Document:

EX-4.2

 Exhibit 4.2 

THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE
“ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED (I) UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR
(II) WITHOUT AN OPINION OF COUNSEL, IN FORM AND SUBSTANCE REASONABLY SATISFACTORY TO THE COMPANY, THAT SUCH OFFER, SALE, PLEDGE OR OTHER TRANSFER IS EXEMPT FROM SUCH REGISTRATION. 

WARRANT TO PURCHASE STOCK 1 
  

			
	 Company
	  	 BIONANO GENOMICS, INC.

		
	 Number of Shares
	  	[                    ] [Note: Number of shares to equal 3.75% of the applicable Term Loan funding amount, divided by the Warrant
Price]
		
	 Type/Series of Stock
	  	 Common Stock, par value $0.0001 per share, of the Company (“Common Stock”)

		
	 Warrant Price
	  	 $4.63 per share

		
	 Issue Date
	  	
[                    ]

		
	 Expiration Date
	  	 [                    ]
[Note: Expires 10 years after issuance date] (See also Section 5.1(b))

		
	 Credit Facility
	  	 This Warrant to Purchase Stock (“Warrant”) is issued in connection with that certain Loan and Security
Agreement, dated March 14, 2019, among Innovatus Life Sciences Lending Fund I, LP, as Lender and Collateral Agent, the Lenders from time to time party thereto, including East West Bank, and the Company (as modified, amended and/or restated from
time to time, the “Loan Agreement”).

 THIS WARRANT CERTIFIES THAT, for good and valuable consideration, INNOVATUS LIFE
SCIENCES LENDING FUND I, LP (“Innovatus”), a Delaware limited partnership with an office located at 777 Third Avenue, 25th Floor, New York, NY 10017 (together with any successor or permitted assignee or transferee of this Warrant or of any
shares issued upon exercise hereof, “Holder”) is entitled to purchase the number of fully paid and non-assessable shares (the “Shares”) of the above-stated Type/Series of
Stock (the “Class”) of the above-named company (the “Company”) at the above-stated Warrant Price, all as set forth above and as adjusted pursuant to Section 2 of this Warrant, subject to the provisions and upon
the terms and conditions set forth in this Warrant. 
 SECTION 1.    EXERCISE. 

1.1    Method of Exercise. Holder may at any time and from time to time exercise this Warrant, in
whole or in part, by delivering to the Company the original of this Warrant together with a 
  

	1	 The Company acknowledges and agrees that this Warrant is issued in connection with the Term A1 Loan under, and
as defined in, the Loan Agreement, and that, in the event the Company draws the Term A2 Loan and/or the Term B Loan, each as defined therein, the Company shall issue the Holder additional Warrants to purchase shares of the Common Stock, in each case
for a number of shares equal to 3.75% of the funded amount of such Term A2 and Term B Loans, respectively, divided by the Warrant Price as defined in this Warrant, and with an exercise price equal to such Warrant Price, subject to any adjustments to
the shares and/or price, on substantially the terms and conditions set forth in this Warrant. 

 
duly executed Notice of Exercise in substantially the form attached hereto as Appendix 1 and, unless Holder is exercising this Warrant pursuant to a cashless exercise set forth in
Section 1.2, a check, wire transfer of same-day funds (to an account designated by the Company), or other form of payment acceptable to the Company for the aggregate Warrant Price for the Shares being
purchased. 
 1.2    Cashless Exercise. On any exercise of this Warrant, in lieu of payment of
the aggregate Warrant Price in the manner as specified in Section 1.1 above, but otherwise in accordance with the requirements of Section 1.1, Holder may elect to receive Shares equal to the value of this Warrant, or portion hereof as to
which this Warrant is being exercised. Thereupon, the Company shall issue to the Holder such number of fully paid and non-assessable Shares as are computed using the following formula: 

 

	 	X =	 Y(A-B)/A 

where: 
  

	 	X =	 the number of Shares to be issued to the Holder; 

 

	 	Y =	 the number of Shares with respect to which this Warrant is being exercised (inclusive of the Shares
surrendered to the Company in payment of the aggregate Warrant Price); 

  

	 	A =	 the Fair Market Value (as determined pursuant to Section 1.3 below) of one Share; and

  

	 	B =	 the Warrant Price. 

1.3    Fair Market Value. If the Common Stock is then traded or quoted on a nationally recognized
securities exchange, inter-dealer quotation system or over-the-counter market (a “Trading Market”), the fair market value of a Share shall be the
closing price of a share of Common Stock reported for the Business Day immediately before the date on which Holder delivers this Warrant together with its Notice of Exercise to the Company. If the Common Stock is not traded in a Trading Market, the
Board of Directors of the Company shall determine the fair market value of a Share in its reasonable good faith judgment. 

1.4    Delivery of Certificate and New Warrant. Promptly after Holder exercises this Warrant in the
manner set forth in Section 1.1 or 1.2 above, the Company shall deliver to Holder a certificate (via an electronic shares program, if applicable) representing the Shares issued to Holder upon such exercise and, if this Warrant has not been
fully exercised and has not expired, a new warrant of like tenor representing the Shares not so acquired. 

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

1.6    Treatment of Warrant Upon Acquisition of Company. 

(a)    Acquisition. For the purpose of this Warrant, “Acquisition” means any
transaction or series of related transactions involving: (i) the sale, lease, exclusive license or other 

  
 2 

 
disposition of all or substantially all of the assets of the Company; (ii) any merger or consolidation of the Company into or with another person or entity (other than a merger or
consolidation effected exclusively to change the Company’s domicile), or any other corporate reorganization, in which the stockholders of the Company in their capacity as such immediately prior to such merger, consolidation or reorganization,
own less than a majority of the Company’s (or the surviving or successor entity’s) outstanding voting power immediately after such merger, consolidation or reorganization; or (iii) any sale or other transfer by the stockholders of the
Company of shares representing a majority of the Company’s then-total outstanding combined voting power. For the avoidance of doubt, “Acquisition” shall exclude any sale and issuance by the Company of shares of its capital
stock, or securities or instruments exercisable for or convertible into or otherwise representing the right to acquire shares of capital stock, to one or more investors in a transaction or series of related transactions the primary purpose of which
is a bona fide equity financing of the Company. 
 (b)    Treatment of Warrant at Acquisition.
In the event of an Acquisition in which the consideration to be received by the Company’s stockholders consists solely of cash, solely of Marketable Securities or a combination of cash and Marketable Securities (a “Cash/Public
Acquisition”), either (i) Holder shall exercise this Warrant pursuant to Section 1.1 and/or 1.2 and such exercise will be deemed effective immediately prior to and contingent upon the consummation of such Acquisition or
(ii) if Holder elects not to exercise the Warrant, this Warrant will expire immediately prior to the consummation of such Acquisition. 

(c)    The Company shall provide Holder with written notice of its request relating to the Cash/Public
Acquisition (together with such reasonable information as Holder may reasonably require regarding the treatment of this Warrant in connection with such contemplated Cash/Public Acquisition giving rise to such notice), which is to be delivered to
Holder not less than seven (7) Business Days prior to the closing of the proposed Cash/Public Acquisition. Notwithstanding the foregoing, if, immediately prior to the Cash/Public Acquisition, the fair market value of one Share (or other
security issuable upon the exercise hereof) as determined in accordance with Section 1.3 above would be greater than the Warrant Price in effect on such date, then this Warrant shall automatically be deemed on and as of such date to be
exercised pursuant to Section 1.2 above as to all Shares (or such other securities) for which it shall not previously have been exercised, and the Company shall promptly notify the Holder of the number of Shares (or such other securities)
issued upon such exercise to the Holder. 
 (d)    Upon the closing of any Acquisition other than a
Cash/Public Acquisition defined above, the acquiring, surviving or successor entity shall assume the obligations of this Warrant, and this Warrant shall thereafter be exercisable for the same securities and/or other property as would have been paid
for the Shares issuable upon exercise of the unexercised portion of this Warrant as if such Shares were outstanding on and as of the closing of such Acquisition, subject to further adjustment from time to time in accordance with the provisions of
this Warrant. 
 (e)    As used in this Warrant, “Marketable Securities” means
securities meeting all of the following requirements: (i) the issuer thereof is then subject to the reporting requirements of Section 13 or Section 15(d) of the Securities Exchange Act of 1934, as amended (the “Exchange
Act”), and is then current in its filing of all required reports and other information under the Act and the Exchange Act; (ii) the class and series of shares or other security of the issuer that would be received by Holder in
connection with the Acquisition were Holder to exercise this Warrant on or prior to the closing thereof is then traded in Trading Market; and (iii) Holder would be able to publicly re-sell, within six
(6) months following the closing of such Acquisition, all of the issuer’s shares and/or other 

  
 3 

 
securities that would be received by Holder in such Acquisition were Holder to exercise this Warrant in full on or prior to the closing of such Acquisition. 

1.7    Beneficial Ownership Limitation. The Company shall not issue any shares of Common Stock
under this Warrant to Holder if such shares, when aggregated with all other shares of Common Stock then beneficially owned (as calculated pursuant to Section 13(d) of the Exchange Act and Rule 13d-3
promulgated thereunder) by the Holder and its affiliates would result in the beneficial ownership by the Holder and its affiliates of more than 19.99% of the then issued and outstanding shares of Common Stock. 

SECTION 2.    ADJUSTMENTS TO THE SHARES AND WARRANT PRICE. 

2.1    Stock Dividends, Splits, Etc. If the Company declares or pays a dividend or distribution on
the outstanding shares of the Class payable in common stock or other securities or property (other than cash), then upon exercise of this Warrant, for each Share acquired, Holder shall receive, without additional cost to Holder, the total
number and kind of securities and property which Holder would have received had Holder owned the Shares of record as of the date the dividend or distribution occurred. If the Company subdivides the outstanding shares of the Class by
reclassification or otherwise into a greater number of shares, the number of Shares purchasable hereunder shall be proportionately increased and the Warrant Price shall be proportionately decreased. If the outstanding shares of the Class are
combined or consolidated, by reclassification or otherwise, into a lesser number of shares, the Warrant Price shall be proportionately increased and the number of Shares shall be proportionately decreased. 

2.2    Reclassification, Exchange, Combinations or Substitution. Upon any event whereby all of the
outstanding shares of the Class are reclassified, exchanged, combined, substituted, or replaced for, into, with or by Company securities of a different class and/or series, then from and after the consummation of such event, this Warrant will
be exercisable for the number, class and series of Company securities that Holder would have received had the Shares been outstanding on and as of the consummation of such event, and subject to further adjustment thereafter from time to time in
accordance with the provisions of this Warrant. The provisions of this Section 2.2 shall similarly apply to successive reclassifications, exchanges, combinations substitutions, replacements or other similar events. 

2.3    Intentionally Omitted. 

2.4    Intentionally Omitted. 

2.5    No Fractional Share. No fractional Share shall be issuable upon exercise of this Warrant and
the number of Shares to be issued shall be rounded down to the nearest whole Share. If a fractional Share interest arises upon any exercise of the Warrant, the Company shall eliminate such fractional Share interest by paying Holder in cash the
amount computed by multiplying the fractional interest by (a) the fair market value (as determined in accordance with Section 1.3 above) of a full Share, less (b) the then-effective Warrant Price. 

2.6    Notice/Certificate as to Adjustments. Upon each adjustment of the Warrant Price,
Class and/or number of Shares, the Company, at the Company’s expense, shall notify Holder in writing within a reasonable time setting forth the adjustments to the Warrant Price, Class and/or number of Shares and facts upon which such
adjustment is based. The Company shall, upon written request from Holder, furnish Holder with a certificate of its Chief Financial Officer, including computations of such 

  
 4 

 
adjustment and the Warrant Price, Class and number of Shares in effect upon the date of such adjustment. 

SECTION 3.    REPRESENTATIONS AND COVENANTS OF THE COMPANY. 

3.1    Representations and Warranties. The Company represents and warrants to, and agrees with, the
Holder as follows: 
 (a)    The initial Warrant Price referenced on the first page of this Warrant is
not greater than the price per share at which shares of the Class were last sold and issued prior to the Issue Date hereof in an arms-length transaction in which at least $500,000 of such shares were sold. 

(b)    All Shares which may be issued upon the exercise of this Warrant, and all securities, if any,
issuable upon conversion of the Shares, shall, upon issuance, be duly authorized, validly issued, fully paid and non-assessable, and free of any liens and encumbrances except for restrictions on transfer
provided for herein or under applicable federal and state securities laws. The Company covenants that it shall at all times cause to be reserved and kept available out of its authorized and unissued capital stock such number of shares of the
Class as will be sufficient to permit the exercise in full of this Warrant. 
 (c)    The
Company’s capitalization table attached hereto as Schedule 1 is true and complete, in all material respects, as of the Issue Date. 

3.2    Notice of Certain Events. If the Company proposes at any time to: 

(a)    declare any dividend or distribution upon the outstanding shares of the Class, whether in cash,
property, stock, or other securities and whether or not a regular cash dividend; 
 (b)    offer for
subscription or sale pro rata to the holders of the outstanding shares of the Class any additional shares of any class or series of the Company’s stock (other than pursuant to contractual pre-emptive
rights); 
 (c)    effect any reclassification, exchange, combination, substitution, reorganization or
recapitalization of the outstanding shares of the Class; or 
 (d)    effect an Acquisition or to
liquidate, dissolve or wind up; 
 then, in connection with each such event, the Company shall give Holder: 

(1) at least seven (7) Business Days prior written notice of the date on which a record will be taken for
such dividend, distribution, or subscription rights (and specifying the date on which the holders of outstanding shares of the Class will be entitled thereto) or for determining rights to vote, if any, in respect of the matters referred to in
(a) and (b) above; and 
 (2) in the case of the matters referred to in (c) and (d) above at least
seven (7) Business Days prior written notice of the date when the same will take place (and specifying the date on which the holders of outstanding shares of the Class will be entitled to exchange their shares for the securities or other
property deliverable upon the occurrence of such event). 

  
 5 

 Reference is made to Section 1.6(c) whereby this Warrant will be deemed to be exercised
pursuant to Section 1.2 hereof if the Company does not give written notice to Holder of a Cash/Public Acquisition as required by the terms hereof. Company will also provide information requested by Holder that is reasonably necessary to enable
Holder to comply with Holder’s accounting or reporting requirements. 
 3.3    Registration
Rights. The Company agrees that the Holder shall have the “Piggyback” and S-3 registration rights pursuant to and as set forth in the Company’s Fifth Amended and Restated Investors’
Rights Agreement, dated as of August 5, 2016, as amended (the “Rights Agreement”), on a pari passu basis with the holders of outstanding shares of the Company’s convertible preferred stock who are parties thereto. The
provisions set forth in the Rights Agreement or similar agreement relating to such registration rights in effect as of the Issue Date may not be amended, modified or waived without the prior written consent of the Holder unless such amendment,
modification or waiver affects the rights associated with the Shares issued and issuable upon exercise hereof (and the shares of the Common Stock issued and issuable upon conversion of the Shares) in the same manner as such amendment, modification
or waiver affects the rights associated with all outstanding shares of the Company’s convertible preferred stock whose holders are parties thereto. 

SECTION 4.    REPRESENTATIONS, WARRANTIES OF THE HOLDER. 

The Holder represents and warrants to the Company as follows: 

4.1    Purchase for Own Account. This Warrant and the securities to be acquired upon exercise of
this Warrant by Holder are being acquired for investment for Holder’s account, not as a nominee or agent, and not with a view to the public resale or distribution within the meaning of the Act. Holder also represents that it has not been formed
for the specific purpose of acquiring this Warrant or the Shares. 
 4.2    Disclosure of
Information. Holder is aware of the Company’s business affairs and financial condition and has received or has had full access to all the information it considers necessary or appropriate to make an informed investment decision with respect
to the acquisition of this Warrant and its underlying securities. Holder further has had an opportunity to ask questions and receive answers from the Company regarding the terms and conditions of the offering of this Warrant and its underlying
securities and to obtain additional information (to the extent the Company possessed such information or could acquire it without unreasonable effort or expense) necessary to verify any information furnished to Holder or to which Holder has access.

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

 4.4    Accredited Investor Status. Holder is an “accredited investor” within the
meaning of Regulation D promulgated under the Act. 

  
 6 

 4.5    The Act. Holder understands that this
Warrant and the Shares issuable upon exercise hereof have not been registered under the Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of the Holder’s investment
intent as expressed herein. Holder understands that this Warrant and the Shares issued upon any exercise hereof must be held indefinitely unless subsequently registered under the Act and qualified under applicable state securities laws, or unless
exemption from such registration and qualification are otherwise available. Holder is aware of the provisions of Rule 144 promulgated under the Act. 

4.6    No Voting Rights. Holder, as a Holder of this Warrant, will not have any voting rights until
the exercise of this Warrant. 
 SECTION 5.    MISCELLANEOUS. 

5.1    Term and Automatic Conversion Upon Expiration. 

(a)    Term. Subject to the provisions of Section 1.6 above, this Warrant is exercisable in
whole or in part at any time and from time to time on or before 6:00 P.M., Eastern time, on the Expiration Date and shall be void thereafter. 

(b)    Automatic Cashless Exercise upon Expiration. In the event that, upon the Expiration Date,
the fair market value of one Share (or other security issuable upon the exercise hereof) as determined in accordance with Section 1.3 above is greater than the Warrant Price in effect on such date, then this Warrant shall automatically be
deemed on and as of such date to be exercised pursuant to Section 1.2 above as to all Shares (or such other securities) for which it shall not previously have been exercised, and the Company shall, within a reasonable time, deliver a
certificate (via an electronic shares program, if applicable) representing the Shares (or such other securities) issued upon such exercise to Holder. 

5.2    Legends. 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: 
 THE SHARES EVIDENCED BY THIS
CERTIFICATE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “ACT”), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN THAT CERTAIN WARRANT TO PURCHASE STOCK ISSUED BY THE ISSUER TO INNOVATUS
LIFE SCIENCES LENDING FUND I, LP DATED [                    ], MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED (I) UNLESS AND UNTIL
REGISTERED UNDER SAID ACT AND LAWS OR (II) WITHOUT AN OPINION OF COUNSEL, IN FORM AND SUBSTANCE REASONABLY SATISFACTORY TO THE ISSUER, THAT SUCH OFFER, SALE, PLEDGE OR OTHER TRANSFER IS EXEMPT FROM SUCH REGISTRATION. 

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 except in compliance with applicable federal and state securities laws by
the transferor and the transferee (including, without limitation, the delivery of investment representation letters and legal opinions 

  
 7 

 
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. Additionally, the Company shall also not require an opinion of counsel if there is no material question as to the availability of Rule 144 promulgated under the Act. 

5.4    Transfer Procedure. Subject to the provisions of Section 5.3 and upon providing the
Company with written notice, Holder may transfer all or part of this Warrant or the Shares issuable upon exercise of this Warrant (or the securities issuable directly or indirectly, upon conversion of the Shares, if any) to any transferee,
provided, however, in connection with any such transfer, Holder will give the Company notice of the portion of the Warrant being transferred with the name, address and taxpayer identification number of the transferee and Holder will
surrender this Warrant to the Company for reissuance to the transferee(s) (and Holder if applicable); and provided further, that any subsequent transferee shall agree in writing with the Company to be bound by all of the terms and
conditions of this Warrant. 
 5.5    Notices. All notices and other communications hereunder
from the Company to the Holder, or vice versa, shall be deemed delivered and effective (i) when given personally, (ii) on the third (3rd) Business Day after being mailed by first-class
registered or certified mail, postage prepaid, (iii) upon actual receipt if given by facsimile or electronic mail and such receipt is confirmed in writing by the recipient, or (iv) on the first Business Day following delivery to a reliable
overnight courier service, courier fee prepaid, in any case at such address as may have been furnished to the Company or Holder, as the case may be, in writing by the Company or such Holder from time to time in accordance with the provisions of this
Section 5.5. All notices to Holder shall be addressed as follows until the Company receives notice of a change of address in connection with a transfer or otherwise: 

INNOVATUS LIFE SCIENCES LENDING FUND I, LP 

777 Third Avenue, 25th Floor 

New York, NY 10017 

Attention: Claes Ekstrom 

Email: cekstrom@innovatuscp.com 

Notice to the Company shall be addressed as follows until Holder receives notice of a change in address: 

BIONANO GENOMICS, INC. 

9540 Towne Centre Drive 

Suite 100 

Attn: Chief Financial Officer 

Email: mward@bionanogenomics.com 

With a copy (which shall not constitute notice) to: 

Cooley LLP 

4401 Eastgate Mall 

San Diego, CA 92121 

Attn: Thomas A. Coll 

Facsimile No.: (858) 550-6420 

Email: collta@cooley.com 

  
 8 

 5.6    Waiver. This Warrant and any term hereof
may be changed, waived, discharged or terminated (either generally or in a particular instance and either retroactively or prospectively) only by an instrument in writing signed by the party against which enforcement of such change, waiver,
discharge or termination is sought. 
 5.7    Attorneys’ Fees. In the event of any dispute
between the parties concerning the terms and provisions of this Warrant, the party prevailing in such dispute shall be entitled to collect from the other party all costs incurred in such dispute, including reasonable attorneys’ fees. 

5.8    Counterparts; Facsimile/Electronic Signatures. This Warrant may be executed in counterparts,
all of which together shall constitute one and the same agreement. Any signature page delivered electronically or by facsimile shall be binding to the same extent as an original signature page with regards to any agreement subject to the terms
hereof or any amendment thereto. 
 5.9    Governing Law. This Warrant shall be governed by and
construed in accordance with the laws of the State of New York, without giving effect to its principles regarding conflicts of law. 

5.10    Headings. The headings in this Warrant are for purposes of reference only and shall not
limit or otherwise affect the meaning of any provision of this Warrant. 
 5.11    Business Days.
“Business Day” is any day that is not a Saturday, Sunday or a day on which banks in New York, New York are closed. 

[Signature page follows] 

  
 9 

 IN WITNESS WHEREOF, the parties have caused this Warrant to Purchase Stock
to be executed by their duly authorized representatives effective as of the Issue Date written above. 
 “COMPANY” 

 

			
	 BIONANO GENOMICS, INC.

		
	 By:
	 	
                  
                       

	 Name:
	 	  

		 	 (Print)

	 Title:
	 	
	
	 “HOLDER”

	
	 INNOVATUS LIFE SCIENCES LENDING FUND I, LP

		
	 By:
	 	  

	 Name:
	 	  

		 	 (Print)

	 Title:
	 	  

  
 10 

 APPENDIX 1 

NOTICE OF EXERCISE 

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

	
	 ☐   check in the amount of
$             payable to order of the Company enclosed herewith

	
	 ☐   Wire transfer of immediately available funds to the
Company’s account

	
	 ☐   Cashless Exercise pursuant to Section 1.2 of the
Warrant

	
	 ☐   Other [Describe]
                                         
                                         
      

 2.    Please issue a certificate or certificates representing the Shares
in the name specified below: 
  

			
	  
	 	
	 Holder’s Name
	 	
		
	  
	 	
		
	  
	 	
	 (Address)
	 	

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

			
	 HOLDER:

	
	  

		
	 By:
	 	
                  
                                         
  

	 Name:
	 	  

	 Title:
	 	  

	 (Date):
	 	  

  
 Appendix 1 

 SCHEDULE 1 

Company Capitalization Table 

[see attached] 

  
 Schedule 1EX-4.3

 Exhibit 4.3 

BIONANO GENOMICS, INC. 

REGISTRATION RIGHTS AGREEMENT 

THIS REGISTRATION RIGHTS AGREEMENT (this
“Agreement”) is entered into as of March 14, 2019, by and among BIONANO GENOMICS, INC., a Delaware corporation (the “Company”),
INNOVATUS LIFE SCIENCES LENDING FUND I, LP and INNOVATUS LIFE SCIENCES OFFSHORE FUND I,
LP (collectively, “Investor”). The Company and Investor may be referred to hereinafter collectively as the “Parties” and each individually as a “Party.” 

RECITALS 

WHEREAS, in connection with the purchase of shares of the Common Stock of
the Company by Investor pursuant to that certain Common Stock Purchase Agreement dated as of the date hereof (the “Purchase Agreement”), the parties desire to enter into this Agreement in order to grant registration rights to
Investor as set forth below. 
 NOW, THEREFORE, in consideration of these premises and
for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows: 
 SECTION
1. DEFINITIONS. 
 Capitalized terms used herein and not defined elsewhere herein have the meanings set forth in Exhibit A. 

SECTION 2. REGISTRATION RIGHTS. 

2.1    Resale Registration. At any time on or after October 1, 2019, Holder may make a
written request that the Company register the resale of the Registrable Securities under the Securities Act on Form S-3 (or any successor to Form S-3) or any
similar short-form registration statement. Upon receipt of such notice, the Company will (i) as soon as practicable, and no later than sixty (60) days following receipt of such notice, file such registration statement, and any
qualifications and compliances as may be so requested as would permit or facilitate the sale and distribution of all or such portion of Holder’s Registrable Securities as are specified in such request and (ii) use its commercially
reasonable efforts to cause such registration statement to be declared effective by the SEC as soon as practicable and no later than the Effectiveness Deadline, and shall use its commercially reasonable efforts to keep such registration statement
continuously effective under the Securities Act until the earlier of (1) such time as all of the Registrable Securities covered by such registration statement have been publicly sold by the 

  
 1 

 
Holder, or (2) four (4) years from the date hereof; provided, however, that the Company will not be obligated to effect any such registration, qualification or compliance pursuant to
this Section 2.1: 
 (a)    if within thirty (30) days of receipt of a written request
from Holder pursuant to this Section 2.1, the Company gives notice to Holder of the Company’s intention to make a public offering within ninety (90) days, other than pursuant to a Special Registration Statement; provided,
however, that the Company shall not utilize this right more than once in any twelve (12) month period, and provided further, that the Company shall not register any other of its shares during such ninety (90)-day period other than pursuant to a
Special Registration Statement; 
 (b)    if the Company will furnish to Holder a certificate
signed by the Chairman of the Board stating that in the good faith judgment of the Company’s Board of Directors, it would be seriously detrimental to the Company and its stockholders for such
Form S-3 registration to be effected at such time, in which event the Company will have the right to defer the filing of the Form S-3 registration statement
for a period of not more than ninety (90) days after receipt of the request of Holder under this Section 2.1; provided, that such right to delay a request will be exercised by the Company not more than once in any twelve
(12)-month period and provided that the Company shall not register any other of its shares during such ninety (90)-day period other than pursuant to a Special Registration Statement; 

(c)    if the Company has, within the twelve (12)-month period preceding the date of such request,
already effected one (1) registration on Form S-3 for Holder pursuant to this Section 2.1, or 

(d)    in any particular jurisdiction in which the Company would be required to qualify to do
business or to execute a general consent to service of process in effecting such registration, qualification or compliance, unless the Company is already subject to service in such jurisdiction and except as may be required by the Securities Act.

 If the Company is ineligible for any reason to register the resale of the Registrable Securities on Form
S-3, then such registration shall be on such other form then available to the Company (including a Form S-1) to register for resale of the Registrable Securities as a
secondary offering. 
 2.2    Piggyback Registration. If the Company at any time that the
Registrable Securities are not registered pursuant to a registration statement required to be filed pursuant to Section 2.1, proposes to register any of its securities under the Securities Act for sale to the public, whether for its own account
or for the account of other security holders or both (except with respect to a Special Registration Statement or a registration statement required to be filed pursuant to Section 2.1), each such time it will give written notice to all Holders
of outstanding Registrable Securities of its intention so to do. Upon the written request of any such Holder, received by the Company within thirty (30) days after the giving of any such notice by the

  
 2 

 
Company, to register any of its Registrable Securities, the Company will use its reasonable best efforts to cause the Registrable Securities as to which registration shall have been so requested
to be included in the securities to be covered by the registration statement proposed to be filed by the Company, all to the extent requisite to permit the sale or other disposition by the holder of such Registrable Securities so registered.
Notwithstanding any other provision of this Agreement, in the event that any registration pursuant to this Section 2.2 shall be, in whole or in part, an underwritten public offering of Common Stock, if the underwriter determines in good faith
that marketing factors require a limitation of the number of shares to be underwritten, the number of shares that may be included in the underwriting will be allocated, first, to the Company; second, to the “Investors” under that certain
Fifth Amended and Restated Investors’ Rights Agreement dated August 5, 2016, as amended, by and among the Company and the Investors named therein; and third, to Investor. If Investor disapproves of the terms of any such underwriting,
Investor may elect to withdraw therefrom by written notice to the Company and the underwriter, delivered at least ten (10) business days prior to the effective date of the registration statement. Any Registrable Securities excluded or withdrawn
from such underwriting will be excluded and withdrawn from the registration. Notwithstanding the foregoing, the Company may withdraw any registration statement referred to in this Section 2.2 without thereby incurring any liability to the
holders of Registrable Securities. 
 2.3    Expenses of Registration. Except as
specifically provided herein, all Registration Expenses incurred in connection with any registration, qualification or compliance pursuant to Section 2.1 or Section 2.2 will be borne by the Company. All Selling Expenses incurred in
connection with any registrations hereunder will be borne by the holders of the securities so registered pro rata on the basis of the number of shares so registered. The Company will not, however, be required to pay for expenses of any
registration statement filed pursuant to Section 2.1 the request of which has been subsequently withdrawn by Holder unless (a) the withdrawal is based upon material adverse information concerning the Company of which Holder was not aware
at the time of such request or (b) Holder agrees to deem such registration to have been effected as of the date of such withdrawal for purposes of determining whether the Company will be obligated pursuant to Section 2.1(c), to undertake
any subsequent registration, in which event such right will be forfeited by Holder. If Holder is required to pay the Registration Expenses, such expenses will be borne by the holders of securities (including Registrable Securities) requesting such
registration in proportion to the number of shares for which registration was requested. If the Company is required to pay the Registration Expenses of a withdrawn offering pursuant to clause (a) above, then such registration will not be deemed
to have been effected for purposes of determining whether the Company will be obligated pursuant to Section 2.1(c) to undertake any subsequent registration. 

2.4    Obligations of the Company. Whenever required to effect the registration of any
Registrable Securities, the Company will, as expeditiously as reasonably possible: 

  
 3 

 (a)    prepare and file with the SEC a
registration statement with respect to such Registrable Securities and use all commercially reasonable efforts to cause such registration statement to become effective; 

(b)    at any time, upon written notice to Holder and for a period not to exceed sixty
(60) days thereafter (the “Suspension Period”), the Company may suspend the use of any registration statement (and Holder hereby agrees not to offer or sell any Registrable Securities pursuant to such registration
statement during the Suspension Period) if the Company reasonably believes that there is or may be in existence material nonpublic information or events involving the Company, the failure of which to be disclosed in the prospectus included in the
registration statement could result in a Violation (as defined below). In the event that the Company will exercise its right to suspend the use of a registration statement hereunder, the applicable time period during which the registration statement
is to remain effective will be extended by a period of time equal to the duration of the Suspension Period. The Company may extend the Suspension Period for an additional consecutive sixty (60) days with the consent of Holder, which consent
will not be unreasonably withheld. If so directed by the Company, Holder will (i) not offer to sell any Registrable Securities pursuant to the registration statement during the period in which the suspension is in effect after receiving
notice of such suspension; and (ii) use its commercially reasonable efforts to deliver to the Company (at the Company’s expense) all copies, other than permanent file copies then in Holder’s possession, of the prospectus relating to
such Registrable Securities current at the time of receipt of such notice. 
 (c)    Prepare and
file with the SEC such amendments and supplements to such registration statement and the prospectus used in connection with such registration statement as may be necessary to comply with the provisions of the Securities Act with respect to the
disposition of all securities covered by such registration statement. 
 (d)    Furnish to Holder
such number of copies of a prospectus, including a preliminary prospectus, in conformity with the requirements of the Securities Act, and such other documents as it may reasonably request in order to facilitate the disposition of Registrable
Securities owned by it. 
 (e)    Use its commercially reasonable efforts to register and qualify
the securities covered by such registration statement under such other securities or Blue Sky laws of such jurisdictions as will be reasonably requested by Holder; provided that the Company will not be required in connection therewith or as a
condition thereto to qualify to do business or to file a general consent to service of process in any such states or jurisdictions, unless the Company is already subject to service in such jurisdiction and except as may be required by the Securities
Act. 
 (f)    Notify Holder at any time when a prospectus relating to Holder’s Registrable
Securities is required to be delivered under the Securities Act of the happening of 

  
 4 

 
any event as a result of which the prospectus included in such registration statement, as then in effect, includes an untrue statement of a material fact or omits to state a material fact
required to be stated therein or necessary to make the statements therein not misleading in the light of the circumstances then existing. The Company will use commercially reasonable efforts to amend or supplement such prospectus in order to cause
such prospectus not to include any untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary to make the statements therein not misleading in the light of the circumstances then existing. 

2.5    Delay of Registration; Furnishing Information. 

(a)    Holder will not have any right to obtain or seek an injunction restraining or otherwise
delaying any such registration as the result of any controversy that might arise with respect to the interpretation or implementation of this Section 2. 

(b)    It will be a condition precedent to the obligations of the Company to take any action
pursuant to Section 2.1 that Holder will furnish to the Company such information regarding Holder, the Registrable Securities held by it and the intended method of disposition of such securities as will be required to effect the registration of
their Registrable Securities. 
 2.6    Indemnification. In the event any Registrable
Securities are included in a registration statement under Section 2.1 or 2.2: 
 (a)    To
the extent permitted by law, the Company will indemnify and hold harmless Holder, the partners, members, stockholders, officers, advisers and directors of Holder, as applicable, any underwriter (as defined in the Securities Act) for Holder and each
person, if any, who controls Holder or underwriter within the meaning of the Securities Act or the Exchange Act, and against any losses, claims, damages, or liabilities (joint or several) to which they may become subject under the Securities Act,
the Exchange Act or other federal or state law, insofar as such losses, claims, damages or liabilities (or actions in respect thereof) arise out of or are based upon any of the following statements, omissions or violations (collectively a
“Violation”) by the Company: (i) any untrue statement or alleged untrue statement of a material fact contained in such registration statement or incorporated by reference therein, including any preliminary prospectus or
final prospectus contained therein or any amendments or supplements thereto, (ii) the omission or alleged omission to state therein a material fact required to be stated therein, or necessary to make the statements therein not misleading, or
(iii) any violation or alleged violation by the Company of the Securities Act, the Exchange Act, any state securities law or any rule or regulation promulgated under the Securities Act, the Exchange Act or any state securities law in connection
with the offering covered by such registration statement; and the Company will reimburse Holder and each such partner, member, stockholder, officer, director, underwriter or controlling person for any legal or other expenses reasonably incurred by
them in connection with investigating or defending any such loss, claim, damage, liability or 

  
 5 

 
action; provided however, that the indemnity agreement contained in this Section 2.6(a) will not apply to amounts paid in settlement of any such loss, claim, damage, liability or
action if such settlement is effected without the consent of the Company, which consent will not be unreasonably withheld, nor will the Company be liable in any such case for any such loss, claim, damage, liability or action to the extent that it
arises out of or is based upon a Violation which occurs in reliance upon and in conformity with written information furnished expressly for use in connection with such registration by Holder or any partner, member, officer, director, underwriter or
controlling person of Holder. 
 (b)    To the extent permitted by law, Holder will, if
Registrable Securities held by Holder are included in the securities as to which such registration qualifications or compliance is being effected, indemnify and hold harmless the Company, each of its directors, its officers and each person, if any,
who controls the Company within the meaning of the Securities Act, and any underwriter against any losses, claims, damages or liabilities (joint or several) to which the Company or any such director, officer, controlling person, underwriter,
partner, director, officer or controlling person of Holder may become subject under the Securities Act, the Exchange Act or other federal or state law, insofar as such losses, claims, damages or liabilities (or actions in respect thereto) arise out
of or are based upon any of the following statements: (i) any untrue statement or alleged untrue statement of a material fact contained in such registration statement or incorporated reference therein, including any preliminary prospectus or
final prospectus contained therein or any amendments or supplements thereto, (ii) the omission or alleged omission to state therein a material fact required to be stated therein, or necessary to make the statements therein not misleading, or
(iii) any violation or alleged violation by the Company of the Securities Act (collectively, a “Holder Violation”), in each case to the extent (and only to the extent) that such Holder Violation occurs in reliance upon
and in conformity with written information furnished by Holder under an instrument duly executed by Holder and stated to be specifically for use in connection with such registration; and Holder will reimburse any legal or other expenses reasonably
incurred by the Company or any such director, officer, controlling person, or underwriter in connection with investigating or defending any such loss, claim, damage, liability or action if it is judicially determined that there was such a Holder
Violation; provided, however, that the indemnity agreement contained in this Section 2.5(b) will not apply to amounts paid in settlement of any such loss, claim, damage, liability or action if such settlement is effected without the
consent of Holder, which consent will not be unreasonably withheld; provided further, that in no event will any indemnity under this Section 2.5 exceed the net proceeds from the offering actually received by Holder. 

(c)    Promptly after receipt by an indemnified party under this Section 2.6 of notice of the
commencement of any action (including any governmental action), such indemnified party will, if a claim in respect thereof is to be made against any indemnifying party under this Section 2.6, deliver to the indemnifying party a written notice
of the commencement thereof and the indemnifying party will have the right to participate in, and, to the extent the indemnifying party so desires, jointly with any other indemnifying party similarly noticed, to

  
 6 

 
assume the defense thereof with counsel mutually satisfactory to the parties; provided, however, that an indemnified party will have the right to retain its own counsel, with the fees and
expenses thereof to be paid by the indemnifying party, if representation of such indemnified party by the counsel retained by the indemnifying party would be inappropriate due to actual or potential differing interests between such indemnified party
and any other party represented by such counsel in such proceeding. The failure to deliver written notice to the indemnifying party within a reasonable time of the commencement of any such action will relieve such indemnifying party of any liability
to the indemnified party under this Section 2.6 to the extent, and only to the extent, prejudicial to its ability to defend such action, but the omission so to deliver written notice to the indemnifying party will not relieve it of any
liability that it may have to any indemnified party otherwise than under this Section 2.6. 

(d)    If the indemnification provided for in this Section 2.6 is held by a court of competent
jurisdiction to be unavailable to an indemnified party with respect to any losses, claims, damages or liabilities referred to herein, the indemnifying party, in lieu of indemnifying such indemnified party thereunder, will to the extent permitted by
applicable law contribute to the amount paid or payable by such indemnified party as a result of such loss, claim, damage or liability in such proportion as is appropriate to reflect the relative fault of the indemnifying party on the one hand and
of the indemnified party on the other in connection with the Violation(s) or Holder Violation(s) that resulted in such loss, claim, damage or liability, as well as any other relevant equitable considerations. The relative fault of the indemnifying
party and of the indemnified party will be determined by a court of law by reference to, among other things, whether the untrue or alleged untrue statement of a material fact or the omission to state a material fact relates to information supplied
by the indemnifying party or by the indemnified party and the parties’ relative intent, knowledge, access to information and opportunity to correct or prevent such statement or omission; provided, that in no event will any
contribution by Holder hereunder exceed the net proceeds from the offering received by Holder. 

(e)    The obligations of the Company and Holder under this Section 2.6 will survive
completion of any offering of Registrable Securities in a registration statement and, with respect to liability arising from an offering to which this Section 2.6 would apply that is covered by a registration filed before termination of this
Agreement, such termination. No indemnifying party, in the defense of any such claim or litigation, will, except with the consent of each indemnified party, consent to entry of any judgment or enter into any settlement which does not include as an
unconditional term thereof the giving by the claimant or plaintiff to such indemnified party of a release from all liability in respect to such claim or litigation. 

2.7    Agreement to Furnish Information. Holder hereby agrees to execute and deliver such
other agreements as may be reasonably requested by the Company that are consistent with Holder’s obligations under this Agreement or that are necessary to give further effect thereto. 

  
 7 

 2.8    Rule 144 Reporting. With a view to
making available to Holder the benefits of certain rules and regulations of the SEC which may permit the sale of the Registrable Securities to the public without registration, the Company agrees to use its best efforts to: 

(a)    Make and keep public information available, as those terms are understood and defined in
Rule 144 or any similar or analogous rule promulgated under the Securities Act, at all times after the effective date of the first registration filed by the Company for an offering of its securities to the general public; 

(b)    File with the SEC, in a timely manner, all reports and other documents required of the
Company under the Exchange Act; and 
 (c)    So long as Holder owns any Registrable Securities,
as applicable, furnish to Holder forthwith upon request: a written statement by the Company as to its compliance with the reporting requirements of said Rule 144, and of the Exchange Act (at any time after it has become subject to such reporting
requirements); a copy of the most recent annual or quarterly report of the Company filed with the SEC; and such other reports and documents as Holder may reasonably request in connection with availing itself of any rule or regulation of the SEC
allowing it to sell any such securities without registration. 
 2.9    Assignment of
Registration Rights. The rights to cause the Company to register Registrable Securities pursuant to this Section 2 may be assigned by Holder to a transferee or assignee of Registrable Securities (for so long as such shares remain
Registrable Securities) that is a subsidiary, Affiliate, parent, general partner, limited partner, retired partner, member, stockholder or retired member, of a Holder that is a corporation, partnership or limited liability company; provided,
however, (i) the transferor shall, within ten (10) days after such transfer, furnish to the Company written notice of the name and address of such transferee or assignee and the securities with respect to which such registration rights
are being assigned and (ii) such transferee shall agree to be subject to all restrictions set forth in this Agreement. 

2.10    Termination of Registration Rights. The right of Holder to request registration or
inclusion of Registrable Securities in any registration pursuant to Section 2.1 or Section 2.2 will terminate upon the date that is four (4) years following the date hereof. Upon such termination, such shares will cease to be
“Registrable Securities” hereunder for all purposes. 
 SECTION 3. MISCELLANEOUS. 

3.1    Governing Law. This Agreement will in all respects be governed by and construed in
accordance with the substantive laws of the State of New York, without regard to its choice of law rules. 

3.2    Successors and Assigns. Except as otherwise expressly provided herein, the provisions
hereof will inure to the benefit of, and be binding upon, the parties hereto and their 

  
 8 

 
respective successors, permitted assigns, heirs, executors, and administrators and shall inure to the benefit of and be enforceable by each person who shall be a holder of Registrable Securities
from time to time. Investor may directly or indirectly assign this Agreement to its parent, Affiliate or subsidiary in connection with a direct or indirect transfer of Registrable Securities to such assignee but may not otherwise assign this
Agreement or, other than pursuant to Section 2.9, its rights under this Agreement without the express prior written consent of the Company. Any attempted assignment by Investor of any rights under this Agreement other than in accordance with
the terms of this Agreement will be null and void. 
 3.3    Entire Agreement. This
Agreement, including the exhibits and schedules hereto, constitutes the entire agreement between the Company and Investor with respect to the specific subject matter hereof, and supersedes all prior and contemporaneous agreements, representations,
and understandings of the parties with respect to such specific subject matter. No party hereto will be liable or bound to the other in any manner by any warranties, representations or covenants with respect to the subject matter hereof except as
specifically set forth herein. 
 3.4    Severability. If one or more provisions of this
Agreement are held by a proper court or arbitral tribunal to be unenforceable under applicable law, the unenforceable portions of such provisions, or such provisions in their entirety, to the extent necessary and permitted by law, will be severed
herefrom, and the balance of this Agreement will be enforceable in accordance with its terms. 

3.5    Amendment and Waiver. Except as otherwise expressly provided, this Agreement
may be amended or modified, and the rights and obligations under this Agreement may be waived, only upon the written consent of the Company and Investor. 

3.6    Delays or Omissions. It is agreed that no delay or omission to exercise any right,
power, or remedy accruing to any party, upon any breach, default or noncompliance by another party under this Agreement will impair any such right, power, or remedy, nor will it be construed to be a waiver of any such breach, default or
noncompliance, or any acquiescence therein, or of any similar breach, default or noncompliance thereafter occurring. It is further agreed that any waiver, permit, consent, or approval of any kind or character on any party’s part of any breach,
default or noncompliance under this Agreement or any waiver on such party’s part of any provisions or conditions of this Agreement must be in writing and will be effective only to the extent specifically set forth in such writing. All remedies,
either under this Agreement, by law, or otherwise afforded to any party, will be cumulative and not alternative. 

3.7    Notices. Except where otherwise specifically provided in this Agreement, all notices,
requests, consents, approvals and statements will be in writing and will be deemed to have been properly given by (i) personal delivery, (ii) electronic facsimile transmission, (iii) 

  
 9 

 
electronic mail, or by (iv) nationally recognized overnight courier service, addressed in each case, to the intended recipient as set forth below: 

 

			
	 To the Company:
	  	 Bionano Genomics, Inc.

9640 Towne Centre Drive, Suite 100

San Diego, California 92121

Attention: Chief Executive Officer

		
	 With a copy to:
	  	 Cooley LLP
 4401
Eastgate Mall
 San Diego, CA 92121

Attention: Thomas A. Coll, Esq.

		
	 To Investor:
	  	 Innovatus Life Sciences Lending Fund I, LP

777 Third Avenue, 25th Floor
 New
York, NY 10017
 Attention: Claes Ekstrom

		
	 With a copy to:
	  	 Greenberg Traurig, LLP

One International Place, Suite 2000

Boston, MA 02110
 Attention:
Abdullah Malik

 Such notice, request, demand, claim or other communication will be deemed to have been duly given on
(a) the date of personal delivery, (b) the date actually received if by facsimile or electronic mail; or (c) on the third business day after delivery to a nationally recognized overnight courier service, as the case may be. Either
Party may change the address to which notices, requests, demands, claims, and other communications hereunder are to be delivered by giving the other Party notice in the manner herein set forth. 

3.8    Fees and Expenses. Each party will pay all costs and expenses that it incurs with
respect to the negotiation, execution, delivery and performance of this Agreement. If any action at law or in equity is necessary to enforce or interpret the terms of any of this Agreement, the prevailing party will be entitled to reasonable
attorneys’ fees, costs and necessary disbursements in addition to any other relief to which such party may be entitled. For purposes of this Section 3.8, “prevailing party” means the net winner of a dispute, taking into account
the claims pursued, the claims on which the pursuing party was successful, the amount of money sought, the amount of money awarded, and offsets or counterclaims pursued (successfully or unsuccessfully) by the other Party. If a written settlement
offer is rejected and the judgment or award finally obtained is equal to or more favorable to the offeror than an offer made in writing to settle, the offeror is deemed to be the prevailing party from the date of the offer forward. 

  
 10 

 3.9    Titles and Subtitles; Form of Pronouns;
Construction and Definitions. The titles of the Sections and paragraphs of this Agreement are for convenience only and are not to be considered in construing this Agreement. All pronouns used in this Agreement will be deemed to include
masculine, feminine and neuter forms, the singular number includes the plural and the plural number includes the singular and will not be interpreted to preclude the application of any provision of this Agreement to any individual or entity. Unless
the context otherwise requires, (i) each reference in this Agreement to a designated “Section,” “Schedule,” “Exhibit,” or “Appendix” is to the corresponding Section, Schedule, Exhibit, or Appendix of or
to this Agreement; (ii) the word “or” will not be applied in its exclusive sense; (iii) “including” will mean “including, without limitation”; (iv) references to “$” or “dollars” will mean the
lawful currency of the United States; and (v) “herein,” “hereof,” “hereunder” and other words of similar import refer to this Agreement as a whole and not to any particular Section or other subdivision. References in
this Agreement to particular sections of the Securities Act or to any provisions of California law will be deemed to refer to such sections or provisions as they may be amended or succeeded after the date of this Agreement. 

3.10    Counterparts. This Agreement may be executed in counterparts, each of which will be
deemed an original, but all of which together will constitute one and the same instrument, and will become effective when there exist copies hereof which, when taken together, bear the authorized signatures of each of the parties hereto. Only one
such counterpart signed by the party against whom enforceability is sought needs to be produced to evidence the existence of this Agreement. 

3.11    Aggregation of Stock. All shares of Registrable Securities held or acquired by
affiliated entities or persons or persons or entities under common management or control will be aggregated together for the purpose of determining the availability of any rights under this Agreement. 

3.12    Specific Performance. The failure of either party to this Agreement to perform its
agreements and covenants hereunder, including but not limited to Section 2, may cause irreparable injury to the other party to this Agreement for which monetary damages, even if available, will not be an adequate remedy. Accordingly, each of
the parties hereto hereby consents to the granting of equitable relief (including specific performance and injunctive relief) by any court of competent jurisdiction to enforce any Party’s obligations hereunder. The parties further agree to
waive any requirement for the securing or posting of any bond in connection with the obtaining of any such equitable relief and that this Section 3.12 is without prejudice to any other rights that the Company and Investor may have for any
failure to perform this Agreement. 
 3.13    Termination. This Agreement will terminate
and be of no further force or effect upon the termination of Holder’s registration rights hereunder pursuant to Section 2.10 above. 

  
 11 

 [THIS SPACE INTENTIONALLY LEFT BLANK] 

  
 12 

 IN WITNESS WHEREOF, the
parties hereto have executed this REGISTRATION RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 

COMPANY: 
  

			
	BIONANO GENOMICS, INC.
		
	 By:
	 	 /s/ R. Erik Holmlin, Ph.D.

	 Name:
	 	 R. Erik Holmlin, Ph.D.

	 Title:
	 	 President and Chief Executive Officer

 IN WITNESS WHEREOF, the
parties hereto have executed this REGISTRATION RIGHTS AGREEMENT as of the date set forth in the first paragraph hereof. 

INVESTOR: 
 INNOVATUS
LIFE SCIENCES LENDING FUND I, LP 
 By: Innovatus Life Sciences GP, LP 

Its: General Partner 
 By:
Innovatus Flagship Parent GP, LLC 
 Its: General Partner 
  

			
	 By:
	 	 /s/ Andrew Dym

	 Name:
	 	 Andrew Dym

	 Title:
	 	 Authorized Signatory

		
	 Address:
	 	 777 Third Avenue

		 	 25th Floor

		 	 New York, NY 10017

	 Facsimile:
	 	
                  
                       

 INNOVATUS LIFE SCIENCES OFFSHORE FUND I, LP

 By: Innovatus Life Sciences Offshore GP, LP 

Its: General Partner 
 By:
Innovatus Flagship Offshore Parent GP, LLC 
 Its: General Partner 
  

			
	 By:
	 	 /s/ Andrew Dym

	 Name:
	 	 Andrew Dym

	 Title:
	 	 Authorized Signatory

		
	 Address:
	 	 777 Third Avenue

		 	 25th Floor

		 	 New York, NY 10017

	 Facsimile:
	 	  

 EXHIBIT A 

DEFINITIONS 

1.1    “Affiliate” means with
respect to any specified person, any other person who or which, directly or indirectly, controls, is controlled by, or is under common control with such specified person, including, without limitation, any general partner, officer, director or
manager of such person and any venture capital fund now or hereafter existing that is controlled by one or more general partners or managing members of, or is under common investment management with, such person. 

1.2    “Common Stock” means the Common Stock of the Company. 

1.3    “Effectiveness Deadline” means, with respect to a registration
statement filed pursuant to Section 2.1, the earlier of (i) the 30th calendar day following the date the registration statement was filed (or the 60th calendar day following the date the registration statement was filed if such
registration statement is subject to review by the SEC) and (ii) the 5th trading day after the date the Company is notified (orally or in writing, whichever is earlier) by the SEC that such registration statement will not be
“reviewed” or will not be subject to further review and that the SEC is prepared to declare such registration statement effective; provided, that if the Effectiveness Deadline falls on a Saturday, Sunday or other day that the SEC is closed
for business, the Effectiveness Deadline shall be extended to the next business day on which the SEC is open for business. 

1.4    “Exchange Act” means the Securities Exchange Act of 1934, as
amended. 
 1.5    “Form S-3”
means such form under the Securities Act as in effect on the date hereof or any successor or similar registration form under the Securities Act subsequently adopted by the SEC which permits inclusion or incorporation of substantial
information by reference to other documents filed by the Company with the SEC. 

1.6    “Holder” means Investor or transferee pursuant to Section 2.10,
so long as it owns of record Registrable Securities that have not been sold to the public. 

1.7     “Register,” “registered,” and
“registration” refer to a registration effected by preparing and filing a registration statement in compliance with the Securities Act, and the declaration or ordering of effectiveness of such registration statement or
document. 
 1.8    “Registrable
Securities” means (a) Common Stock issued pursuant to the Purchase Agreement and (b) any Common Stock issued as (or issuable upon the conversion or exercise of any warrant, right or other security
which is issued as) a dividend or other 

 
distribution with respect to, or in exchange for or in replacement of, such above-described securities. Notwithstanding the foregoing, Registrable Securities will not include any securities
(i) sold by a person to the public either pursuant to a registration statement or Rule 144, or (ii) sold in a private transaction where registration rights are not transferred in accordance with Section 2.10. 

1.9    “Registration Expenses” means all expenses incurred by the Company
in complying with Sections 2.1 or 2.2, including, without limitation, all registration and filing fees, printing expenses, fees and disbursements of counsel for the Company, reasonable fees and disbursements not to exceed ten thousand dollars
($10,000) of a single special counsel for Holder, if applicable, blue sky fees and expenses and the expense of any special audits incident to or required by any such registration (but excluding the compensation of regular employees of the
Company which will be paid in any event by the Company). 
 1.10    “Rule
144” means Rule 144 promulgated under the Securities Act, as in effect from time to time. 

1.11    “SEC” means the Securities and Exchange Commission. 

1.12    “Securities Act” means the Securities Act of 1933, as amended. 

1.13    “Selling Expenses” means any underwriting discounts and selling
commissions applicable to the sale. 
 1.14    “Special Registration
Statement” means (i) a registration statement relating to any employee benefit plan or (ii) with respect to any corporate reorganization or transaction under Rule 145 of the Securities Act, any registration statements
related to the issuance or resale of securities issued in such a transaction. 

  
 A-1

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