BNGO 10-K & 10-Q changes, risk factors and insider trading

Investing in our common stock involves a high degree of risk. You should consider and read carefully all of the risks and uncertainties described below, as well as other information included in this Annual Report, including our financial statements and related notes appearing below, and our other filings with the SEC, before making investment decisions regarding our securities. The occurrence of any of the following risks could harm our business, financial condition, results of operations and/or growth prospects or cause our actual results to differ materially from those contained in forward-looking statements we have made in this report and those we may make from time to time. The risks described below are not the only risks facing our company. Additional risks and uncertainties not currently known to us or that we currently deem to be immaterial also may materially adversely affect our business, financial condition or future results. In such case, the trading price of our securities could decline. This Annual Report also contains forward-looking statements and estimates that involve risks and uncertainties. Our actual results could differ materially from those anticipated in the forward-looking statements as a result of specific factors, including the risks and uncertainties described below. Please see the section titled “Forward-Looking Statements.”

Our recurring losses, negative cash flows and significant accumulated deficit have raised substantial doubt regarding our ability to continue as a going concern. We will need to raise additional capital, which may not be available on acceptable terms, if at all, to fund our existing operations. If we are unable to raise sufficient additional capital in the very near term, we willmay be required to further curtail our operations, liquidate or otherwise dispose of assets, wind-down or cease operations entirely. In these circumstances, investors may not receive full value, or any value, for their investment.

Since inception, we have experienced recurring operating losses and negative cash flows from operating activities, and have significant accumulated deficit. We expect to continue to generate operating losses and consume significant cash resources for the foreseeable future. We believe that with receipt of the net proceeds from our registered direct offerings in April 2024 from the April Registered Direct Offering,2024, July 2024 from the July 2024 Offering,2024, October 2024 and January 2025, from theour OctoberSeptember 20242025 Offering, January 2025 from theour JanuaryATM 2025 OfferingAgreement and May 2024 from the transaction pursuant to that certain securities purchase agreement dated May 24, 2024 and amended on December 31, 2024, between us and certain accredited investors and JGB Collateral LLC, as collateral agent for the investors (the “JGB Purchase Agreement”) and the restructuring of redemption terms for our debt instruments in January 2025, together with the Company’s existing cash and, cash equivalents and short-term investments, and after taking into account inaccessible “restricted cash” under the terms of the transaction under the JGB Purchase Agreement, based on the Company’s current business plans we will be able to fund our operating expenses and capital expenditure requirements into the first quarter of 2026.2027. See Note 9 and 10 (Debt and Stockholders’ Equity and Stock-Based Compensation) in the accompanying notes to our consolidated financial statements included elsewhere in this Annual Report for a further discussion of our recent debt and equity financings. Our existing cash and cash equivalents and short-term investments will not be sufficient for us to achieve cash-flow break even and we expect to need to seek additional capital based on favorable market conditions or strategic considerations alternatives in the future. Without additional financing, these conditions raise substantial doubt about our ability to continue as a going concern, meaning that we may be unable to continue operations for the foreseeable future or realize assets and discharge liabilities in the ordinary course of operations. As a result, our financial statements include an explanatory paragraph expressing substantial doubt about our ability to continue as a going concern. We will continue to seek to raise additional capital, but without sufficient additional financing in the near term we will not be able to continue as a going concern, we may have to reorganize or liquidate our business and may receive less than the value at which those assets are carried on our consolidated financial statements, further curtail planned operations or cease operations entirely and wind down our business. Any of these could materially and adversely affect our liquidity, financial condition and business prospects and, as a result, our investors may lose all or a part of their investment. In light of our existing cash and cash equivalents and our current obligations, such a liquidation or disposition process may occur subject to bankruptcy protections, which may further reduce the value that we may receive for our assets. If we seek additional financing to fund our business activities in the future and there remains doubt about our ability to continue as a going concern, investors or other financing sources may be unwilling to provide additional funding on commercially reasonable terms or at all. TheFrom time to time, the board of directors has establishedmaintains a strategy committee to work with the Company and outside advisors in evaluating our options and considering alternatives that we believe will maximize stakeholder value, including any of the following or a combination thereof: debt financing, equity investments, combinations with other companies, or the sale of all or part of the company.Company. There can be no assurances that any transactions will be available to us or completed and if we are not able to raise sufficient additional capital in the near term to fund our operations, we may seek relief available under applicable insolvency laws. We do not intend to make further announcements regarding this process unless and until the board of directors approves a specific transaction or otherwise determines that further disclosure is appropriate.

Our corporate cost saving initiatives and the associated headcount reductions we announced in May 2023, October 2023, March 2024,2023 and September 2024 could disrupt our business, and may not achieve our intended objectives.

In May 2023, October 2023, March 2024,2023 and September 2024, we undertook a series of cost saving initiatives intended to decrease expenses and maintain a streamlined organization to support key programs and customers, and that are expected to conserve cash. These initiatives primarily related to the Company’s efforts on the current installed base of OGM systems with less emphasis on new placements of OGM systems and more emphasis on ensuring customers are able to maximize their utilization of the OGM systems and included a reduction in force. These initiatives may be disruptive to our operations and there is no guarantee that they will achieve the intended benefits. For example, our headcount reductions could yield unanticipated consequences and costs, such as increased difficulties in implementing our business strategy due to the loss of institutional knowledge and expertise, reduced strength of our sales force and marketing efforts, attrition beyond the intended number of employees, decreased morale among our remaining employees, and the risk that we may not achieve the anticipated benefits of the reduction in force. In addition, while certain positions have been eliminated, certain functions necessary to our operations remain, and we may be unsuccessful in distributing the duties and obligations of departed employees among our remaining employees. The reduction in workforce could also make it difficult for us to pursue, or prevent us from pursuing, new opportunities and initiatives, including restricting the strength of our sales force and marketing efforts, due to insufficient personnel, or require us to incur additional and unanticipated costs to hire new personnel to pursue such opportunities or initiatives. Moreover, any employee litigation related to the headcount reductions could be costly and prevent management from fully concentrating on the business. In addition, Bionano Laboratories’ phase out of the offering of certain testing services related to neurodevelopmental disorders (“NDDs”), including autism spectrum disorders (“ASDs”), and other disorders of childhood development effective as of December 31, 2024 could have a negative impact on our cash flow, financial conditions or results of operations. In 2023, these products generated approximately $7.0 million of our overall $36.1 million in revenues. The revenue from these products in 2024 was immaterial, and there was no revenue from these products in 2025. Further, our reduction in personnel through these headcount reductions and voluntary attrition could limit our ability to segregate responsibility for certain accounting and related treasury functions within our organization.

Our future financial performance and our ability to develop our product candidates or additional assets will depend, in part, on our ability to effectively manage future growth or restructuring, as the case may be. In addition, if we are unable to realize the anticipated benefits from our cost saving initiatives including those we discussed under “Part II. Item 7. Management’s Discussion and Analysis of Operations – Liquidity and Capital Resources”,initiatives, or if we experience significant adverse consequences of such initiatives, our business, financial condition, and results of operations may be materially adversely affected.

We are an early commercial-stage company and have a limited commercial history. Our limited commercial history may make it difficult to evaluate our current business and, especially when combined with the other risk factors listed in this section, makes predictions about our future success or viability subject to significant uncertainty. For example, in recentpast years we significantly grew our headcount through acquisitions of other businesses and, the expansion of our sales, marketing and research and development teams, and, more recently, have undertaken several rounds of reductions to our work force and the discontinuation of certain product offerings, all of which have resulted in significant fluctuations in our operating costs in a manner not historically reflected in our consolidated financial statements. Because our business model has evolved over time and may continue to evolve, this has impacted the composition and concentration of our revenues, and which may continue to change in the future. These changes in revenue and expenses, among others, may make it difficult to evaluate our current business, assess our future performance relative to prior performance and accurately predict our future performance. We have encountered in the past, and will continue to encounter in the future, risks and difficulties frequently experienced by early commercial-stage companies, including those associated with scaling up our infrastructure, increasing and decreasing the size of our organization, integrating acquired businesses and implementing cost saving initiatives. If we do not address these risks successfully, or if our assumptions regarding these risks and uncertainties are incorrect or change over time, our results of operations could differ materially from our expectations and our business, financial condition and results of operations could be materially and adversely affected.

•adoption of our OGM solutions onand our OGM systems, Ionic® Purification system or successor systems;

•the rate of utilization of consumables by our customers;

•reductions in or other difficulties relating to staffing, capacity, shutdowns or slowdowns of laboratories and other institutions in our customer base, such as reduced or delayed investment in new technologies or spending on products, technologies or consumables;

•differences in purchasing patterns across our customer base, including potential differences in consumables spending between earlier adopters of our technologies and more recent customers and variances in rates of increase of consumables spending following new technology purchases;

•geopolitical and macroeconomic developments, such as theinternational conflict between Ukraine and Russia and related sanctions, conflicts in the Middle East,conflicts, potential future disruptions in access to bank deposits or lending commitments due to bank failures, global pandemics, inflation, increased cost of goods, supply chain issues, international trade policies (including trade protection measures, such as tariffs, sanctions and other trade barriers), changes in monetary and fiscal policy, United States political developments and global financial market conditions;

•our ability to successfully integrate new personnel, technology and other assets that we may acquire into our company;

•any cost saving and restructuring initiatives and our ability to successfully maintain our business operations and customer support at historic levels;

•the timing of the introduction of new systems, products, technologies, system and product enhancements and services;

•changes in governmental funding of life sciences research and development or other changes that impact budgets, budget cycles or seasonal or other spending patterns of our customers;

•future accounting pronouncements or changes in our accounting policies; and the outcome of any current or future litigation or governmental investigations involving us or other third parties with whom we do business.

We may not achieve substantial growth rates in future periods. In particular as part of our cost saving plans we have also made a change in itsour business strategy and refocused our efforts on the current installed base of OGM systems with less emphasis on new placements of OGM systems and more emphasis on ensuring customers are able to maximize their utilization of the OGM systems. Investors should not rely on our operating results for any prior periods as an indication of our future operating performance. To effectively manage any future growth, we must continue to maintain and enhance our financial, accounting, manufacturing, customer support and sales administration systems, processes and controls, and to integrate such systems, processes and controls into our acquired businesses. Failure to effectively manage any future growth could lead us to over-invest or under-invest in development, operational and administrative infrastructure; result in weaknesses in our infrastructure, systems, or controls; give rise to operational mistakes, losses, loss of customers, productivity or business opportunities; and result in loss of employees and reduced productivity of remaining employees.

Any continued growth is likely to require significant capital expenditures and might divert financial resources from other projects such as the development or integration of new products, technologies and services. As additional products and technologies are commercialized, we may need to incorporate new equipment, implement new technology systems, or hire new personnel with different qualifications. Failure to manage this growth or transition could result in turnaround time delays, higher product costs, declining product quality, deteriorating customer service, and slower responses to competitive challenges. A failure in any one of these areas could make it difficult for us to meet market expectations for our products and technologies, and could damage our reputation and the prospects for our business.

Our future capital needs are uncertainuncertain, and we will require additional funding in the future to advance the commercialization of our OGM systems, Ionic® Purification system, VIA™ software, and our other products, technologies and services, as well as continue our research and development efforts. If we fail to obtain sufficient additional funding, we will be forced to delay, reduce or eliminate significant portions of our commercialization and development efforts which could negatively impact our revenue opportunities.

•maintain and expand our sales and marketing efforts to further commercialize our products, technologies and services and address competitive developments;

•maintain and expand our research and development efforts to improve our existing products, technologies and services and develop and launch new products, technologies and services, particularly if any of our products, technologies and services are deemed by the FDA to be medical devices or otherwise subject to additional regulation by the FDA;

•pursue a regulatory path with the FDA, or a regulatory body outside the United States, to market our existing RUO products or new products utilized for diagnostic purposes;

•lease additional facilities or build-out existing facilities to grow our inventory and research and development;

•further expand our operations within or outside the United States;

•enter into collaboration arrangements, if any, or in-license products and technologies;

•acquire or invest in complementary businesses or assets; and add operational, financial and management information systems.

•the cost of integrating our acquired businesses or of acquiring future businesses;

•market acceptance of our products, technologies and services, and the variability in costs to achieve such acceptance;

•the cost and timing of establishing additional sales, marketing and distribution capabilities;

•the cost of our research and development activities;

•our ability to satisfy any outstanding or future debt obligations;

•high interest rates;

•supply chain disruptions;

•the success of our existing distribution and marketing arrangements and our ability to enter into additional arrangements in the future;

•the effects of geopolitical or macroeconomic developments, such as the ongoing military conflicts between Russia and Ukraine and in the Middle East, and relatedincluding sanctions, recent and, potential future disruptions in access to bank deposits or lending commitments due to bank failuresfailures, international trade policies (including trade protection measures, such as tariffs, sanctions and other trade barriers), changes in monetary and fiscal policy, United States political developments and global pandemics; and the effect of competing technological and market developments.

As of December 31, 2024,2025, we had $9.2$3.0 million in cash and cash equivalents, $0.3$16.3 million in short-term investments, and $11.4$10.3 million in restricted cash and cash equivalents and restricted short-term investments.

We received net proceeds of approximately $9.3 million after deducting placement agent fees and offering expenses, from the issuance and sale of our securities in thean April 2024 Registeredregistered Directdirect Offeringoffering; net proceeds of approximately $9.3 million after deducting placement agent fees and offering expenses, from the issuance and sale of our securities in thea July 2024 Offeringregistered direct offering; net proceeds of approximately $2.7 million after deducting placement agent fees and offering expenses, from the issuance and sale of our securities in thean October 2024 Offeringregistered direct offering and net proceeds of approximately $9.3 million after deducting placement agent fees and offering expenses, from the issuance and sale of our securities in a January 2025 registered direct offering, and net proceeds of approximately $9.2 million after deducting placement agent fees and offering expenses, from the Januaryissuance and sale of our securities in a September 2025 Offering. Based on our current business plans, we believe the net proceeds from such financings together with our existing cash and cash equivalents and short-term investments, and after taking into account inaccessible “restricted cash and restricted investments” under the terms of the JGB Purchase AgreementAgreement, and that certain settlement and amendment, dated December 31, 2024, with certain accredited investors and JGB (the “Debentures Amendment”), will be sufficient to fund our operating expenses and capital expenditure requirements into at least the first quarter of 2026.2027. Nevertheless, our existing cash and cash equivalents and short-term investments, will not be sufficient for us to achieve cash-flow break even and we expect to need to seek additional capital in the near future.

Global economic conditions have been challenging, with disruptions to, and volatility in, the credit and financial markets in the U.S. and worldwide resulting from the effects of ongoing geopolitical or macroeconomic developments. If these conditions persist or worsen, we could experience an inability to access additional capital. If we do not have, or are not able to obtain, sufficient funds, we will have to delay, reduce or eliminate significant portions of our development and commercialization efforts related to our technologies and products, any of which could, among other things, negatively impact our revenue opportunities. For example, in September 2024, we decided to focus our efforts on the current installed base of OGM systems with less emphasis on new placements of OGM systems and more emphasis on ensuring customers are able to maximize their utilization of the OGM systems. As a result, we anticipatemay experience a reduction in our future product revenue. Bionano Laboratories’ phase out of the offering of certain testing services related to OGM-Dx, NDDs, including ASDs, and other disorders of childhood development could also have a negative impact on our cash flow, financial conditions or results of operations. We also may have to further reduce marketing, customer support or other resources devoted to our products or technologies or cease operations entirely. Any of these factors could have a material adverse effect on our financial condition, operating results and business. Any of the foregoing could significantly harm our business, prospects, financial condition and results of operation and could cause the price of our securities to decline. Any additional fundraising efforts may divert our management from their day-to-day activities, which may adversely affect our ability to conduct our strategic operations.

Our results of operations could be adversely affected by general conditions in the global economy, the global financial markets and adverse geopolitical and macroeconomic developments, including without limitation inflation, potential future disruptions in access to bank deposits or lending commitments due to bank failures, slowing growth, risinghigh interest rates and recessionthe risk of a recession, international conflicts, and theinternational conflictstrade betweenpolicies Ukraine(including trade protection measures, such as tariffs, sanctions and Russiaother trade barriers), changes in monetary and infiscal thepolicy, MiddleUnited East.States political developments and other sources of instability. A severe or prolonged global economic downturn could result in a variety of risks to our business. For example, although inflation rates have been recently declining, particularly in the United States, they remain at elevated levels notcompared seento inthe recent years. Continuing high inflation rates may result in decreased demand for our products and services, increases in our operating costs (including our labor costs), prolonged unemployment, reduced liquidity and has limited and may continue to limit our ability to access credit or otherwise raise capital on acceptable terms, if at all. Risks of a prolonged economic downturn are particularly true in Europe, which is undergoing a continued severe economic crisis. A weak or declining economy, regardless of the reason for the decline, could also strain our suppliers, possibly resulting in supply disruption. For example, higher energy prices in Europe are causing an increase in cloud computing expenses, which impacts the cost for us and our partners. Any actual or perceived disruption in our product distribution channel could alter customer buying decisions, prompting customers to delay or cancel their orders, which would negatively impact our sales revenue and could harm our reputation.

As of December 31, 2024,2025, we had federal and state tax net operating loss carryforwards of $488.3$531.2 million and $195.0$199.9 million, respectively. The federal tax loss carryforwards include $446.7$489.6 million that do not expire, but utilization of such tax loss carryforwards is limited to 80% of our taxable income. The remaining federal tax loss carryforwards of $41.6 million begin to expire in 2027 unless previously utilized.2027. Our state tax loss carryforwards began to expire in 20242026 and will continue to expire unless previously utilized.expire. As of December 31, 2024,2025, we also had federal and California research credit carryforwards of $7.1$7.3 million and $10.2$10.6 million, respectively. The federal research credit carryforwards begin to expire in 2027 unless previously utilized.2027. The California research credits carry forward indefinitely.

You should read theThe following discussion and analysis of our financial condition and results of operations togethershould be read in conjunction with our consolidated financial statements and the related notes included elsewhere in this Annual Report. All dollar amounts and share counts presented below have been rounded to the nearest thousand and, thus are approximate. Some of the information contained in this discussion and analysis or set forth elsewhere in this Annual Report, including information with respect to our plans and strategy for our business and expected financial results, includes forward-looking statements that involve risks and uncertainties. You should review the section titled “Forward-Looking Statements” and the risks described in Part I, Item 1A Risk Factors and elsewhere in this Annual Report.

We expect to see OGM adoption in cytogenomics, in discovery research and in cell bioprocessingand qualitygene controltherapy (“QC”).applications. Within cytogenetics and molecular pathology, we estimate thethat numberthere ofare approximately 10,000 cytogenetic labs on a worldwide basis (excluding India and developing countries) to be approximately 10,000.. We estimate that these labs analyze approximately 10.0 million samples per year. Additionally, we estimate thethat numberapproximately of1,400 pharmaceutical and biotech companies that are engaged in research and development of various cell therapies that rely on methods, including cytogenetics, for QC of the cell modification and manufacturing process to be approximately 1,400.cytogenetics. Based on these estimates, we believe the economic potential for OGM in these markets is approximately $10.0 billion annually, $3.0 billion of which we attribute to cell bioprocessingand QC.gene therapy applications. We believe there are additional potential future market opportunities for OGM to streamline workflows, reduce the number of technologies required to deliver results, lower costs, and improve findings in the broader pathology market across multiple subdisciplines including newborn screening, population genomics, and neurological and cardiological risk assessment which are not included in our estimates above. Additionally, we believe the market for our platform-agnostic software solution, which can be used in next-generation sequencing and microarray data analysis, includes the clinical NGS market which The Business Research Company has estimated toat beapproximately $3.4$4.1 billion in 20242025 and growingpredicted atwould grow to approximately $8.2 billion in 2029, representing a 20% compound annual growth rate.rate of 18.8%.

We are subject to additional risks and uncertainties as a result of adverse geopolitical and macroeconomic developments, such as recent and potential future bank failures, the ongoing conflictsinternational between Ukraine and Russia and in the Middle East,conflicts, related sanctions, and any effects of global pandemics and uncertain market conditions, including inflation and supply chain disruptions, which,and international trade policies (including trade protection measures, such as tariffs, sanctions and other trade barriers), changes in monetary and fiscal policy, United States political developments and other sources of instability, which have not had a material impact on our business and financial results to date, but could result in a material impact to our business or financial results in the future. Additionally, we have experienced a slowdown in our Asia Pacific business, including as a result of headwinds in the region, which negatively impacted our manufacturing partners who are reliant on government funding. While our manufacturing partners in the Asia Pacific region have obtained some approvals from the National Medical Products Administration, and are waiting on more, we do not anticipate that the funding headwinds will change in the near term.

We generate product revenue from sales of our OGM and Ionic® Purification systems and consumables, which includes our instruments, and our VIA™ software. At the end of July 2023 we began installations of VIA™ software asis aour replacement to our NxClinical software. Like NxClinical, VIA has a simple integrated workflow for visualization, interpretation and reporting of NGS and microarray data. VIA additionally incorporates OGM data to that workflow creating a standard software tool for use across molecular pathology and cytogenomics applications. We currently sell our systems for research use only applications and our customers are primarily laboratories associated with academic and governmental research institutions, academic and commercial clinical laboratories, as well as pharmaceutical, biotechnology and contract research companies. In addition, we provide instruments to certain customers at no cost under our reagent rental program, and the customers agree to purchase minimum quantities of consumables. Consumable revenue consists of sales of reagents and chips necessary to process a sample. Sales of our VIA™ software, which provides customers with solutions for analysis, interpretation and reporting of genomics data, are made on a subscription basis. We generate service revenue from the sale of diagnostic testing services through Bionano Laboratories, as well as services performed related to customer sample evaluations using an OGM system. Other revenue consists of warranty and other service-based revenue, including support, repair and maintenance services.

The following table reflects total revenue by geography and as a percentage of total revenue, based on the billing address of our customers. Americas consists of North America and South America. EMEA consists of Europe, the Middle East and Africa. Asia Pacific includes China, Japan, South Korea, Singapore, AustraliaIndia and India.Australia.

Research and development expenses consist of salaries and other personnel costs, stock-based compensation, research supplies, third-party development costs for new products, materials for prototypes, equipment depreciation, and allocated overhead costs that include facility and other overhead costs. We have made substantial investments in research and development since our inception, and plan to continue to make investments in the future.inception. Our research and development efforts have focused primarily on the tasks required to support development and commercialization of existing products. We believe that our continued investment in research and development is essential to our long-term competitive position.

The following table sets forth our resultsComparison of operations for the yearsYears endedEnded December 31, 20242025 and 2023:2024

Total revenue decreased $5.3by $2.3 million, or 15%7%, to $30.8$28.5 million for the year ended December 31, 2024,2025, as compared to $36.1$30.8 million for the same period in 2023,2024, driven primarily by a decrease in service and other revenue.

Instrument revenue decreased $2.0by $1.7 million, or 20%,21%, to $6.4 million for the year ended December 31, 2025, as compared to $8.0 million for the year ended December 31, 2024, as compared to $10.0 million for the year ended December 31, 2023, due to a decrease in the number of OGM and Ionic® instruments sold. For the year ended December 31, 2024,2025, our installed base grew to 371387 OGM systems compared to the 326371 OGM systems for the year ended December 31, 2023,2024, which only represented a 14%4% increase year-over-year as compared to a 36%14% year-over-year increase in the prior year. In September 2024, we announced a change in our business strategy to focus on driving utilization and adoption of OGM from our existing installed base, with less emphasis on new placements of our OGM systems. We anticipatedexpected that this change in strategy would slow the pace of our instrument revenue growth when compared to historical growth ratesrates, and we anticipate that the reduced pace of our revenue growth will continue into 2025.2026.

Software revenue increased $0.6by $0.2 million, or 11%,4%, to $6.4 million for the year ended December 31, 2025, as compared to $6.2 million for the year ended December 31, 2024, as compared to $5.6 million for the year ended December 31, 2023.2024. The increase is primarily attributed to an increase in salesthe number of ourVIA VIA™software software.licenses sold.

Service and other revenue decreased $5.6by $2.0 million, or 60%,53%, to $1.8 million for the year ended December 31, 2025, as compared to $3.8 million for the year ended December 31, 2024,2024. asThe compareddecrease was primarily due to $9.4 million for the year ended December 31, 2023, which is the result of discontinuing salesdiscontinuation of certain clinical service offerings from Bionano Laboratories effective March 2024. SuchThese clinical service offerings from Bionano Laboratories contributed $1.7 million in revenue for the year ended December 31, 2024, as compared to $7.1 million for the same period in 2023. We expect service2024 and other revenue to decline in 2025 relative to 2024 as these service offerings have beenwere fully phased outout. asNo ofcomparable Decemberrevenue 31,was 2024.recorded in 2025.

Cost of service and other revenue decreased $4.2$1.1 million, or 68%,54%, to $0.9 million for the year ended December 31, 2025, compared to $1.9 million for the year ended December 31, 2024, compared to $6.1 million for the year ended December 31, 2023.2024. The decrease in cost of service and other revenue was primarily due to discontinuingthe salesdiscontinuation of certain clinical service offerings from Bionano Laboratories effective March 2024. WeThese expectservices cost of service and other revenue to remain relatively flat in 2025 as these service offerings have beenwere fully phased out as ofby December 31, 2024.2024 and no comparable costs were incurred in 2025.

Research and Development (“R&D”) Expenses

Research and development (“R&D”) expenses decreased by $29.2$13.4 million, or 54%, to $24.8$11.4 million for the year ended December 31, 2024,2025, as compared to $54.0$24.8 million for the same period in 2023.2024. The decrease was partiallyprimarily due to decreases of $16.1$8.7 million in salaries, wages and benefits driven by headcount reductions announced throughout 2023 andin 2024 and $7.7a decrease of $2.2 million in professional and consulting fees, including decreases in costs incurred to support clinical research studies, development of the Stratys™ development,system, foundry expenses, and cloud computing. Lastly, in 2025 we reduced internal consumption of inventory, materials and supplies by $1.6 million and we reduced information technology and rent and facility costs by $0.8 million, and we reduced our internal consumption of inventory, materials and supplies by $4.2$0.3 million. We anticipate that R&D expenses will continue to decrease throughout 2025 as a result of our cost saving initiatives announced in March and September 2024.

Selling, General and Administrative (“SG&A”) Expenses

Selling, general and administrative (“SG&A”) expenses decreased $40.9by $16.7 million, or 44%,32%, to $51.9$35.2 million for the year ended December 31, 2024,2025, as compared to $92.8$51.9 million for the same period in 2023.2024. The decrease was primarily due to a $21.0$12.6 million decrease in salaries, wages and benefits driven by headcount reductions announced in 2023 and 2024,2024; a $9.4 million decrease in the gain/loss recorded on fair value of the contingent consideration due for Purigen and BioDiscovery milestones, a $8.9$8.7 million decrease in professional and consulting fees which is primarily marketing, software, and legal expenses,expenses; a $1.3 million decrease in information technology and rent and facility costs; a $2.6$1.4 million decrease in depreciation and amortization; a $2.5 million decrease in the losses on disposal of property and equipment recorded; a $0.9 million decrease in travel and entertainment.entertainment; Weand anticipatea that$0.4 SG&Amillion expenseschange willin continuethe gain on lease modification. These decreases were offset by a $10.9 million gain recorded on the fair value of the contingent consideration due for the Purigen milestones during the same period in 2024 as compared to decreaseno throughoutgain 2025recorded asfor athe resultyear ofended ourDecember cost31, saving initiatives announced in March and September 2024.2025.

The Company recognized $19.7 million inno impairment losses on intangible assets and other long-lived assets during the year ended December 31, 2025, as compared to $19.7 million for the same period in 2024. These 2024 losses were due to our restructuring initiatives and change in business strategy.strategy Theannounced Companyin recognized no additional impairment losses during the year ended December 31, 2023.2024. See Note 2 (Summary of Significant Accounting Policies) to our condensed consolidated financial statements included elsewhere in this Annual Report for further discussion on the impairment charges that were recorded during the period.

Interest income decreased by $1.2$1.0 million, or 37%,47%, to $2.1$1.1 million for the year ended December 31, 2024,2025, as compared to $3.3$2.1 million for the same period in 20232024 resulting from a reduction in investments offset by higher returns. Our total short-term investments balance was $0.3 million as of December 31, 2024, as compared to $48.8 million for the same period in 2023.

Other expensesIncome (Expense)

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our unaudited condensed consolidated financial statements and related notes included in this Quarterly Report on Form 10-Q for the three and six months ended MarchJune 31,30, 2026 (this “Quarterly Report”) and the audited consolidated financial statements and notes thereto as of and for the year ended December 31, 2025 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 for the year ended December 31, 2025 (“Annual Report”), filed with the Securities and Exchange Commission (“SEC”) on March 23, 2026. Unless the context requires otherwise, references in this Quarterly Report to “we,” “us,” and “our” refer to Bionano Genomics, Inc. and its subsidiaries or, as the context may require, Bionano Genomics, Inc. only. “Lineagen” (doing business as “Bionano Laboratories”), “BioDiscovery” and “Purigen” refer to our wholly owned subsidiaries, Lineagen, Inc., BioDiscovery, LLC and Purigen Biosystems, Inc., respectively.

Grew our installed base to 399397 as of MarchJune 31,30, 2026, an increase of approximately 5% from a total installed base of 379378 as of MarchJune 31,30, 2025. Installed base represents the global number of OGM instruments installed at end-customer locations and therefore having the technology to process OGM.

Sold 8,1789,219 flowcells in the three-month period ended MarchJune 31,30, 2026, an increase of approximately 17%27 % from 6,9947,233 flowcells sold in the same period of 2025. Sold 17,397 flowcells in the six-month period ended June 30, 2026, an increase of approximately 22% from 14,227 flowcells sold in the same period of 2025. The OGM cartridge is the consumable that packages nanochannel arrays for DNA linearization. In its current form, the OGM cartridge can comprise one, twoone or three flowcells per cartridge. Flowcells sold refers to the units of genome mapping consumables used for analyzing one genome, purchased by customers to process samples for optical genome mapping.

We are subject to additional risks and uncertainties as a result of adverse geopolitical and macroeconomic developments, such as recent and potential future bank failures, ongoing international conflicts, related sanctions, any effects of global pandemics and uncertain market conditions, including inflation and supply chain disruptions, and international trade policies (including trade protection measures, such as tariffs, sanctions and other trade barriers), changes in monetary and fiscal policy, United States political developments and other sources of instability, which have not had a material impact on our business and financial results to date, but could result in a material impact to our business or financial results in the future. Additionally,Also, we have seen, and expect to continue to see, an impact on our costs due to higher computing component costs, specifically memory, which may result in material cost pressures and supply constraints in future periods. Additionally, for the three months ended June 30, 2026, we experienced aslower slowdowngrowth in our Asia Pacific business, including as a result of headwinds in the region,region. which negatively impacted our manufacturing partners who are reliant on government funding. While our manufacturing partners in the Asia Pacific region have obtained some approvals from the National Medical Products Administration, and are waiting on more, weWe do not anticipate that the fundingthese headwinds will change in the near term.

We closely monitor and comply with various applicable guidelines and legal requirements in the jurisdictions in which we operate. In the past, we have experienced supply chain challenges, attributable to such adverse geopolitical and macroeconomic developments including increased costs to secure certain component parts in our products and to produce our products at our contract manufacturers. During the threesix months ended MarchJune 31,30, 2026, we did not experience overall material increases in our supply chain costs, but we have and may continue to experience increases in our computing component costs, specifically memory, and may experience such increases in future fiscal periods.periods for other parts of our business as well. We expect our costs to remain high for the foreseeable future. As global economic conditions recover,continue to be volatile, business activity may not recovergrow as quickly as anticipated, and it is not possible at this time to estimate the long-term impact that these and related events could have on our business, as the impact will depend on future developments, which are highly uncertain and cannot be predicted. For instance, product demand may be reduced due to an economic recession, a decrease in corporate capital expenditures, prolonged unemployment, high inflation rates, labor shortages, reduction in consumer confidence, adverse geopolitical and macroeconomic developments, or any similar negative economic condition. These negative effects could have a material impact on our operations, business, earnings, and liquidity.

We generate product revenue from sales of our OGM and Ionic® Purification systems and consumables, which includes our instruments, and our VIA™ software. VIA software is our replacement to our NxClinical software. Like NxClinical, VIA has a simple integrated workflow for visualization, interpretation and reporting of NGS andNGS, microarray data. VIA additionally incorporatesand OGM data to that workflow creatingcreate a standard software tool for use across molecular pathology and cytogenomics applications. We currently sell our systems for research use only applications and our customers are primarily laboratories associated with academic and governmental research institutions, academic and commercial clinical laboratories, as well as pharmaceutical, biotechnology and contract research companies. In addition, we provide instruments to certain customers at no cost under our reagent rental program, andwhere the customerscost agreeof the instrument is factored into the price of a consumable and, the customer agrees to purchase minimum quantities of consumables. Consumable revenue consists of sales of reagents and chips necessary to process a sample. We believe that the growth in our consumable sales has been primarily driven by increased clinical adoption, and we expect future growth will continue to be driven by clinical adoption and increased utilization at existing and new clinical sites. Sales of our VIA software, which provides customers with solutions for analysis, interpretation and reporting of genomics data, are made on a subscription basis. We generate service revenue from the sale of diagnostic testing services through Bionano Laboratories, as well as services performed related to customer sample evaluations using an OGM system. Other revenue consists of warranty and other service-based revenue, including support, repair and maintenance services.

We have incurred losses in each year since our inception. Our net loss was $8.3$7.4 million and $3.1$15.7 million for the three and six months ended MarchJune 31,30, 2026 and 2025,2026, respectively. As of MarchJune 31,30, 2026, we had an accumulated deficit of $727.9$735.3 million.

Comparison of the Three Months Ended MarchJune 31,30, 2026 and 2025

The following table sets forth our results of operations for the three months ended MarchJune 31,30, 2026 and 2025 (in thousands):

Total revenue increased by $0.2$1.4 million, or 4%21% to $6.7$8.2 million for the three months ended MarchJune 31,30, 2026, as compared to $6.5$6.7 million for the same period in 2025, driven primarily by an increase in instrument, consumables, service and other revenue, partially offset by a decrease in software revenue.

Instrument revenue increased by $0.3$0.6 million, or 40%,46%, to $1.0$2.0 million for the three months ended MarchJune 31,30, 2026, as compared to $0.7$1.4 million for the three months ended MarchJune 31,30, 2025, due to an increase in the number of OGM and Ionic instruments sold. ForAs theof threeJune months ended March 31,30, 2026, our installed base grew to 399397 OGM systems compared to the 379378 OGM systems foras theof threeJune months ended March 31,30, 2025, which represented a 5% increase year-over-year as compared to a 9% year-over-year increase in the prior year. In September 2024, we announced a change in our business strategy to focus on driving utilization and adoption of OGM from our existing installed base, with less emphasis on new placements of our OGM systems. We expected that this change in strategy would slow the pace of our instrument revenue growth when compared to historical growth rates.year-over-year.

Consumables revenue increased by $0.7$1.0 million, or 20%,31%, to $3.9$4.3 million for the three months ended MarchJune 31,30, 2026, as compared to $3.2$3.3 million for the three months ended MarchJune 31,30, 2025. The increase is primarily driven by an increase in both the number and the average selling price of flowcells sold, partially offset by certain supply constraints due to manufacturing delays that were initiated in the fourth quarter of 2025.2025 and continued through the current period. For the three months ended MarchJune 31,30, 2026, we sold 8,1789,219 flowcells, an increase of approximately 17%27% from 6,9947,233 flowcells sold in the same period of 2025.

Software revenue decreased by $0.8$0.3 million, or 40%,16%, to $1.2$1.4 million for the three months ended MarchJune 31,30, 2026, as compared to $2.1$1.6 million for the three months ended MarchJune 31,30, 2025. The decrease is primarily attributed to a decrease in the number of VIA software licenses sold.

Cost of product revenue increased by $0.2$0.6 million or 5%,18%, to $3.7 million for the three months ended June 30, 2026, as compared to $3.2 million for the three months ended MarchJune 31, 2026, as compared to $3.1 million for the three months ended March 31,30, 2025. The increase was primarily attributable to higher instrument and consumable sales. We expect cost of product revenue to vary with sales volume and product mix.

Service and otherProduct gross profit increased by $0.4$0.8 millionmillion, or 26%, to $0.4$4.0 million for the three months ended MarchJune 31,30, 2026, compared to a gross loss of $(0.01)$3.2 million for the three months ended MarchJune 31,30, 2025. The increase in service and other gross profit was primarily driven by the non-recurringan increase in warrantyinstrument expenseand recognizedconsumable sales, offset by a decrease in thesoftware prior period. In addition, revenues increased from clinical service offerings through Bionano Laboratories and instrument service contracts.sales.

R&D expenses increased by $0.8$0.1 million, or 32%,2%, to $3.1$3.0 million for the three months ended MarchJune 31,30, 2026, as compared to $2.4$2.9 million for the same period in 2025. The increase was primarily due to increases of $0.2 million in salaries, wages and benefits driven by a slight increase in headcount and an increase in salaries and bonuses which were not offered during the same period in 2025 due to the cost savings initiatives announced in 2024; an increase of $0.4$0.3 million in professional and consulting fees, including increases in costs incurred to support development of the Stratys system and foundry expenses. Lastly,These weincreases increasedwere offset by decreases in our internal consumption of inventory, materials and suppliessupplies, depreciation, and rent and facilities costs by a combined total of $0.3 million. Lastly, in the prior period we recognized a loss on disposal of assets of $0.2 million.million which did not reoccur in the current period.

Selling, general and administrative (“SG&A”) expenses decreasedincreased by $1.0$0.2 million, or 11%,2%, to $8.0$8.5 million for the three months ended MarchJune 31,30, 2026, as compared to $9.0$8.3 million for the same period in 2025. The decreaseincrease was primarily due to a net decrease of headcount-related expenses of $0.3$0.5 million including a reduction in stock-basedcombined compensationone-time dueexecutive totransition acosts reduction in the number of grants awarded, offset byand an increase in salaries and accrued bonuses, and a $1.3$0.2 million increase in information technology, travel, rent and facility costs. These increases were partially offset by a $0.5 million decrease in professional and consulting fees which is primarily marketing, software, and legal expenses. These decreases were partially offset by the absence of a $0.4 million gain on lease modification recorded in the prior period and a $0.2 million increase in information technology, travel, rent and facility costs.

Interest income decreased by $0.1 million, or 23%,47%, to $0.2$0.1 million for the three months ended MarchJune 31,30, 2026, as compared to $0.3 million for the same period in 2025 resulting from a reduction in investments offset by higher returns.

Since our inception, we have incurred net losses and negative cash flows from operations. We incurred net losses of $8.3$15.7 million and $3.1$10.0 million, and used $5.7$10.4 million and $2.8$6.3 million of cash from our operating activities for the threesix months ended MarchJune 31,30, 2026 and 2025, respectively. As of MarchJune 31,30, 2026, we had an accumulated deficit of $727.9$735.3 million, cash and cash equivalents of $3.4$3.7 million, $11.0$6.2 million in short-term investments and $10.3$0.5 million in restricted cash and short-term investments.cash.

In the threesix months ended MarchJune 31,30, 2026, we generated cash flows from sales of common stock and other equity instruments. We anticipate that future sources of liquidity will principally come from sales of common stock and other equity instruments, borrowings from credit facilities and revenue from our commercial operations. See Note 5 (Debt) and Note 6 (Stockholder’s Equity and Stock-Based Compensation) in the accompanying notes to our unaudited condensed consolidated financial statements included elsewhere in this Quarterly Report for a discussion of our recent debt and equity activity.

AsThe $10.3 million outstanding principal balance was redeemed in full shortly after the May 24, 2026 maturity date, and no principal remained outstanding under the Debentures as of MarchJune 31,30, 2026, the Company reported $10.2 million of Debentures at fair value, which is classified as current on the unaudited condensed consolidated balance sheet.2026. For the threesix months ended MarchJune 31,30, 2026, the Company paid $0.3$0.5 million in interest and zero$10.3 million in principal redemption amounts on the Debentures. As of March 31, 2026, the Company may be required to redeem up to $10.3 million of principal and expects to pay an additional $0.2 million in interest on the Debentures for the remainder of 2026. See Note 5 (Debt) in the accompanying notes to our unaudited condensed consolidated financial statements included elsewhere in this Quarterly Report for further information.

Based on our current business plans, we will continue to require additional capital in the very near term to fund our operating expenses and capital expenditure requirements, or we may need to further curtail or cease operations and seek protection by filing a voluntary petition for relief under the United States Bankruptcy Code. If this were to occur, the value available to our various stakeholders, including our creditors and stockholders, is uncertain and trading prices for our securities may bear little or no relationship to the actual recovery, if any, by holders of our securities in bankruptcy proceedings, if any. This estimate assumes the inclusion of the amount equal to the outstanding principal amount of the Debentures. Our existing cash and cash equivalents and short-term investments,investments will not be sufficient for us to achieve cash-flow break eveneven, and we expect to need to seek additional capital. Based on the Company’s current business plans we believe we will be able to fund our operating expenses and capital expenditure requirements into at least the first quarter of 2027.

As of MarchJune 31,30, 2026, we had $3.4$3.7 million in cash and cash equivalents, $11.0$6.2 million in short-term investments and $10.3$0.5 million in restricted cash and short-term investments. The amount we are required to hold as restricted cash or restricted investments is equal to the lesser of (a) $11.0 million and (b) the then outstanding principal balance of the Debentures.cash. As of MarchJune 31,30, 2026, the Company had $10.3fully millionredeemed ofthe outstanding principal outstandingbalance under the Debentures. Based on recurring losses from operations incurred since inception and the expectation of continued operating losses, we anticipate our available cash balance will not be sufficient to operate our business for the next twelve months from the issuance of this Quarterly Report. Accordingly, we determined that there is substantial doubt about our ability to continue as a going concern within 12 months after the date that the financial statements included in this Quarterly Report are issued. In order to continue to operate our business beyond that time, we will need to raise substantial additional capital. We are actively evaluating debt and equity financing sources available to us as well as cost reduction strategies, but there can be no assurance that financing will be available on terms acceptable to us, on a timely basis, or at all, or that we are able to effectively reduce our operating expenses. To the extent that we raise additional capital through the sale of equity or convertible debt securities, the ownership interest of our stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of common stockholders. Debt financing and preferred equity financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making acquisitions or capital expenditures or declaring dividends. Any disruptions to, or volatility in, the credit and financial markets or any deterioration in overall economic conditions may make any necessary debt or equity financing more difficult to obtain, more costly and/or more dilutive. If we are unable to raise additional funds through debt or equity financing or other arrangements when needed, we may be required to delay, limit, reduce or terminate our research and development activities or future commercialization efforts. Even if we raise additional capital, we may also be required to modify, delay or abandon some of our plans which could have a material adverse effect on our business, operating results and financial condition and our ability to achieve our intended business objectives.

Net cash used in operating activities was $5.7$10.4 million during the threesix months ended MarchJune 31,30, 2026, as compared to $2.8$6.3 million during the same period in 2025. The increase in cash used in operating activities of $3.0$4.1 million was primarily attributed to an increase in inventory purchases and an increase in salaries, wages, and benefits driven by a slight increase in headcount and an increase in accrued salaries, wages, and bonuses.

Historically, our primary investing activities have consisted of capital expenditures for the purchase of capital equipment to support our expanding infrastructure, as well as the acquisitions of Lineagen, BioDiscovery and Purigen to grow our business. We expect to continue to incur additional costs for capital expenditures related to these efforts in future periods. During the threesix months ended MarchJune 31,30, 2026, net cash provided by investing activities was $5.5$19.1 million, as compared to net cash used in investing activities was $14.1$12.1 million during the same period in 2025. The increase in cash provided by investing activities of $19.5$31.2 million was primarily attributed to the maturity of $54.1$99.3 million in available for sale securities, which was offset by the purchase of available for sale securities of $48.7$80.1 million during the threesix months ended MarchJune 31,30, 2026, as compared to the maturity of $50.7$104.6 million in available for sale securities, which was offset by a higher purchase of available for sale securities of $64.8$116.6 million during the same period in 2025.

Net cash used in financing activities was $9.0 million during the six months ended June 30, 2026 as compared to net cash provided by financing activities wasof $0.7 million during the three months ended March 31, 2026 as compared to $10.9$12.4 million during the same period in 2025, a decrease of $10.2$21.4 million. During the threesix months ended MarchJune 31,30, 2026, the Company madefully noredeemed the outstanding principal paymentsbalance towardsof $10.3 million of the convertible debentures payable, as compared to principal payments of $1.5$3.0 million during the same period in 2025, and $0.7$1.3 million in gross proceeds from executing sales under our at-the-market facilities with H.C. Wainwright & Co., LLC (“Wainwright”) during the threesix months ended MarchJune 31,30, 2026, as compared to $13.3$16.4 million in gross proceeds from executing sales under our at-the-market facilities with Cowen and Company, LLC (“Cowen”) and Wainwright during the same period in 2025.

As of MarchJune 31,30, 2026, we had approximately $3.4$3.7 million in cash and cash equivalents, $11.0$6.2 million in short-term investments, $10.3$0.5 million in restricted cash and short-term investments and working capital of $17.7$14.8 million. The amount we are required to hold as restricted cash or restricted investments is equal to the lesser of (a) $11.0 million and (b) the then outstanding principal balance of the Debentures (as defined in Note 5 (Debt) to our unaudited condensed consolidated financial statements). As of MarchJune 31,30, 2026, the Company had $10.3fully millionredeemed ofthe outstanding principal outstandingbalance under the Debentures.