For Nonqualified Options Only 

 I elect to have any withholding tax
obligations resulting from the exercise of the Option satisfied as follows: 
  

					
	 ☐
	  	Check to be given to the Company on the date of exercise.	  	Approximately $                    
			
	 ☐
	  	Share withholding, not to exceed minimum applicable withholding amount.	  	Approximately                  shares

  

	 	4.	Representations and Agreements 

 I hereby represent and agree as follows: 

 

	 	(a)	I am acquiring the shares underlying the Option solely for investment purposes, with no present intention of distributing or reselling any of the shares or any interest therein. I acknowledge that the shares have not
been registered under the Securities Act of 1933, as amended (the “Securities Act”). I am aware of the limitations under the Securities Act and under the Plan relating to a subsequent sale, transfer, pledge or other assignment or
encumbrance of the shares. I acknowledge that the shares must be held indefinitely unless they are subsequently registered under the Securities Act and applicable state securities laws or an exemption from such registration is available.

  

	 	(b)	Except as required by the Option grant agreement, I will not sell, transfer, pledge, donate, assign, mortgage, hypothecate or otherwise encumber the shares underlying the Option unless the shares are registered under
the Securities Act or the Company is given an opinion of counsel reasonably acceptable to the Company that such registration is not required under the Securities Act. I realize that there is no public market for the shares underlying the Option,
that no market may ever develop for them, and that they have not been approved or disapproved by any governmental agency. 

  
 -8- 

	 	(c)	In the event of an initial public offering of the Company’s stock, I will not sell or otherwise transfer or dispose of the shares of Company stock to be issued pursuant to the exercise of the Option for a period
specified by the representatives of the underwriters of the Company stock, which generally shall not exceed 180 days following the effective date of the initial registration statement of the Company filed under the Securities Act. 

 

	 	(d)	I hereby acknowledge that the shares of Company stock that I receive upon the exercise of the Option are subject to the Company’s right of first refusal and repurchase rights as set forth in the Plan, and other
restrictions set forth in the Plan and the Option grant agreement, and that the Company may require me to execute a stockholder’s agreement with respect to Company stock issued pursuant to the exercise of the Option. 

 

									
	 	 	 	 	 	 	Grantee
				
	Date:	 	  
	 		 	  

				
	 	 	 	 	 	 	Received and Accepted by the Company
	 	 	 	 	 	 	BioNanomatrix, Inc.
					
	Date:	 	  
	 		 	By:	 	
                     
                                         
                                   

  
 -9- 

 Attestation to Ownership of 

Company Common Stock 
 Pursuant to the
Notice of Stock Option Exercise that I have submitted to BioNanomatrix, Inc. (the “Company”) dated                     , I am
electing to pay the exercise price for the option shares by attesting to ownership of the shares listed below, and I hereby tender such shares in payment thereof. I hereby certify that: 

 

	1.	I beneficially own                  shares of Company common stock (the “Swap Shares”) as of the date hereof. These Swap
Shares are: 

  

	 	[    ]	Held in my name individually and a photocopy of the stock certificate evidencing my ownership is attached. 

  

	 	[    ]	Held in a brokerage account in my name. A photocopy of a brokerage statement of this account, dated within the preceding 15-day period and showing evidence of ownership of the
Swap Shares, is attached. (The Grantee may black out information not relevant to Company stock ownership on the account statement.) 

  

	2.	The Swap Shares are held by me as described above and are not held for my benefit by a trustee or custodian in an IRA account or in any other type of employee benefit or tax deferral plan. The Swap Shares are not
subject to any liens, claims or encumbrances. 

  

	3.	The Swap Shares have been owned by me as described above for at least six months and have not been used or acquired in a stock-for-stock
swap transaction within the preceding six months. 

  

					
	  
 Date
	 		  	  

Signature of Grantee

			
	  
 Date
	 		  	  
 Witness

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