Document:

EX-10.15

 Exhibit 10.15 

BIONANO GENOMICS, INC. 

WESTERN ALLIANCE BANK, AN ARIZONA CORPORATION 

LOAN AND SECURITY AGREEMENT 

 This LOAN AND SECURITY
AGREEMENT is entered into as of March 8, 2016, by and between WESTERN ALLIANCE BANK, an Arizona corporation (“Bank”) and BIONANO
GENOMICS, INC. (“Borrower”). 
 RECITALS 

Borrower wishes to obtain credit from time to time from Bank, and Bank desires to extend credit to Borrower. This Agreement
sets forth the terms on which Bank will advance credit to Borrower, and Borrower will repay the amounts owing to Bank. 

AGREEMENT 

The parties agree as follows: 
  

	 	 1.
	 DEFINITIONS AND CONSTRUCTION.

 1.1 Definitions. As used in this Agreement, the following terms shall have the following
definitions: 
 “Accounts” means all presently existing and hereafter arising accounts, contract rights, payment
intangibles, and all other forms of obligations owing to Borrower arising out of the sale or lease of goods (including, without limitation, the licensing of software and other technology) or the rendering of services by Borrower, whether or not
earned by performance, and any and all credit insurance, guaranties, and other security therefor, as well as all merchandise returned to or reclaimed by Borrower and Borrower’s Books relating to any of the foregoing. 

“Affiliate” means, with respect to any Person, any Person that owns or controls directly or indirectly such Person,
any Person that controls or is controlled by or is under common control with such Person, and each of such Person’s senior executive officers, directors, and partners. 

“Amortization Date” is April 8, 2017; provided, however, if Borrower achieves the Irys Milestone, then the
Amortization Date shall be extended to October 8, 2017. 
 “Bank Expenses” means all: reasonable costs or
expenses (including reasonable attorneys’ fees and expenses) incurred in connection with the preparation, negotiation, administration, and enforcement of the Loan Documents; reasonable Collateral audit fees; and Bank’s reasonable
attorneys’ fees and expenses incurred in amending, enforcing or defending the Loan Documents (including fees and expenses of appeal), incurred before, during and after an Insolvency Proceeding, whether or not suit is brought. 

“Borrower’s Books” means all of Borrower’s books and records including: ledgers; records concerning
Borrower’s assets or liabilities, the Collateral, business operations or financial condition; and all computer programs, or tape files, and the equipment, containing such information. 

“Business Day” means any day that is not a Saturday, Sunday, or other day on which banks in the State of California
are authorized or required to close. 
 “Change in Control” shall mean a transaction in which any
“person” or “group” (within the meaning of Section 13(d) and 14(d)(2) of the Securities Exchange Act of 1934) becomes the “beneficial owner” (as defined in Rule 13d-3 under
the Securities Exchange Act of 1934), directly or indirectly, of a sufficient number of shares of all classes of stock then outstanding of Borrower ordinarily entitled to vote in the election of directors, empowering such “person” or
“group” to elect a majority of the Board of Directors of Borrower, who did not have such power before such transaction. 

“Closing Date” means the date of this Agreement. 

“Code” means the California Uniform Commercial Code. 

  
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 “Collateral” means the property described on Exhibit A attached
hereto. 
 “Contingent Obligation” means, as applied to any Person, any direct or indirect liability, contingent
or otherwise, of that Person with respect to (i) any indebtedness, lease, dividend, letter of credit or other obligation of another; (ii) any obligations with respect to undrawn letters of credit, corporate credit cards, or merchant
services issued or provided for the account of that Person; and (iii) all obligations arising under any agreement or arrangement designed to protect such Person against fluctuation in interest rates, currency exchange rates or commodity prices;
provided, however, that the term “Contingent Obligation” shall not include endorsements for collection or deposit in the ordinary course of business. The amount of any Contingent Obligation shall be deemed to be an amount equal to the
stated or determined amount of the primary obligation in respect of which such Contingent Obligation is made or, if not stated or determinable, the maximum reasonably anticipated liability in respect thereof as determined by Bank in good faith;
provided, however, that such amount shall not in any event exceed the maximum amount of the obligations under the guarantee or other support arrangement. 

“Copyrights” means any and all copyright rights, copyright applications, copyright registrations and like
protections in each work or authorship and derivative work thereof. 
 “Credit Extension” means each Term Loan, or
any other extension of credit by Bank for the benefit of Borrower hereunder. 
 “Daily Balance” means the
principal amount of the Obligations owed at the end of a given day. 
 “Designated Deposit Account” means
Borrower’s primary depository or operating account with Bank. 
 “Domestic Subsidiary” means a Subsidiary
organized under the laws of the United States or any state or territory thereof or the District of Columbia. 

“Equipment” means all present and future machinery, equipment, tenant improvements, furniture, fixtures, vehicles,
tools, parts and attachments in which Borrower has any interest. 
 “Equity Event’ means Borrower’s receipt,
on or before the Closing Date, of at least Seven Million Dollars ($7,000,000) of net cash proceeds from the sale of its equity securities to investors and on terms and conditions reasonably acceptable to Bank. 

“ERISA” means the Employee Retirement Income Security Act of 1974, as amended, and the regulations thereunder. 

“Event of Default” has the meaning assigned in Article 8. 

“Existing Indebtedness” is the indebtedness of Borrower to PWB in the aggregate principal outstanding amount as of
the Closing Date of approximately Five Million Dollars ($5,000,000) pursuant to that certain Loan and Security Agreement, dated September 18, 2008, as amended from time to time, entered into by and between PWB and Borrower. 

“Final Payment” is a payment (in addition to and not a substitution for the regular monthly payments of principal
plus accrued interest) due on the earliest to occur of (a) the Term Loan Maturity Date, or (b) the acceleration of any Term Loan, or (c) the prepayment of a Term Loan pursuant to Section 2.2(c) or (d), equal to the original
principal amount of the Term Loan multiplied by the Final Payment Percentage, payable to Bank. 
 “Final Payment
Percentage” is three and one quarter percent (3.25%). 
 “Foreign Exchange Reserve Percentage” is defined in
Section 2.1(d)(ii) hereof. 
 “Foreign Subsidiary” means any Subsidiary which is not a Domestic Subsidiary.

  
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 “Foreign Support Account” is defined in the Schedule. 

“Funding Date” is any date on which a Credit Extension is made to or on account of Borrower which shall be a
Business Day. 
 “GAAP” means generally accepted accounting principles as in effect from time to time. 

“Indebtedness” means (a) all indebtedness for borrowed money or the deferred purchase price of property or
services, including without limitation reimbursement and other obligations with respect to surety bonds and letters of credit, (b) all obligations evidenced by notes, bonds, debentures or similar instruments, (c) all capital lease
obligations and (d) all Contingent Obligations. 
 “Index Rate” means the thirty (30) day U.S. LIBOR
rate reported in the Wall Street Journal. 
 “Insolvency Proceeding” means any proceeding commenced by or against
any person or entity under any provision of the United States Bankruptcy Code, as amended, or under any other bankruptcy or insolvency law, including assignments for the benefit of creditors, formal or informal moratoria, compositions,
extension generally with its creditors, or proceedings seeking reorganization, arrangement, or other relief. 

“Intellectual Property” means all of Borrower’s right, title, and interest in and to the following: Copyrights,
Trademarks and Patents; all trade secrets, all design rights, claims for damages by way of past, present and future infringement of any of the rights included above, all licenses or other rights to use any of the Copyrights, Patents or Trademarks,
and all license fees and royalties arising from such use to the extent permitted by such license or rights; all amendments, renewals and extensions of any of the Copyrights, Trademarks or Patents; and all proceeds and products of the foregoing,
including without limitation all payments under insurance or any indemnity or warranty payable in respect of any of the foregoing. 

“Inventory” means all inventory in which Borrower has or acquires any interest, including work in process and
finished products intended for sale or lease or to be furnished under a contract of service, of every kind and description now or at any time hereafter owned by or in the custody or possession, actual or constructive, of Borrower, including such
inventory as is temporarily out of its custody or possession or in transit and including any returns upon any accounts or other proceeds, including insurance proceeds, resulting from the sale or disposition of any of the foregoing and any documents
of title representing any of the above, and Borrower’s Books relating to any of the foregoing. 

“Investment” means any beneficial ownership of (including stock, partnership interest or other securities) any
Person, or any loan, advance or capital contribution to any Person. 
 “IRC” means the Internal Revenue Code of
1986, as amended, and the regulations thereunder. 
 “Irys Milestone” means Borrower’s successful placement
of a minimum of twenty (20) Irys Instruments, at prices not less than Two Hundred Twenty-Five Thousand Dollars ($225,000) per instrument, during the 2016 fiscal year. 

“Lien” means any mortgage, lien, deed of trust, charge, pledge, security interest or other encumbrance. 

“Loan Documents” means, collectively, this Agreement, any note or notes executed by Borrower, and any other
agreement entered into in connection with this Agreement, all as amended or extended from time to time. 
 “Material
Adverse Effect” means a material adverse effect on (i) the business operations or condition (financial or otherwise) of Borrower and its Subsidiaries taken as a whole or (ii) the ability of Borrower to repay the Obligations or
otherwise perform its obligations under the Loan Documents or (iii) the value or priority of Bank’s security interests in the Collateral. 

  
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 “Negotiable Collateral” means all letters of credit of which Borrower
is a beneficiary, notes, drafts, instruments, securities, documents of title, and chattel paper, and Borrower’s Books relating to any of the foregoing. 

“Obligations” means all debt, principal, interest, the Prepayment Fee, the Final Payment, Bank Expenses and other
amounts owed to Bank by Borrower pursuant to this Agreement or any other agreement, whether absolute or contingent, due or to become due, now existing or hereafter arising, including any interest that accrues after the commencement of an Insolvency
Proceeding and including any debt, liability, or obligation owing from Borrower to others that Bank may have obtained by assignment or otherwise. Notwithstanding the foregoing, the “Obligations” shall not include any of Borrower’s
obligations under the Warrant. 
 “Patents” means all patents, patent applications and like protections including
without limitation improvements, divisions, continuations, renewals, reissues, extensions and continuations-in-part of the same. 

“Payment Date” means the first (1st) calendar day of each calendar month. 

“Periodic Payments” means all installments or similar recurring payments that Borrower may now or hereafter become
obligated to pay to Bank pursuant to the terms and provisions of any instrument, or agreement now or hereafter in existence between Borrower and Bank. 

“Permitted Indebtedness” means: 

(a) Indebtedness of Borrower in favor of Bank arising under this Agreement or any other Loan Document; 

(b) Indebtedness existing on the Closing Date and disclosed in the Schedule; 

(c) Indebtedness secured by a lien described in clause (c) of the defined term “Permitted Liens,”
provided (i) such Indebtedness does not exceed the lesser of the cost or fair market value of the equipment and software financed with such Indebtedness and (ii) such Indebtedness does not exceed Two Hundred Fifty Thousand Dollars
($250,000) in the aggregate at any given time; 
 (d) Subordinated Debt; 

(e) Unsecured Indebtedness to trade creditors incurred in the ordinary course of business; 

(f) Indebtedness incurred as a result of endorsing negotiable instruments received in the ordinary course of business;

 (g) Indebtedness that also constitutes a Permitted Investment; 

(h) Indebtedness consisting of reimbursement obligations with respect to letters of credit having a face amount not to
exceed One Hundred Fifty Thousand Dollars ($150,000) in the aggregate issued by PWB to secure Borrower’s obligations under real estate leases, and indebtedness related to a corporate credit facility not to exceed Fifty Thousand Dollars
($50,000) in the aggregate provided by PWB to Borrower, in each case for a period ending not later than ninety (90) days after the Closing Date; 

(i) Indebtedness related to a corporate credit facility not to exceed Fifty Thousand Dollars ($50,000) in the
aggregate provided by American Express to Borrower (which facility will replace the corporate credit facility provided by PWB to Borrower unless such facility is provided by Bank to Borrower instead); 

(j) extensions, refinancings, modifications, amendments and restatements of any items of Permitted Indebtedness
(a) through (i) above, provided that the principal amount thereof is not increased or 

  
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the terms thereof are not modified to impose more burdensome terms upon Borrower or its Subsidiary, as the case may be. 

“Permitted Investment” means: 

(a) Investments existing on the Closing Date disclosed in the Schedule; 

(b) (i) marketable direct obligations issued or unconditionally guaranteed by the United States of America or any
agency or any State thereof maturing within one (1) year from the date of acquisition thereof, (ii) commercial paper maturing no more than one (1) year from the date of creation thereof and currently having rating of at least A-2 or P-2 from either Standard & Poor’s Corporation or Moody’s Investors Service, (iii) certificates of deposit maturing no more than one
(1) year from the date of investment therein issued by Bank and (iv) Bank’s money market accounts; 

(c) Investments consisting of the endorsement of negotiable instruments for deposit or collection or similar
transactions in the ordinary course of Borrower; 
 (d) Investments consisting of deposit accounts or securities
accounts in which Bank has a perfected security interest, except as provided in Section 6.7; 
 (e) Investments
accepted in connection with Transfers permitted by Section 7.1; 
 (f) Investments consisting of the creation
of a Subsidiary for the purpose of consummating a merger transaction permitted by Section 7.3 of this Agreement, which is otherwise a Permitted Investment; 

(g) Investments by Borrower in Subsidiaries and by Subsidiaries in other Subsidiaries not to exceed Two Million
Five Hundred Thousand Dollars ($2,500,000) in the aggregate in any fiscal year; 
 (h) Investments consisting
of (i) travel advances and employee relocation loans and other employee loans and advances in the ordinary course of business, and (ii) loans to employees, officers or directors relating to the purchase of equity securities of Borrower or
its Subsidiaries pursuant to employee stock purchase plans or agreements approved by Borrower’s Board of Directors; not to exceed in the aggregate for (i) and (ii), One Hundred Fifty Thousand Dollars ($150,000) in any fiscal year; 

(i) Investments (including debt obligations) received in connection with the bankruptcy or reorganization of customers
or suppliers and in settlement of delinquent obligations of, and other disputes with, customers or suppliers arising in the ordinary course of business; 

(j) Investments consisting of notes receivable of, or prepaid royalties and other credit extensions, to customers and
suppliers who are not Affiliates, in the ordinary course of business; provided that this paragraph (j) shall not apply to Investments of Borrower in any Subsidiary; 

(k) Repurchases of stock permitted by Section 7.6(i); and 

(l) joint ventures or strategic alliances in the ordinary course of Borrower’s business consisting of the non-exclusive licensing of technology, the development of technology or the providing of technical support, provided that any cash investments by Borrower do not exceed One Hundred Thousand Dollars ($100,000) in the
aggregate in any fiscal year. 
 “Permitted Liens” means the following: 

(a) Any Liens existing on the Closing Date and disclosed in the Schedule or arising under this Agreement or the other
Loan Documents; 

  
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 (b) Liens for taxes, fees, assessments or other governmental charges or
levies, either not delinquent or being contested in good faith by appropriate proceedings, provided the same have no priority over any of Bank’s security interests; 

(c) Liens (including capital leases) (i) upon or in any equipment and related software which was not financed by
Bank acquired or held by Borrower or any of its Subsidiaries to secure the purchase price of such equipment and software or indebtedness incurred solely for the purpose of financing the acquisition of such equipment and software, or
(ii) existing on such equipment and software at the time of its acquisition, provided that the Lien is confined solely to the property so acquired and improvements thereon, and the proceeds of such equipment and software; 

(d) Liens of carriers, warehousemen, suppliers, or other Persons that are possessory in nature arising in the ordinary
course of business so long as such Liens secure liabilities in the aggregate amount not to exceed Two Hundred Fifty Thousand Dollars ($250,000) and are not delinquent or remain payable without penalty or are being contested in good faith and by
appropriate proceedings which proceedings have the effect of preventing the forfeiture or sale of the property subject thereto; 

(e) Liens to secure payment of workers’ compensation, employment insurance,
old-age pensions, social security and other like obligations incurred in the ordinary course of business (other than Liens imposed by ERISA); 

(f) leases or subleases of real property granted in the ordinary course of Borrower’s business (or, if referring
to another Person, in the ordinary course of such Person’s business), and leases, subleases, non-exclusive licenses or sublicenses of personal property (other than Intellectual Property) granted in the
ordinary course of Borrower’s business (or, if referring to another Person, in the ordinary course of such Person’s business), if the leases, subleases, licenses and sublicenses do not prohibit granting Bank a security interest therein;

 (g) non-exclusive licenses of Intellectual Property granted to third
parties in the ordinary course of business, and licenses of Intellectual Property that could not result in a legal transfer of title of the licensed property that may be exclusive in respects other than territory and that may be exclusive as to
territory only as to discreet geographical areas outside of the United States; 
 (h) statutory or common law Liens
of landlords; 
 (i) deposits in the aggregate not to exceed $250,000 securing the performance of real estate leases
entered into in the ordinary course of business; 
 (j) Liens in favor of customs and revenue authorities arising as
a matter of law to secure payment of custom duties that are promptly paid on or before the date they become due; 

(k) Liens arising from attachments or judgments, orders, or decrees in circumstances not constituting an Event of
Default under Sections 8.4 and 8.7; 
 (l) Liens in favor of other financial institutions arising in connection with
Borrower’s deposit and/or securities accounts held at such institutions, provided that Borrower is permitted under the terms of this Agreement to maintain such accounts and Bank has a perfected security interest in the amounts held in such
deposit and/or securities accounts, except as provided in Section 6.7. 
 (m) Liens on cash collateral to
secure the obligations described in clause (h) of the definition of “Permitted Indebtedness”; and 

(n) Liens incurred in connection with the extension, renewal or refinancing of the indebtedness secured by Liens of
the type described in clauses (a) through (m) above, provided that any extension, renewal or replacement Lien shall be limited to the property encumbered by the existing Lien and the principal amount of the indebtedness being extended, renewed
or refinanced does not increase. 

  
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 “Person” means any individual, sole proprietorship, partnership,
limited liability company, joint venture, trust, unincorporated organization, association, corporation, institution, public benefit corporation, firm, joint stock company, estate, entity or governmental agency. 

“Prepayment Fee” is, with respect to any Term Loan subject to prepayment prior to the Term Loan Maturity Date,
whether by mandatory or voluntary prepayment, acceleration or otherwise, an additional fee payable to Bank in an amount equal to: 

(i) for a prepayment made on or after the Funding Date of the Term Loan and prior to the one year anniversary of the
Closing Date, three percent (3.0%) of the principal amount of the Term Loan prepaid; 
 (ii) for a prepayment made on
or after the one year anniversary of the Closing Date and prior to the two year anniversary of the Closing Date, two percent (2.0%) of the principal amount of the Term Loan prepaid; and 

(iii) for a prepayment made on or after the two year anniversary of the Closing Date, one percent (1.0%) of the
principal amount of the Term Loan prepaid. 
 “PWB” is Pacific Western Bank, a California state chartered bank, as
successor in interest by merger with SQUARE 1 BANK, a North Carolina corporation 
 “Responsible Officer” means
each of the Chief Executive Officer and the Chief Financial Officer of Borrower. 
 “Schedule” means the schedule
of exceptions attached hereto and approved by Bank, if any, as the same may be updated from time to time, subject to Bank’s prior written approval. 

“Shares” is (i) one hundred percent (100%) of the issued and outstanding capital stock, membership units or
other securities owned or held of record by Borrower or Borrower’s Subsidiary, in any Domestic Subsidiary; and (ii) sixty-five percent (65%) of the issued and outstanding capital stock, membership units or other securities owned or held of
record by Borrower or any Domestic Subsidiary in any Foreign Subsidiary. 
 “Square 1 Accounts” is defined in the
Schedule. 
 “Square 1 Cash Collateral Accounts” is defined in the Schedule. 

“Subordinated Debt” means any debt incurred by Borrower that is subordinated to the debt owing by Borrower to Bank
on terms acceptable to Bank (and identified as being such by Borrower and Bank). 
 “Subsidiary” means any
corporation, company or partnership in which (i) any general partnership interest or (ii) more than 50% of the stock or other units of ownership which by the terms thereof has the ordinary voting power to elect the Board of Directors,
managers or trustees of the entity, at the time as of which any determination is being made, is owned by Borrower, either directly or through an Affiliate. 

“SVB Accounts” is defined in the Schedule. 

“Term Loan” is defined in Section 2.2(a)(ii) hereof. 

“Term Loan Maturity Date” means April 1, 2020. 

“Total Liabilities” means at any date as of which the amount thereof shall be determined, all obligations that
should, in accordance with GAAP be classified as liabilities on the consolidated balance sheet of Borrower, including in any event all Indebtedness. 

  
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 “Trademarks” means any trademark and servicemark rights, whether
registered or not, applications to register and registrations of the same and like protections, and the entire goodwill of the business of Borrower connected with and symbolized by such trademarks. 

“Warrant” means that certain Warrant to Purchase Stock issued by Borrower to Bank on the Closing Date, as the same
may be amended from time to time. 
 1.2 Accounting Terms. All accounting terms not specifically defined
herein shall be construed in accordance with GAAP and all calculations made hereunder shall be made in accordance with GAAP. When used herein, the terms “financial statements” shall include the notes and schedules thereto. 

 

	 	 2.
	 LOAN AND TERMS OF
PAYMENT. 

 2.1 Credit Extensions. 

Borrower promises to pay to the order of Bank, in lawful money of the United States of America, the aggregate unpaid principal
amount of all Credit Extensions made by Bank to Borrower hereunder. Borrower shall also pay interest on the unpaid principal amount of such Credit Extensions at rates in accordance with the terms hereof. 

2.2 Term Loan. 

(a) Availability. Subject to the terms and conditions of this Agreement, Bank agrees to make a term loan to
Borrower on the Closing Date in an aggregate amount of Seven Million Dollars ($7,000,000) Dollars. After repayment, no Term Loan may be re-borrowed. 

(b) Repayment. Borrower shall make monthly payments of interest only, in arrears, commencing on the first (1st)
Payment Date following the Funding Date of the Term Loan, and continuing on the Payment Date of each successive month thereafter through and including the Payment Date immediately preceding the Amortization Date. Borrower agrees to pay, on the
Funding Date of the Term Loan, any initial partial monthly interest payment otherwise due for the period between the Funding Date of the Term Loan and the first Payment Date thereof. Commencing on the Amortization Date, and continuing on the Payment
Date of each month thereafter, Borrower shall make equal monthly payments of principal, together with applicable interest, in arrears, to Bank, as calculated by Bank (which calculations shall be deemed correct absent manifest error) based upon:
(1) the amount of the Term Loan, (2) the effective rate of interest, as determined in Section 2.4(a), and (3) a repayment schedule equal to (i) if the Amortization Date is April 8, 2017,
thirty-six (36) months and (ii) if the Amortization Date is October 8, 2017, thirty (30) months. All unpaid principal and accrued and unpaid interest with respect to the Term Loan is due
and payable in full on the Term Loan Maturity Date. The Term Loan may only be prepaid in accordance with Sections 2.2(c) and 2.2(d). 

(c) Mandatory Prepayments. If the Term Loan is accelerated following the occurrence of an Event of Default,
Borrower shall immediately pay to Bank, payable to Bank, an amount equal to the sum of: (i) all outstanding principal of the Term Loan plus accrued and unpaid interest thereon through the prepayment date, (ii) the Final Payment,
(iii) the Prepayment Fee, plus (iv) all other Obligations that are due and payable, including Bank’s Expenses and interest at the Default Rate with respect to any past due amounts. Notwithstanding (but without duplication with) the
foregoing, on the Term Loan Maturity Date, if the Final Payment had not previously been paid in full in connection with the prepayment of the Term Loan in full, Borrower shall pay to Bank the Final Payment in respect of the Term Loan. 

(d) Permitted Prepayment of Term Loan. Borrower shall have the option to prepay all, but not less than all, of
the Term Loan advanced by Bank under this Agreement, provided Borrower (i) provides written notice to Bank of its election to prepay the Term Loan at least thirty (30) days prior to such prepayment, and (ii) pays to Bank on the date
of such prepayment, payable to Bank, an amount equal to the sum of (A) all outstanding principal of the Term Loan plus accrued and unpaid interest thereon through the prepayment date, (B) 

  
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the Final Payment, (C) the Prepayment Fee, plus (D) all other Obligations that are due and payable, including Bank’s Expenses and interest at the Default Rate with respect to any
past due amounts. 
 2.3 Intentionally Omitted. 

2.4 Interest Rates, Payments, and Calculations. 

(a) Interest Rate. Except as set forth in Section 2.4(b), the Term Loan shall bear interest, on the
outstanding Daily Balance thereof, at a floating per annum rate equal to the Index Rate plus six and fifty-two hundredths of one percent (6.52%). 

(b) Late Fee; Default Rate. If any payment is not made within ten (10) days after the date such payment is
due, Borrower shall pay Bank a late fee equal to the lesser of (i) five percent (5%) of the amount of such unpaid amount or (ii) the maximum amount permitted to be charged under applicable law, not in any case to be less than $25.00. All
Obligations shall bear interest, from and after the occurrence and during the continuance of an Event of Default, at a rate equal to five (5) percentage points above the interest rate applicable immediately prior to the occurrence of the Event
of Default. 
 (c) Payments. Interest hereunder shall be due and payable on the first calendar day of each
month during the term hereof. Bank shall, at its option, charge such interest, all Bank Expenses, and all Periodic Payments against any of Borrower’s deposit accounts (including but not limited to the Designated Deposit Account), in which case
those amounts shall thereafter accrue interest at the rate then applicable hereunder. Any interest not paid when due shall be compounded by becoming a part of the Obligations, and such interest shall thereafter accrue interest at the rate then
applicable hereunder. All payments shall be free and clear of any taxes, withholdings, duties, impositions or other charges, to the end that Bank will receive the entire amount of any Obligations payable hereunder, regardless of source of payment.

 (d) Computation. In the event the Index Rate is changed from time to time hereafter, the applicable rate
of interest hereunder shall be increased or decreased, effective as of the day the Index Rate is changed, by an amount equal to such change in the Index Rate. All interest chargeable under the Loan Documents shall be computed on the basis of a three
hundred sixty (360) day year for the actual number of days elapsed. 
 2.5 Crediting Payments. Prior to
the occurrence of an Event of Default, Bank shall credit a wire transfer of funds, check or other item of payment to such deposit account or Obligation as Borrower specifies. After the occurrence of an Event of Default, the receipt by Bank of any
wire transfer of funds, check, or other item of payment shall be immediately applied to conditionally reduce Obligations, but shall not be considered a payment on account unless such payment is of immediately available federal funds or unless and
until such check or other item of payment is honored when presented for payment. Notwithstanding anything to the contrary contained herein, any wire transfer or payment received by Bank after 12:00 noon Pacific time shall be deemed to have been
received by Bank as of the opening of business on the immediately following Business Day. Whenever any payment to Bank under the Loan Documents would otherwise be due (except by reason of acceleration) on a date that is not a Business Day, such
payment shall instead be due on the next Business Day, and additional fees or interest, as the case may be, shall accrue and be payable for the period of such extension. 

2.6 Fees. Borrower shall pay to Bank the following: 

(a) Facility Fee. On the Closing Date, a Facility Fee equal to Thirty-Five Thousand Dollars ($35,000) which
shall be nonrefundable; Borrower has paid to Bank a deposit of $35,000 (the “Good Faith Deposit”) to initiate Bank’s due diligence review process. The Good Faith Deposit will be applied to the Facility Fee due on the Closing Date;

 (b) Final Payment. The Final Payment, when due hereunder; 

(c) Prepayment Fee. The Prepayment Fee, when due hereunder; 

  
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 (d) Bank Expenses. On the Closing Date, all Bank Expenses incurred
through the Closing Date, including reasonable attorneys’ fees and expenses and, after the Closing Date, all Bank Expenses, including reasonable attorneys’ fees and expenses, as and when they are incurred by Bank. 

2.7 Term. This Agreement shall become effective on the Closing Date and, subject to Section 13.7, shall
continue in full force and effect for so long as any Obligations (other than inchoate indemnity obligations) remain outstanding or Bank has any obligation to make Credit Extensions under this Agreement. Notwithstanding the foregoing, Bank shall have
the right to terminate its obligation to make Credit Extensions under this Agreement immediately and without notice upon the occurrence and during the continuance of an Event of Default. Notwithstanding termination, Bank’s Lien on the
Collateral shall remain in effect for so long as any Obligations (other than inchoate indemnity obligations) are outstanding. Upon full and final payment and satisfaction, in cash, of all Obligations (other than inchoate indemnity obligations), and
the full and final termination of all of Bank’s obligations and commitments to make Credit Extensions, Bank shall, at Borrower’s sole cost and expense, release the security interest in the Collateral granted under this Agreement and any
other Loan Document. 
 2.8 Extension of Maturity. Notwithstanding anything contained herein to the contrary,
Bank shall have the right, in its sole and absolute discretion, to extend the Term Loan Maturity Date to the tenth day of the month next following the actual Term Loan Maturity Date as stated in this Agreement. 

 

	 	 3.
	 CONDITIONS OF LOANS. 

3.1 Conditions Precedent to Initial Credit Extension. The obligation of Bank to make the initial Credit Extension
is subject to the condition precedent that Bank shall have received, in form and substance satisfactory to Bank, the following: 

(a) this Agreement; 

(b) a certificate of the Secretary of Borrower with respect to incumbency and resolutions authorizing the execution
and delivery of this Agreement; 
 (c) UCC National Form Financing Statement; 

(d) the Warrant; 

(e) agreement to provide insurance; 

(f) payment of the fees and Bank Expenses then due specified in Section 2.6 hereof; 

(g) current financial statements of Borrower; 

(h) evidence that Borrower has consummated the Equity Event, receipt of which hereby is acknowledged by Bank; 

(i) a payoff letter from PWB, in respect of the Existing Indebtedness; 

(j) evidence that (i) the Liens securing the Existing Indebtedness will be terminated and (ii) the documents
and/or filings evidencing the perfection of such Liens, including without limitation any financing statements and/or control agreements, have or will, concurrently with the initial Credit Extension, be terminated; and 

(k) such other documents, and completion of such other matters, as Bank may reasonably deem necessary or appropriate.

 3.2 Conditions Precedent to all Credit Extensions. The obligation of Bank to make each Credit Extension,
including the initial Credit Extension, is further subject to the following conditions: 

  
 10 

 (a) timely receipt by Bank of (i) the Advance Request Form in the
form of Exhibit B-1 attached hereto; and (ii) the Disbursement Letter in the form of Exhibit B-2 attached hereto; 

(b) the representations and warranties contained in Section 5 shall be true and correct in all material respects
on and as of the date of such Advance Request Form and Disbursement Letter, and on the Funding Date of each Credit Extension as though made at and as of each such date, provided that those representations and warranties expressly referring to
another date shall be true, correct and complete in all material respects as of such date, and no Event of Default shall have occurred and be continuing, or would exist after giving effect to such Credit Extension. The making of each Credit
Extension shall be deemed to be a representation and warranty by Borrower on the date of such Credit Extension as to the accuracy of the facts referred to in this Section 3.2; and 

(c) to the extent not delivered at the Closing Date, a duly executed original Warrants, in number, form and content
acceptable to Bank with respect to each Credit Extension made by Bank after the Closing Date. 
 3.3 Post-Closing
Condition. As soon as possible, but no later than thirty (30) days after the Closing Date, Borrower shall deliver to Bank, in form and substance satisfactory to Bank, the following: 

(a) a landlord waiver for each of Borrower’s leased locations at (i) 9540 Towne Centre Drive #100, San Diego,
CA 92121 and (ii) 9640 Towne Centre Drive #100, San Diego, CA 92121; and 
 (b) an equipment holder’s
acknowledgment for each of (i) 5206 Eastgate Mall, San Diego CA 92121 and (ii) 9890 Pacific Heights Blvd. San Diego CA 92121. 

3.4 Procedures for Borrowing. Subject to the prior satisfaction of all other applicable conditions to the making
of the Term Loan set forth in this Agreement, to obtain the Term Loan, Borrower shall notify Bank (which notice shall be irrevocable) by electronic mail, facsimile, or telephone by 12:00 noon Pacific time three (3) Business Days prior to the
date the Term Loan is to be made. Together with any such electronic, facsimile or telephonic notification, Borrower shall deliver to Bank by electronic mail or facsimile a completed Disbursement Letter executed by a Responsible Officer or his or her
designee, together with the Warrant, in form and content reasonably acceptable to Bank. Bank may rely on any telephone notice given by a person whom Bank reasonably believes is a Responsible Officer or designee. On the Funding Date, Bank shall
credit and/or transfer (as applicable) to the Designated Deposit Account, the amount of the Term Loan. 
  

	 	 4.
	 CREATION OF SECURITY
INTEREST. 

 4.1 Grant of Security Interest. Borrower
grants and pledges to Bank a continuing security interest in all presently existing and hereafter acquired or arising Collateral in order to secure prompt repayment of any and all Obligations and in order to secure prompt performance by Borrower of
each of its covenants and duties under the Loan Documents (other than the Warrant). Except as set forth in the Schedule and Permitted Liens, such security interest constitutes a valid, first priority security interest in the presently existing
Collateral, and will constitute a valid, first priority security interest in Collateral acquired after the date hereof. 

4.2 Delivery of Additional Documentation Required. Borrower shall from time to time execute and deliver to Bank,
at the request of Bank, all Negotiable Collateral, all financing statements and other documents that Bank may reasonably request, in form satisfactory to Bank, to perfect and continue the perfection of Bank’s security interests in the
Collateral and in order to fully consummate all of the transactions contemplated under the Loan Documents. Borrower from time to time may deposit with Bank specific time deposit accounts to secure specific Obligations. Borrower authorizes Bank to
hold such balances in pledge and to decline to honor any drafts thereon or any request by Borrower or any other Person to pay or otherwise transfer any part of such balances for so long as such Obligations are outstanding. 

4.3 Right to Inspect. Bank (through any of its officers, employees, or agents) shall have the right, upon
reasonable prior notice, from time to time during Borrower’s usual business hours but no more than once 

  
 11 

 
a year (unless an Event of Default has occurred and is continuing), to inspect Borrower’s Books and to make copies thereof and to check, test, and appraise the Collateral in order to verify
Borrower’s financial condition or the amount, condition of, or any other matter relating to, the Collateral. 

4.4 Pledge of Collateral. Borrower hereby pledges, assigns and grants to Bank, a security interest in all the
Shares, together with all proceeds and substitutions thereof, all cash, stock and other moneys and property paid thereon, all rights to subscribe for securities declared or granted in connection therewith, and all other cash and noncash proceeds of
the foregoing, as security for the performance of the Obligations. No later than thirty (30) days after the Closing Date, the certificate or certificates for the Shares will be delivered to Bank, accompanied by an instrument of assignment duly
executed in blank by Borrower. To the extent required by the terms and conditions governing the Shares, Borrower shall cause the books of each entity whose Shares are part of the Collateral and any transfer agent to reflect the pledge of the Shares.
Upon the occurrence and during the continuance of an Event of Default hereunder, Bank may effect the transfer of any securities included in the Collateral (including but not limited to the Shares) into the name of Bank and cause new (as applicable)
certificates representing such securities to be issued in the name of Bank or its transferee. Borrower will execute and deliver such documents, and take or cause to be taken such actions, as Bank may reasonably request to perfect or continue the
perfection of Bank’s security interest in the Shares. Unless an Event of Default shall have occurred and be continuing, Borrower shall be entitled to exercise any voting rights with respect to the Shares and to give consents, waivers and
ratifications in respect thereof, provided that no vote shall be cast or consent, waiver or ratification given or action taken which would be inconsistent with any of the terms of this Agreement or which would constitute or create any violation of
any of such terms. All such rights to vote and give consents, waivers and ratifications shall terminate upon the occurrence and during the continuance of an Event of Default. 
  

	 	 5.
	 REPRESENTATIONS AND WARRANTIES.

 Borrower represents and warrants as follows: 

5.1 Due Organization and Qualification. Borrower is a corporation duly existing under the laws of its state of
incorporation and qualified and licensed to do business in any other state in which the conduct of its business or its ownership of property requires that it be so qualified. except where the failure to do so could not reasonably be expected to have
a Material Adverse Effect. Each Subsidiary of Borrower is a corporation or other organization duly existing under the laws of its jurisdiction of formation and qualified and licensed to do business in any other jurisdiction in which the conduct of
its business or its ownership of property requires that it be so qualified except where the failure to do so could not reasonably be expected to have a Material Adverse Effect. 

5.2 Due Authorization; No Conflict. The execution, delivery, and performance of the Loan Documents are within
Borrower’s powers, have been duly authorized, and are not in conflict with nor constitute a breach of any provision contained in Borrower’s Certificate of Incorporation or Bylaws, nor will they constitute an event of default under any
material agreement to which Borrower is a party or by which Borrower is bound. Borrower is not in default under any material agreement to which it is a party or by which it is bound. 

5.3 No Prior Encumbrances. Borrower has good and marketable title to its property, free and clear of Liens,
except for Permitted Liens. 
 5.4 Bona Fide Accounts. The Accounts are bona fide existing obligations. The
property and services giving rise to such Accounts have been delivered or rendered to the account debtor or to the account debtor’s agent for immediate and unconditional acceptance by the account debtor. Borrower has not received notice of
actual or imminent Insolvency Proceeding of any account debtor. 
 5.5 Merchantable Inventory. All Inventory
is in all material respects of good and marketable quality, free from all material defects, except for Inventory for which adequate reserves have been made. 

5.6 Intellectual Property. Borrower is the sole owner of the Intellectual Property, except for non-exclusive licenses granted by Borrower to its customers in the ordinary course of business. To the best of Borrower’s knowledge, each of the Patents is valid and enforceable, and no part of the Intellectual
Property material 

  
 12 

 
to Borrower’s business has been judged invalid or unenforceable, in whole or in part, and no claim has been made that any part of the Intellectual Property material to Borrower’s
business violates the rights of any third party. Except as set forth in the Schedule, Borrower’s rights as a licensee of intellectual property do not give rise to more than five percent (5%) of its gross revenue in any given month, including
without limitation revenue derived from the sale, licensing, rendering or disposition of any product or service. Except as set forth in the Schedule, Borrower is not a party to, or bound by, any material agreement that restricts the grant by
Borrower of a security interest in Borrower’s rights under such agreement except for Permitted Liens and customary anti-assignment provisions. 

5.7 Name; Location of Chief Executive Office. Except as disclosed in the Schedule, Borrower has not done
business under any name other than that specified on the signature page hereof. The chief executive office of Borrower is located at the address indicated in Section 10 hereof. or as notified to Bank in compliance with Section 7.2. Except
as set forth in the Schedule and except for locations containing (i) less than Two Hundred Fifty Thousand Dollars ($250,000) in Borrower’s assets or property in the aggregate or (ii) mobile equipment consisting of laptop computers and
related hardware and software, all Borrower’s Inventory and Equipment is located only at the location set forth in Section 10 hereof. 

5.8 Litigation. Except as set forth in the Schedule or in a written notice to Bank in accordance with
Section 6.3(d), there are no actions or proceedings pending by or against Borrower or any Subsidiary before any court or administrative agency in which an adverse decision could have a Material Adverse Effect, or a material adverse effect on
Borrower’s interest or Bank’s security interest in the Collateral. 
 5.9 No Material Adverse Change in
Financial Statements. All consolidated and consolidating financial statements related to Borrower and any Subsidiary that Bank has received from Borrower fairly present in all material respects Borrower’s financial condition as of the date
thereof and Borrower’s consolidated and consolidating results of operations for the period then ended. There has not been a material adverse change in the consolidated or the consolidating financial condition of Borrower since the date of the
most recent of such financial statements submitted to Bank. 
 5.10 Solvency, Payment of Debts. Borrower is
solvent and able to pay its debts (including trade debts) as they mature. 
 5.11 Regulatory Compliance.
Borrower and each Subsidiary have met the minimum funding requirements of ERISA with respect to any employee benefit plans subject to ERISA, and no event has occurred resulting from Borrower’s failure to comply with ERISA that could result in
Borrower’s incurring any material liability. Borrower is not an “investment company” or a company “controlled” by an “investment company” within the meaning of the Investment Company Act of 1940. Borrower is not
engaged principally, or as one of the important activities, in the business of extending credit for the purpose of purchasing or carrying margin stock (within the meaning of Regulations T and U of the Board of Governors of the Federal Reserve
System). Borrower has complied with all the provisions of the Federal Fair Labor Standards Act. Borrower has not violated any statutes, laws, ordinances or rules applicable to it, violation of which could have a Material Adverse Effect. 

5.12 Environmental Condition. Except as disclosed in the Schedule, none of Borrower’s or any
Subsidiary’s properties or assets has ever been used by Borrower or any Subsidiary or, to the best of Borrower’s knowledge, by previous owners or operators, in the disposal of, or to produce, store, handle, treat, release, or transport,
any hazardous waste or hazardous substance other than in accordance with applicable law; to the best of Borrower’s knowledge, none of Borrower’s properties or assets has ever been designated or identified in any manner pursuant to any
environmental protection statute as a hazardous waste or hazardous substance disposal site, or a candidate for closure pursuant to any environmental protection statute; no lien arising under any environmental protection statute has attached to any
revenues or to any real or personal property owned by Borrower or any Subsidiary; and neither Borrower nor any Subsidiary has received a summons, citation, notice, or directive from the Environmental Protection Agency or any other federal, state or
other governmental agency concerning any action or omission by Borrower or any Subsidiary resulting in the releasing, or otherwise disposing of hazardous waste or hazardous substances into the environment. 

5.13 Taxes. Borrower and each Subsidiary have filed or caused to be filed all tax returns, or extensions to file
such returns, required to be filed, and have paid, or have made adequate provision for the payment 

  
 13 

 
of, all taxes reflected therein, except for taxes that are currently being contested in good faith, by appropriate proceedings promptly instituted and diligently prosecuted by the Borrower or
Subsidiary and for which adequate reserves are maintained. 
 5.14 Subsidiaries. Borrower does not own any
stock, partnership interest or other equity securities of any Person, except for Permitted Investments. 
 5.15
Government Consents. Borrower and each Subsidiary have obtained all material consents, approvals and authorizations of, made all declarations or filings with, and given all notices to, all governmental authorities that are necessary for the
continued operation of Borrower’s business as currently conducted. 
 5.16 Accounts. Except as disclosed
on the Schedule or permitted by Section 6.7, none of Borrower’s nor any Subsidiary’s cash or cash equivalents is maintained or invested with a Person other than Bank or Bank’s affiliates. 

5.17 Shares. Borrower has full power and authority to create a first lien on the Shares and no disability or
contractual obligation exists that would prohibit Borrower from pledging the Shares pursuant to this Agreement. To Borrower’s knowledge, there are no subscriptions, warrants, rights of first refusal or other restrictions on transfer relative
to, or options exercisable with respect to the Shares. The Shares have been and will be duly authorized and validly issued, and are fully paid and non-assessable. To Borrower’s knowledge, the Shares are
not the subject of any present or threatened suit, action, arbitration, administrative or other proceeding, and Borrower knows of no reasonable grounds for the institution of any such proceedings. 

5.18 Use of Proceeds. Borrower shall use the proceeds of the Credit Extensions solely as working capital and to
fund its general business requirements in accordance with the provisions of this Agreement, and not for personal, family, household or agricultural purposes. A portion of the proceeds of the Term Loan shall be used by Borrower to repay the Existing
Indebtedness in full on the Closing Date. 
 5.19 Full Disclosure. No representation, warranty or other
statement made by Borrower in any certificate or written statement furnished to Bank contains any untrue statement of a material fact or omits to state a material fact necessary in order to make the statements contained in such certificates or
statements not misleading. The Bank acknowledges that the projections and forecasts provided by Borrower in good faith and based upon reasonable assumptions are not to be viewed as facts and that actual results during the period or periods covered
by any such projections and forecasts may differ from the projected or forecasted results. 
  

	 	 6.
	 AFFIRMATIVE COVENANTS. 

Borrower shall do all of the following: 

6.1 Good Standing. Borrower shall maintain its corporate existence and good standing in its jurisdiction of
incorporation and maintain qualification in each other jurisdiction in which it is required under applicable law except where the failure to be so qualified could not reasonably be expected to have a Material Adverse Effect. Borrower shall cause
each of its Subsidiaries to maintain its organizational existence and good standing in its jurisdiction of formation and maintain qualification in each other jurisdiction in which it is required under applicable law except where the failure to be so
qualified could not reasonably be expected to have a Material Adverse Effect. Borrower shall maintain, and shall cause each of its Subsidiaries to maintain, in force all licenses, approvals and agreements, the loss of which could have a Material
Adverse Effect. 
 6.2 Government Compliance. Borrower shall meet, and shall cause each Subsidiary to meet,
the minimum funding requirements of ERISA with respect to any employee benefit plans subject to ERISA. Borrower shall comply, and shall cause each Subsidiary to comply, with all statutes, laws, ordinances and government rules and regulations to
which it is subject, noncompliance with which could have a Material Adverse Effect. 

  
 14 

 6.3 Financial Statements, Reports, Certificates. Borrower shall
deliver the following to Bank: (a) as soon as available, but in any event within thirty (30) days after the end of each calendar month, a company prepared consolidated balance sheet, income statement, and cash flow statement covering
Borrower’s consolidated operations during such period, prepared in accordance with GAAP, consistently applied, in a form acceptable to Bank and certified by a Responsible Officer; (b) as soon as available, but in any event within one
hundred eighty (180) days after the end of Borrower’s fiscal year, audited consolidated financial statements of Borrower prepared in accordance with GAAP, consistently applied, together with an unqualified opinion on such financial
statements of an independent certified public accounting firm reasonably acceptable to Bank; (c) copies of all statements, reports and notices sent or made available generally by Borrower to its security holders or to any holders of
Subordinated Debt and, if applicable, all reports on Forms 10-K and 10-Q filed with the Securities and Exchange Commission; (d) promptly upon receipt of notice
thereof, a report of any legal actions pending or threatened against Borrower or any Subsidiary that could result in damages or costs to Borrower or any Subsidiary of One Hundred Thousand Dollars ($100,000) or more; (e) as soon as available,
but in any event within forty-five (45) days after the end of each fiscal year of Borrower, (i) annual operating budgets (including income statements, balance sheets and cash flow statements, by month) for the upcoming fiscal year of
Borrower, and (ii) annual financial projections for the following fiscal year as approved by Borrower’s board of directors, together with any related business forecasts used in the preparation of such annual financial projections; and
(f) such budgets, sales projections, operating plans or other financial information as Bank may reasonably request from time to time. 

Borrower shall deliver to Bank with the monthly financial statements a Compliance Certificate signed by a Responsible Officer
in substantially the form of Exhibit D hereto. 
 Bank shall have a right from time to time hereafter to audit
Borrower’s Accounts and appraise Collateral at Borrower’s expense, provided that such audits will be conducted no more often than once per year unless an Event of Default has occurred and is continuing. 

6.4 Inventory; Returns. Borrower shall keep all Inventory in good and marketable condition, free from all
material defects except for Inventory for which adequate reserves have been made. Returns and allowances, if any, as between Borrower and its account debtors shall be on the same basis and in accordance with the usual customary practices of
Borrower, as they exist at the time of the execution and delivery of this Agreement. Borrower shall promptly notify Bank of all returns and recoveries and of all disputes and claims, where the return, recovery, dispute or claim involves more than
One Hundred Thousand Dollars ($100,000). 
 6.5 Taxes. Borrower shall make, and shall cause each Subsidiary to
make, due and timely payment or deposit of all material federal, state, and local taxes, assessments, or contributions required of it by law, and will execute and deliver to Bank, on demand, appropriate certificates attesting to the payment or
deposit thereof; and Borrower will make, and will cause each Subsidiary to make, timely payment or deposit of all material tax payments and withholding taxes required of it by applicable laws, including, but not limited to, those laws concerning
F.I.C.A., F.U.T.A., state disability, and local, state, and federal income taxes, and will, upon request, furnish Bank with proof satisfactory to Bank indicating that Borrower or a Subsidiary has made such payments or deposits; provided that
Borrower or a Subsidiary need not make any payment if the amount or validity of such payment is contested in good faith by appropriate proceedings and is reserved against (to the extent required by GAAP) by Borrower. 

6.6 Insurance. 

(a) Borrower, at its expense, shall keep the Collateral insured against loss or damage by fire, theft, explosion,
sprinklers, and all other hazards and risks, and in such amounts, as ordinarily insured against by other owners in similar businesses conducted in the locations where Borrower’s business is conducted on the date hereof. Borrower shall also
maintain insurance relating to Borrower’s business, ownership and use of the Collateral in amounts and of a type that are customary to businesses similar to Borrower’s. 

(b) All such policies of insurance shall be in such form, with such companies, and in such amounts as are reasonably
satisfactory to Bank. All such policies of property insurance shall contain a lender’s loss payable endorsement, in a form reasonably satisfactory to Bank, showing Bank as an additional loss payee thereof, and all liability insurance policies
shall show the Bank as an additional insured and shall specify that the 

  
 15 

 
insurer must give at least twenty (20) days (ten (10) days notice for non-payment of premium) notice to Bank before canceling its policy for any
reason. Upon Bank’s request, Borrower shall deliver to Bank certified copies of such policies of insurance and evidence of the payments of all premiums therefor. All proceeds payable under any such policy shall, at the option of Bank, be
payable to Bank to be applied on account of the Obligations. 
 6.7 Accounts. Borrower shall (i) within
ninety (90) days of the Closing Date (the “Transition Period”), maintain and shall cause each of its Domestic Subsidiaries to maintain its primary depository, operating, and investment accounts with Bank or Bank’s affiliates, and
(ii) endeavor to utilize and shall cause each of its Subsidiaries to endeavor to utilize Bank’s International Banking Division for any international banking services required by Borrower, including, but not limited to, foreign currency
wires, hedges, and swaps. Notwithstanding the foregoing, during the Transition Period (x) Borrower and its Domestic Subsidiaries shall not maintain more than One Million Dollars ($1,000,000) in the aggregate in accounts outside of Bank or
Bank’s affiliate; provided that, in addition to the foregoing amount, the Foreign Support Account may maintain up to Two Hundred Fifty Thousand Dollars ($250,000.00) and the Square 1 Cash Collateral Accounts may maintain up to Two Hundred
Thousand Dollars ($200,000.00); and (y) all such primary depository, operating, and investment accounts of Borrower and its Domestic Subsidiaries, except for the Square 1 Cash Collateral Accounts, shall, within ten (10) days of the Closing
Date, be subject to control agreements in favor of, and in form and content reasonably acceptable to, Bank. For sake of clarity, but subject to the preceding requirements and limitations, Borrower (A) shall be permitted to maintain the SVB
Accounts indefinitely, and (B) must close the Square 1 Accounts within ninety (90) days of the Closing Date. 

6.8 Term Sheet and Funding Milestone; Minimum Cash. On or before May 31, 2016, Borrower shall have received
a term sheet (the “Post-Close Term Sheet”) for the sale of at least Fifteen Million Dollars ($15,000,000) of Borrower’s equity securities (the “Post-Close Equity”), on terms and from investors reasonably acceptable to Bank,
which Post-Close Term sheet must be executed on or before June 30, 2016. Borrower shall have received the Post-Close Equity on or before August 31, 2016. Notwithstanding anything to the contrary in Section 6.7, Borrower shall at all
times from the Closing Date through receipt of the Post-Close Equity maintain in an account with Bank not less than One Million Dollars ($1,000,000). 

6.9 Performance to Plan; Minimum Cash. Borrower’s actual trailing
six-month revenues, as of any date of determination, shall be no less than seventy-five percent (75%) of Borrower’s projected revenues (the “Revenue Covenant”), as set forth in the table
attached as Exhibit C hereto; provided that Borrower shall not be required to comply with the Revenue Covenant as long as Borrower at all times maintains a ratio of (i) minimum unrestricted cash in accounts with Bank to (ii) Indebtedness
to Bank, of at least 1.25 to 1.00. 
 6.10 Intellectual Property Rights. 

(a) Borrower shall, concurrently with the delivery of the monthly Compliance Certificate, give Bank written notice of
any applications or registrations of intellectual property rights filed with the United States Patent and Trademark Office, including the date of such filing and the registration or application numbers, if any, and the filing of any applications or
registrations with the United States Copyright Office, including the title of such intellectual property rights to be registered, as such title will appear on such applications or registrations, and the date such applications or registrations
will be filed. 
 (b) Bank may audit Borrower’s Intellectual Property to confirm compliance with this Section,
provided such audit may not occur more often than once per year, unless an Event of Default has occurred and is continuing. Bank shall have the right, but not the obligation, to take, at Borrower’s sole expense, any actions that Borrower is
required under this Section to take but which Borrower fails to take, after 15 days’ notice to Borrower. Borrower shall reimburse and indemnify Bank for all reasonable costs and reasonable expenses incurred in the reasonable exercise of its
rights under this Section. 
 6.11 Formation or Acquisition of Subsidiaries. Notwithstanding and without
limiting the negative covenants contained in Sections 7.3 and 7.7 hereof, at the time that Borrower or any guarantor forms any direct or indirect Subsidiary or acquires any direct or indirect Subsidiary after the Closing Date, Borrower and such
guarantor shall (a) cause such new Domestic Subsidiary to provide to Bank (i) a joinder to this Agreement, to cause such Domestic Subsidiary to become a co-borrower hereunder or (ii) a Guaranty
and security agreement, to cause 

  
 16 

 
such Domestic Subsidiary to become a guarantor hereunder; in each case, together with such appropriate financing statements and/or Control Agreements, all in form and substance satisfactory to
Bank (including being sufficient to grant Bank a first priority Lien (subject to Permitted Liens) in and to the assets of such newly formed or acquired Domestic Subsidiary), (b) provide to Bank appropriate certificates and powers and financing
statements, pledging all of the Shares in such new Subsidiary, in form and substance satisfactory to Bank, and (c) provide to Bank all other documentation in form and substance satisfactory to Bank, which in its opinion is appropriate with
respect to the execution and delivery of the applicable documentation referred to above. Any document, agreement, or instrument executed or issued pursuant to this Section shall be a Loan Document. 

6.12 Further Assurances. At any time and from time to time Borrower shall execute and deliver such further
instruments and take such further action as may reasonably be requested by Bank to effect the purposes of this Agreement. 
  

	 	 7.
	 NEGATIVE COVENANTS. 

Borrower will not do any of the following without the Bank’s prior written consent (not to be unreasonably withheld): 

7.1 Dispositions. Convey, sell, lease, transfer or otherwise dispose of (collectively, a “Transfer”),
or permit any of its Subsidiaries to Transfer, all or any part of its business or property, other than: (i) Transfers of Inventory in the ordinary course of business; (ii) Transfers of non-exclusive
licenses and similar arrangements for the use of the property of Borrower or its Subsidiaries in the ordinary course of business; and licenses of Intellectual Property that could not result in a legal transfer of title of the licensed property that
may be exclusive in respects other than territory and that may be exclusive as to territory only as to discrete geographical areas outside of the United States; (iii) Transfers of worn-out or obsolete
Equipment which was not financed by Bank.; (iv) Permitted Liens and Permitted Investments; (v) Transfers between Borrower and one or more Domestic Subsidiaries that are guarantors of the Obligations or
co-borrowers hereunder; (vi) Transfers from any Subsidiary to Borrower; and (vii) Transfers from Borrower to one or more Foreign Subsidiaries in the form of payment by Borrower for services provided
by such Subsidiary(ies) pursuant to cost plus expense reimbursement arrangements entered into in the ordinary course of business. 

7.2 Change in Business; Change in Control or Executive Office. Engage in any business, or permit any of its
Subsidiaries to engage in any business, other than the businesses currently engaged in by Borrower and any business substantially similar or related thereto (or incidental thereto); or cease to conduct business in the manner conducted by Borrower as
of the Closing Date; or suffer or permit a Change in Control; or without thirty (30) days prior written notification to Bank, relocate its chief executive office or state of incorporation or change its legal name; or without Bank’s prior
written consent, change the date on which its fiscal year ends. 
 7.3 Mergers or Acquisitions. Merge or
consolidate, or permit any of its Subsidiaries to merge or consolidate, with or into any other business organization (other than mergers or consolidations of a Subsidiary into another Subsidiary or into Borrower, with Borrower being the surviving
entity), or acquire, or permit any of its Subsidiaries to acquire, all or substantially all of the capital stock or property of another Person. 

7.4 Indebtedness. Create, incur, assume or be or remain liable with respect to any Indebtedness, or permit any
Subsidiary so to do, other than Permitted Indebtedness. 
 7.5 Encumbrances. Create, incur, assume or suffer
to exist any Lien with respect to any of its property (including without limitation, its Intellectual Property), or assign or otherwise convey any right to receive income, including the sale of any Accounts, or permit any of its Subsidiaries to do
so, except for Permitted Liens, or agree with any Person other than Bank not to grant a security interest in, or otherwise encumber, any of its property (including without limitation, its Intellectual Property), or permit any Subsidiary to do so,
except for Permitted Liens and customary anti-assignment provisions. 
 7.6 Distributions. Pay any dividends
or make any other distribution or payment on account of or in redemption, retirement or purchase of any capital stock, or permit any of its Subsidiaries to do so, except 

  
 17 

 
that (i) Borrower may repurchase the stock of former employees pursuant to stock repurchase agreements as long as an Event of Default does not exist prior to such repurchase or would not
exist after giving effect to such repurchase., (ii) Borrower may convert any of its convertible securities into other securities pursuant to the terms of such convertible securities or otherwise in exchange thereof, (iii) Borrower may pay
dividends solely in common stock, and (iv) Subsidiaries of Borrower may pay dividends or make distributions to Borrower. 

7.7 Investments. Directly or indirectly acquire or own, or make any Investment in or to any Person, or permit
any of its Subsidiaries so to do, other than Permitted Investments; or maintain or invest any of its cash or cash equivalents with a Person other than Bank or Bank’s affiliates or permit any of its Subsidiaries to do so unless such Person has
entered into an account control agreement with Bank in form and substance satisfactory to Bank except as provided in Section 6.7; or suffer or permit any Subsidiary to be a party to, or be bound by, an agreement that restricts such Subsidiary
from paying dividends or otherwise distributing property to Borrower. 
 7.8 Transactions with Affiliates.
Directly or indirectly enter into or permit to exist any material transaction with any Affiliate of Borrower except for (i) transactions that are in the ordinary course of Borrower’s business, upon fair and reasonable terms that are no
less favorable to Borrower than would be obtained in an arm’s length transaction with a non-affiliated Person., (ii) sales of equity securities and unsecured debt financings so long as all such
Indebtedness is Subordinated Debt, (iii) Investments permitted under sub-clauses (a), (f), (g), (h), or (k) of the definition of Permitted Investments, and (iv) transactions between or among
Borrower and any of its Subsidiaries that are otherwise permitted hereunder. 
 7.9 Subordinated Debt. Make
any payment in respect of any Subordinated Debt, or permit any of its Subsidiaries to make any such payment, except in compliance with the terms of such Subordinated Debt, or amend any provision contained in any documentation relating to the
Subordinated Debt, except in compliance with the terms of such Subordinated Debt, without Bank’s prior written consent. 

7.10 Inventory and Equipment. Store the Inventory or the Equipment with a bailee, warehouseman, or other third
party in an aggregate amount of more than Two Hundred Fifty Thousand Dollars ($250,000) unless the third party has been notified of Bank’s security interest and Bank (a) has received an acknowledgment from the third party that it is
holding or will hold the Inventory or Equipment for Bank’s benefit or (b) is in pledge possession of the warehouse receipt, where negotiable, covering such Inventory or Equipment. Except as set forth on the Schedule and except for mobile
equipment consisting of laptop computers and related hardware and software, store or maintain any Equipment or Inventory in an aggregate amount of more than Two Hundred Fifty Thousand Dollars ($250,000) at a location other than the location set
forth in Section 10 of this Agreement. 
 7.11 Compliance. Become an “investment company” or be
controlled by an “investment company,” within the meaning of the Investment Company Act of 1940, or become principally engaged in, or undertake as one of its important activities, the business of extending credit for the purpose of
purchasing or carrying margin stock, or use the proceeds of any Credit Extension for such purpose. Fail to meet the minimum funding requirements of ERISA, permit a Reportable Event or Prohibited Transaction, as defined in ERISA, to occur, fail to
comply with the Federal Fair Labor Standards Act or violate any law or regulation, which violation could have a Material Adverse Effect, or a material adverse effect on the Collateral or the priority of Bank’s Lien on the Collateral, or permit
any of its Subsidiaries to do any of the foregoing. 
 7.12 Assets in Foreign Subsidiaries. Permit Foreign
Subsidiaries to hold or maintain, at any time, assets of an aggregate value in excess of (i) Two Hundred Fifty Thousand Dollars ($250,000.00) in the case of BioNano Genomics UK, Ltd. and (ii) One Hundred Fifty Thousand Dollars
($150,000.00) in the case of BioNano Genomics (Shanghai) Trading Co., Ltd., calculated on a dollar equivalent basis. 

  
 18 

	 	 8.
	 EVENTS OF DEFAULT. 

Any one or more of the following events shall constitute an Event of Default by Borrower under this Agreement: 

8.1 Payment Default. If Borrower fails to pay, when due, any of the Obligations; 

8.2 Covenant Default. 

(a) If Borrower fails to perform any obligation under Article 6 or violates any of the covenants contained in Article 7
of this Agreement; or 
 (b) If Borrower fails or neglects to perform or observe any other material term, provision,
condition, covenant contained in this Agreement, in any of the Loan Documents, or in any other present or future agreement between Borrower and Bank and as to any default under such other term, provision, condition or covenant that can be cured, has
failed to cure such default within ten days after Borrower receives notice thereof or any officer of Borrower becomes aware thereof; provided, however, that if the default cannot by its nature be cured within the ten day period or cannot after
diligent attempts by Borrower be cured within such ten day period, and such default is likely to be cured within a reasonable time, then Borrower shall have an additional reasonable period (which shall not in any case exceed 30 days) to attempt to
cure such default, and within such reasonable time period the failure to have cured such default shall not be deemed an Event of Default but no Credit Extensions will be made. 

8.3 Material Adverse Effect. If there occurs any circumstance or circumstances that could reasonably be expected
to have a Material Adverse Effect; 
 8.4 Attachment. If any portion of Borrower’s assets valued in
excess of Two Hundred Fifty Thousand Dollars ($250,000) is attached, seized, subjected to a writ or distress warrant, or is levied upon, or comes into the possession of any trustee, receiver or person acting in a similar capacity and such
attachment, seizure, writ or distress warrant or levy has not been removed, discharged or rescinded within twenty (20) days, or if Borrower is enjoined, restrained, or in any way prevented by court order from continuing to conduct all or any
material part of its business affairs, or if a judgment or other claim becomes a lien or encumbrance upon any material portion of Borrower’s assets valued in excess of Two Hundred Fifty Thousand Dollars ($250,000), or if a notice of lien, levy,
or assessment is filed of record with respect to any of Borrower’s assets valued in excess of Two Hundred Fifty Thousand Dollars ($250,000) by the United States Government, or any department, agency, or instrumentality thereof, or by any state,
county, municipal, or governmental agency, and the same is not paid within twenty (20) days after Borrower receives notice thereof, provided that none of the foregoing shall constitute an Event of Default where such action or event is stayed or
an adequate bond has been posted pending a good faith contest by Borrower (provided that no Credit Extensions will be required to be made during such cure period); 

8.5 Insolvency. If Borrower becomes insolvent, or if an Insolvency Proceeding is commenced by Borrower, or if an
Insolvency Proceeding is commenced against Borrower and is not dismissed or stayed within forty-five (45) days (provided that no Credit Extensions will be made prior to the dismissal of such Insolvency Proceeding); 

8.6 Other Agreements. If there is a default by Borrower or other failure of Borrower to perform in any agreement
to which Borrower is a party or by which it is bound resulting in a right by a third party or parties, whether or not exercised, to accelerate the maturity of any Indebtedness in an amount in excess of Two Hundred Fifty Thousand Dollars ($250,000)
or which could reasonably be expected to have a Material Adverse Effect; provided, however, that the Event of Default under this Section caused by the occurrence of a breach or default under such other agreement shall be cured or waived for purposes
of this Agreement upon Bank receiving written notice from the party asserting such breach or default of such cure or waiver of the breach or default under such other agreement, if at the time of such cure or waiver under such other agreement
(x) Bank has not declared an Event of Default under this Agreement and/or exercised any rights with respect thereto; (y) any such cure or waiver does not result in an Event of Default under any other provision of this Agreement or any Loan
Document; and (z) 

  
 19 

 
in connection with any such cure or waiver under such other agreement, the terms of any agreement with such third party are not modified or amended in any manner which could in the good faith
business judgment of Bank be materially less advantageous to Borrower or any guarantor; 
 8.7 Judgments. If a
judgment or judgments for the payment of money in an amount, individually or in the aggregate, of at least One Hundred Thousand Dollars ($100,000) (not covered by independent third-party insurance as to which liability has been accepted by such
insurance carrier) shall be rendered against Borrower and shall remain unsatisfied and unstayed for a period of twenty (20) days (provided that no Credit Extensions will be made prior to the satisfaction or stay of such judgment); or 

8.8 Misrepresentations. If any material misrepresentation or material misstatement exists now or hereafter in
any warranty or representation set forth herein or in any certificate delivered to Bank by any Responsible Officer pursuant to this Agreement or to induce Bank to enter into this Agreement or any other Loan Document. 

8.9 Guaranty. If any guaranty of all or a portion of the Obligations (a “Guaranty”)
ceases for any reason to be in full force and effect, or any guarantor fails to perform any obligation under any Guaranty or a security agreement securing any Guaranty (collectively, the “Guaranty Documents”), or any event of default
occurs under any Guaranty Document or any guarantor revokes or purports to revoke a Guaranty, or any material misrepresentation or material misstatement exists now or hereafter in any warranty or representation set forth in any Guaranty Document or
in any certificate delivered to Bank in connection with any Guaranty Document, or if any of the circumstances described in Sections 8.3 through 8.8 occur with respect to any guarantor or any guarantor dies or becomes subject to any criminal
prosecution. 
  

	 	 9.
	 BANK’S RIGHTS AND
REMEDIES. 

 9.1 Rights and Remedies. Upon the occurrence
and during the continuance of an Event of Default, Bank may, at its election, without notice of its election and without demand, do any one or more of the following, all of which are authorized by Borrower: 

(a) Declare all Obligations, whether evidenced by this Agreement, by any of the other Loan Documents, or otherwise,
immediately due and payable (provided that upon the occurrence of an Event of Default described in Section 8.5, all Obligations shall become immediately due and payable without any action by Bank); 

(b) Cease advancing money or extending credit to or for the benefit of Borrower under this Agreement or under any
other agreement between Borrower and Bank; 
 (c) Settle or adjust disputes and claims directly with account debtors
for amounts, upon terms and in whatever order that Bank reasonably considers advisable; 
 (d) Make such payments
and do such acts as Bank considers necessary or reasonable to protect its security interest in the Collateral. Borrower agrees to assemble the Collateral if Bank so requires, and to make the Collateral available to Bank as Bank may designate.
Borrower authorizes Bank to enter the premises where the Collateral is located, to take and maintain possession of the Collateral, or any part of it, and to pay, purchase, contest, or compromise any encumbrance, charge, or lien which in Bank’s
determination appears to be prior or superior to its security interest and to pay all expenses incurred in connection therewith. With respect to any of Borrower’s owned premises, Borrower hereby grants Bank a license to enter into possession of
such premises and to occupy the same, without charge, in order to exercise any of Bank’s rights or remedies provided herein, at law, in equity, or otherwise; 

(e) Set off and apply to the Obligations any and all (i) balances and deposits of Borrower held by Bank, or
(ii) indebtedness at any time owing to or for the credit or the account of Borrower held by Bank; 

  
 20 

 (f) Ship, reclaim, recover, store, finish, maintain, repair, prepare for
sale, advertise for sale, and sell (in the manner provided for herein) the Collateral. Bank is hereby granted a license or other right, solely pursuant to the provisions of this Section 9. 1, to use, without charge, Borrower’s labels,
patents, copyrights, rights of use of any name, trade secrets, trade names, trademarks, service marks, and advertising matter, or any property of a similar nature, as it pertains to the Collateral, in completing production of, advertising for sale,
and selling any Collateral and, in connection with Bank’s exercise of its rights under this Section 9. 1, Borrower’s rights under all licenses and all franchise agreements shall inure to Bank’s benefit; 

(g) Dispose of the Collateral by way of one or more contracts or transactions, for cash or on terms, in such manner
and at such places (including Borrower’s premises) as Bank determines is commercially reasonable, and apply any proceeds to the Obligations in whatever manner or order Bank deems appropriate; 

(h) Bank may credit bid and purchase at any public sale; and 

(i) Any deficiency that exists after disposition of the Collateral as provided above will be paid immediately by
Borrower. 
 9.2 Power of Attorney. Effective only upon the occurrence and during the continuance of an Event
of Default, Borrower hereby irrevocably appoints Bank (and any of Bank’s designated officers, or employees) as Borrower’s true and lawful attorney to: (a) send requests for verification of Accounts or notify account debtors of
Bank’s security interest in the Accounts; (b) endorse Borrower’s name on any checks or other forms of payment or security that may come into Bank’s possession; (c) sign Borrower’s name on any invoice or bill of lading
relating to any Account, drafts against account debtors, schedules and assignments of Accounts, verifications of Accounts, and notices to account debtors; (d) dispose of any Collateral; (e) make, settle, and adjust all claims under and
decisions with respect to Borrower’s policies of insurance; (f) settle and adjust disputes and claims respecting the accounts directly with account debtors, for amounts and upon terms which Bank determines to be reasonable; and (g) to
file, in its sole discretion, one or more financing or continuation statements and amendments thereto, relative to any of the Collateral. The appointment of Bank as Borrower’s attorney in fact, and each and every one of Bank’s rights and
powers, being coupled with an interest, is irrevocable until all of the Obligations (other than inchoate indemnity obligations) have been fully repaid and performed and Bank’s obligation to provide Credit Extensions hereunder is terminated.

 9.3 Accounts Collection. At any time after the occurrence and during the continuance of an Event of
Default, (i) Bank may notify any Person owing funds to Borrower of Bank’s security interest in such funds and verify the amount of such Account and (ii) Borrower shall collect all amounts owing to Borrower for Bank, receive in trust
all payments as Bank’s trustee, and immediately deliver such payments to Bank in their original form as received from the account debtor, with proper endorsements for deposit. 

9.4 Bank Expenses. If Borrower fails to pay any amounts or furnish any required proof of payment due to third
persons or entities, as required under the terms of this Agreement, then Bank may do any or all of the following after reasonable notice to Borrower: (a) make payment of the same or any part thereof; (b) set up such reserves under a loan
facility in Section 2.1 as Bank deems necessary to protect Bank from the exposure created by such failure; or (c) obtain and maintain insurance policies of the type discussed in Section 6.6 of this Agreement, and take any action with
respect to such policies as Bank deems prudent. Any amounts so paid or deposited by Bank shall constitute Bank Expenses, shall be immediately due and payable, and shall bear interest at the then applicable rate hereinabove provided, and shall be
secured by the Collateral. Any payments made by Bank shall not constitute an agreement by Bank to make similar payments in the future or a waiver by Bank of any Event of Default under this Agreement. 

9.5 Bank’s Liability for Collateral. So long as Bank complies with reasonable banking practices, Bank shall
not in any way or manner be liable or responsible for: (a) the safekeeping of the Collateral; (b) any loss or damage thereto occurring or arising in any manner or fashion from any cause; (c) any diminution in the value thereof; or
(d) any act or default of any carrier, warehouseman, bailee, forwarding agency, or other person whomsoever. All risk of loss, damage or destruction of the Collateral shall be borne by Borrower. 

  
 21 

 9.6 Remedies Cumulative. Bank’s rights and remedies under this
Agreement, the Loan Documents, and all other agreements shall be cumulative. Bank shall have all other rights and remedies not inconsistent herewith as provided under the Code, by law, or in equity. No exercise by Bank of one right or remedy shall
be deemed an election, and no waiver by Bank of any Event of Default on Borrower’s part shall be deemed a continuing waiver. No delay by Bank shall constitute a waiver, election, or acquiescence by it. No waiver by Bank shall be effective
unless made in a written document signed on behalf of Bank and then shall be effective only in the specific instance and for the specific purpose for which it was given. 

9.7 Demand; Protest. Borrower waives demand, protest, notice of protest, notice of default or dishonor, notice
of payment and nonpayment, notice of any default, nonpayment at maturity, release, compromise, settlement, extension, or renewal of accounts, documents, instruments, chattel paper, and guarantees at any time held by Bank on which Borrower may in any
way be liable. 
  

	 	 10.
	 NOTICES. 

All notices, consents, requests, approvals, demands, or other communication by any party to this Agreement or any other Loan
Document must be in writing and shall be deemed to have been validly served, given, or delivered: (a) upon the earlier of actual receipt and three (3) Business Days after deposit in the U.S. mail, first class, registered or certified mail
return receipt requested, with proper postage prepaid; (b) upon transmission, when sent by electronic mail or facsimile transmission; (c) one (1) Business Day after deposit with a reputable overnight courier with all charges prepaid; or
(d) when delivered, if hand-delivered by messenger, all of which shall be addressed to the party to be notified and sent to the address, facsimile number, or email address indicated below. Bank or Borrower may change its mailing or electronic
mail address or facsimile number by giving the other party written notice thereof in accordance with the terms of this Section 10. 
  

			
	 If to Borrower:
	  	 BIONANO GENOMICS, INC.

		  	 9640 Towne Centre Dr., #100

		  	 San Diego, CA 92121

		  	 Attn: Robert Erik Holmlin, Ph.D., CEO

		  	 EMAIL: eholmlin@bionanogenomics.com

		
	 If to Bank:
	  	 Bridge Bank, a division of Western Alliance Bank

		  	 55 Almaden Boulevard, Suite 100

		  	 San Jose, CA 95113

		  	 Attn: Loan Operations

		
	 With a copy to:
	  	 Bridge Bank, a division of Western Alliance Bank

		  	 12220 El Camino Real, Suite 100

		  	 San Diego, CA 2130

		  	 Attn: Robert C. Lake, SVP, Head of Life Sciences

		  	 EMAIL: rob.lake@bridgebank.com

 The parties hereto may change the address at which they are to receive notices hereunder, by
notice in writing in the foregoing manner given to the other. 
  

	 	 11.
	 CHOICE OF LAW AND VENUE; JURY TRIAL WAIVER. 

This Agreement shall be governed by, and construed in accordance with, the internal laws of the State of California, without
regard to principles of conflicts of law. Each of Borrower and Bank hereby submits to the exclusive jurisdiction of the state and Federal courts located in the County of Santa Clara, State of California. BORROWER AND BANK EACH HEREBY WAIVE THEIR
RESPECTIVE RIGHTS TO A JURY TRIAL OF ANY CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF ANY OF THE LOAN DOCUMENTS OR ANY OF THE TRANSACTIONS CONTEMPLATED THEREIN, INCLUDING CONTRACT CLAIMS, TORT CLAIMS, BREACH OF DUTY CLAIMS, AND ALL OTHER
COMMON LAW OR STATUTORY CLAIMS. EACH PARTY RECOGNIZES AND AGREES THAT THE FOREGOING WAIVER CONSTITUTES A MATERIAL INDUCEMENT FOR IT TO ENTER INTO THIS AGREEMENT. EACH 

  
 22 

 
PARTY REPRESENTS AND WARRANTS THAT IT HAS REVIEWED THIS WAIVER WITH ITS LEGAL COUNSEL AND THAT IT KNOWINGLY AND VOLUNTARILY WAIVES ITS JURY TRIAL RIGHTS FOLLOWING CONSULTATION WITH LEGAL COUNSEL.

  

	 	 12.
	 JUDICIAL REFERENCE PROVISION. 

12.1 In the event the Jury Trial Waiver set forth above is not enforceable, the parties elect to proceed under this
Judicial Reference Provision. 
 12.2 With the exception of the items specified in Section 12.3, below, any
controversy, dispute or claim (each, a “Claim”) between the parties arising out of or relating to this Agreement or any other document, instrument or agreement between the undersigned parties (collectively in this Section, the
“Loan Documents”), will be resolved by a reference proceeding in California in accordance with the provisions of Sections 638 et seq. of the California Code of Civil Procedure (“CCP”), or their successor sections,
which shall constitute the exclusive remedy for the resolution of any Claim, including whether the Claim is subject to the reference proceeding. Except as otherwise provided in the Loan Documents, venue for the reference proceeding will be in the
state or federal court in the county or district where the real property involved in the action, if any, is located or in the state or federal court in the county or district where venue is otherwise appropriate under applicable law (the
“Court”). 
 12.3 The matters that shall not be subject to a reference are the following:
(i) nonjudicial foreclosure of any security interests in real or personal property, (ii) exercise of self-help remedies (including, without limitation, set-off), (iii) appointment of a receiver and
(iv) temporary, provisional or ancillary remedies (including, without limitation, writs of attachment, writs of possession, temporary restraining orders or preliminary injunctions). This reference provision does not limit the right of any party
to exercise or oppose any of the rights and remedies described in clauses (i) and (ii) or to seek or oppose from a court of competent jurisdiction any of the items described in clauses (iii) and (iv). The exercise of, or opposition to, any
of those items does not waive the right of any party to a reference pursuant to this reference provision as provided herein. 

12.4 The referee shall be a retired judge or justice selected by mutual written agreement of the parties. If the
parties do not agree within ten (10) days of a written request to do so by any party, then, upon request of any party, the referee shall be selected by the Presiding Judge of the Court (or his or her representative). A request for appointment
of a referee may be heard on an ex parte or expedited basis, and the parties agree that irreparable harm would result if ex parte relief is not granted. Pursuant to CCP § 170.6, each party shall have one peremptory challenge to the referee
selected by the Presiding Judge of the Court (or his or her representative). 
 12.5 The parties agree that time is
of the essence in conducting the reference proceedings. Accordingly, the referee shall be requested, subject to change in the time periods specified herein for good cause shown, to (i) set the matter for a status and trial-setting conference
within fifteen (15) days after the date of selection of the referee, (ii) if practicable, try all issues of law or fact within one hundred twenty (120) days after the date of the conference and (iii) report a statement of
decision within twenty (20) days after the matter has been submitted for decision. 
 12.6 The referee will have
power to expand or limit the amount and duration of discovery. The referee may set or extend discovery deadlines or cutoffs for good cause, including a party’s failure to provide requested discovery for any reason whatsoever. Unless otherwise
ordered based upon good cause shown, no party shall be entitled to “priority” in conducting discovery, depositions may be taken by either party upon seven (7) days written notice, and all other discovery shall be responded to within
fifteen (15) days after service. All disputes relating to discovery which cannot be resolved by the parties shall be submitted to the referee whose decision shall be final and binding. 

12.7 Except as expressly set forth herein, the referee shall determine the manner in which the reference proceeding is
conducted including the time and place of hearings, the order of presentation of evidence, and all other questions that arise with respect to the course of the reference proceeding. All proceedings and hearings conducted before the referee, except
for trial, shall be conducted without a court reporter, except that when any party so requests, a court reporter will be used at any hearing conducted before the referee, and the referee will be provided a courtesy copy of the transcript. The party
making such a request shall have the obligation to arrange 

  
 23 

 
for and pay the court reporter. Subject to the referee’s power to award costs to the prevailing party, the parties will equally share the cost of the referee and the court reporter at trial.

 12.8 The referee shall be required to determine all issues in accordance with existing case law and the statutory
laws of the State of California. The rules of evidence applicable to proceedings at law in the State of California will be applicable to the reference proceeding. The referee shall be empowered to enter equitable as well as legal relief, enter
equitable orders that will be binding on the parties and rule on any motion which would be authorized in a court proceeding, including without limitation motions for summary judgment or summary adjudication. The referee shall issue a decision at the
close of the reference proceeding which disposes of all claims of the parties that are the subject of the reference. Pursuant to CCP § 644, such decision shall be entered by the Court as a judgment or an order in the same manner as if the
action had been tried by the Court and any such decision will be final, binding and conclusive. The parties reserve the right to appeal from the final judgment or order or from any appealable decision or order entered by the referee. The parties
reserve the right to findings of fact, conclusions of laws, a written statement of decision, and the right to move for a new trial or a different judgment, which new trial, if granted, is also to be a reference proceeding under this provision. 

12.9 If the enabling legislation which provides for appointment of a referee is repealed (and no successor statute is
enacted), any dispute between the parties that would otherwise be determined by reference procedure will be resolved and determined by arbitration. The arbitration will be conducted by a retired judge or justice, in accordance with the California
Arbitration Act § 1280 through § 1294.2 of the CCP as amended from time to time. The limitations with respect to discovery set forth above shall apply to any such arbitration proceeding. 

12.10 THE PARTIES RECOGNIZE AND AGREE THAT ALL CONTROVERSIES, DISPUTES AND CLAIMS RESOLVED UNDER THIS REFERENCE
PROVISION WILL BE DECIDED BY A REFEREE AND NOT BY A JURY. AFTER CONSULTING (OR HAVING HAD THE OPPORTUNITY TO CONSULT) WITH COUNSEL OF ITS, HIS OR HER OWN CHOICE, EACH PARTY KNOWINGLY AND VOLUNTARILY, AND FOR THE MUTUAL BENEFIT OF ALL PARTIES, AGREES
THAT THIS REFERENCE PROVISION WILL APPLY TO ANY CONTROVERSY, DISPUTE OR CLAIM BETWEEN OR AMONG THEM ARISING OUT OF OR IN ANY WAY RELATED TO, THIS AGREEMENT OR THE OTHER LOAN DOCUMENTS. 

 

	 	 13.
	 GENERAL PROVISIONS. 

13.1 Successors and Assigns. This Agreement shall bind and inure to the benefit of the respective successors and
permitted assigns of each of the parties; provided, however, that neither this Agreement nor any rights hereunder may be assigned by Borrower without Bank’s prior written consent, which consent may be granted or withheld in Bank’s sole
discretion. Bank shall have the right without the consent of or notice to Borrower to sell, transfer, negotiate, or grant participation in all or any part of, or any interest in, Bank’s obligations, rights and benefits hereunder. 

13.2 Indemnification. Borrower shall defend, indemnify and hold harmless Bank and its officers, employees, and
agents against: (a) all obligations, demands, claims, and liabilities (collectively, “Claims”) claimed or asserted by any other party in connection with the transactions contemplated by this Agreement; and (b) all losses or Bank
Expenses in any way suffered, incurred, or paid by Bank as a result of or in any way arising out of, following, or consequential to transactions between Bank and Borrower whether under this Agreement, or otherwise (including without limitation
reasonable attorneys’ fees and expenses), except as to (a) or (b) for Claims, losses or Bank Expenses caused by Bank’s gross negligence or willful misconduct. 

13.3 Time of Essence. Time is of the essence for the performance of all obligations set forth in this Agreement.

 13.4 Severability of Provisions. Each provision of this Agreement shall be severable from every other
provision of this Agreement for the purpose of determining the legal enforceability of any specific provision. 

  
 24 

 13.5 Amendments in Writing, Integration. Neither this Agreement nor
the Loan Documents can be amended or terminated orally. All prior agreements, understandings, representations, warranties, and negotiations between the parties hereto with respect to the subject matter of this Agreement and the Loan Documents, if
any, are merged into this Agreement and the Loan Documents. 
 13.6 Counterparts. This Agreement may be
executed in any number of counterparts and by different parties on separate counterparts, each of which, when executed and delivered, shall be deemed to be an original, and all of which, when taken together, shall constitute but one and the same
Agreement. 
 13.7 Survival. All covenants, representations and warranties made in this Agreement shall continue in full
force and effect so long as any Obligations (other than inchoate indemnity obligations) remain outstanding or Bank has any obligation to make Credit Extensions to Borrower. The obligations of Borrower to indemnify Bank with respect to the expenses,
damages, losses, costs and liabilities described in Section 13.2 shall survive until all applicable statute of limitations periods with respect to actions that may be brought against Bank have run. 

13.8 Confidentiality. In handling any confidential information Bank and all employees and agents of Bank,
including but not limited to accountants, shall exercise the same degree of care that it exercises with respect to its own proprietary information of the same types to maintain the confidentiality of any
non-public information thereby received or received pursuant to this Agreement except that disclosure of such information may be made (i) to the subsidiaries or affiliates of Bank in connection with their
present or prospective business relations with Borrower, provided that such subsidiaries or affiliates are bound by confidentiality obligations substantially the same as those of this Section, (ii) to prospective transferees or purchasers of
any interest in the Credit Extensions, provided that commercially reasonable efforts have been undertaken to cause them to enter into a comparable confidentiality agreement in favor of Borrower, (iii) as required by law, regulations, rule or
order, subpoena, judicial order or similar order, (iv) as may be required in connection with the examination, audit or similar investigation of Bank and (v) as Bank may determine in connection with the enforcement of any remedies
hereunder. Confidential information hereunder shall not include information that either: (a) is in the public domain or in the knowledge or possession of Bank when disclosed to Bank, or becomes part of the public domain after disclosure to Bank
through no fault of Bank; or (b) is disclosed to Bank by a third party, provided Bank does not have actual knowledge that such third party is prohibited from disclosing such information. 

13.9 Patriot Act Notice. Bank notifies Borrower that, pursuant to the requirements of the USA Patriot Act, Title
III of Pub. L. 107-56 (signed into law on October 26, 2001) (the “ Patriot Act “), it is required to obtain, verify and record information that identifies Borrower, which information
includes names and addresses and other information that will allow Bank to identify the Borrower in accordance with the Patriot Act. 
  

	 	 14.
	 NOTICE OF FINAL AGREEMENT. 

BY SIGNING THIS DOCUMENT EACH PARTY REPRESENTS AND AGREES THAT: (A) THIS WRITTEN AGREEMENT REPRESENTS THE FINAL
AGREEMENT BETWEEN THE PARTIES, (B) THERE ARE NO UNWRITTEN ORAL AGREEMENTS BETWEEN THE PARTIES, AND (C) THIS WRITTEN AGREEMENT MAY NOT BE CONTRADICTED BY EVIDENCE OF ANY PRIOR, CONTEMPORANEOUS, OR SUBSEQUENT ORAL AGREEMENTS OR
UNDERSTANDINGS OF THE PARTIES. 
 [Balance of Page Intentionally Left Blank] 

  
 25 

 IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be executed
as of the date first above written. 
  

			
	 BIONANOGENOMICS,
INC., a Delaware corporation

		
	 By:
	 	 /s/ R. Erik Holmlin

	 Title:
	 	 CEO

	
	 WESTERN ALLIANCE BANK,
an Arizona Corporation

		
	 By:
	 	  

	 Title:
	 	

  
 [Signature Page to
Loan and Security Agreement] 

 IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be executed
as of the date first above written. 
  

			
	 BIONANOGENOMICS, INC., a Delaware
corporation

		
	 By:
	 	  

	 Title:
	 	
	
	 WESTERN ALLIANCE BANK, an Arizona Corporation

		
	 By:
	 	 /s/ Lindsay Schwallie

	 Title:
	 	 VP, Portfolio Management

  
 [Signature Page to
Loan and Security Agreement] 

 EXHIBIT A 
  

			
	 DEBTOR:
	  	 BIONANO GENOMICS, INC.

		
	 SECURED PARTY:
	  	 WESTERN ALLIANCE BANK, an Arizona Corporation

 COLLATERAL DESCRIPTION ATTACHMENT 

TO LOAN AND SECURITY AGREEMENT 

All personal property of Borrower (herein referred to as “Borrower” or “Debtor”) whether presently
existing or hereafter created or acquired, and wherever located, including, but not limited to: 
 (a) all accounts
(including health-care-insurance receivables), chattel paper (including tangible and electronic chattel paper), deposit accounts, documents (including negotiable documents), equipment (including all accessions and additions thereto), general
intangibles (including payment intangibles and software), goods (including fixtures), instruments (including promissory notes), inventory (including all goods held for sale or lease or to be furnished under a contract of service, and including
returns and repossessions), investment property (including securities and securities entitlements), letter of credit rights, money, and all of Debtor’s books and records with respect to any of the foregoing, and the computers and equipment
containing said books and records; 
 (b) any and all cash proceeds and/or noncash proceeds of any of the foregoing,
including, without limitation, insurance proceeds, and all supporting obligations and the security therefor or for any right to payment. All terms above have the meanings given to them in the California Uniform Commercial Code, as amended or
supplemented from time to time. 
 Notwithstanding the foregoing, the Collateral shall not include any Intellectual Property
(as defined in the Loan and Security Agreement dated as of March 8, 2016 between Debtor and Secured Party), now owned or hereafter acquired; provided, however, that the Collateral shall include all accounts and general intangibles that consist
of rights to payment and proceeds from the sale, licensing or disposition of all or any part, or rights in, the foregoing (the “Rights to Payment”). Notwithstanding the foregoing, if a judicial authority (including a U.S. Bankruptcy Court)
holds that a security interest in the underlying Intellectual Property is necessary to have a security interest in the Rights to Payment, then the Collateral shall automatically, and effective as of the Closing Date, include the Intellectual
Property to the extent necessary to permit perfection of Bank’s security interest in the Rights to Payment. 

Notwithstanding the foregoing, the Collateral shall not include (i) more than 65% of the presently existing and hereafter
arising issued and outstanding shares of capital stock owned by Borrower of any Foreign Subsidiary which shares entitle the holder thereof to vote for directors or any other matter. or (ii) any property that is financed by a third party
permitted by clause (a) or (c) of the definition of “Permitted Liens” hereunder to the extent prohibited by the terms of such agreement, provided that upon the termination or lapse of any such prohibition, such property (and any
accessions, attachments, replacements or improvements thereon) shall be deemed to be Collateral hereunder and shall be subject to the security interest granted. 

 EXHIBIT B-1 

ADVANCE REQUEST FORM 

(To be submitted no later than 3:00 PM to be considered for same day processing) 

 

			
	 To:
	  	 Western Alliance Bank, an Arizona corporation

		
	 Fax:
	  	 (408) 282-1681

		
	 Date:
	  	  

		
	 From:
	  	 BIONANO GENOMICS, INC.

		  	 Borrower’s Name

		
		  	 /s/ R. Erik Holmlin

		  	 Authorized Signature

		
		  	 R. Erik Holmlin

		  	 Authorized Signer’s Name (please print)

		
		  	 1-858-888-7610

		  	 Phone Number

			
		
	 To Account #
	    	 2003069        

 Borrower hereby requests funding in the amount of $7,000,000 in accordance with the Term Loan as defined in
the Loan and Security Agreement dated as of March     , 2016. 
 Borrower hereby authorizes Bank to rely on facsimile
stamp signatures and treat them as authorized by Borrower for the purpose of requesting the above advance. 
 All representations and
warranties of Borrower stated in the Loan and Security Agreement are true, correct and complete in all material respects as of the date of this Advance Request; provided that those representations and warranties expressly referring to another
date shall be true, correct and complete in all material respects as of such date. 
 Capitalized terms used herein and not otherwise
defined have the meanings set forth in the Loan and Security Agreement. 

 EXHIBIT B-2 

Form of Disbursement Letter 

[see attached] 

 DISBURSEMENT LETTER 

March 8, 2016 

The undersigned, being the duly elected and acting
                     of BIONANO GENOMICS, INC. (“Borrower”), does hereby certify to WESTERN ALLIANCE BANK, an Arizona
corporation (“Bank”), in connection with that certain Loan and Security Agreement dated as of March 8, 2016, by and among Borrower and Bank (the “Loan Agreement”; with other capitalized terms used below having
the meanings ascribed thereto in the Loan Agreement) that: 
 1. The representations and warranties made by Borrower in
Section 5 of the Loan Agreement and in the other Loan Documents are true and correct in all material respects as of the date hereof; provided that those representations and warranties expressly referring to another date shall be true, correct
and complete in all material respects as of such date. 
 2. No event or condition has occurred and is continuing that would
constitute an Event of Default under the Loan Agreement or any other Loan Document. 
 3. Borrower is in compliance with the
covenants and requirements contained in Sections 4, 6 and 7 of the Loan Agreement. 
 4. All conditions referred to in
Section 3 of the Loan Agreement to the making of the Loan to be made on or about the date hereof have been satisfied or waived by Bank. 

5. No Material Adverse Effect has occurred. 

6. The undersigned is a Responsible Officer. 

[Balance of Page Intentionally Left Blank] 

 7. The proceeds of the Term Loan shall be disbursed as follows: 

 

					
	 Disbursement from Bank:
	  			
	 Loan Amount
	  	$	7,000,000	 
	 Plus:
	  			
	 —Deposit Received
	  	$	35,000	 
		
	 Less:
	  			
	 —Facility Fee
	  	($	35,000	) 
	 —Existing Debt Payoff to be remitted to Pacific Western Bank per the Payoff
Letter dated March     , 2016
	  	($	5,006,808.34	) 
	 — Bank’s Legal Fees
	  	($	            	)* 
	 Net Proceeds due from Bank:
	  	$	            	 
		
	 TOTAL TERM LOAN NET PROCEEDS FROM BANK
	  	$	            	 

 8. The aggregate net proceeds of the Term Loan shall be transferred to the Designated Deposit
Account as follows: 
  

			
	 Account Name:
	 	 BIONANO GENOMICS, INC.

		
	 Bank Name:
	 	 Bridge Bank, a division of Western Alliance Bank

		
	 Bank Address:
	 	 55 Almaden Boulevard

		 	 San Jose, CA 95113

		
	 Account Number:
	 	 101608149

		
	 ABA Number:
	 	 121143260

 [Balance of Page Intentionally Left Blank] 

 

	 *
	 Legal fees and costs are through the Closing Date. Post-closing legal fees and costs, payable after the
Closing Date, to be invoiced and paid post-closing. 

 Dated as of the date first set forth above. 

 

			
	 BORROWER:
	 	

			
	
	 BIONANO GENOMICS, INC., a Delaware corporation

			
		
	 By
	 	  

			
	 Name:
	 	
	 Title:
	 	

			
		
	 BANK:
	 	

			
	
	 WESTERN ALLIANCE BANK, an Arizona corporation

			
		
	 By
	 	  

			
	 Name:
	 	
	 Title:
	 	

  
 [Signature Page to
Disbursement Letter] 

 EXHIBIT C 
  

																																																	
	 	  	Jan-16	 	  	Feb-16	 	  	Mar-16	 	  	Apr-16	 	  	May-16	 	  	Jun-16	 	  	Jul-16	 	  	Aug-16	 	  	Sep-16	 	  	Oct-16	 	  	Nov-16	 	  	Dec-16	 
	 Revenues (Proj)
	  	$	496,409	 	  	$	512,852	 	  	$	518,575	 	  	$	662,925	 	  	$	684,821	 	  	$	692,502	 	  	$	835,745	 	  	$	863,412	 	  	$	873,090	 	  	$	953,446	 	  	$	984,975	 	  	$	1,064,599	 
	 T6M Revenues
	  				  				  				  				  				  				  				  				  	$	4,612,495	 	  	$	4,903,016	 	  	$	5,203,170	 	  	$	5,575,267	 
	 75% of Plan
	  				  				  				  				  				  				  				  				  	$	3,459,371	 	  	$	3,677,262	 	  	$	3,902,378	 	  	$	4,181,450	 
	 Tested
	  				  				  				  				  				  				  				  				  	 	16-Oct	 	  	 	16-Nov	 	  	 	16-Dec	 	  	 	17-Jan	 
													
	 	  	Jan-17	 	  	Feb-17	 	  	Mar-17	 	  	Apr-17	 	  	May-17	 	  	Jun-17	 	  	Jul-17	 	  	Aug-17	 	  	Sep-17	 	  	Oct-17	 	  	Nov-17	 	  	Dec-17	 
	 Revenues (Proj)
	  	$	910,065	 	  	$	949,203	 	  	$	957,147	 	  	$	1,654,226	 	  	$	1,725,883	 	  	$	1,752,225	 	  	$	1,814,216	 	  	$	1,891,057	 	  	$	1,906,653	 	  	$	2,407,623	 	  	$	2,508,047	 	  	$	2,549,533	 
	 T6M Revenues
	  	$	5,649,586	 	  	$	5,735,378	 	  	$	5,819,435	 	  	$	6,520,216	 	  	$	7,261,124	 	  	$	7,948,750	 	  	$	8,852,901	 	  	$	9,794,754	 	  	$	10,744,260	 	  	$	11,497,657	 	  	$	12,279,821	 	  	$	13,077,129	 
	 75% of Plan
	  	$	4,237,190	 	  	$	4,301,533	 	  	$	4,364,576	 	  	$	4,890,162	 	  	$	5,445,843	 	  	$	5,961,562	 	  	$	6,639,676	 	  	$	7,346,066	 	  	$	8,058,195	 	  	$	8,623,243	 	  	$	9,209,865	 	  	$	9,807,846	 
	 Tested
	  	 	17-Feb	 	  	 	17-Mar	 	  	 	17-Apr	 	  	 	17-May	 	  	 	17-Jun	 	  	 	17-Jul	 	  	 	17-Aug	 	  	 	17-Sep	 	  	 	17-Oct	 	  	 	17-Nov	 	  	 	17-Dec	 	  	 	18-Jan	 
													
	 	  	Jan-18	 	  	Feb-18	 	  	Mar-18	 	  	Apr-18	 	  	May-18	 	  	Jun-18	 	  	Jul-18	 	  	Aug-18	 	  	Sep-18	 	  	Oct-18	 	  	Nov-18	 	  	Dec-18	 
	 Revenues (Proj)
	  	$	2,256,687	 	  	$	2,321,830	 	  	$	2,360,944	 	  	$	3,082,118	 	  	$	3,170,082	 	  	$	3,224,082	 	  	$	4,672,129	 	  	$	4,804,822	 	  	$	4,887,110	 	  	$	5,477,237	 	  	$	5,631,587	 	  	$	5,738,380	 
	 T6M Revenues
	  	$	13,519,599	 	  	$	13,950,372	 	  	$	14,404,663	 	  	$	15,079,158	 	  	$	15,741,193	 	  	$	16,415,743	 	  	$	18,831,185	 	  	$	21,314,178	 	  	$	23,840,343	 	  	$	26,235,462	 	  	$	28,696,967	 	  	$	31,211,265	 
	 75% of Plan
	  	$	10,139,699	 	  	$	10,462,779	 	  	$	10,803,497	 	  	$	11,309,368	 	  	$	11,805,895	 	  	$	12,311,807	 	  	$	14,123,389	 	  	$	15,985,633	 	  	$	17,880,258	 	  	$	19,676,596	 	  	$	21,522,725	 	  	$	23,408,449	 
	 Tested
	  	 	18-Feb	 	  	 	18-Mar	 	  	 	18-Apr	 	  	 	18-May	 	  	 	18-Jun	 	  	 	18-Jul	 	  	 	18-Aug	 	  	 	18-Sep	 	  	 	18-Oct	 	  	 	18-Nov	 	  	 	18-Dec	 	  	 	19-Jan	 

  

 EXHIBIT D 

COMPLIANCE CERTIFICATE 

TO:         WESTERN ALLIANCE BANK, an Arizona corporation 

FROM:    BIONANO GENOMICS, INC. 

The undersigned authorized officer of BIONANO GENOMICS, INC. hereby certifies that in accordance with the terms and conditions
of the Loan and Security Agreement between Borrower and Bank (the “Agreement”), (i) Borrower is in complete compliance for the period ending
                         with all required covenants except as noted below and (ii) all representations and
warranties of Borrower stated in the Agreement are true and correct in all material respects as of the date hereof except as noted below; provided that those representations and warranties expressly referring to another date shall be true, correct
and complete in all material respects as of such date. Attached herewith are the required documents supporting the above certification. The Officer further certifies that these are prepared in accordance with Generally Accepted Accounting Principles
(GAAP) and are consistently applied from one period to the next except as explained in an accompanying letter or footnotes. 
 Please
indicate compliance status by circling Yes/No under “Complies” column. 
  

									
	 Reporting Covenant
	  	 Required
	  	
Complies

				
	 Annual financial statements (CPA Audited)
	  	 FYE within 180 days
	  	Yes 	  	No
				
	 Monthly financial statements and Compliance Certificate
	  	 Prior to each Credit Extension, and monthly within 30 days
	  	Yes 	  	No
				
	 10K and 10Q
	  	 (as applicable)
	  	Yes 	  	No
				
	 Annual operating budget, sales projections and operating plans approved by board of directors
	  	 Annually no later than 45 days after the beginning of each fiscal year
	  	Yes 	  	No
				
	 Deposit balances with Bank
	  	 $
                                         
     
	  		  	
	 Deposit balance outside Bank
	  	 $
                                         
     
	  		  	

											
					
	 Financial Covenant
	    	 Required
	    	 Actual
	    	  	    	
Complies

											
	 Term Sheet and Funding Milestone ($15MM)
	    	 Term sheet received by 5/31/2016
	    	
$                       
 
	  		    	 Yes 
	    	 No

	 	    	 Term sheet executed by
6/30/2016
	    	
$                       
 
	  	 	    	 Yes 
	    	 No

	 	    	 Funded by 8/31/2016
	    	
$                       
 
	  	 	    	 Yes 
	    	 No

						
	 Minimum Cash with Bank
	    	 $1,000,000, through receipt of $15MM
	    	
                       
 ;
	  		    	 Yes 
	    	 No

	 	    	 Funding Milestone
	    	 	  	 	    	 	    	 
	 Performance to Plan (monthly; T6M)
	    	 At least 75% of the projections (see Exhibit C)
	    	          %
	  		    	 Yes 
	    	 No

  

					
	 Comments Regarding Exceptions: See Attached.

 
 Sincerely,

 
	  	 	  	
BANK USE ONLY

 

Received by:             
                                         
                       

                 
               AUTHORIZED SIGNER
  

Date:
                                         
                                         
      
  

		  	 	  	 Verified:
                                         
                                         

	 SIGNATURE
	  	 	  	
                
                AUTHORIZED SIGNER

		  	 	  	 Date:
                                         
                                         
    

	 TITLE
	  	 	  	 

					
		  	 	  	 Compliance
Status                                    Yes    
            No

	 DATE
	  	 	  	 

  
 [Signature Page to
Disbursement Letter] 

 SCHEDULE OF EXCEPTIONS 

Permitted Indebtedness (Section 1.1) 

None 
 Permitted Investments
(Section 1.1) 
 Two Subsidiaries: 
  

	 (1)
	 BioNano Genomics UK, Ltd. 

 

	 (2)
	 BioNano Genomics (Shanghai) Trading Co., Ltd. 

Borrower maintains cash Investments in the above two Subsidiaries not exceeding the amounts set forth in Section 7.12. 

Permitted Liens (Section 1.1) 

Liens on the collateral described in that certain financing statement # 2012 2040246 filed by Webbank in the State of Delaware on May 25,
2012 [to be terminated soon after the Closing Date] 
 Inbound Licenses (Section 5.6) 

Borrower’s rights as a licensee of intellectual property under the inbound licenses set forth below may give rise to more than five
percent (5%) of its gross revenue in any given month, including without limitation revenue derived from the sale, licensing, rendering or disposition of any product or service. 

 

	 	 •
	 	 License Agreement by and between Princeton University and the Company, effective as of January 7, 2004,
as amended 

  

	 	 •
	 	 Supply and License Agreement by and between Life Technologies Corporation and the Company effective as of
February 15, 2010 

  

	 	 •
	 	 License Agreement by and between Howard Florey Institute and the Company effective as of January 1, 2010

  

	 	 •
	 	 Sublicense Agreement by and between Industry 3200 and the Company effective as of December 27, 2013

  

	 	 •
	 	 License Agreement by and between Q Biotechnology C.V. and the Company effective as of May 1, 2014

  

	 	 •
	 	 License Agreement by and between New York University and the Company effective as of November 4,
2013 

 Prior Names (Section 5.7) 

BioNanomatrix, Inc. 

Locations (Section 5.7; Section 7.10) 

(1) Borrower has engaged the following company for self-storage space: 

Public Storage, 9890 Pacific Heights Blvd., San Diego, CA 92121 

Storage West, 5206 Eastgate Mall, San Diego, CA 92121 

(2) Borrower maintains a second office at the following location: 

9540 Towne Centre Drive, Suite 100 

San Diego, CA 92121 

Litigation (Section 5.8) 

None 

 Environmental Condition (Section 5.12) 

None 
 Accounts (Section 5.16)

  

	 	 1.
	 SQ1 Bank Business Checking account # 2003069; 

 

	 	 2.
	 SQ1 Bank Money Market Business account # 2003150; 

 

	 	 3.
	 SQ1 Bank Money Market Collateral account # 7057099; and 

 

	 	 4.
	 SQ1 Bank Money Market Collateral account # 2020048;Collectively, the accounts referred to in 1-4 above, the “Square 1 Accounts,” and the accounts referred to in 3-4 above, the “Square 1 Cash Collateral Accounts;”

  

	 	 5.
	 Silicon Valley Bank US General Account # 3300928342 USD (the “Foreign Support Account”);

  

	 	 6.
	 Silicon Valley Bank Corporate Deposit Account #20113773 EUR; 

 

	 	 7.
	 Silicon Valley Bank Operating Account # 20106483 GBP; and 

 

	 	 8.
	 Silicon Valley Bank China Capital Account # 100 100 1000000918 USD. 

	 	  
	 Collectively, the accounts referred to in 5-8 above, the “SVB
Accounts.” 

  
 [Signature Page to
Disbursement Letter] 

 CORPORATE RESOLUTIONS TO BORROW 

 
  

			
	 Borrower: BIONANO GENOMICS, INC.
	  	Date: March 8, 2016

  

I, the undersigned Secretary or Assistant Secretary of BIONANO GENOMICS, INC. (the “Corporation”), HEREBY CERTIFY
that the Corporation is organized and existing under and by virtue of the laws of the State of Delaware. 
 I FURTHER
CERTIFY that attached hereto as Attachments 1 and 2 are true and complete copies of the Certificate of Incorporation, as amended, and the Restated Bylaws of the Corporation, each of which is in full force and effect on the date hereof. 

I FURTHER CERTIFY that at a meeting of the Directors of the Corporation, duly called and held, at which a quorum was present
and voting (or by other duly authorized corporate action in lieu of a meeting), the following resolutions (the “Resolutions”) were adopted. 

BE IT RESOLVED, that any one (1) of the following named officers, employees, or agents of this Corporation, whose actual
signatures are shown below: 
  

									
	 NAMES
	  	 	  	 POSITION
	  	 	  	 ACTUAL
SIGNATURES

	  
	  		  	  
	  		  	  

	  
	  		  	  
	  		  	  

	  
	  		  	  
	  		  	  

	  
	  		  	  
	  		  	  

 acting for and on behalf of this Corporation and as its act and deed be, and they hereby are, authorized and
empowered: 
 Borrow Money. To borrow from time to time from Western Alliance Bank, an Arizona corporation
(“Bank”), on such terms as may be agreed upon between the officers, employees, or agents of the Corporation and Bank, such sum or sums of money as in their judgment should be borrowed, without limitation. 

Execute Loan Documents. To execute and deliver to Bank that certain Loan and Security Agreement dated as of (the
“Loan Agreement”) and any other agreement entered into between Corporation and Bank in connection with the Loan Agreement, including any amendments, all as amended or extended from time to time (collectively, with the Loan Agreement, the
“Loan Documents”), and also to execute and deliver to Bank one or more renewals, extensions, modifications, refinancings, consolidations, or substitutions for the Loan Documents, or any portion thereof. 

Grant Security. To grant a security interest to Bank in the Collateral described in the Loan Documents, which security
interest shall secure all of the Corporation’s Obligations, as described in the Loan Documents. 
 Negotiate
Items. To draw, endorse, and discount with Bank all drafts, trade acceptances, promissory notes, or other evidences of indebtedness payable to or belonging to the Corporation or in which the Corporation may have an interest, and either to
receive cash for the same or to cause such proceeds to be credited to the account of the Corporation with Bank, or to cause such other disposition of the proceeds derived therefrom as they may deem advisable. 

Warrants. To issue Bank warrants to purchase the Corporation’s capital stock. 

 Letters of Credit. To execute letter of credit applications and other
related documents pertaining to Bank’s issuance of letters of credit. 
 Corporate Credit Cards. To execute
corporate credit card applications and agreements and other related documents pertaining to Bank’s provision of corporate credit cards. 

Further Acts. In the case of lines of credit, to designate additional or alternate individuals as being authorized to
request advances thereunder, and in all cases, to do and perform such other acts and things, to pay any and all fees and costs, and to execute and deliver such other documents and agreements as they may in their discretion deem reasonably necessary
or proper in order to carry into effect the provisions of these Resolutions. 
 BE IT FURTHER RESOLVED, that any and all
acts authorized pursuant to these resolutions and performed prior to the passage of these resolutions are hereby ratified and approved, that these Resolutions shall remain in full force and effect and Bank may rely on these Resolutions until written
notice of their revocation shall have been delivered to and received by Bank. Any such notice shall not affect any of the Corporation’s agreements or commitments in effect at the time notice is given. 

I FURTHER CERTIFY that the officers, employees, and agents named above are duly elected, appointed, or employed by or for the
Corporation, as the case may be, and occupy the positions set forth opposite their respective names; that the foregoing Resolutions now stand of record on the books of the Corporation; and that the Resolutions are in full force and effect and have
not been modified or revoked in any manner whatsoever. 
 IN WITNESS WHEREOF, I have hereunto set my hand on the date set
forth above and attest that the signatures set opposite the names listed above are their genuine signatures. 
  

	
	 CERTIFIED AND ATTESTED BY:

	
	
X                       
                                         
    

	 Secretary or Assistant Secretary of Borrower

  
  

 ATTACHMENT A 

CERTIFICATE OF INCORPORATION 

 ATTACHMENT B 

BYLAWS OF THE CORPORATION 

 INSURANCE AUTHORIZATION LETTER 

In accordance with the insurance coverage requirements of the Loan and Security Agreement     ,
2016 (the “Agreement”) between Western Alliance Bank, an Arizona corporation (“Bank”), and BIONANO GENOMICS, INC. (“Borrower”), coverage is to be provided as set forth below: 

 

	 COVERAGE:
	     All risk including liability and property damage. 

 

	 INSURED:
	         BIONANO GENOMICS, INC. 

LOCATION(s) OF COLLATERAL: 

1. 
  

			
	 Insuring Agent:
	  	 Barney and Barney

		
	 Address:
	  	 9171 Towne Centre Drive, Suite 510

		  	 San Diego, CA 92122

		  	 Attn: Mark Nash

		
	 Phone Number:
	  	 (858) 587-7595

		
	 Fax Number:
	  	 (858) 909-9813

 ADDITIONAL INSURED AND LOSS PAYEE: 

Bank, as its interests may appear below. 

BANK: 
 Bridge
Bank, a division of Western Alliance Bank 
 55 Almaden Blvd. 

San Jose, CA 95113 

Attn: Note Department 

Fax # 408-689-8542 

Phone # 408-423-8500 

The above coverage is to be provided prior to funding the Agreement. Borrower hereby agrees to pay for the coverage above and
by signing below acknowledges its obligation to do so. 
  

					
		  	 Signature:
	  	 /s/ R. Erik Holmlin

			
		  	 Title:
	  	 CEO

			
		  	 Date:EX-10.16

 Exhibit 10.16 

FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT 

This First Amendment to Loan and Security Agreement (this “Amendment”) is entered into as of December 9, 2016,
by and between WESTERN ALLIANCE BANK, an Arizona corporation (“Bank”) and BIONANO GENOMICS, INC. (“Borrower”). 

RECITALS 

Borrower and Bank are parties to that certain Loan and Security Agreement dated as of March 8, 2016, as amended from time
to time (the “Agreement”). The parties desire to amend the Agreement in accordance with the terms of this Amendment. 

NOW, THEREFORE, the parties agree as follows: 

1. The following defined terms in Section 1.1 of the Agreement hereby are added, amended or restated as follows: 

“Amortization Date” is April 8, 2017; provided, however, if Borrower achieves either
(i) the Irys Milestone or (ii) the New Equity Milestone, then the Amortization Date shall be extended to October 8, 2017; provided further, however, that if Borrower achieves both (i) the Irys Milestone and (ii) the New
Equity Milestone, then the Amortization Date shall be further extended to April 8, 2018. 
 “First
Amendment Effective Date” means December 9, 2016. 
 “New Equity Milestone” means
Borrower’s receipt, on or after December 1, 2016 and on or before the date immediately preceding the date that would otherwise be the Amortization Date, of at least Fifteen Million Dollars ($15,000,000) of gross cash proceeds (provided
that Borrower shall only incur a reasonable amount of transaction expenses in connection therewith) from the sale or issuance of its equity securities or Subordinated Debt to investors and on terms and conditions reasonably acceptable to Bank.”

 “Warrant” means that certain Warrant to Purchase Stock issued by Borrower to Bank on the Closing
Date and that certain Warrant to Purchase Stock issued by Borrower to Bank on the First Amendment Effective Date, as the same may be amended from time to time. 

2. Section 2.2(b) of the Agreement hereby is amended and restated in its entirety to read as follows: 

“(b) Repayment. Borrower shall make monthly payments of interest only, in arrears, commencing on
the first (1st) Payment Date following the Funding Date of the Term Loan, and continuing on the Payment Date of each successive month thereafter through and including the Payment Date immediately preceding the Amortization Date. Borrower agrees to
pay, on the Funding Date of the Term Loan, any initial partial monthly interest payment otherwise due for the period between the Funding Date of the Term Loan and the first Payment Date thereof. Commencing on the Amortization Date, and continuing on
the Payment Date of each month thereafter, Borrower shall make equal monthly payments of principal, together with applicable interest, in arrears, to Bank, as calculated by Bank (which calculations shall be deemed correct absent manifest error)
based upon: (1) the amount of the Term Loan, (2) the effective rate of interest, as determined in Section 2.4(a), and (3) a repayment schedule equal to (i) if the Amortization Date is April 8, 2017, thirty-six (36) months, (ii) if the Amortization Date is October 8, 2017, thirty (30) months and (iii) if the Amortization Date is April 8, 2018, twenty-four (24) months. All unpaid
principal and accrued and unpaid interest with respect to the Term Loan is due and payable in full on the Term Loan Maturity Date. The Term Loan may only be prepaid in accordance with Sections 2.2(c) and 2.2(d).” 

  
 1 

 3. Section 6.8 of the Agreement hereby is amended and restated in its entirety to
read as follows: 
 “6.8 Funding Milestone. On or after December 1, 2016 and on or before
April 30, 2017, Borrower shall have received at least Five Million Dollars ($5,000,000) of gross cash proceeds (provided that Borrower shall only incur a reasonable amount of transaction expenses in connection therewith) from the sale or
issuance of its equity securities or Subordinated Debt to investors and on terms and conditions reasonably acceptable to Bank.” 

4. Section 6.9 of the Agreement hereby is amended and restated in its entirety to read as follows: 

“6.9 Performance to Plan; Minimum Cash. Borrower’s actual trailing six-month revenues, as of any date of determination, shall be no less than seventy-five percent (75%) of Borrower’s projected revenues (the “Revenue Covenant”), as set forth in the table attached as
Exhibit C hereto and updated in accordance with Borrower’s annual financial projections delivered to Bank pursuant to Section 6.3(e) hereof; provided that Borrower shall not be required to comply with the Revenue Covenant as long as
Borrower at all times maintains a ratio of (i) minimum unrestricted cash in accounts with Bank to (ii) Indebtedness to Bank, of at least 0.75 to 1.00.” 

5. Exhibit D to the Agreement hereby is replaced with Exhibit D attached hereto. 

6. No course of dealing on the part of Bank or its officers, nor any failure or delay in the exercise of any right by Bank,
shall operate as a waiver thereof, and any single or partial exercise of any such right shall not preclude any later exercise of any such right. Bank’s failure at any time to require strict performance by Borrower of any provision shall not
affect any right of Bank thereafter to demand strict compliance and performance. Any suspension or waiver of a right must be in writing signed by an officer of Bank. 

7. Unless otherwise defined, all initially capitalized terms in this Amendment shall be as defined in the Agreement. The
Agreement, as amended hereby, shall be and remain in full force and effect in accordance with its respective terms and hereby is ratified and confirmed in all respects. Except as expressly set forth herein, the execution, delivery, and performance
of this Amendment shall not operate as a waiver of, or as an amendment of, any right, power, or remedy of Bank under the Agreement, as in effect prior to the date hereof. 

8. Borrower represents and warrants that the Representations and Warranties contained in the Agreement are true and correct as
of the date of this Amendment, and that no Event of Default has occurred and is continuing. 
 9. As a condition to the
effectiveness of this Amendment, Bank shall have received, in form and substance satisfactory to Bank, the following: 

(a) this Amendment, duly executed by Borrower; 

(b) a Certificate of the Secretary of Borrower with respect to incumbency and resolutions authorizing the execution and
delivery of this Amendment; 
 (c) a Warrant to Purchase Stock, duly executed by Borrower; 

(d) an amendment fee in the amount of Fifteen Thousand Dollars ($15,000), which may be debited from any of Borrower’s
accounts; 
 (e) all reasonable Bank Expenses incurred through the date of this Amendment, which may be debited from any of
Borrower’s accounts; and 
 (f) such other documents, and completion of such other matters, as Bank may reasonably
deem necessary or appropriate. 

 10. This Amendment may be executed in two or more counterparts, each of which
shall be deemed an original, but all of which together shall constitute one instrument. 
 [Balance of Page Intentionally Left
Blank] 

 IN WITNESS WHEREOF, the undersigned have executed this Amendment as of the first
date above written. 
  

			
	 BIONANOGENOMICS, INC.

			
		
	 By:
	 	 /s/ R. Erik Holmlin

	 Title:
	 	 CEO

 
			
	
	 WESTERN ALLIANCE BANK, an Arizona
Corporation

 
			
		
	 By:
	 	  

	 Title:
	 	

  
 [Signature Page to
First Amendment to Loan and Security Agreement] 

 IN WITNESS WHEREOF, the undersigned have executed this Amendment as of the first
date above written. 
  

			
	 BIONANOGENOMICS, INC.

			
		
	 By:
	 	  

	 Title:
	 	

 
			
	
	 WESTERN ALLIANCE BANK, an Arizona
Corporation

 
			
		
	 By:
	 	 /s/ Lindsay Schwallie

	 Title:
	 	 VP, Portfolio Management

  
 [Signature Page to
First Amendment to Loan and Security Agreement] 

 EXHIBIT C 

[see attached] 

																																																											
	 	 	 	 	Financial Performance for 2017	 	 	 	 
	 	 	 	 	January	 	 	February	 	 	March	 	 	April	 	 	May	 	 	June	 	 	July	 	 	August	 	 	September	 	 	October	 	 	November	 	 	December	 	 	Full Year	 	 	 	 
	 Revenue:
	 		 			 	 				 				 				 			 	 				 			 	 				 			 	 				 				 				 			 	 			
	 Instrument
	 		 	 	$395,000	 	 	 	$691,250	 	 	 	$987,500	 	 	 	$691,250	 	 	 	$691,250	 	 	 	$1,234,375	 	 	 	$691,250	 	 	 	$691,250	 	 	 	$1,481,250	 	 	 	$641,875	 	 	 	$395,000	 	 	 	$1,283,750	 	 	 	$9,875,000	 	 			
	 Cartridge
	 		 	 	$76,320	 	 	 	$133,560	 	 	 	$190,800	 	 	 	$133,560	 	 	 	$133,560	 	 	 	$238,500	 	 	 	$133,560	 	 	 	$133,560	 	 	 	$286,200	 	 	 	$124,020	 	 	 	$76,320	 	 	 	$248,040	 	 	 	$1,908,000	 	 			
	 Kit
	 		 	 	$38,160	 	 	 	$66,780	 	 	 	$95,400	 	 	 	$66,780	 	 	 	$66,780	 	 	 	$119,250	 	 	 	$66,780	 	 	 	$66,780	 	 	 	$100,966	 	 	 	$62,010	 	 	 	$38,160	 	 	 	$62,010	 	 	 	$849,856	 	 			
	 Other
	 		 	 	$35,000	 	 	 	$38,000	 	 	 	$41,000	 	 	 	$45,000	 	 	 	$55,000	 	 	 	$58,000	 	 	 	$65,000	 	 	 	$69,000	 	 	 	$75,000	 	 	 	$75,000	 	 	 	$75,000	 	 	 	$44,000	 	 	 	$675,000	 	 			
	 Service
	 		 	 	$29,167	 	 	 	$29,167	 	 	 	$29,167	 	 	 	$29,167	 	 	 	$29,167	 	 	 	$29,167	 	 	 	$29,167	 	 	 	$29,167	 	 	 	$29,167	 	 	 	$29,167	 	 	 	$29,167	 	 	 	$29,167	 	 	 	$350,000	 	 			
	 Grant
	 		 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	$0	 	 			
	 Total Revenue
	 		 	 	$573,647	 	 	 	$958,757	 	 	 	$1,343,867	 	 	 	$965,757	 	 	 	$975,757	 	 	 	$1,679,292	 	 	 	$985,757	 	 	 	$989,757	 	 	 	$1,972,582	 	 	 	$932,072	 	 	 	$613,647	 	 	 	$1,666,967	 	 	 	$13,657,856	 	 			
			 		 	 	 		 		 		 	 	 	
	 COGS:
	 		 			 	 				 				 				 			 	 				 			 	 				 			 	 				 				 				 			 	 			
	 Total COGS
	 		 	 	$224,940	 	 	 	$367,896	 	 	 	$585,852	 	 	 	$367,896	 	 	 	$367,896	 	 	 	$704,982	 	 	 	$367,896	 	 	 	$367,896	 	 	 	$832,258	 	 	 	$344,070	 	 	 	$224,940	 	 	 	$754,004	 	 	 	$5,510,521	 	 			
		 		 			 	 				 				 				 			 	 				 			 	 				 			 	 				 				 				 			 	 			
	 Gross Margin
	 		 	 	$348,707	 	 	 	$590,861	 	 	 	$758,015	 	 	 	$597,861	 	 	 	$607,861	 	 	 	$974,310	 	 	 	$617,861	 	 	 	$621,861	 	 	 	$1,140,324	 	 	 	$588,002	 	 	 	$388,707	 	 	 	$912,963	 	 	 	$8,147,334	 	 			
	 GM%
	 		 	 	60.8%	 	 	 	61.6%	 	 	 	56.4%	 	 	 	61.9%	 	 	 	62.3%	 	 	 	58.0%	 	 	 	62.7%	 	 	 	62.8%	 	 	 	57.8%	 	 	 	63.1%	 	 	 	63.3%	 	 	 	54.8%	 	 	 	59.7%	 	 			
			 		 	 	 		 		 		 	 	 	
	 Operating Expenses:
	 		 			 	 				 				 				 			 	 				 			 	 				 			 	 				 				 				 			 	 			
	 Operations
	 		 	 	$51,667	 	 	 	$51,667	 	 	 	$51,667	 	 	 	$51,667	 	 	 	$51,667	 	 	 	$51,667	 	 	 	$51,667	 	 	 	$51,667	 	 	 	$51,667	 	 	 	$51,667	 	 	 	$51,667	 	 	 	$51,667	 	 	 	$620,000	 	 			
	 General & Administrative
	 		 	 	$508,333	 	 	 	$508,333	 	 	 	$508,333	 	 	 	$508,333	 	 	 	$508,333	 	 	 	$508,333	 	 	 	$508,333	 	 	 	$508,333	 	 	 	$508,333	 	 	 	$508,333	 	 	 	$508,333	 	 	 	$508,333	 	 	 	$6,100,000	 	 			
	 Sales & Marketing
	 		 	 	$551,750	 	 	 	$551,750	 	 	 	$551,750	 	 	 	$551,750	 	 	 	$551,750	 	 	 	$551,750	 	 	 	$551,750	 	 	 	$551,750	 	 	 	$551,750	 	 	 	$551,750	 	 	 	$551,750	 	 	 	$551,750	 	 	 	$6,621,000	 	 			
	 Research
	 		 	 	$205,691	 	 	 	$205,691	 	 	 	$205,691	 	 	 	$205,691	 	 	 	$205,691	 	 	 	$205,691	 	 	 	$205,691	 	 	 	$205,691	 	 	 	$205,691	 	 	 	$205,691	 	 	 	$205,691	 	 	 	$205,691	 	 	 	$2,468,293	 	 			
	 Development
	 		 	 	$890,810	 	 	 	$890,810	 	 	 	$890,810	 	 	 	$890,810	 	 	 	$890,810	 	 	 	$890,810	 	 	 	$890,810	 	 	 	$890,810	 	 	 	$890,810	 	 	 	$890,810	 	 	 	$890,810	 	 	 	$890,810	 	 	 	$10,689,721	 	 			
	 Total Operating Expenses
	 		 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$2,208,251	 	 	 	$26,499,014	 	 			
	 % of Rev

 
	 	 	 	   
	384.9%  
	   
	 	   
	230.3%  
	   
	 	   
	164.3%  
	   
	 	   
	228.7%  
	   
	 	   
	226.3%  
	   
	 	   
	131.5%  
	   
	 	   
	224.0%  
	   
	 	   
	223.1%  
	   
	 	   
	111.9%  
	   
	 	   
	236.9%  
	   
	 	   
	359.9%  
	   
	 	   
	132.5%  
	   
	 	   
	194.0%  
	   
	 			
	Total Operating Income	 	 	 	 	($1,859,544	) 	 	 	($1,617,390	) 	 	 	($1,450,236	) 	 	 	($1,610,390	) 	 	 	($1,600,390	) 	 	 	($1,233,941	) 	 	 	($1,590,390	) 	 	 	($1,586,390	) 	 	 	($1,067,927	) 	 	 	($1,620,249	) 	 	 	($1,819,544	) 	 	 	($1,295,288	) 	 	 	($18,351,680	) 	 			
			 		 	 	 		 		 		 	 	 	
	 Other Expense/Income

 
	 	 	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $42,000 
	   
	 	   
	 $504,000 
	   
	 			
	 Net
Income
	 	 	 	 	($1,901,544	) 	 	 	($1,659,390	) 	 	 	($1,492,236	) 	 	 	($1,652,390	) 	 	 	($1,642,390	) 	 	 	($1,275,941	) 	 	 	($1,632,390	) 	 	 	($1,628,390	) 	 	 	($1,109,927	) 	 	 	($1,662,249	) 	 	 	($1,861,544	) 	 	 	($1,337,288	) 	 	 	($18,855,680	) 	 			
	 	 	 			

 EXHIBIT D 

COMPLIANCE CERTIFICATE 
  

			
	 TO:
	  	 WESTERN ALLIANCE BANK, an Arizona corporation

		
	 FROM:
	  	 BIONANO GENOMICS, INC.

 The undersigned authorized officer of BIONANO GENOMICS, INC. hereby certifies that in
accordance with the terms and conditions of the Loan and Security Agreement between Borrower and Bank (the “Agreement”), (i) Borrower is in complete compliance for the period ending
                     with all required covenants except as noted below and (ii) all representations and warranties of Borrower stated in
the Agreement are true and correct in all material respects as of the date hereof except as noted below; provided that those representations and warranties expressly referring to another date shall be true, correct and complete in all material
respects as of such date. Attached herewith are the required documents supporting the above certification. The Officer further certifies that these are prepared in accordance with Generally Accepted Accounting Principles (GAAP) and are consistently
applied from one period to the next except as explained in an accompanying letter or footnotes. 
 Please indicate compliance status by
circling Yes/No under “Complies” column. 
  

									
	 Reporting Covenant
	  	 Required
	 	
Complies

				
	 Annual financial statements (CPA Audited)
	  	 FYE within 180 days
	 	Yes 	  	No
				
	 Monthly financial statements and Compliance Certificate
	  	 Prior to each Credit Extension, and monthly within 30 days
	 	Yes 	  	No
				
	 10K and 10Q
	  	 (as applicable)
	 	Yes 	  	No
				
	 Annual operating budget, sales projections and operating plans approved by board of directors
	  	 Annually no later than 45 days after the beginning of each fiscal year
	 	Yes 	  	No
				
	 Deposit balances with Bank
	  	
$                       
                         
	 		  	
	 Deposit balance outside Bank
	  	
$                       
                         
	 		  	
				
	 Financial Covenant
	  	 Required
	  	 Actual
	 	
Complies

	 Term Sheet and Funding Milestone ($5MM)
	  	 Receipt of $5,000,000 of gross cash proceeds from the sale or issuance of its equity securities or Subordinated
Debt
	  	
$                       
 
  

$                       
 
  

$                       
 
	 	 Yes 
  

Yes 
  

Yes 
	  	 No
  

No
  

No

					
	 Minimum Cash with Bank
	  	 ratio of (i) minimum unrestricted cash in accounts with Bank to (ii) Indebtedness to Bank, of at least 0.75 to
1.00
	  	
                       
   ;
  
	 	Yes 	  	No
	 	  	 Funding Milestone
	  	
                       
   
	 	 	  	 
	 Performance to Plan (monthly; T6M)
	  	 At least 75% of the projections (see Exhibit C)
	  	               %
	 	Yes 	  	No

  

					
	 Comments Regarding Exceptions: See Attached.

 
 Sincerely,

 
	 		  	
BANK USE ONLY
  

Received by:             
                                         
                       

AUTHORIZED SIGNER

 

Date:               
                                         
                                 

 
  

					
	 SIGNATURE
	 		  	
Verified:               
                                         
                           

AUTHORIZED SIGNER

 

Date:               
                                         
                                 

	 TITLE

 
	 		  	 
	 DATE
	 		  	
Compliance Status             
                       Yes                No

 

  

 CORPORATE RESOLUTIONS TO BORROW 

 
  

Borrower: BIONANO GENOMICS, INC. 

 
 I, the undersigned
Secretary or Assistant Secretary of BIONANO GENOMICS, INC. (the “Corporation”), HEREBY CERTIFY that the Corporation is organized and existing under and by virtue of the laws of the State of Delaware. 

I FURTHER CERTIFY that attached hereto as Attachments 1 and 2 are true and complete copies of the Certificate of
Incorporation, as amended, and the Bylaws of the Corporation, each of which is in full force and effect on the date hereof. 

I FURTHER CERTIFY that at a meeting of the Directors of the Corporation, duly called and held, at which a quorum was present
and voting (or by other duly authorized corporate action in lieu of a meeting), the following resolutions (the “Resolutions”) were adopted. 

BE IT RESOLVED, that any one (1) of the following named officers, employees, or agents of this Corporation, whose actual
signatures are shown below: 
  

					
	 NAMES
	    	 POSITION
	    	 ACTUAL
SIGNATURES

			
	 R. Erik Holmlin
	    	 CEO
	    	 /s/ R. Erik Holmlin

			
	  
	    	  
	    	  

			
	  
	    	  
	    	  

			
	  
	    	  
	    	  

 acting for and on behalf of this Corporation and as its act and deed be, and they hereby are, authorized and
empowered: 
 Borrow Money. To borrow from time to time from Western Alliance Bank, an Arizona corporation
(“Bank”), on such terms as may be agreed upon between the officers, employees, or agents of the Corporation and Bank, such sum or sums of money as in their judgment should be borrowed, without limitation. 

Execute Loan Documents. To execute and deliver to Bank that certain Loan and Security Agreement dated as March 8, 2016
(the “Loan Agreement”) and any other agreement entered into between Corporation and Bank in connection with the Loan Agreement, including any amendments, all as amended or extended from time to time, including but not limited to that
certain First Amendment to Loan and Security Agreement dated as of December     , 2016 (collectively, with the Loan Agreement, the “Loan Documents”), and also to execute and deliver to Bank one or more
renewals, extensions, modifications, refinancings, consolidations, or substitutions for the Loan Documents, or any portion thereof. 

Grant Security. To grant a security interest to Bank in the Collateral described in the Loan Documents, which security
interest shall secure all of the Corporation’s Obligations, as described in the Loan Documents. 
 Negotiate
Items. To draw, endorse, and discount with Bank all drafts, trade acceptances, promissory notes, or other evidences of indebtedness payable to or belonging to the Corporation or in which the Corporation may have an interest, and either to
receive cash for the same or to cause such proceeds to be credited to the account of the Corporation with Bank, or to cause such other disposition of the proceeds derived therefrom as they may deem advisable. 

 Warrants. To issue Bank warrants to purchase the Corporation’s
capital stock. 
 Letters of Credit. To execute letter of credit applications and other related documents pertaining
to Bank’s issuance of letters of credit. 
 Corporate Credit Cards. To execute corporate credit card
applications and agreements and other related documents pertaining to Bank’s provision of corporate credit cards. 

Further Acts. In the case of lines of credit, to designate additional or alternate individuals as being authorized to
request advances thereunder, and in all cases, to do and perform such other acts and things, to pay any and all fees and costs, and to execute and deliver such other documents and agreements as they may in their discretion deem reasonably necessary
or proper in order to carry into effect the provisions of these Resolutions. 
 BE IT FURTHER RESOLVED, that any and all
acts authorized pursuant to these resolutions and performed prior to the passage of these resolutions are hereby ratified and approved, that these Resolutions shall remain in full force and effect and Bank may rely on these Resolutions until written
notice of their revocation shall have been delivered to and received by Bank. Any such notice shall not affect any of the Corporation’s agreements or commitments in effect at the time notice is given. 

I FURTHER CERTIFY that the officers, employees, and agents named above are duly elected, appointed, or employed by or for the
Corporation, as the case may be, and occupy the positions set forth opposite their respective names; that the foregoing Resolutions now stand of record on the books of the Corporation; and that the Resolutions are in full force and effect and have
not been modified or revoked in any manner whatsoever. 
 IN WITNESS WHEREOF, I have hereunto set my hand on December
    , 2016 and attest that the signatures set opposite the names listed above are their genuine signatures. 
  

			
		  	 CERTIFIED AND ATTESTED BY:

		
		  	
/s/ Tom Coll

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