Document:

EX-4.8

 Exhibit 4.8 

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR
THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AND PURSUANT TO THE PROVISIONS OF ARTICLE 5 BELOW, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND APPLICABLE STATE SECURITIES
LAW, OR SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION CAN BE MADE IN COMPLIANCE WITH RULE 144 OF THE ACT, OR IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE REASONABLY SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR
TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION. 
 WARRANT TO PURCHASE STOCK 

 

			
	 Company:
	  	 BioNano Genomics, Inc., a Delaware corporation

	 Number of Shares:
	  	 [____________] (Subject to adjustment as hereinafter provided)

	 Class of Stock:
	  	 Series D-1 Preferred Stock (Subject to Section 1.7)

	 Warrant Price:
	  	 $0.48 per Share (Subject to adjustment as hereinafter provided)

	 Issue Date:
	  	 [    ], 2018

	 Expiration Date:
	  	 The earlier to occur of the (i) expiration of this Warrant pursuant to Section 1.6 hereof or (ii) 10th
anniversary of the Issue Date

	 Credit Facility:
	  	 This Warrant is issued in connection with the Credit and Security Agreement, dated as of June 29, 2018, among the
Company, the other Borrowers (as defined therein) from time to time party thereto, MidCap Financial Trust, a Delaware statutory trust, as Agent and the lenders from time to time party thereto (as amended, restated, supplemented or otherwise modified
from time to time, the “Credit Agreement”).

 THIS WARRANT TO PURCHASE STOCK (this “Warrant”) CERTIFIES THAT, for good and
valuable consideration, including without limitation the mutual promises contained in the Credit Agreement (defined above), MidCap Funding XXVIII Trust, a Delaware statutory trust (together with any registered holder from time to time of this
Warrant or any holder of the Shares issuable or issued upon the exercise or conversion of this Warrant, “Holder”) is entitled to purchase the number of fully paid and nonassessable shares of the class and series of capital stock of the
Company at the Warrant Price, all as set forth above or herein below and as adjusted pursuant to the terms of this Warrant, subject to the provisions and upon the terms and conditions set forth in this Warrant. As used herein, “Share” or
“Shares” shall refer to either (i) the shares of stock issuable upon the exercise or conversion of this Warrant and any shares of capital stock into which such shares may be converted or exchanged, or (ii) the authorized or
issued and outstanding shares of capital stock of the Company which are of the same class and series as the shares of stock issuable upon the exercise or conversion of this Warrant, in either case as the specific provisions of this Warrant or the
context may require. 
 ARTICLE 1 EXERCISE. 

1.1 Method of Exercise. Holder may at any time and from time to time exercise this Warrant, in whole or in part, by
delivering a duly completed and executed Notice of Exercise in substantially the form attached as Appendix 1 to the principal office of the Company. Unless Holder is exercising the conversion right set forth in Section 1.2, Holder shall also
deliver to the Company a check, wire transfer (to an account designated by the Company), or other form of 

  
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payment acceptable to the Company for the aggregate Warrant Price for the Shares being purchased. 

1.2 Conversion Right. In lieu of exercising this Warrant as specified in Section 1.1, Holder may at any time and
from time to time after the Issue Date convert this Warrant, in whole or in part, into a number of Shares determined by dividing (a) the aggregate Fair Market Value of the number of Shares or the securities otherwise issuable upon exercise of
this Warrant with respect to which Holder elects to convert this Warrant minus the aggregate Warrant Price of such Shares by (b) the Fair Market Value of one Share, and by delivering a duly completed and executed Notice of Exercise in
substantially the form attached as Appendix 1 to the principal office of the Company. The “Fair Market Value” of a Share shall be determined pursuant to Section 1.3. 

1.3 Fair Market Value. If the Company’s common stock is traded on a nationally recognized securities exchange,
inter-dealer quotation system or over-the-counter market (a “Trading Market”) and the Shares are common stock, the Fair Market Value of each Share shall be the
closing price of a Share reported for the business day immediately before Holder delivers its Notice of Exercise to the Company (or in the instance where the Warrant is exercised immediately prior to the effectiveness of the Company’s initial
public offering of its common stock (“IPO”), the “price to public” per share specified in the final prospectus relating to such offering). If the Company’s common stock is traded in a Trading Market and the Shares are
preferred stock, the Fair Market Value of each Share shall be the closing price of such common stock reported for the business day immediately before Holder delivers its Notice of Exercise to the Company (or in the instance where the Warrant is
exercised immediately prior to the effectiveness of an IPO, the initial “price to public” per share specified in the final prospectus relating to the IPO), in either case, multiplied by the number of shares of the Company’s common
stock into which a Share is then convertible. In the event of an exercise in connection with an Acquisition, the Fair Market Value of a Share shall be the value to be received per Share by all holders of such Shares in such transaction. If the
Company’s common stock is not traded in a Trading Market and other than in the event of an exercise in connection with an IPO or Acquisition, the Board of Directors of the Company shall determine the Fair Market Value in its reasonable good
faith judgment. 
 1.4 Delivery of Certificate and New Warrant. Promptly after Holder exercises or converts this
Warrant pursuant to Section 1.1 or 1.2, respectively, and, if applicable, the Company receives payment of the aggregate Warrant Price, the Company shall promptly deliver to Holder certificates for the Shares acquired and, if this Warrant has
not been fully exercised or converted and has not expired, a new Warrant of like tenor representing the Shares not so acquired. This Warrant shall be deemed to have been exercised and such certificates deemed issued, and Holder shall become the
holder of record of the Shares for all purposes, as of the date of Holder’s delivery of the exercise notice pursuant to Section 1.1 or 1.2 and payment of the Warrant Price, if applicable. 

1.5 Replacement of Warrants. On receipt of evidence reasonably satisfactory to the Company of the loss, theft,
destruction or mutilation of this Warrant and, in the case of loss, theft or destruction, on delivery of an indemnity agreement reasonably satisfactory in form and amount to the Company or, in the case of mutilation on surrender and cancellation of
this Warrant, the Company shall execute and deliver, in lieu of this Warrant, a new warrant of like tenor. 

  
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 1.6 Treatment of Warrant Upon Acquisition of Company. 

1.6.1 “Acquisition”. For the purpose of this Warrant, “Acquisition” means (a) any sale,
exclusive license, or other disposition of all or substantially all of the assets of the Company, or (b) any reorganization, consolidation, share exchange or merger of the Company with or into another person or entity, or sale of outstanding
securities of the Company by the holders thereof, in each case where the holders of the Company’s securities before the transaction beneficially own less than fifty percent (50%) of the outstanding voting securities of the successor, acquiring
or surviving person or entity after the transaction. 
 1.6.2 Treatment of Warrant Upon Acquisition. 

(A) Upon the written request of the Company, Holder agrees that, in the event of an Acquisition that (i) is not described in
Section 1.6.1(a), (ii) in which the sole consideration is cash, and (iii) in connection with or as a result of which all holders of the Shares are receiving or have the right to receive solely cash in the same proportions in respect of all
of their Shares, then either (a) Holder shall exercise its conversion or purchase right under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such Acquisition, or (b) if Holder elects not to
exercise the Warrant, this Warrant will expire upon the consummation of such Acquisition, subject to Section 5.8. The Company shall provide Holder with written notice of its request relating to the foregoing (together with such reasonable
information as Holder may reasonably request in connection with such contemplated Acquisition giving rise to such notice), which notice is to be delivered to Holder not less than ten (10) business days prior to the closing of the proposed
Acquisition. 
 (B) Upon the written request of the Company, Holder agrees that, in the event of an Acquisition that is described in
Section 1.6.1(a) and is an “arms’-length” transaction with a third party that is not an Affiliate (as defined below) of the Company (a “True Asset Sale”), Holder may (a) exercise its conversion or purchase right
under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such True Asset Sale, (b) permit this Warrant to continue (unless exercised in the interim) until the earlier of the Expiration Date or the
dissolution and/or liquidation of the Company following the closing of any such True Asset Sale, subject to Section 5.8, or (c) elect to have the terms of Section 1.6.2(D) below apply. The Company shall provide Holder with written
notice of its request relating to the foregoing (together with such reasonable information as Holder may request in connection with such contemplated Acquisition giving rise to such notice), which notice is to be delivered to Holder not less than
ten (10) business days prior to the closing of the proposed True Asset Sale. 
 (C) Upon the written request of the Company, Holder
agrees that, in the event of an Acquisition (i) in which the consideration is a combination of cash and equity securities of the acquirer listed for trading on a U.S. national securities exchange and which may be freely resold pursuant to a
resale registration statement or under Rule 144 of the Act without any restriction or limitation (including without limitation volume and manner of sale restrictions), (ii) in connection with or as a result of which all holders of the Shares are
receiving or have the right to receive solely cash and/or such securities in the same proportions in respect of all of their Shares, and (iii) on the record date for which the Fair Market Value of one Share (or other securities issuable upon
exercise of this Warrant) is greater than the Warrant Price, Holder may (a) exercise its conversion or purchase right under this Warrant and such exercise will be deemed effective immediately prior to the consummation of such Acquisition, or
(b) if Holder elects not to exercise the Warrant, this Warrant will expire upon the consummation of such Acquisition, subject to 

  
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Section 5.8. The Company shall provide Holder with written notice of its request relating to the foregoing (together with such reasonable information as Holder may reasonably request in
connection with such contemplated Acquisition giving rise to such notice), which notice is to be delivered to Holder not less than ten (10) business days prior to the closing of the proposed Acquisition. 

(D) Upon the closing of any Acquisition other than those particularly described in subsections (A), (B) and (C) above (or in the case of
an Acquisition described in Section 1.6.2(B) above if Holder elects to have the terms of this Section 1.6.2(D) apply), the successor, surviving or acquiring entity shall assume in writing the obligations of this Warrant, including
agreements to deliver to Holder in exchange for this Warrant a written instrument issued by the successor, surviving or acquiring entity pursuant to which this Warrant shall thereafter be exercisable for the kind, amount and value of securities,
cash, and property as would have been payable for the Shares issuable upon exercise of the unexercised portion of this Warrant had such Shares been outstanding on the record date for the Acquisition and subsequent closing. The Warrant Price and/or
number of Shares shall be adjusted accordingly. 
 (E) Conditional Exercise. Notwithstanding any other provision hereof, if an
exercise of this Warrant is to be made in connection with an IPO or an Acquisition, such exercise may at the election of Holder be conditioned upon the consummation of such transaction, in which case such exercise shall not be deemed to be effective
until immediately prior to the consummation of such transaction. 
 As used herein “Affiliate” shall mean any person or entity
that owns or controls directly or indirectly ten percent (10%) or more of the voting securities of the Company, any person or entity that controls, is controlled by or is under common control with any such person or entity, and each of such
person’s or entity’s officers, directors, members, managers, joint venturers or partners, as applicable (whether as a result of the ownership of voting securities, by contract or otherwise). 

1.7 Adjustment in Number, Class and/or Series of Shares and Warrant Price in Certain Equity
Financings. In the event of an equity financing in which the Company issues shares of its preferred stock after the Issue Date (the “Next Round”), if the price per share (the “Next Round Price”) of any class or series of
Company’s preferred stock issued in such financing (the “Next Round Stock”) is less than the Warrant Price, Holder and any permitted transferee shall have the right, in Holder’s sole discretion, to elect to cause this Warrant to
be (and this Warrant shall be deemed automatically upon such election to be) exercisable for shares of the Next Round Stock at the Next Round Price (with the number of such shares subject to this Warrant automatically adjusted to equal (i) $0.48
divided by (ii) the Next Round Price). The Shares for which this Warrant is exercisable upon such election, if at all, shall bear the same rights, preferences, and privileges applicable to all holders of such Next Round Stock. Company shall
provide Holder no less than ten (10) business days’ written notice prior to any sale of Next Round Stock; and Holder shall provide Company written notice of its election, if at all, under this Section 1.7, no less than five
(5) business days’ prior to such sale. Any adjustment to the number of Shares, class or series of Shares and/or Warrant Price made as a result of this Section 1.7 shall be in addition to any adjustment(s) to be made in accordance with
Article 2 hereof. 
 ARTICLE 2 ADJUSTMENTS TO THE SHARES. 

2.1 Stock Dividends, Subdivisions and Combinations. If the Company declares or pays a dividend on the Shares payable in
common stock or other securities, then upon exercise 

  
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of this Warrant, for each Share acquired, Holder shall receive, without cost to Holder, the total number and kind of securities to which Holder would have been entitled had Holder owned the
Shares of record as of the date the dividend occurred. If the Company subdivides the Shares by reclassification, stock split, split-up or otherwise into a greater number of shares or takes any other action
which increases the number of shares of any class or series of capital stock into which the Shares are convertible, the number of Shares purchasable hereunder shall be proportionately increased and the Warrant Price shall be proportionately
decreased. If the outstanding Shares are combined or consolidated, by reclassification or otherwise, into a lesser number of shares, the Warrant Price shall be proportionately increased and the number of Shares shall be proportionately decreased.

 2.2 Reclassification, Exchange, Combination or Substitution. Upon any reclassification, exchange, combination,
substitution, reorganization, merger, consolidation or other event that results in a change of the number and/or class of the underlying securities as to which purchase rights under this Warrant exist, Holder shall be entitled to receive, upon
exercise or conversion of this Warrant, the number, amount and kind of securities, money and property that Holder would have ultimately received upon the completion of such reclassification, exchange, combination, substitution, reorganization,
merger, consolidation or other event if this Warrant had been exercised immediately before such reclassification, exchange, combination, substitution, reorganization, merger, consolidation or other event. Such an event shall include any automatic
conversion of the outstanding or issuable securities of the Company of the same class or series as the Shares to common stock pursuant to the terms of the Company’s Amended and Restated Certificate of Incorporation, as amended (the
“Certificate”). The Company or its successor shall promptly issue to Holder an amendment to this Warrant setting forth the number and kind of such new securities or other property issuable upon exercise or conversion of this Warrant as a
result of such reclassification, exchange, combination, substitution, reorganization, merger, consolidation or other event that results in a change of the number and/or class of securities issuable upon exercise or conversion of this Warrant. The
amendment to this Warrant shall provide for adjustments which shall be as nearly equivalent as may be practicable to the adjustments provided for in this Article 2 including, without limitation, adjustments to the Warrant Price and to the number of
securities or property issuable upon exercise of the amended Warrant. The provisions of this Section 2.2 shall similarly apply to successive reclassifications, exchanges, combinations, substitutions, reorganizations, mergers, consolidations or
other events. 
 2.3 Adjustments for Diluting Issuances. In the event of the issuance (a “Diluting
Issuance”) by the Company, after the Issue Date, of securities at a price per share less than the then Warrant Price, then the number of shares of common stock issuable upon conversion of the Shares, and the conversion price, shall be adjusted
in accordance with those provisions of the Certificate which apply to Diluting Issuances with the same effect as though the shares were outstanding at the time of the Diluting Issuance. The provisions set forth for the Shares in the Certificate
relating to the above in effect as of the Issue Date may not be amended, modified or waived, without the prior written consent of Holder unless such amendment, modification or waiver affects the rights associated with the Shares in the same manner
as such amendment, modification or waiver affects the rights associated with all other shares of the same series and class as the Shares. 

2.4 No Impairment. Without the prior written consent of Holder, the Company shall not, by amendment of the Certificate,
the Stockholders Agreements (as defined below) or its by-laws, or through any reorganization, recapitalization, share exchange, transfer of assets, consolidation, merger, dissolution, issuance or sale of
securities, or any other voluntary action, 

  
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avoid or seek to avoid the observance or performance of any of the terms of this Warrant, and shall at all times in good faith assist in carrying out of all such terms and in taking all such
action as may be necessary or appropriate to protect Holder’s rights against such avoidance or impairment. 
 2.5
Fractional Shares. No fractional Shares shall be issuable upon exercise or conversion of this Warrant and the number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional share interest arises upon any
exercise or conversion of the Warrant, the Company shall eliminate such fractional share interest by paying Holder the amount computed by multiplying the fractional interest by the Fair Market Value of a full Share. 

2.6 Certificate as to Adjustments. Upon each adjustment of the Warrant Price or the kind or number of securities
issuable under this Warrant pursuant to this Article 2, the Company shall promptly notify Holder in writing, and, at the Company’s expense, promptly compute such adjustment, and furnish Holder with a certificate of its Chief Executive Officer,
Corporate Secretary or a senior financial officer setting forth such adjustment and the facts upon which such adjustment is based. The Company shall, upon written request, furnish Holder a certificate setting forth the Warrant Price and the number
and kind of securities issuable under this Warrant in effect upon the date thereof and the series of adjustments leading to such Warrant Price and such number and kind of securities. 

ARTICLE 3 REPRESENTATIONS, WARRANTIES AND COVENANTS OF THE COMPANY. 

3.1 Representations and Warranties. The Company represents and warrants and covenants to Holder as follows: 

(a) The Company has all requisite legal and corporate power and authority, and has taken all corporate action on the part of
itself, its officers, directors and stockholders necessary, to execute, issue and deliver this Warrant, to issue the Shares issuable upon exercise or conversion of this Warrant and the securities issuable upon conversion of the Shares, and to carry
out and perform its obligations under this Warrant, and this Warrant constitutes the legally binding and valid obligation of the Company enforceable in accordance with its terms, except as enforceability may be limited by applicable bankruptcy,
insolvency, reorganization, or similar laws relating to or affecting the enforcement of creditors’ rights, or to principles of equity. 

(b) This Warrant has been validly issued and is free of restrictions on transfer other than restrictions on transfer set
forth herein and under applicable state and federal securities laws. All Shares which may be issued upon the exercise of the purchase or conversion right represented by this Warrant, and all securities, if any, issuable upon conversion of the
Shares, shall, upon issuance, be duly authorized, validly issued, fully paid and nonassessable, and free of any liens and encumbrances (including preemptive or other similar rights) except for restrictions on transfer provided for herein or under
applicable federal and state securities laws. 
 (c) The execution, delivery, and performance of this Warrant will not
result in a violation of, be in conflict with, or constitute a default under, with or without the passage of time or giving of notice, any provision of the Certificate, the Stockholders Agreements or the Company’s
by-laws, any provision of any judgment, decree, or order to which the Company is a party, by which it is bound, or to which any of its material assets are subject, any contract, obligation, or commitment to
which the Company is a party or by which it is bound, or any statute, 

  
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rule, or governmental regulation applicable to the Company, or the creation of any lien, charge, or encumbrance upon any assets of the Company. 

(d) The Company has provided Holder with a capitalization table of the Company, and such capitalization table is complete and
accurate as of the date hereof and reflects all outstanding capital stock of the Company and all outstanding warrants, options, conversion privileges, preemptive rights and other rights or agreements to purchase or otherwise acquire or issued any
equity securities or convertible debt securities of the Company. The Company has reserved a sufficient number of Shares for issuance upon the exercise of this Warrant and a sufficient number of shares of the securities issuable upon conversion of
the Shares. 
 (e) The Warrant Price is no greater than the lowest price at which the Company has issued Series D-1 Preferred Stock. 
 3.2 Notice of Certain Events; Information. If the Company
proposes at any time (a) to declare any dividend or distribution upon any of its stock, whether in cash, property, stock, or other securities and whether or not a regular cash dividend; (b) to effect any reclassification or
recapitalization of any of its stock; (c) to merge or consolidate with or into any other corporation, or sell, lease, license, or convey all or substantially all of its assets, (d) to approve or participate in any Acquisition or an IPO,
(e) to liquidate, dissolve or wind up or approve or consummate any Liquidation Event (as defined in the Certificate), or (f) to take any action or to effect any transaction which requires the Company to provide notice to other holders of
the Shares, then, in connection with each such event, the Company shall give Holder: (1) at least ten (10) business days prior written notice of the date on which a record will be taken for such dividend or distribution (and specifying the
date on which the holders of stock will be entitled thereto) or for determining rights to vote, if any, in respect of the matters referred to in (a) above; and (2) in the case of the matters referred to in (b), (c), (d), (e) or
(f) above, at least ten (10) business days prior written notice of the date when the same will take place (and, if applicable, specifying the date on which the holders of stock will be entitled to exchange their common stock for securities
or other property deliverable upon the occurrence of such event). The Company will also provide such information in its possession as is requested by Holder and as is reasonably necessary to enable Holder to comply with Holder’s accounting or
reporting requirements, including without limitation, a capitalization table, to be provided to Holder within thirty (30) days after the end of each fiscal quarter of the Company, including the per share price of the Company’s equity
securities most recently issued prior to the date such capitalization table and indication are so provided; provided, that the Company’s obligations set forth in this sentence shall terminate immediately prior to the Company’s IPO. 

3.3 Stockholders Agreements; No Other Stockholder Rights. Except as provided in this Warrant and subject to the
following provisions of this Section 3.3, Holder will not have any rights as a stockholder of the Company until the exercise of this Warrant. Effective upon any exercise or conversion of this Warrant, Holder and any permitted transferee of the
Warrant or the Shares shall be entitled to all of the rights and benefits provided to all other holders of the Shares pursuant to, and the Company and Holder agree that Holder (and any permitted transferee of the Warrant or the Shares) will execute
a counterpart signature page and become a party to (a) the Fifth Amended and Restated Stockholders Agreement, dated as of August 5, 2016 and the Fifth Amended and Restated Investor Rights Agreement, dated as of August 5, 2016, in each
case, by and among the Company and certain of its stockholders (as hereafter amended, restated or superseded, together, the “Stockholders Agreements”), provided that no such amendment shall

  
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in any respect restrict Holder’s or such permitted transferee’s right and ability to transfer this Warrant or the Shares to any affiliate of Holder or such permitted transferee and
(b) provided Holder or any permitted transferee agrees to become a party to any such agreement entered into hereafter (such agreement not to be unreasonably withheld), any agreement to which holders of the Shares may hereafter become parties
and the Shares may become bound (including, without limitation, any stockholders, investor rights, registration rights, right of refusal, voting and co-sale rights or similar agreement); and provided, that
(v) Holder and any permitted transferee shall have all of the rights of each other holder of Shares under all such agreements without regard to any applicable minimum share ownership or other requirement on which such rights are conditioned,
(w) with respect to Holder and its permitted transferees and assigns, notwithstanding any term or restriction on transfer contained in the Stockholders Agreements, Holder and its permitted transferees shall have the unrestricted right to
transfer all or any portion of the Shares to any assignee of or purchaser from Holder or its affiliate of their rights under the Credit Agreement (to the extent permitted by the Credit Agreement) or any interest or participation therein,
(x) Holder and its permitted transferees may transfer its rights under the Stockholders Agreements to any affiliate of Holder or any assignee of or purchaser from Holder or its affiliates of their rights under the Credit Agreement (to the
extent permitted by the Credit Agreement) or any interest or participation therein, (y) Holder and its permitted transferees shall have any purchase, participation, preemptive and registration rights granted to any other holders of the Shares,
and (z) in the event any term, restriction or condition of the Stockholders Agreements or any such agreement conflicts with, is inconsistent with or would otherwise prohibit or restrict the exercise of any right of Holder under this Warrant,
the terms of this Warrant shall control and this Warrant and Holder shall not be subject to such term, restriction or condition. As an illustration and not by way of limitation as to the purpose and intent of this Section 3.3, the Company shall
grant registration rights to Holder for any Shares acquired by Holder upon exercise or conversion of this Warrant or conversion of such Shares in parity to the registration rights granted to any other holder of the Shares. 

ARTICLE 4 REPRESENTATIONS AND WARRANTIES OF HOLDER. Holder represents and warrants to the Company as follows: 

4.1 Purchase for Own Account. This Warrant and the securities to be acquired upon exercise of this Warrant by Holder
will be acquired for investment for Holder’s account, not as a nominee or agent, and not with a view to the public resale or distribution within the meaning of the Act and Holder has no present intention of selling or engaging in any public
distribution of the same except pursuant to a registration or exemption or any transfer contemplated by or permitted under Section 3.3. Holder also represents that Holder has not been formed for the specific purpose of acquiring this Warrant or
the Shares. 
 4.2 Disclosure of Information. Holder has received or has had full access to all the information it
considers necessary or appropriate to make an informed investment decision with respect to the acquisition of this Warrant and its underlying securities. Holder further has had an opportunity to ask questions and receive answers from the Company
regarding the terms and conditions of the offering of this Warrant and its underlying securities and to obtain additional information (to the extent the Company possessed such information or could acquire it without unreasonable effort or expense)
necessary to verify any information furnished to Holder or to which Holder has access. 
 4.3 Investment Experience.
Holder understands that the purchase of this Warrant and its underlying securities involves substantial risk. Holder has experience as an 

  
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investor in securities of companies in the development stage and acknowledges that Holder can bear the economic risk of Holder’s investment in this Warrant and its underlying securities and
has such knowledge and experience in financial or business matters that Holder is capable of evaluating the merits and risks of its investment in this Warrant and its underlying securities and/or has a preexisting personal or business relationship
with the Company and certain of its officers, directors or controlling persons of a nature and duration that enables Holder to be aware of the character, business acumen and financial circumstances of such persons. 

4.4 Accredited Investor Status. Holder is an “accredited investor” within the meaning of Regulation D
promulgated under the Act. 
 4.5 The Act. Holder understands that this Warrant and the Shares issuable upon exercise
or conversion hereof have not been registered under the Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of Holder’s investment intent as expressed herein. Holder
understands that this Warrant and the Shares issued upon any exercise or conversion hereof must be held indefinitely unless subsequently registered under the Act and qualified under applicable state securities laws, or unless exemption from such
registration and qualification are otherwise available. 
 4.6 Market
Stand-Off. Holder hereby agrees that, in connection with the Company’s IPO it shall not to the extent requested by the Company’s underwriter(s) sell, make any short sale of, loan, grant any
option for the purchase of, or otherwise dispose of any securities of the Company (other than any disposed of in the registration and those acquired by Holder in the IPO or thereafter in open market transactions, or any disposed of in a private
transaction to a transferee who agrees to be bound by the terms of this Section 4.6) for up to one hundred eighty (180) days from the effective date of the registration statement filed in connection with the IPO; provided, however, that
such one hundred eighty (180) day period may be extended to the extent necessary to permit any managing underwriter to comply with applicable law; provided further, however, that Holder shall not be bound by the restrictions set forth in this
Section 4.6 unless all five percent (5%) or greater (in terms of ownership of the issued and outstanding capital stock of the Company) stockholders of the Company also agree to such restrictions; and provided, further, that any discretionary
waiver or termination of the foregoing restrictions by the Company or the underwriters shall apply to all holders of the Company’s equity securities subject to such restrictions pro rata based on the number of shares subject to such
restrictions. Holder agrees to enter into the form of lock-up agreement as reasonably requested by the underwriter(s) in connection with this Section 4.6. 

ARTICLE 5 MISCELLANEOUS. 

5.1 Term. This Warrant is exercisable in whole or in part at any time and from time to time on or before the Expiration
Date. The conditions under which the Warrant shall automatically convert on the Expiration Date are set forth in Section 5.8 below. 

5.2 Legends. 

(a) This Warrant and the Shares (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any)
shall be imprinted with a legend in substantially the following form: 

  
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 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE
SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT PURSUANT TO THE PROVISIONS OF ARTICLE 5, MAY NOT BE OFFERED, SOLD OR OTHERWISE TRANSFERRED, PLEDGED OR HYPOTHECATED UNLESS REGISTERED UNDER
SAID ACT AND APPLICABLE STATE SECURITIES LAW, OR UNLESS SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION CAN BE MADE IN COMPLIANCE WITH RULE 144 OF THE ACT, OR UNLESS, IN THE OPINION OF LEGAL COUNSEL IN FORM AND SUBSTANCE REASONABLY
SATISFACTORY TO THE ISSUER OF THESE SECURITIES, SUCH OFFER, SALE OR TRANSFER, PLEDGE OR HYPOTHECATION IS EXEMPT FROM REGISTRATION. 

THE SECURITIES EVIDENCED BY THIS CERTIFICATE ARE SUBJECT TO RESTRICTIONS ON TRANSFERABILITY AND RESALE, INCLUDING A MARKET STAND-OFF PERIOD OF UP TO 180 DAYS IN THE EVENT OF A PUBLIC OFFERING, OR FOR A LONGER PERIOD IF THE ISSUER’S TRANSFER AGENT IS NOTIFIED BY THE ISSUER OR THE ISSUER’S COUNSEL THAT THIS MARKET STAND-OFF RESTRICTION HAS BEEN EXTENDED FOR THE PURPOSE OF COMPLYING WITH APPLICABLE LAW. 

(b) Notwithstanding the foregoing, neither this Warrant nor any certificate or instrument evidencing this Warrant or the
Shares shall bear, and the Company hereby agrees to remove, within ten (10) days of any written request (together with such evidence or documentation described in the following provisions) by Holder, pursuant to the following provisions of this
Section 5.2(b), or not to affix, as applicable, any restrictive or other legend, notice or provision restricting the sale or transfer of this Warrant or the Shares, in each case provided that Holder has provided reasonable evidence to the
Company (including any customary broker’s or transferring stockholder’s letters but expressly excluding an opinion of counsel other than with respect to clause (D) below) that: (A) a transfer of this Warrant or the Shares, as
applicable, has been made pursuant to SEC Rule 144 (assuming the transferor is not an “affiliate” (as defined in SEC Rule 144) of the Company); (B) the Warrant or the Shares, as applicable, are then eligible for transfer pursuant to SEC
Rule 144; (C) a transfer of this Warrant or the Shares has been made for no consideration to an affiliate of Holder or any assignee or purchaser of Holder’s or its affiliate’s rights under the Credit Agreement or any interest or
participation therein or has otherwise been made to any affiliate of Holder who is an “accredited investor” as defined in Regulation D promulgated under the Act, and that is otherwise in compliance with all applicable securities laws; or
(D) in connection with any other sale or transfer, provided that upon the request of the Company, such Holder provides the Company with an opinion of counsel to such Holder, in a reasonably acceptable form to the Company, to the effect that
either such sale or transfer may be made without registration under the applicable requirements of the Act or that such a legend, notice or provision is not required by, and is not required in order to establish compliance with any provisions of,
the Act. For all purposes of Section 1.4, the Company shall not be deemed to have delivered to Holder Shares unless and until the Company shall have fully complied with all of the terms and conditions of this Section 5.2(b) (if removal has
been requested by Holder in compliance with this Section 5.2(b)). 
 5.3 Compliance with Securities Laws on
Transfer. This Warrant and the Shares issuable upon exercise of this Warrant (and the securities issuable, directly or indirectly, upon conversion of the Shares, if any) may not be transferred or assigned in whole or in part

  
 -10- 

 
without compliance with applicable federal and state securities laws by the transferor and the transferee (including, without limitation, the delivery of investment representation letters and,
subject to Section 5.2(b), legal opinions reasonably satisfactory to the Company, as reasonably requested by the Company). The Company shall not require Holder to provide an opinion of counsel if the transfer is to an affiliate of Holder or any
assignee or purchaser of Holder’s or its affiliate’s rights under the Credit Agreement or any interest or participation therein. Additionally, the Company shall also not require an opinion of counsel if there is no material question as to
the availability of Rule 144. 
 5.4 Transfer Procedure. Subject to the provisions of Section 5.3 and upon and
effective immediately as of providing Company with written notice substantially in the form attached as Appendix 2, Holder and any permitted transferee may transfer all or part of this Warrant or the Shares issuable upon exercise of this Warrant (or
the Shares issuable directly or indirectly, upon conversion of the Shares, if any) to any transferee, provided, however, in connection with any such transfer, Holder or such transferee will give the Company notice of the portion of the Warrant being
transferred with the name, address and taxpayer identification number of the transferee and, in the case of transfer to a transferee who is not an affiliate of the Holder, Holder or such transferee promptly thereafter surrenders this Warrant to the
Company for reissuance to the transferee(s) (and Holder if applicable). The Company may refuse to transfer this Warrant or the Shares to any person who directly competes with the Company, unless, in either case, the stock of the Company is publicly
traded. 
 5.5 Notices. All notices, requests, documents and other communications (collectively, “Notices”)
from the Company to Holder, or vice versa, shall be in writing and deemed validly delivered effective as of the earliest to occur of (a) when actually received, (b) when transmitted by facsimile or electronic mail (PDF), (c) the first
business day after mailing by first-class registered or certified mail, postage prepaid, or after deposit with a reputable overnight courier with all charges paid, in each case other than actual receipt at such mailing, facsimile or electronic mail
address as may have been furnished to the Company or Holder, as the case may be. As used in this Warrant, “business days” shall refer to all days other than any Saturday, Sunday or day on which the Company’s primary depository bank is
closed. All notices to Holder shall be addressed as follows until the Company receives notice of a change of address in connection with a transfer or otherwise: 

MIDCAP FUNDING XXVIII TRUST 

c/o MidCap Financial Services, LLC, as servicer 

7255 Woodmont Avenue, Suite 200 

Bethesda, MD 20814 

Attention: Portfolio Management – BioNano transaction 

Facsimile: (301) 941-1450 

E-mail: notices@midcapfinancial.com 

with a copy to: 

c/o MidCap Financial Services, LLC, as servicer 

7255 Woodmont Avenue, Suite 200 

Bethesda, Maryland 20814 

Attn: General Counsel 

Facsimile: 301-941-1450 

E-mail: legalnotices@midcapfinancial.com 

  
 -11- 

 Notice to the Company shall be addressed as follows until Holder receives notice of a change in
address: 
 BioNano Genomics, Inc. 

9640 Towne Centre Dr #100 

San Diego CA 92121 

5.6 Waiver. This Warrant and any term hereof may be changed, waived, discharged or terminated only by an instrument in
writing signed by the party against which enforcement of such change, waiver, discharge or termination is sought. 
 5.7
Attorneys’ Fees. In the event of any dispute between the parties concerning the terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such
dispute, including reasonable attorneys’ fees. 
 5.8 Automatic Conversion upon Expiration. Unless Holder
notifies the Company in writing to the contrary prior to such automatic conversion, in the event that, upon the earliest to occur of the Expiration Date or any expiration, involuntary termination or cancellation of this Warrant, the Fair Market
Value of one Share as determined in accordance with Section 1.3 above is greater than the Warrant Price in effect on such date, then this Warrant shall automatically be deemed as of immediately before such date to have been converted pursuant
to Section 1.2 above as to all Shares for which it shall not previously have been exercised or converted, and the Company shall promptly deliver a certificate representing the Shares issued upon such conversion to the Holder. 

5.9 Counterparts. This Warrant may be executed in counterparts, all of which together shall constitute one and the same
agreement. 
 5.10 Governing Law. This Warrant shall be governed by and construed in accordance with the laws of the
State of New York, in each case (except to the extent the General Corporation Law of the State of Delaware applies) without giving effect to its principles regarding conflicts of law (other than
Section 5-1401 of the General Obligations Law). 
 5.11 Headings. The
various headings in this Warrant are inserted for convenience only and shall not affect the meaning or interpretation of this Warrant or any provisions hereof. 

5.12 Severability. In the event any one or more of the provisions of this Warrant shall for any reason be held invalid,
illegal or unenforceable, the remaining provisions of this Warrant shall be unimpaired, and the invalid, illegal or unenforceable provision shall be replaced by a mutually acceptable valid, legal and enforceable provision. 

[Balance of Page Intentionally Left Blank] 

  
 -12- 

			
	“COMPANY”
	
	BIONANO GENOMICS, INC.
		
	By:	 	 
	Name:	 	 
		 	(Print)
	Title:	 	Chief Executive Officer

			
	“HOLDER”
	
	MIDCAP FUNDING XXVIII TRUST
	
	By: Apollo Capital Management, L.P.,
	its investment manager
	
	By: Apollo Capital Management GP, LLC,
	its general partner

  

			
	By:	 	 

			
	Name:	 	
	Title:	 	

 APPENDIX 1 

NOTICE OF EXERCISE 

1. Holder elects to purchase ____________ shares of the [Preferred/Common] Stock of BioNano Genomics, Inc. pursuant to the
terms of the attached Warrant, and tenders payment of the purchase price of the shares in full. 
 [or] 

1. Holder elects to convert the attached Warrant into Shares/cash [strike one] in the manner specified in the Warrant. This
conversion is exercised for ____________________ of the Shares covered by the Warrant. 
 [Strike paragraph that does not
apply.] 
 2. Please issue a certificate or certificates representing the shares in the name specified below: 

 

			
	
		
		 	 
		 	 Holder’s Name

		
		 	 
		 	 
		 	 (Address)

		 	

 3. By its execution below and for the benefit of the Company, Holder hereby restates each of
the representations and warranties in Article 4 of the Warrant as the date hereof. 
  

			
	HOLDER:
	
	 

 
			
		
	By:	 	 

 
			
		
	Name:	 	 

 
			
		
	Title:	 	 

 
			
		
	(Date):	 	 

 APPENDIX 2 

ASSIGNMENT 

For value received, MIDCAP FUNDING XXVIII TRUST hereby sells, assigns and transfers unto 

Name: 

Address: 

Tax ID: 

that certain Warrant to Purchase Stock issued by BioNano Genomics, Inc. (the “Company”), on June 29, 2018 (the
“Warrant”) together with all rights, title and interest therein. 
  

					
	MIDCAP FUNDING XXVIII TRUST	 	
		
	By: Apollo Capital Management, L.P.,	 	
	its investment manager	 	
		
	By: Apollo Capital Management GP, LLC,	 	
	its general partner	 	
			
	By:	 	 	 	)
	Name:	 	 	 	
		 	(Print)	 	
	Title:	 	 	 	

 Date:
                                 

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

			
	[NAME OF TRANSFEREE]

 
			
		
	By:	 	 

 
			
		
	Name:	 	 

 
			
		
	Title:EX-10.39

 Exhibit 10.39 

***Text Omitted and Filed Separately 

with the Securities and Exchange Commission 

Confidential Treatment Requested 

Under 17 C.F.R. Sections 200.80(b)(4) 

and 230.406 
 AMENDMENT
TO PATENT SUBLICENSE AGREEMENT 
 THIS AMEDMENT TO PATENT SUBLICENSE AGREEMENT (this
“Amendment”) is made this 28th day of June, 2018 (the “Amendment Effective Date”) between: 

Industry 3200, Inc., a Delaware Corporation with a principal office located at 1155 Camino Del Mar #118, Del Mar, CA
92014 (“Sublicensor”); and 
 BioNano Genomics, Inc., a Delaware corporation with a place of business at
9640 Town Centre Drive, Suite 100, San Diego, CA 92121 (“Sublicensee”), 
 individually a “Party” and together
the “Parties”. 
 WHEREAS, on December 27, 2013, the Sublicensor and Sublicensee entered into a Patent
Sublicense Agreement (the “Agreement”). 
 WHEREAS, the Sublicensor and Sublicensee now wish to amend certain terms
of the Agreement as set forth herein; 
 NOW, THEREFORE, in consideration of the mutual covenants contained in this Amendment and
other good and valuable consideration, the receipt and sufficiency of which each Party acknowledges, the Sublicensor and Sublicensee hereto agree the following: 
  

	 	1.	 The terms utilized in this Amendment shall have the same meanings set forth in the Agreement, unless otherwise
indicated herein. 

  

	 	2.	 Section 3.1 of the Agreement is hereby amended and restated in its entirety as
follows: 

 “3.1. Sublicense Fees: As consideration for the grant and maintenance of this
Agreement, Sublicensee shall pay, and Sublicensor shall accept, a sublicense fee as follows: 
 3.1.1. $[...***...]
within thirty (30) days of the full execution of this Agreement or of the Master License Agreement, whichever is later. 

3.1.2. $[...***...] on July 1 of the second Agreement Year. 

3.1.3. $[...***...] on July 1 of the third Agreement Year. 

3.1 .4. $[...***...] on July 1 of the fourth Agreement Year. 

3.1.5. $[...***...] on July 1 of the fifth Agreement Year. 

  

***Confidential Treatment Requested 

 3.1.6. $[...***...] on October 1 of the sixth Agreement Year. 

3.1.7. $[...***...] on July 1 of each subsequent Agreement Year, if the term of this Agreement is extended to
include such Agreement Year.” 
  

	 	3.	 Section 4.1 under Section 4 “TERM AND TERMINATION” of the Agreement
is hereby amended and restated in its entirety as follows: 

 “4.1. Unless otherwise terminated under
any other provision of this Agreement, this Agreement shall expire on the earlier of the end of the sixth (6th) Agreement Year or upon the termination of the Master License Agreement.” 

 

	 	4.	 All terms and conditions of the Agreement not expressly amended by this Amendment shall remain in full force
and effect. · 

  

	 	5.	 In the event of any dispute, conflict or ambiguity between the terms and conditions of this Amendment and the
License Agreement, this Amendment shall control. 

  

	 	6.	 This Amendment, and the Agreement (where herein referenced), together constitute the entire agreement of the
Parties as to the subject matter of this Amendment, and supersede all prior negotiations, representations, agreements and understandings regarding the same. 

  

	 	7.	 This Amendment shall be effective upon full execution by facsimile or original, and a facsimile signature
shall be deemed to be and shall be as effective as an original signature. This Amendment may be executed in any number of counterparts, each of which will be deemed an original, but all of which taken together shall constitute one and the same
instrument. 

 IN WITNESS WHEREOF, the Parties hereto have caused this Amendment to be signed by their
duly authorized representatives. 
  

							
	Industry 3200, Inc.	 	BioNano Genomics, Inc.
				
	 By :
	 	 /s/ Leslie A. Hickle
	 	 By :
	 	 /s/ R. Erik Holmlin

	 Name :
	 	 Leslie A. Hickle
	 	 Name :
	 	 R. Erik Holmlin

	 Title :
	 	 CEO
	 	 Title :
	 	 CEO

  

***Confidential Treatment Requested

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