10-Q 1 bngo-20220331.htm 10-Q bngo-20220331
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UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
WASHINGTON, D.C. 20549
_________________________________________________________
FORM 10-Q
_________________________________________________________
(Mark One)
QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
FOR THE QUARTERLY PERIOD ENDED MARCH 31, 2022
TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
FOR THE TRANSITION PERIOD FROM             TO
Commission file number: 001-38613
_________________________________________________________
Bionano Genomics, Inc.
(Exact name of registrant as specified in its charter)
Delaware 26-1756290
(State or Other Jurisdiction of Incorporation or Organization) (I.R.S. Employer Identification No.)
9540 Towne Centre Drive, Suite 100,
San Diego, CA
 
 
92121
(Address of Principal Executive Offices) (Zip Code)
(858) 888-7600
(Registrant’s Telephone Number, Including Area Code)
_________________________________________________________

Securities registered pursuant to Section 12(b) of the Act:
Title of each classTrading Symbol(s)Name of each exchange on which registered
Common Stock, $0.0001 par value per shareBNGOThe Nasdaq Stock Market, LLC
Warrants to purchase Common StockBNGOWThe Nasdaq Stock Market, LLC

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.   Yes  x No  ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files).    Yes  x   No  ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and ‘‘emerging growth company’’ in Rule 12b-2 of the Exchange Act.
Large accelerated filer Accelerated filer
Non-accelerated filer Smaller reporting company
   Emerging growth company


If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).   Yes   No x

As of April 28, 2022, the registrant had 289,697,045 shares of Common Stock ($0.0001 par value) outstanding.




BIONANO GENOMICS, INC.
TABLE OF CONTENTS
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2

PART I. FINANCIAL INFORMATION
ITEM 1. FINANCIAL STATEMENTS
BIONANO GENOMICS, INC.
Condensed Consolidated Balance Sheets
(Unaudited)
 March 31,
2022
December 31,
2021
Assets  
Current assets:  
Cash and cash equivalents$24,048,000 $24,571,000 
Investments 192,420,000 226,041,000 
Accounts receivable, net of allowance for doubtful accounts of $463,000 and $690,000 as of March 31, 2022 and December 31, 2021, respectively
5,514,000 4,934,000 
Inventory16,268,000 12,387,000 
Prepaid expenses and other current assets4,110,000 4,481,000 
Total current assets242,360,000 272,414,000 
Property and equipment, net12,661,000 10,318,000 
Operating lease right-of-use assets6,817,000 6,691,000 
Finance lease right-of-use assets, related party3,897,000 3,926,000 
Intangible assets, net25,424,000 26,842,000 
Goodwill56,254,000 56,160,000 
Other long-term assets798,000 749,000 
Total assets$348,211,000 $377,100,000 
Liabilities and stockholders’ equity
Current liabilities:
Accounts payable$6,590,000 $9,696,000 
Accrued expenses8,936,000 9,694,000 
Contract liabilities1,107,000 684,000 
Operating lease liability1,730,000 1,467,000 
Finance lease liability, related party296,000 299,000 
Total current liabilities18,659,000 21,840,000 
Operating lease liability, net of current portion5,451,000 5,288,000 
Finance lease liability, net of current portion, related party3,638,000 3,642,000 
Contingent consideration9,145,000 9,066,000 
Long-term contract liabilities133,000 146,000 
Total liabilities37,026,000 39,982,000 
Commitments and contingencies (Note 7)
Stockholders’ equity:
Preferred stock, $0.0001 par value; 10,000,000 shares authorized and no shares issued or outstanding as of March 31, 2022 and December 31, 2021
  
Common stock, $0.0001 par value, 400,000,000 shares authorized at March 31, 2022 and December 31, 2021; 289,688,000 and 289,602,000 shares issued and outstanding at March 31, 2022 and December 31, 2021, respectively
29,000 29,000 
Additional paid-in capital558,864,000 553,747,000 
Accumulated deficit(246,071,000)(216,119,000)
Accumulated other comprehensive loss(1,637,000)(539,000)
Total stockholders’ equity311,185,000 337,118,000 
Total liabilities and stockholders’ equity$348,211,000 $377,100,000 
See accompanying notes to the unaudited condensed consolidated financial statements
3

BIONANO GENOMICS, INC.
Condensed Consolidated Statements of Operations
(Unaudited)
Three Months Ended
March 31,
 20222021
Revenue:  
Product revenue$3,116,000 $2,049,000 
Service and other revenue2,580,000 1,119,000 
Total revenue5,696,000 3,168,000 
Cost of revenue:
Cost of product revenue3,576,000 1,513,000 
Cost of service and other revenue1,259,000 612,000 
Total cost of revenue4,835,000 2,125,000 
Operating expenses:
Research and development10,527,000 2,678,000 
Selling, general and administrative20,277,000 9,528,000 
Total operating expenses30,804,000 12,206,000 
Loss from operations(29,943,000)(11,163,000)
Other income (expense):
Interest income110,000 65,000 
Interest expense(77,000)(603,000)
Gain on forgiveness of Paycheck Protection Program loan 1,775,000 
Other income (expense)(33,000)(15,000)
Total other income (expense) 1,222,000 
Loss before income taxes(29,943,000)(9,941,000)
Benefit (provision) for income taxes(9,000)(6,000)
Net loss$(29,952,000)$(9,947,000)
Net loss per share, basic and diluted$(0.11)$(0.04)
Weighted-average common shares outstanding basic and diluted284,613,000 263,939,000 
See accompanying notes to the unaudited condensed consolidated financial statements.
4

BIONANO GENOMICS, INC.
Condensed Consolidated Statements of Comprehensive Loss
(Unaudited)
Three Months Ended
March 31,
 20222021
Net Loss:$(29,952,000)$(9,947,000)
Unrealized (loss) on investment securities
(1,098,000) 
Comprehensive Loss$(31,050,000)$(9,947,000)
See accompanying notes to the unaudited condensed consolidated financial statements.
5

BIONANO GENOMICS, INC.
Condensed Consolidated Statements of Stockholders’ Equity (Deficit) (Unaudited)
Common StockAdditional
Paid-in
Capital
Accumulated
Deficit
Accumulated Other Comprehensive LossTotal Stockholders’ Equity (Deficit)
SharesAmount
Balance at January 1, 2021189,953,000 $19,000 $178,747,000 $(143,684,000)$— $35,082,000 
Stock option exercises102,000 — 333,000 — — 333,000 
Stock-based compensation expense— — 371,000 — — 371,000 
Issue common stock, net of issuance costs78,000,000 8,000 327,478,000 — — 327,486,000 
Issue stock for warrant exercises10,739,000 1,000 9,392,000 — — 9,393,000 
Net loss— — — (9,947,000)— (9,947,000)
Balance at March 31, 2021278,794,000 $28,000 $516,321,000 $(153,631,000)$— $362,718,000 
Balance at January 1, 2022289,602,000 $29,000 $553,747,000 $(216,119,000)$(539,000)$337,118,000 
Stock option exercises21,000 — 15,000 — — 15,000 
Stock-based compensation expense— — 5,102,000 — — 5,102,000 
Issuance of common stock due to the vesting of restricted stock units, net of shares withheld to cover taxes65,000 — — — — — 
Net loss— — — (29,952,000)— (29,952,000)
Other comprehensive loss— — $— — (1,098,000)(1,098,000)
Balance at March 31, 2022289,688,000 $29,000 $558,864,000 $(246,071,000)$(1,637,000)$311,185,000 
See accompanying notes to the unaudited condensed consolidated financial statements
6

BIONANO GENOMICS, INC.
Condensed Consolidated Statements of Cash Flows
(Unaudited)
  Three Months Ended
March 31,
 20222021
Operating activities:  
Net loss$(29,952,000)$(9,947,000)
Adjustments to reconcile net loss to net cash used by operating activities:
Depreciation and amortization expense2,210,000 448,000 
Amortization of financing lease right-of-use asset29,000  
Amortization of interest on securities299,000  
Non-cash lease expense299,000  
Non-cash interest expense 315,000 
Stock-based compensation5,102,000 371,000 
Change in fair value of contingent consideration79,000  
Gain on forgiveness of PPP Loan (1,775,000)
Changes in operating assets and liabilities:
Accounts receivable(640,000)783,000 
Inventory(5,938,000)(961,000)
Prepaid expenses and other current assets(371,000)(1,049,000)
Accounts payable(3,168,000)(1,045,000)
Accrued expenses and contract liabilities(443,000)(1,044,000)
Net cash used in operating activities(32,494,000)(13,904,000)
Investing Activities:
BioDiscovery acquisition, return of purchase consideration from escrow694,000  
Purchases of property and equipment(150,000)(24,000)
Purchase of available for sale securities(14,954,000) 
Sale and maturity of available for sale securities47,179,000  
Construction in progress(832,000) 
Sale of property and equipment27,000  
Net cash provided by / (used in) investing activities31,964,000 (24,000)
Financing activities:
Principal payments of financing lease liability(8,000) 
Proceeds from sale of common stock 328,635,000 
Offering expenses on sale of common stock (825,000)
Proceeds from warrant and option exercises15,000 9,726,000 
Net cash provided by financing activities7,000 337,536,000 
Net increase in cash and cash equivalents(523,000)323,608,000 
Cash and cash equivalents at beginning of period24,571,000 38,449,000 
Cash and cash equivalents at end of period$24,048,000 $362,057,000 
Supplemental cash flow disclosures:
Cash paid for interest$70,000 $287,000 
Cash paid for operating lease liabilities $217,000 $206,000 
Supplemental disclosure of non-cash investing and financing activities:
Transfer of instruments and servers from inventory to property and equipment, net$2,056,000 $1,240,000 
Operating Lease Liabilities resulting from obtaining right-of-use assets$513,000 $2,013,000 
Forgiveness of PPP Loan$ $1,775,000 
Offering costs in accounts payable$ $324,000 
Warrant exercise pursuant to cashless exercise$ $129,000 
See accompanying notes to the unaudited condensed consolidated financial statements
7

BIONANO GENOMICS, INC.
NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
(Unaudited)
1. Organization and Basis of Presentation
Description of Business
Bionano Genomics, Inc. (collectively, with its consolidated subsidiaries, the “Company”) is a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. The Company’s mission is to transform the way the world sees the genome through optical genome mapping (“OGM”) solutions, diagnostic services and software. The Company offers OGM solutions for applications across basic, translational and clinical research. Through its Lineagen, Inc. (“Lineagen”) business, the Company also provides diagnostic testing for patients with clinical presentations consistent with autism spectrum disorder and other neurodevelopmental disabilities. Through its BioDiscovery, LLC. (“BioDiscovery”) business, the Company also offers an industry-leading, platform-agnostic software solution, which integrates next-generation sequencing and microarray data designed to provide analysis, visualization, interpretation and reporting of copy number variants, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view.
Basis of Presentation
The accompanying financial information has been prepared by the Company pursuant to the rules and regulations of the Securities and Exchange Commission (the “SEC”) for interim reporting purposes. The condensed consolidated financial statements are unaudited. The unaudited condensed consolidated financial statements reflect, in the opinion of the Company’s management, all adjustments, consisting of only normal recurring adjustments, necessary for a fair presentation of financial position, results of operations, changes in equity, and comprehensive loss and cash flows for each period presented in accordance with United States generally accepted accounting principles (“U.S. GAAP”). All intercompany transactions and balances have been eliminated. These interim condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and related notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2021.
Liquidity
As of March 31, 2022, the Company had approximately $24.0 million in cash and cash equivalents, $192.4 million in available for sale investment securities, and working capital of $223.7 million as a result of common stock offerings executed in the quarters ended December 31, 2020, March 31, 2021, and September 30, 2021. In February 2021, the Company applied for forgiveness of its Paycheck Protection Program Loan of approximately $1.8 million (the “PPP Loan”), and in March 2021, the PPP Loan, including all accrued interest, was forgiven in full.
The Company believes its available cash, cash equivalents, and available for sale securities will be sufficient to fund operations, obligations as they become due and capital investments for at least the next 12 months. However, the Company expects to continue to incur net losses for the foreseeable future. The Company plans to continue to fund its losses from operations and capital funding needs through a combination of equity offerings, debt financings or other sources, including potential collaborations, licenses and other similar arrangements. If the Company is not able to secure adequate additional funding, the Company may be forced to make reductions in spending, potentially harming the Company’s business.
COVID-19
The Company is subject to additional risks and uncertainties as a result of the continued spread of COVID-19 and uncertain market conditions, which could continue to have a material impact on the Company’s business and financial results. The Company closely monitors and complies with various applicable guidelines and legal requirements in the jurisdictions in which it operates, which may continue to result in reduced business operations in response to new or existing stay-at-home orders, travel restrictions and other social distancing measures. If restrictions related to COVID-19 persist, the Company could see additional supply chain disruptions that impact its ability to produce its products and may cause the Company to make strategic determinations regarding, among other things, the cost and quality of the components and supplies it acquires. The Company may also see negative effects on study enrollment in its ongoing or future studies. At various times throughout the pandemic, the Company has been unable to visit certain customer sites to support installation or service of its OGM systems. The Company’s manufacturing partners, suppliers, and customers, have implemented similar operational reductions. Despite reporting an increase in revenue for the three months ended March 31, 2022 when compared to the same period in 2021, the Company experienced supply chain constraints that negatively impacted the Company’s first quarter 2022 financial results. Given the continued evolution of the COVID-19 pandemic and the related complexities and uncertainties associated with the additional variants, the future effects of COVID-19 are unknown and the Company’s financial results may continue to be negatively affected in the future.
8

During the three months ended March 31, 2022, the Company experienced supply chain challenges, which it largely attributes to the COVID-19 pandemic. While the COVID-19 pandemic did not prevent the Company from operating its business during the three months ended March 31, 2022, it experienced increased cost to secure certain component parts in its products and to produce its products at its contract manufacturers.
There may be long-term negative effects of the COVID-19 pandemic, even after it has subsided. Specifically, product demand may be reduced due to an economic recession, a decrease in corporate capital expenditures, prolonged unemployment, reduction in consumer confidence, or any similar negative economic condition. Further, the travel restrictions on the Company’s business have limited its ability to support its global and domestic operations, including providing installation and training and customer service, which has and may continue to slow the pace of its commercial strategy, sales and marketing efforts. These negative effects could have a material impact on the Company’s operations, business, earnings, and liquidity.
Significant Accounting Policies
During the three months ended March 31, 2022, there were no changes to the Company’s significant accounting policies as described in the Company’s Annual Report on Form 10-K for the year ended December 31, 2021.
Recently Issued But Not Yet Adopted Accounting Pronouncements
In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments - Credit Losses: Measurement of Credit Losses on Financial Instruments (ASU 2016-13), which amends the impairment model by requiring entities to use a forward looking approach based on expected losses to estimate credit losses on certain types of financial instruments, including trade receivables and available for sale debt securities. The standard is effective for the company beginning in the first quarter of 2023, with early adoption permitted. The Company is currently evaluating the expected impact of ASU 2016-13 on its financial statements.
Recently Adopted Accounting Pronouncements
In February 2016, the Financial Accounting Standards Board issued Accounting Standards Update 2016-02, “Leases (Topic 842)” (“ASC 842”) which requires lessees to recognize leases on the balance sheet and disclose key information about leasing arrangements. ASC 842 establishes a right-of-use model that requires a lessee to recognize a ROU asset and lease liability on the balance sheet for all leases with a term longer than 12 months. ASC 842 also requires disclosures to meet the objective of enabling users of financial statements to assess the amount, timing, and uncertainty of cash flows arising from leases. The standard was adopted on January 1, 2021, as the Company lost its status as an Emerging Growth Company effective December 31, 2021, and therefore was required to adopt the standard for the year ending December 31, 2021, using the modified retrospective method. Under this transition method, the Company recognized and measured leases that existed at the adoption date in the consolidated balance sheet as of January 1, 2021. In connection with the adoption of ASC 842, the Company elected the package of practical expedients requiring no reassessment of whether any expired or existing contracts contain leases, the lease classification of any expired or existing leases, or initial direct costs for any existing leases. The Company also made accounting policy elections not to apply the recognition requirements under ASC 842 to any short-term leases and to account for each separate lease and associated non-lease components as a single lease component for all the Company’s leases. The adoption of this new accounting standard resulted in increased qualitative and quantitative disclosures regarding the amount, timing, and uncertainty of cash flows arising from leases. For further details, see Note 7, Commitments and Contingencies. The adoption of the new standard did not materially impact the Company’s consolidated results of operations.
In May 2021, the FASB issued ASU No. 2021-04, Issuer’s Accounting for Certain Modifications or Exchanges for Freestanding Equity-Classified Written Call Options to clarify the accounting for modifications or exchanges of equity-classified warrants. The standard is effective for fiscal years beginning after December 15, 2021. Early adoption is permitted. The Company’s adoption of this accounting standard on January 1, 2022, did not have a material impact on the Company’s consolidated financial statements and related disclosures.
2. Net Loss Per Share
Basic net loss per share is calculated by dividing the net loss by the weighted-average number of common shares outstanding for the period. Diluted net loss per share is computed by dividing the net loss by the weighted average number of common shares and common share equivalents outstanding for the period. Common share equivalents are only included when their effect is dilutive. Pre-funded warrants from the Company’s follow-on offering have been treated as if they were common shares outstanding on the date of issuance. The Company’s potentially dilutive securities which include outstanding warrants to purchase stock and outstanding stock options under the Company’s equity incentive plans have been excluded from the computation of diluted net loss per share as they would be anti-dilutive to the net loss per share. Restricted stock is treated as outstanding for accounting purposes. For all periods presented, there is no difference in the number of shares used to calculate basic and diluted shares outstanding due to the Company’s net loss position.
Potentially dilutive securities not included in the calculation of diluted net loss per share attributable to common stockholders because to do so would be anti-dilutive are as follows (in common stock equivalent shares):
9

March 31,
2022
March 31,
2021
Stock options21,531,000 5,126,000 
Unvested restricted stock4,257,000 
Warrants4,356,000 4,411,000 
RSUs296,000  
PSUs290,000  
Total30,730,000 9,537,000 
3. Revenue Recognition
Revenue by Source
Three Months Ended March 31,
20222021
Instruments$1,596,000 $882,000 
Consumables1,520,000 1,167,000 
Total product revenue3,116,000 2,049,000 
Service and other2,580,000 1,119,000 
Total revenue$5,696,000 $3,168,000 

Revenue by Geographic Location
Three Months Ended March 31,
20222021
$%$%
Americas$3,328,000 58 %$1,498,000 47 %
EMEIA1,739,000 31 %1,587,000 50 %
Asia Pacific629,000 11 %83,000 3 %
Total$5,696,000 100 %$3,168,000 100 %
The table above provides revenue from contracts with customers by source and geographic region (based on the customer’s billing address) on a disaggregated basis. Americas consists of North America and South America. EMEIA consists of Europe, the Middle East, India and Africa. Asia Pacific includes China, Japan, South Korea, Singapore and Australia. For the three months ended March 31, 2022 and 2021, the United States represented 45.0% and 44.8% of total revenue, respectively. No other countries represented greater than 10% of revenue during the three months ended March 31, 2022 and 2021.
Remaining Performance Obligations
As of March 31, 2022, the estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied was approximately $1.2 million. These remaining performance obligations primarily relate to extended warranty and support and maintenance obligations. The Company expects to recognize approximately 75.8% of this amount as revenue during the remainder of 2022, 20.9% in 2023, and 3.3% in 2024 and thereafter. Warranty revenue is included in service and other revenue.
The Company recognized revenue of approximately $0.3 million and $0.2 million during the three months ended March 31, 2022 and 2021, respectively, which was included in the contract liability balance at the end of the previous year.
4. Balance Sheet Account Details
Accounts Receivable
March 31,
2022
December 31,
2021
Accounts receivable, net:
Accounts receivable, trade$5,977,000 $5,624,000 
Less allowance for doubtful accounts(463,000)(690,000)
$5,514,000 $4,934,000 
10

Inventory
The components of inventories are as follows:
 March 31,
2022
December 31,
2021
Inventory:
Raw materials$1,139,000 $745,000 
Finished goods15,129,000 11,642,000 
$16,268,000 $12,387,000 
Intangible Assets
Intangible assets that are subject to amortization consisted of the following for the periods presented:
March 31, 2022
December 31, 2021
Gross Carrying AmountAccumulated AmortizationNet Carrying AmountGross Carrying AmountAccumulated AmortizationNet Carrying Amount
Trade name$1,630,000 $(290,000)$1,340,000 $1,630,000 $(210,000)$1,420,000 
Customer relationships3,950,000 (576,000)3,374,000 3,950,000 (378,000)3,572,000 
Developed technology22,800,000 (2,090,000)20,710,000 22,800,000 (950,000)21,850,000 
Intangibles, net$28,380,000 $(2,956,000)$25,424,000 $28,380,000 $(1,538,000)$26,842,000 
Accrued Expenses
Accrued expenses consist of the following:
March 31,
2022
December 31,
2021
Compensation expenses$3,946,000 $4,529,000 
Goods received not invoiced1,238,000 1,073,000 
Customer deposits979,000 826,000 
Taxes payable685,000 677,000 
Insurance 389,000 1,011,000 
Professional fees and royalties218,000 288,000 
Warranty liabilities175,000 175,000 
Other1,306,000 1,115,000 
Total$8,936,000 $9,694,000 
5. Debt
Paycheck Protection Program
On April 17, 2020, the Company received the PPP Loan proceeds of approximately $1.8 million pursuant to the Paycheck Protection Program under the Coronavirus Aid, Relief, and Economic Security Act (the “CARES Act”) administered by the U.S. Small Business Administration (the “SBA”). In February 2021, the Company applied for forgiveness of the PPP Loan, and in March 2021, the PPP Loan, including all accrued interest, was forgiven in full. A gain on forgiveness of Paycheck Protection Program loan of $1.8 million was recognized during the three months ended March 31, 2021.
Innovatus Loan and Security Agreement
In May 2021, the outstanding term loan with Innovatus (“Innovatus LSA”) was paid in full, including all accrued interest, the end of term fee, and a prepayment fee for a total of approximately $17.0 million. Interest expense recognized during the three months ended March 31, 2021 totaled approximately $0.6 million.
6. Stockholders’ Equity and Stock-Based Compensation
Follow-on Public Offerings
On January 12, 2021 and January 25, 2021, the Company completed an underwritten public offering of 33.4 million and 38.3 million shares of common stock, respectively. The price to the public in the offerings on January 12, 2021 and January 15,
11

2021 was $3.05 and $6.00 per share, respectively. The net proceeds to the Company from the offerings, after deducting the underwriting discounts and commissions and other offering expenses, were $101.5 million and $229.6 million, respectively.
Shelf Registration Statements; Ladenburg and Cowen At-the-Market Facilities
In August 2020, the Company filed a shelf registration statement on Form S-3 with the SEC covering the offering, issuance and sale of up to $125 million of the Company’s securities, including up to $40 million of common stock, pursuant to an At Market Issuance Sales Agreement, with Ladenburg Thalmann & Co. Inc. acting as sales agent (the “Ladenburg ATM”). During October 2020 through January 2021, the Company sold approximately 27.0 million shares of common stock under the Ladenburg ATM and received net proceeds of $38.0 million after deducting aggregate offering costs. The Company terminated the Ladenburg ATM in March 2021.
On January 19, 2021, the Company filed an automatically effective shelf registration statement on Form S-3 with the SEC as a “well-known seasoned issuer,” allowing for the Company to issue an indeterminate number or amount of its securities from time to time in one or more offerings. On March 23, 2021, the Company entered into a Sales Agreement with Cowen and Company, LLC (“Cowen”) which provides for the sale, in the Company’s sole discretion, of shares of common stock having an aggregate offering price of up to $350.0 million through or to Cowen, acting as sales agent or principal (the “Cowen ATM”). The Company agreed to pay Cowen a commission of up to 3.0% of the aggregate gross proceeds from each sale of shares, reimburse legal fees and disbursements and provide Cowen with customary indemnification and contribution rights. In August and September 2021, the Company sold approximately 2.3 million shares of common stock under the Cowen ATM at an average share price of $6.15 per share, and received gross proceeds of approximately $13.9 million before deducting offering costs of $0.6 million. There were no sales of common stock under the Cowen ATM from January 1, 2022 to March 31, 2022.
Stock Warrants
A summary of the Company’s warrant activity during the three months ended March 31, 2022 was as follows:
Shares of Stock under WarrantsWeighted-
Average
Exercise
Price
Weighted-
Average
Remaining
Contractual
Term
Aggregate
Intrinsic
Value
Outstanding at January 1, 20224,356,000 $5.96 1.76$785,000 
Granted — — — 
Exercised  —  
Canceled  — — 
Outstanding at March 31, 2022
4,356,000 $5.96 1.76$785,000 
Stock Options
A summary of the Company’s stock option activity during the three months ended March 31, 2022 was as follows:   
Shares of Stock under Stock OptionsWeighted-
Average
Exercise
Price
Weighted-
Average
Remaining
Contractual
Term
Aggregate
Intrinsic
Value
Outstanding at January 1, 202212,765,000 $4.97 8.9$7,891,000 
Granted9,691,000 2.19 — — 
Exercised(21,000)0.79 — 32,000 
Canceled(904,000)5.73 — — 
Outstanding at March 31, 2022
21,531,000 $3.69 9.11$10,131,000 
Vested and exercisable at March 31, 2022
4,018,000 $3.66 7.88$3,972,000 
For the three months ended March 31, 2022, the weighted-average grant date fair value of stock options granted was $1.39 per share.
Stock-Based Compensation
The Company recognized stock-based compensation expense for the periods presented as follows: 
12

 Three Months Ended
March 31,
20222021
Research and development$3,328,000 $81,000 
General and administrative1,774,000 290,000 
Total stock-based compensation expense$5,102,000 $371,000 
The weighted-average assumptions used in the Black-Scholes option pricing model to determine the fair value of the employee stock option grants during the periods presented were as follows:
Three Months Ended
March 31,
20222021
Risk-free interest rate1.9 %0.7 %
Expected volatility70.1 %79.3 %
Expected term (in years)6.06.1
Expected dividend yield0.0 %0.0 %
Restricted Stock
Restricted Stock
A restricted stock award in the amount of 5.0 million shares with a grant date fair value of $5.20 a share was granted as part of the acquisition of BioDiscovery. One-third of the Restricted Shares will vest on October 18, 2022 and one-twelfth of the Restricted Shares shall vest every three months following October 18, 2022, subject to continuous service of a key employee. The weighted average remaining contractual term for the restricted stock is 2.6 years as of March 31, 2022. The fair value of the restricted stock award is based on the market value of common stock as of the date of grant and is amortized to expense over the respective vesting period or the service period.
Restricted Stock Units and Performance Stock Units
The following table summarizes restricted share unit (“RSU”) activity during the three months ended March 31, 2022:
Stock UnitsWeighted- Average Grant Date Fair Value per Share
Outstanding at January 1, 2022361,000 $4.74 
Granted
Released(65,000)4.74
Forfeited  
Outstanding at March 31, 2022
296,000$4.74
The total intrinsic value of the RSUs that vested was $0.3 million during the three months ended March 31, 2022, determined as of the date of vesting. The weighted average remaining contractual term for the RSUs is 1.1 years as of March 31, 2022.
The following table summarizes performance share unit (“PSU”) activity during the quarter ended March 31, 2022:
Stock UnitsWeighted- Average Grant Date Fair Value per Share
Outstanding at January 1, 2021290,000$4.74 
Granted
Released
Forfeited
Outstanding at March 31, 2022
290,000$4.74
The weighted average remaining contractual term for the PSUs is 3.1 years as of March 31, 2022.
13

Executive Option Grants
On February 15, 2022, the compensation committee of the Company’s board of directors granted various executive officers stock options to purchase an aggregate of 4.3 million shares of common stock at an exercise price of $2.18 a share, in each case with an effective grant date and vesting commencement date of February 15, 2022 (the “Grant Date”). These stock option grants were issued from the 2018 Stock Plan. The shares subject to the option shall vest monthly over 48 months beginning on the one-month anniversary of the Grant Date, such that the option shall be fully vested and exercisable on the four-year anniversary of the Grant Date.
7. Commitments and Contingencies
The Company discounts its lease payments using its incremental borrowing rate as of the commencement of the lease. The Company has determined a weighted-average discount rate of 7.1% as of March 31, 2022 and December 31, 2021.
The operating lease right-of-use asset and operating lease liability as of March 31, 2022 and December 31, 2021 are as follows:
March 31, 2022December 31, 2021
Operating lease right-of-use assets$6,817,000 $6,691,000 
Operating lease liability
Current1,730,0001,467,000
Non-current5,451,0005,288,000
Total operating lease liability$7,181,000 $6,755,000
For the three months ended March 31, 2022, the Company recorded $0.5 million in expense related to operating leases, including amortized tenant improvement allowances. For the three months ended March 31, 2021, the Company recorded $0.2 million in expense related to operating leases, including amortized tenant improvement allowances.
The finance lease right-of-use asset and finance lease liability as of March 31, 2022 and December 31, 2021 are as follows:
March 31, 2022December 31, 2021
Finance lease right-of-use assets$3,897,000 $3,926,000 
Finance lease liability
Current296,000299,000
Non-current3,638,0003,642,000
Total finance lease liability$3,934,000 $3,941,000
For the three months ended March 31, 2022, the Company recorded $0.1 million in expense related to its finance lease. The Company did not hold a finance lease as of March 31, 2021.
14

The future minimum payments under non-cancellable operating and finance leases as of March 31, 2022, are as follows:
Operating LeasesFinance Lease
Remainder of 2022$1,538,000 $236,000 
20232,149,000 322,000 
20242,219,000 330,000 
20252,305,000 338,000 
2026232,000 347,000 
Thereafter 5,949,000 
Total future lease payments8,443,000 7,522,000 
Less: imputed interest(1,262,000)(3,588,000)
Total lease liabilities$7,181,000 $3,934,000 
Litigation
From time to time, the Company may be subject to potential liabilities under various claims and legal actions that are pending or may be asserted. These matters arise in the ordinary course and conduct of the business. The Company regularly assesses contingencies to determine the degree of probability and range of possible loss for potential accrual in the financial statements. An estimated loss contingency is accrued in the financial statements if it is probable that a liability has been incurred and the amount of the loss can be reasonably estimated. Based on the Company’s assessment, it currently does not have any material loss exposure as it is not a defendant in any claims or legal actions.
Contingent Consideration
See Note 9 to our condensed consolidated financial statements for a discussion of the contingent consideration liability.
8. Acquisitions
BioDiscovery Acquisition
In October 2021, the Company completed the acquisition of BioDiscovery, LLC, for a combination of approximately $52.3 million in cash, $40.0 million in shares of Company common stock, and $10.0 million in cash payable based on the achievement of certain milestones. Of the $40.0 million in shares of Company common stock, approximately $26.0 million is subject to vesting based on continuous service. See Note 6 to our condensed consolidated financial statements for a discussion of the restricted stock vesting terms and accounting treatment.
The purchase price allocation for the acquisition of BioDiscovery is preliminary and subject to revision as additional information about the fair value of assets and liabilities becomes available. As permitted under ASC 805, the Company is allowed a measurement period, which may not exceed one year, in which to complete its accounting for the acquisition. During the first quarter of 2022, the Company recorded an increase to the value of acquired contract liabilities in the amount of $94,000, with the offset recorded to goodwill. The purchase price is still subject to adjustment for the final determination of deferred and current tax assets and liabilities.
The following is the purchase price for the acquisition of BioDiscovery:
Cash$52,291,000 
Estimated fair value of milestone consideration$9,000,000 
Return of cash to buyer from escrow$(694,000)
Shares of common stock issued as consideration2,723,000 
Stock price per share on closing date$5.20 
Value of estimated common stock consideration$14,159,000 
Total purchase price$74,756,000 
The total purchase price was allocated to BioDiscovery’s tangible and identifiable intangible assets acquired and liabilities assumed based on their estimated fair values as of the acquisition date, with the excess recorded as goodwill, as follows:
15

Cash and cash equivalents$3,205,000 
Accounts receivable1,782,000 
Right-of-use assets3,987,000 
Other assets213,000 
Intangible assets26,800,000 
Goodwill49,081,000 
Accounts payable and other accrued liabilities(193,000)
Right-of-use liabilities (short-term and long-term)(3,987,000)
Deferred tax liability(5,777,000)
Contract liabilities(355,000)
Net assets acquired$74,756,000 
The acquisition date fair values of identifiable intangible assets acquired are as follows:
Customer relationships$3,000,000 
Developed technology22,800,000 
Tradename1,000,000 
Fair value of identifiable intangible assets$26,800,000 
The Company uses the income approach to derive the fair value of the identified intangible assets acquired. This approach calculates fair value by estimating future cash flows attributable to the assets and then discounting these cash flows to a present value using a risk-adjusted discount rate.
The developed technology, customer relationships and trade name intangibles are both being amortized on a straight-line basis over their estimated useful lives of five years. Straight-line amortization was determined to be materially consistent with the pattern of expected use of the intangible assets.
As the Company began integrating BioDiscovery’s operations with its existing operations during the fourth quarter of 2021, it is not practical or meaningful to distinguish BioDiscovery’s expenses or net income or loss from that of the combined operations.
Pro forma Financial Information
The unaudited pro forma financial information in the table below summarizes the combined results of operations for the Company and BioDiscovery as if the companies had been combined as of the beginning of the year prior to the acquisition. These amounts have been calculated after applying the Company’s accounting policies and adjusting the results of BioDiscovery to reflect the additional amortization that would have been charged assuming the fair value adjustments to intangible assets had been applied at the beginning of the year prior to the acquisition. The following unaudited pro forma financial information is for informational purposes only and is not necessarily indicative of the results of operations that would have been achieved as if the acquisitions had taken place as of January 1, 2020.
 Three Months Ended March 31,
2021
Revenue$4,154,000 
Net loss(11,159,000)
Basic and diluted net loss per share
$(0.04)
9. Investments and Fair Value Measurements
The Company holds investment securities that consist of highly liquid, investment grade debt securities. The Company determines the fair value of its investment securities based upon one or more valuations reported by its investment accounting and reporting service provider. The investment service provider values the securities using a hierarchical security pricing model that relies primarily on valuations provided by an industry-recognized valuation service. Such valuations may be based on trade prices in active markets for identical assets or liabilities (Level 1 inputs) or valuation models using inputs that are observable either directly or indirectly (Level 2 inputs), such as quoted prices for similar assets or liabilities, yield curves, volatility factors, credit spreads, default rates, loss severity, current market and contractual prices for the underlying instruments or debt, and broker and dealer quotes, as well as other relevant economic measures.
16

The following table presents the Company’s financial assets and liabilities measured at fair value on a recurring basis as of March 31, 2022 and December 31, 2021:
March 31, 2022
Total Fair Value and Carrying Value on Balance SheetFair Value Measurement Category
Level 1Level 2Level 3
Assets:
Commercial Paper$75,642,000 $ $75,642,000 $ 
Corporate Notes/Bonds116,778,000  116,778,000  
Total Investments:$192,420,000 $ $192,420,000 $ 
Money Market Funds$7,700,000 $7,700,000 $ $ 
Liabilities:
Contingent consideration$9,145,000 $ $ $9,145,000 
December 31, 2021
Total Fair Value and Carrying Value on Balance SheetFair Value Measurement Category
Level 1Level 2Level 3
Assets:
Commercial Paper$100,860,000 $ $100,860,000 $ 
Corporate Notes/Bonds125,181,000  125,181,000  
Total Investments:$226,041,000 $ $226,041,000 $ 
Money Market Funds$11,126,000 $11,126,000 $ $ 
Liabilities:
Contingent consideration$9,066,000 $9,066,000 
Money Market Funds are classified as cash equivalents on the balance sheet. As of March 31, 2022 and December 31, 2021, the Company held 51 and 57 securities in an unrealized loss position, respectively. None of the Company’s available for sale investment securities were in a material unrealized loss position at March 31, 2022 or December 31, 2021. As such, the Company has not recognized any impairment in its financial statements related to its available for sale investment securities.
The fair value of the contingent consideration liability is reassessed on a quarterly basis using the income approach. Assumptions used to estimate the acquisition date fair value of the contingent consideration include the probability of achieving certain milestones and a discount rate of 3%. The fair value measurement of the contingent consideration is based on significant inputs not observed in the market (Level 3 inputs). The Company determined the fair value of the milestone consideration using a scenario-based technique, as the trigger for payment is event driven. The outcome of the milestone consideration is binary, meaning the milestone is either achieved or not achieved, and the only other variable factor is the timing of when the milestone is achieved. The Company determined it is highly likely that the milestone will be achieved and therefore used a 95% probability factor which is applied to the $10.0 million milestone consideration. The change in fair value of the contingent consideration during the three month period ended March 31, 2022 was due to the passage of time.
17

Changes in estimated fair value of contingent consideration liability in the three months ended March 31, 2022 is as follows:
Contingent
Consideration
Liability
(Level 3
Measurement)
Balance as of January 1, 2021$9,066,000 
Liability recorded as a result of current period acquisition 
Change in estimated fair value, recorded in selling, general and administrative expenses79,000.00 
Cash payments 
Balance as of March 31, 2022
$9,145,000 
As of March 31, 2022, the following table summarizes the amortized cost and the unrealized gains (losses) of the available for sale securities:
Commercial PaperCorporate Notes/Bonds
Amortized Cost
Unrealized gains (losses)
Amortized Cost
Unrealized gains (losses)
Less than 1 year$75,922,000 $(280,000)$54,179,000 $(370,000)
Due after one year through five years  63,956,000 (987,000)
Total$75,922,000 $(280,000)$118,135,000 $(1,357,000)
As of December 31, 2021, the following table summarizes the amortized cost and the unrealized gains (losses) of the available for sale securities:
Commercial PaperCorporate Notes/Bonds
Amortized Cost
Unrealized loss
Amortized Cost
Unrealized loss
Less than 1 year$100,929,000 $(69,000)$41,173,000 $(61,000)
Due after one year through five years  84,478,000 (409,000)
Total$100,929,000 $(69,000)$125,651,000 $(470,000)
Included in interest income for the three-month period ended March 31, 2022 was interest income related to the Company’s available for sale securities of $0.1 million. All available for sale securities are classified as current assets, even if the maturity when acquired by the Company is greater than one year due to the ability to liquidate within the next 12 months.
10. Related Party Transactions
Through the acquisition of BioDiscovery in October 2021, the Company inherited a building lease with a landlord owned by BioDiscovery’s former Director and Chief Executive Officer, who is now the Company’s Chief Informatics Officer. The Company recorded $0.1 million in finance lease costs related to this lease for the three-month period ended March 31, 2022.
ITEM 2. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS
The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our unaudited consolidated financial statements and related notes included in this Quarterly Report on Form 10-Q and the audited consolidated financial statements and notes thereto as of and for the year ended December 31, 2021 and the related Management’s Discussion and Analysis of Financial Condition and Results of Operations, both of which are contained in our Annual Report on Form 10-K, or our Annual Report, filed with the Securities and Exchange Commission, or the SEC, on March 1, 2022. Unless the context requires otherwise, references in this Quarterly Report on Form 10-Q to “we,” “us,” and “our” refer to Bionano Genomics, Inc. and its subsidiaries or, as the context may require, Bionano Genomics, Inc. only.
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Forward-Looking Statements
The information in this Quarterly Report on Form 10-Q contains forward-looking statements and information within the meaning of Section 27A of the Securities Act of 1933, as amended, or the Securities Act, and Section 21E of the Securities Exchange Act of 1934, as amended, or the Exchange Act, which are subject to the “safe harbor” created by those sections. These forward-looking statements include, but are not limited to any statements concerning the potential effects of the COVID-19 pandemic on our business, statements concerning our strategy, future operations, future financial position, future revenues, projected costs, prospects and plans and objectives of management. The words “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “will,” “would” and similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words. We may not actually achieve the plans, intentions, or expectations disclosed in our forward-looking statements and you should not place undue reliance on our forward-looking statements. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements that we make. These forward-looking statements involve risks and uncertainties that could cause our actual results to differ materially from those in the forward-looking statements, including, without limitation, the risks set forth in our filings with the SEC. The forward-looking statements are applicable only as of the date on which they are made, and we do not assume any obligation to update any forward-looking statements.
Overview
We are a provider of genome analysis solutions that can enable researchers and clinicians to reveal answers to challenging questions in biology and medicine. Our mission is to transform the way the world sees the genome through optical genome mapping, or OGM, solutions, diagnostic services and software. We offer OGM solutions for applications across basic, translational and clinical research. Through our Lineagen, Inc., or Lineagen, business, we also provide diagnostic testing for patients with clinical presentations consistent with autism spectrum disorder and other neurodevelopmental disabilities. Through our BioDiscovery, LLC, or BioDiscovery, business, we also offer an industry-leading, platform-agnostic software solution, which integrates next-generation sequencing and microarray data designed to provide analysis, visualization, interpretation and reporting of copy number variants, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view.
We have incurred losses in each year since our inception. Our net loss was $30.0 million and $9.9 million for the three months ended March 31, 2022, and 2021 respectively. As of March 31, 2022, we had an accumulated deficit of $246.1 million.
We expect to continue to incur significant expenses and operating losses as we:
expand our sales and marketing efforts to further commercialize our products;
continue research and development efforts to improve our existing products;
hire additional personnel;
enter into collaboration arrangements, if any;
add operational, financial and management information systems; and
incur increased costs as a result of operating as a public company.
Recent Highlights
Commercial Adoption of Offerings for Saphyr
In executing on our commercialization strategy, we expanded the utilization of our Saphyr® system and:
Grew our installed base to 176 as of March 31, 2022, an increase of approximately 64% from a total installed base of 107 as of March 31, 2021. Installed base represents the global number of Saphyr instruments installed at end-customer locations and therefore having the technology to process OGM.
Sold 3,225 flowcells in the three-month period ended March 31, 2022, an increase of approximately 24% over the 2,603 flowcells sold during the same quarter of 2021. The Sa