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What changed in Bionano Genomics, Inc.'s 10-K — 2024 vs 2025

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Paragraph-level year-over-year comparison of Bionano Genomics, Inc.'s 2024 and 2025 10-K annual filings, covering the Business, Risk Factors, Legal Proceedings, Cybersecurity, MD&A and Market Risk sections. Every new, removed and edited paragraph is highlighted side-by-side so you can see exactly what management changed in the 2025 report.

+892 added−143 removedSource: 10-K (2026-03-23) vs 10-K (2025-03-31)

Top changes in Bionano Genomics, Inc.'s 2025 10-K

892 paragraphs added · 143 removed · 118 edited across 4 sections

Item 1. Business

Business — how the company describes what it does

110 edited+774 added−18 removed188 unchanged
Biggest changeAdditionally, Bionano Laboratories previously offered molecular genetic clinical testing services for individuals demonstrating clinical presentations consistent with NDDs, including ASDs and other disorders of childhood development, but as of December ,31 2024, has phased out the offering of these products, including: • FirstStepDx PLUS is a CMA designed to identify an underlying genetic cause in individuals with autism spectrum disorder, developmental delay, and intellectual disability; • Fragile X syndrome (“FXS”) testing is designed to detect individuals (both males and females) with FXS, as well as carriers of the condition; and • NextStepDx PLUS is a whole exome sequencing test designed to identify genetic variants that are associated with disorders of childhood development. 15 Table of Contents Market Opportunity According to MarketsandMarkets, the worldwide market for genomics products and services is expected to reach approximately $66.8 billion by 2029, up from approximately $42.4 billion in 2023, representing a compound annual growth rate of 9.4%.
Biggest changeBionano Laboratories previously offered OGM-based LDTs and molecular genetic clinical testing services for individuals demonstrating clinical presentations consistent with NDDs, including ASDs and other disorders of childhood development, but began phasing out the offering of these products beginning December 31, 2024, including: • OGM-Dx TM HemeOne is a test that detects SVs defined by professional & medical guidelines as cytogenomic targets that aid in the diagnosis, prognosis, and therapeutic management of individuals with hematologic malignancies; • OGM-Dx TM Postnatal Whole Genome SV is an assay that detects SVs across the genome and provides comprehensive testing; • OGM-Dx TM Prenatal Whole Genome SV is an assay that detects SVs across the genome and provides comprehensive testing for most common and rare chromosomal abnormalities for prenatal indications; • FirstStepDx PLUS is a CMA designed to identify an underlying genetic cause in individuals with autism spectrum disorder, developmental delay, and intellectual disability; • Fragile X syndrome (“FXS”) testing is designed to detect individuals (both males and females) with FXS, as well as carriers of the condition; and • NextStepDx PLUS is a whole exome sequencing test designed to identify genetic variants that are associated with disorders of childhood development.
We offer OGM solutions for applications across basic, translational and clinical research, and for other applications including bioprocessing. We offer a platform-agnostic software solution, which integrates next-generation sequencing, microarray and OGM 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 offer OGM solutions for applications across basic, translational and clinical research, and for other applications including bioprocessing. We offer a platform-agnostic software solution, which integrates next-generation sequencing (“NGS”), microarray and OGM 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.
OGM has also been shown to identify structural changes in chromosomes that cannot be identified using current commercially available gene sequencing solutions. We market and sell the Ionic ® Purification system, which is able to deliver high quality DNA in a more natural, native form and with fewer contaminants when compared to other isolation and purification solutions.
OGM has also been shown to identify structural changes in chromosomes that cannot be identified using current commercially available gene sequencing solutions. We develop, manufacture, market and sell the Ionic ® Purification system, which is able to deliver high quality DNA in a more natural, native form and with fewer contaminants when compared to other isolation and purification solutions.
Additionally, the Stratys™ system is a higher throughput system designed to meet the needs of medium and high-volume labs and offers approximately 4 times the throughput of a Saphyr® system. The OGM Instruments The OGM instruments are each single-molecule imagers that include high performance optics, automated sample loading based on machine learning algorithms and computational hardware and control software.
Additionally, the Stratys system is a higher throughput system designed to meet the needs of medium and high-volume labs and offers up to 4 times the throughput of a Saphyr system. The OGM Instruments The OGM instruments are each single-molecule imagers that include high performance optics, automated sample loading based on machine learning algorithms and computational hardware and control software.
Additionally, our portfolio includes patents and patent applications directed to related parts of our business, including certain diagnostic tests and methods of diagnosis and analysis of microarray and image data. We have developed a global patent portfolio that includes more than 135 issued patents across approximately 30 patent families that are either owned or exclusively licensed.
Additionally, our portfolio includes patents and patent applications directed to related parts of our business, including certain diagnostic tests and methods of diagnosis and analysis of microarray and image data. We have developed a global patent portfolio that includes more than 125 issued patents across approximately 30 patent families that are either owned or exclusively licensed.
Laboratory services for OGM are performed in our laboratory facilities in San Diego, California and at partner laboratories in the United States and Europe, and serve as solutions for researchers and clinicians who would like to use OGM for various applications in genomics but have yet to acquire an OGM system.
Laboratory services for OGM are performed in our laboratory facilities in San Diego, California and, from time-to-time, at partner laboratories in the United States and Europe, and serve as solutions for researchers and clinicians who would like to use OGM for various applications in genomics but have yet to acquire an OGM system.
Instruments Our first Stratys™ instruments are being manufactured in-house; however, we will eventually be moving manufacturing of the Stratys™ instrument to the same third-party medical device manufacturer that manufactures our Saphyr® instrument. Complete instruments are shipped by the manufacturer to us for final quality control testing.
Instruments Our first Stratys instruments were manufactured in-house; however, we will eventually be moving manufacturing of the Stratys instrument to the same third-party medical device manufacturer that manufactures our Saphyr instrument. Complete instruments are shipped by the manufacturer to us for final quality control testing.
To date, our customers have published over 1,300 papers showcasing the clinical and translational research advancements enabled by OGM. Since the first publication in 2010, the annual volume of research featuring data from our OGM systems has steadily increased.
To date, our customers have published over 1,800 papers showcasing the clinical and translational research advancements enabled by OGM. Since the first publication in 2010, the annual volume of research featuring data from our OGM systems has steadily increased.
We market and sell the VIA™ software which delivers genomic data interpretation solutions tailored for research use in cytogenomics and molecular pathology labs in genetic disease and cancer research markets, with an emphasis on SV.
We develop, manufacture, market and sell the VIA software which delivers genomic data interpretation solutions tailored for research use in cytogenomics and molecular pathology labs in genetic disease and cancer research markets, with an emphasis on SV.
In addition, on April 1, 2014, the Protecting Access to Medicare Act of 2014, or PAMA, was signed into law, which, among other things, significantly altered the payment methodology under the Medicare CLFS. PAMA requires certain laboratories performing clinical diagnostic laboratory tests to report to CMS the amounts paid by private payors for laboratory tests.
In addition, on April 1, 2014, the Protecting Access to Medicare Act of 2014, or PAMA, was signed into law, which, among other things, significantly altered the payment 33 Table of Contents methodology under the Medicare CLFS. PAMA requires certain laboratories performing clinical diagnostic laboratory tests to report to CMS the amounts paid by private payors for laboratory tests.
Their managed care efforts were directed to establishing contracts and/or credentialing with private and governmental insurance carriers that provide coverage for patients with ASD and other forms of NDDs. During 2024, Bionano Laboratories phased out the offering of the ASD and NDD LDTs and is now focused on offering solely their OGM-based LDTs.
Their managed care efforts were directed to establishing contracts and/or credentialing with private and governmental insurance carriers that provide coverage for patients with 21 Table of Contents ASD and other forms of NDDs. During 2024, Bionano Laboratories phased out the offering of the ASD and NDD LDTs and is now focused on offering solely their OGM-based LDTs.
Penalties Failure to comply with the aforementioned fraud and abuse laws could result in significant penalties, including civil, criminal, and administrative penalties, damages, fines, disgorgement, the curtailment or restructuring of our operations, exclusion from participation in federal and state healthcare programs, additional integrity oversight and reporting obligations, imprisonment, contractual damages, and reputational harm.
Penalties Failure to comply with the aforementioned fraud and abuse laws could result in significant penalties, including civil, criminal, and administrative penalties, damages, fines, disgorgement, the curtailment or restructuring of our 32 Table of Contents operations, exclusion from participation in federal and state healthcare programs, additional integrity oversight and reporting obligations, imprisonment, contractual damages, and reputational harm.
In this manner we can expand our network of Bionano customers into our software ecosystem with among the most comprehensive platform- 18 Table of Contents agnostic genome interpretation solution where our proprietary original content in OGM can be adopted when needed to obtain a more comprehensive view of the genome by revealing all classes of SVs.
In this manner we can expand our network of Bionano customers into our software ecosystem with among the most comprehensive platform-agnostic genome interpretation solution where our proprietary original content in OGM can be adopted when needed to obtain a more comprehensive view of the genome by revealing all classes of SVs.
Many states have adopted laws similar to the Anti-Kickback Statute, and some apply to items and services reimbursable by any payor, including private third-party payors. Further, the Eliminating Kickbacks in Recovery Act of 2018 (“EKRA”), prohibits payments for referrals to recovery homes, clinical treatment facilities, and laboratories.
Many states have adopted laws similar to the Anti-Kickback Statute, and some apply to items and services reimbursable by any payor, including private third-party payors. 31 Table of Contents Further, the Eliminating Kickbacks in Recovery Act of 2018 (“EKRA”), prohibits payments for referrals to recovery homes, clinical treatment facilities, and laboratories.
The instrument’s high-performance optics simultaneously image DNA linearized in hundreds of thousands of nanochannels. The instrument’s control interface is the user’s primary control center to design and monitor experiments as they occur in real time. The computational hardware is responsible for the secondary processing of the image data being produced on the instruments.
The instrument’s high-performance optics simultaneously image DNA linearized in hundreds of thousands of nanochannels. The instrument’s control interface is the user’s primary control center to design and monitor experiments as they occur in 15 Table of Contents real time. The computational hardware is responsible for the secondary processing of the image data being produced on the instruments.
We believe these long read lengths overcome the inherent challenges of genome complexity and are the key to our OGM systems’ unprecedented sensitivity and specificity. • Proprietary nanotechnology for massively parallel linearization and analysis of long molecules with single molecule imaging. Analyzing UHMW DNA required invention.
We believe these long read lengths overcome the inherent challenges of genome complexity and are the key to our OGM systems’ unprecedented sensitivity and specificity. 12 Table of Contents • Proprietary nanotechnology for massively parallel linearization and analysis of long molecules with single molecule imaging. Analyzing UHMW DNA required invention.
Bionano Laboratories is subject to prosecution and/or administrative enforcement and increased civil and criminal penalties for non-compliance, including a new, four-tiered system of monetary penalties adopted under HITECH. Bionano Laboratories is also subject to enforcement by state attorneys general who were given authority to enforce HIPAA under HITECH.
Bionano Laboratories is subject to prosecution and/or administrative enforcement and increased civil and criminal penalties for non-compliance, including a new, four-tiered system of monetary penalties adopted under HITECH. Bionano Laboratories 29 Table of Contents is also subject to enforcement by state attorneys general who were given authority to enforce HIPAA under HITECH.
Bionano Laboratories may expand its testing menu with inclusion of OGM to demonstrate workflow implementation in a clinical setting in order to drive adoption as well as serve as a conduit for enabling access for those customers unable to make a capital equipment expenditure.
Bionano Laboratories may expand its testing menu with inclusion of OGM to demonstrate workflow implementation in a clinical setting in order to drive adoption as well as serve as a conduit for enabling access for those customers unable to make a capital 14 Table of Contents equipment expenditure.
We believe that the isolation and purification of DNA using the Ionic® system in an OGM 14 Table of Contents workflow will create a number of opportunities, including, enabling additional sample types not currently available to OGM, increasing sample throughput, decreasing sample preparation complexity.
We believe that the isolation and purification of DNA using the Ionic system in an OGM workflow will create a number of opportunities, including, enabling additional sample types not currently available to OGM, increasing sample throughput, decreasing sample preparation complexity.
Failure to maintain compliance, or changes in state or federal laws regarding privacy or security could result in civil and/or criminal penalties, significant reputational damage and could have a material adverse effect on our business. The General Data Protection Regulation (“GDPR”), which applies to all EU member states from May 25, 2018, also applies to some of our operations.
Failure to maintain compliance, or changes in state or federal laws regarding privacy or security could result in civil and/or criminal penalties, significant reputational damage and could have a material adverse effect on our business. The General Data Protection Regulation (“GDPR”), which applies to all EU member states, also applies to some of our operations.
NGS is capable of measuring genome variants below 500 bp while OGM bridges the gap by enabling detection of all SVs above 500 bp to reveal more answers and resolve previously unresolved cases from using NGS alone.
NGS is capable of measuring genome variants 20 Table of Contents below 500 bp while OGM bridges the gap by enabling detection of all SVs above 500 bp to reveal more answers and resolve previously unresolved cases from using NGS alone.
CLIA certification is also a prerequisite to be eligible to bill state and federal healthcare programs, as well as many commercial third-party payers, for laboratory testing services. The Bionano Laboratories’ facility, located in San Diego, California is CLIA certified. This laboratory must comply with all applicable CLIA requirements.
CLIA certification is also a 28 Table of Contents prerequisite to be eligible to bill state and federal healthcare programs, as well as many commercial third-party payers, for laboratory testing services. The Bionano Laboratories’ facility, located in San Diego, California is CLIA certified. This laboratory must comply with all applicable CLIA requirements.
The Saphyr® system images DNA at a rate of approximately 205 gigabase pairs (“Gbp”) per hour, and the Stratys™ system images nearly 820 Gbp per hour. • Partner with industry-leading companies and laboratories to expand adoption in clinical markets.
The Saphyr system images DNA at a rate of approximately 205 gigabase pairs (“Gbp”) per hour, and the Stratys system images between 530 and 820 Gbp per hour. • Partner with industry-leading companies and laboratories to expand adoption in clinical markets.
These requirements vary by jurisdiction, differ from those in the United States and may require us to implement additional compliance measures or perform additional pre-clinical or clinical testing. For example, the In Vitro Diagnostic Medical Devices (2017/746/EU) (“IVDR”) will replace the existing In Vitro Diagnostic Medical Devices Directive (98/79/EC) (“IVDD”) in the EU.
These requirements vary by jurisdiction, differ from those in the United States and may require us to implement additional compliance measures or perform additional pre-clinical or clinical testing. For example, the In Vitro Diagnostic Medical Devices (2017/746/EU) (“IVDR”) has replaced the existing In Vitro Diagnostic Medical Devices Directive (98/79/EC) (“IVDD”) in the EU.
We are constantly on the look-out for opportunities to better meet the needs of our customers 10 Table of Contents whether that is through partnerships, organic development, or strategic acquisitions that accelerate and up-shift our capabilities.
We are constantly on the look-out for opportunities to better meet the needs of our customers whether that is through partnerships, organic development, or strategic acquisitions that accelerate and up-shift our capabilities.
In its current form, each Saphyr Chip® has three flow cells containing approximately 120,000 nanochannels that are roughly 30 nanometers wide, and each flowcell can hold one unique sample. The Stratys Chip™ is the consumable that packages the nanochannel arrays for DNA linearization for use on the Stratys™ instrument.
OGM Chips The Saphyr Chip® is the consumable that packages the nanochannel arrays for DNA linearization for use in the Saphyr instrument. In its current form, each Saphyr Chip has three flow cells containing approximately 120,000 nanochannels that are roughly 30 nanometers wide, and each flowcell can hold one unique sample.
Genome maps typically span entire chromosome arms in single, contiguous maps. Comparative analysis of maps reveals SV. Our customers use our variant annotation workflow to specifically uncover rare and sample-specific mutations.
Genome maps typically span entire chromosome arms in single, contiguous maps. 17 Table of Contents Comparative analysis of maps reveals SV. Our customers use our variant annotation workflow to specifically uncover rare and sample-specific mutations.
As the scientific, peer-reviewed literature supports this claim, the coding entities such as the Centers for Medicare & Medicaid Services (“CMS”) and the American Medical Association (“AMA”) would need to adopt the proper procedural codes to allow for insurance reimbursement of new testing methodologies before they become mainstream clinical diagnostic instruments.
As the scientific, peer-reviewed literature supports the inclusion of OGM-based testing, the coding entities such as the Centers for Medicare & Medicaid Services (“CMS”) and the American Medical Association (“AMA”) would need to adopt the proper procedural codes to allow for insurance reimbursement of new testing methodologies before they become mainstream clinical diagnostic instruments.
In 2022, we added a portfolio of patents and patent applications related to ITP through the Purigen acquisition, which we plan to continue to pursue and develop.
In 2022, we added a portfolio of patents and patent applications related to ITP through the Purigen acquisition, which we plan to continue to pursue and 23 Table of Contents develop.
We believe we have transformed our business from an instrument company to a provider of a full suite of genomic solutions. We expanded into molecular genetic clinical testing services through our August 2020 acquisition of Lineagen.
We have in recent years transformed our business from an instrument company to a provider of a full suite of genomic solutions. We expanded into molecular genetic clinical testing services through our August 2020 acquisition of Lineagen.
This industry leading, platform agnostic software solution is designed to provide analysis, visualization, interpretation and reporting of SVs, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view. Our software currently enables analysis of OGM, next-generation sequencing (“NGS”) and microarray data.
This industry leading, platform agnostic software solution is designed to provide analysis, visualization, interpretation and reporting of SVs, single-nucleotide variants and absence of heterozygosity across the genome in one consolidated view. Our software currently enables analysis of OGM, NGS and microarray data.
Under this final rule, over the course of four years FDA would phase out its general enforcement discretion approach to LDTs and begin enforcing requirements for premarket review and marketing authorization and compliance with certain elements of the QSR, registration and listing, medical device reporting, labeling, and corrections and removals reporting.
Under this final rule, over the course of four years FDA would phase out its general enforcement discretion approach to LDTs and begin enforcing requirements for premarket review and marketing authorization and compliance with certain elements of the QSR, registration and listing, medical device reporting, labeling, and corrections and removals reporting. However, in March 2025 the U.S.
All statements made in any of our securities filings, including all forward-looking statements or information, are made as of the date of the document in which the statement is included unless otherwise specified, and we do not assume or undertake any obligation to update any of those statements or documents unless we are required to do so by law.
All statements made in any of our securities filings, including all forward-looking statements or information, are made as of the date of the document in which the statement is included unless otherwise specified, and we do not assume or undertake any obligation to update any of those statements or documents unless we are required to do so by law. 35 Table of Contents ITE M 1A.
Notably, more than 75% of these 1,000+ peer-reviewed and preprint papers have been published since 2021, with 26% appearing in 2024 alone. We remain committed to fostering and supporting our customer base, driving further growth in the number of publications leveraging our technology.
Notably, more than 75% of these 1,400+ peer-reviewed and preprint papers have been published since 2021, with 24% appearing in 2025 alone. We remain committed to fostering and supporting our customer base, driving further growth in the number of publications leveraging our technology.
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 at approximately $3.4 billion in 2024 and predicted would grow to approximately $8.5 billion in 2029, representing a compound annual growth rate of 20%.
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 at approximately $4.1 billion in 2025 and predicted would grow to approximately $8.2 billion in 2029, representing a compound annual growth rate of 18.8%.
SVs are well-known to cause diseases such as constitutional genetic disorders and cancer. Many researchers and clinicians now agree that despite major advances in the speed and cost-effectiveness of DNA sequencing, it fails to reliably detect SVs.
SVs may be inherited or arise spontaneously. SVs are well-known to cause diseases such as constitutional genetic disorders and cancer. Many researchers and clinicians now agree that despite major advances in the speed and cost-effectiveness of DNA sequencing, it fails to reliably detect SVs.
ITEM 1. BUSINESS 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 (“OGM”) solutions, diagnostic services and software.
ITEM 1. B USINESS 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 (“OGM”) solutions, nucleic acid extraction and purification systems, diagnostic services and software.
The transitional period was set to end on May 26, 2022, the “Date of Application” of the IVDR but has since been extended to May 26, 2025 for Class D devices, May 26, 2026 for Class C devices, and May 26, 2027 for Class B and Class A sterile devices.
The transitional period was set to end on May 26, 2022, the “Date of Application” of the IVDR but has since been extended to December 31, 2027 for Class D devices, December 31, 2028 for Class C devices, and December 31, 2029 for Class B and Class A sterile devices.
Software Solutions We offer industry leading genome analysis software that enables genomics labs to analyze and interpret data across a wide range of platforms to generate highly informative data visualizations for streamlined and simple reporting of causal variants.
We anticipate continuing to support and expanding this customer base. Software Solutions We offer industry leading genome analysis software that enables genomics labs to analyze and interpret data across a wide range of platforms to generate highly informative data visualizations for streamlined and simple reporting of causal variants.
Additionally, from January 1, 2021, companies have had to comply with the GDPR and also the UK GDPR (“UK GDPR”), which, together with the amended United Kingdom Data Protection Act 2018, retains the GDPR in the UK national law.
Additionally, from January 1, 2021, companies have had to comply with the GDPR and also the UK GDPR (“UK GDPR”), which, together with the amended United Kingdom Data Protection Act 2018 and subsequent reforms such as the Data (Use and Access) Act 2025, retains the GDPR in the UK national law.
SV is one of the most biologically important aspects of the human genome and is a major factor for the cause of genetic disorders and cancer. Each SV involves the rearrangement or repetition of as few as several hundred base pairs to as many as tens of millions of base pairs. SVs may be inherited or arise spontaneously.
SV is 10 Table of Contents one of the most biologically important aspects of the human genome and is a major factor for the cause of genetic disorders and cancer. Each SV involves the rearrangement or repetition of as few as several hundred base pairs to as many as tens of millions of base pairs.
Testing and Laboratory Services Our Bionano Laboratories business offers tests that use CMA for evaluation of patients suspected of having certain genetic diseases, which is recommended by the American College of Medical Genetics and Genomics, the American Academy of Pediatrics, and the American Academy of Neurology, among other renowned societies.
Additionally, Bionano Laboratories previously offered tests that use CMA for evaluation of patients suspected of having certain genetic diseases, which is recommended by the American College of Medical Genetics and Genomics, the American Academy of Pediatrics, and the American Academy of Neurology, among other renowned societies.
Our Solutions We believe that an end-to-end OGM solution begins with the sample and ends with data analysis. The OGM workflow includes several steps: DNA isolation, DNA labeling, DNA mapping, data processing and data analysis. At each step we have either organically developed a solution or partnered with a third party to enable and provide a solution.
The OGM workflow includes several steps: DNA isolation, DNA labeling, DNA mapping, data processing and data analysis. At each step we have either organically developed a solution or partnered with a third party to enable and provide a solution.
In June 2024 the AMA established a category 1 CPT code for 22 Table of Contents use of OGM in cytogenomic genome-wide analysis to detect structural and copy number variations related to hematological malignancies, which became effective January 1, 2025. Additionally, CMS, through its Medicare contractors, can write coverage determinations for molecular testing through their LCD process.
Additionally, in May 2025 the AMA established a category 1 CPT code for use of OGM in cytogenomic genome-wide analysis to detect structural and copy number variations related to constitutional genetic disorders, which became effective January 1, 2026. Also, CMS, through its Medicare contractors, can write coverage determinations for molecular testing through their LCD process.
Information in the investor section and on our website is not part of this Annual Report or any of our other securities filings. Our filings with the SEC may be accessed through the SEC’s website at www.sec.gov.
We do not charge for access to and viewing of these reports. Information in the investor section and on our website is not part of this Annual Report or any of our other securities filings. Our filings with the SEC may be accessed through the SEC’s website at www.sec.gov.
With the integration of OGM into our VIA™ software, we believe that our software is the first software solution delivering a fully integrated interpretation capability for SVs from OGM as well as seamless analysis with NGS, and that this integration will enable complementary OGM and NGS workflows through one software solution.
With the integration of OGM into our VIA software, we believe that our software is the first software solution delivering a fully integrated interpretation capability for SVs from OGM as well as seamless analysis with NGS, and that this integration will enable complementary OGM and NGS workflows through one software solution. 11 Table of Contents Our Solutions We believe that an end-to-end OGM solution begins with the sample and ends with data analysis.
The price we pay is determined according to a mutually agreed-upon pricing formula. We may terminate a purchase order by giving the manufacturer at least 30 days’ written notice and may be required to pay for materials the manufacturer is unable to cancel.
We are obligated to purchase any material deemed in excess pursuant to our agreement with the manufacturer. The price we pay is determined according to a mutually agreed-upon pricing formula. We may terminate a purchase order by giving the manufacturer at least 30 days’ written notice and may be required to pay for materials the manufacturer is unable to cancel.
Bionano Laboratories is working with payers to secure reimbursement alternatives for OGM-based testing. If reimbursements can be established, Bionano Laboratories intends to share its strategies with other labs which may drive demand for the OGM systems.
If reimbursements can be established, Bionano Laboratories intends to share its strategies with other labs which may drive demand for the OGM systems.
In addition, various states have enacted similar laws modeled after the FCA that apply to items and services reimbursed under Medicaid and other state health care programs, and, in several states, such laws apply to claims submitted to any payor. 25 Table of Contents Civil Monetary Penalties Law The federal Civil Monetary Penalties Law (the “CMP Law”), prohibits, among other things, (1) the offering or transfer of remuneration to a Medicare or state health care program beneficiary if the person knows or should know it is likely to influence the beneficiary’s selection of a particular provider, practitioner, or supplier of services reimbursable by Medicare or a state health care program, unless an exception applies; (2) employing or contracting with an individual or entity that the provider knows or should know is excluded from participation in a federal health care program; (3) billing for services requested by an unlicensed physician or an excluded provider; and (4) billing for medically unnecessary services.
Civil Monetary Penalties Law The federal Civil Monetary Penalties Law (the “CMP Law”), prohibits, among other things, (1) the offering or transfer of remuneration to a Medicare or state health care program beneficiary if the person knows or should know it is likely to influence the beneficiary’s selection of a particular provider, practitioner, or supplier of services reimbursable by Medicare or a state health care program, unless an exception applies; (2) employing or contracting with an individual or entity that the provider knows or should know is excluded from participation in a federal health care program; (3) billing for services requested by an unlicensed physician or an excluded provider; and (4) billing for medically unnecessary services.
Installed base represents the global number of OGM instruments installed at end-customer locations to perform optical genome mapping. • For the year ended December 31, 2024, total flowcells sold reached 30,307, an increase of approximately 15% over the 26,444 flowcells sold during the year ended December 31, 2023.
Installed base represents the global number of OGM instruments installed at end-customer locations to perform optical genome mapping. • For the year ended December 31, 2025, total flowcells sold reached 30,171, a decrease of approximately 0.4% over the 30,307 flowcells sold during the year ended December 31, 2024.
The technology was further developed and commercialized by Purigen. The system includes an instrument, consumable and reagents necessary to process samples. The system works by applying an electric field to specially formulated reagents in a consumable. The electric field electrophoretically focuses nucleic acid into a narrow band and purifies the molecules away from other potential inhibitors.
The system works by applying an electric field to specially formulated reagents in a consumable. The electric field electrophoretically focuses nucleic acid into a narrow band and purifies the molecules away from other potential inhibitors.
During 2024, Bionano Laboratories phased out the offering of the non-OGM-based LDT tests. Key Agreements Agreement for the Manufacture of Our Instruments We have engaged a single third-party manufacturer to produce and test our instruments on an as-ordered basis. The manufacturer of our instruments has no obligation to manufacture our instruments without a purchase order.
During 2024, Bionano Laboratories phased out the offering of the non-OGM-based LDT tests and during 2025 phased out the offering of OGM-based LDT tests for hematological malignancies and pre- and postnatal constitutional genetic disorders. Key Agreements Agreement for the Manufacture of Our Instruments We have engaged a single third-party manufacturer to produce and test our instruments on an as-ordered basis.
DNA is the code that is found in all living cells and determines the characteristics and health of all living organisms. Although each organism’s DNA order is unique, all DNA is composed of the same four nucleotides that come in pairs, which are referred to as base pairs.
Although each organism’s DNA order is unique, all DNA is composed of the same four nucleotides that come in pairs, which are referred to as base pairs.
If a vendor is unable to provide sufficient notification, we keep safety stock of the component to minimize disruption to operations. Manufacturing and Supply Our strategy is to outsource instrument and reagent manufacturing, and critical parts of chip manufacturing. Internally, we quality control (“QC”) all outsourced products and perform final assembly and QC of our chips.
If a vendor is unable to provide sufficient notification, we keep safety stock of the component to minimize disruption to operations. Manufacturing and Supply Our strategy is to outsource instrument and reagent manufacturing, and critical parts of chip manufacturing.
The clinical trials must be conducted in accordance with the FDA’s IDE regulations and good clinical practices. A clinical trial may be suspended by the FDA, the sponsor or an IRB at its institution at any time for various reasons, including a belief that the risks to the study participants outweigh the benefits of participation in the trial.
A clinical trial may be suspended by the FDA, the sponsor or an IRB at its institution at any time for various reasons, including a belief that 25 Table of Contents the risks to the study participants outweigh the benefits of participation in the trial.
We expect to see OGM adoption in cytogenomics, in discovery research and in cell and gene therapy applications. Within cytogenetics and molecular pathology, we estimate that there are approximately 10,000 cytogenetic labs on a worldwide basis (excluding India and developing countries). We estimate that these labs analyze approximately 10.0 million samples per year.
Within cytogenetics and molecular pathology, we estimate that there are approximately 10,000 cytogenetic labs on a worldwide basis (excluding India and developing countries). We estimate that these labs analyze approximately 10.0 million samples per year.
In addition, the manufacturer has no obligation to maintain inventory in excess of any open purchase orders or materials in excess of the amount it reasonably determines will be consumed within 90 days. We are obligated to purchase any material deemed in excess pursuant to our agreement with the manufacturer.
The manufacturer of our instruments has no obligation to manufacture our instruments without a purchase order. In addition, the manufacturer has no obligation to maintain inventory in excess of any open purchase orders or materials in excess of the amount it reasonably determines will be consumed within 90 days.
An electric field is applied to the chip and the nucleic acid is isolated in its natural, native form. Traditional methods of isolating nucleic acid, including column-based isolation and bead-based isolation, can be laborious, and result in molecules that are denatured, dehydrated and fragmented, and solutions that are contaminated and have low purity.
Traditional methods of isolating nucleic acid, including column-based isolation and bead-based isolation, can be laborious, and result in molecules that are denatured, dehydrated and fragmented, and solutions that are contaminated and have low purity.
During 2024, Bionano Laboratories phased out the offering of certain testing services for individuals demonstrating clinical presentations consistent with neurodevelopmental disorders (“NDDs”), including autism spectrum disorders (“ASDs”) and other disorders of childhood development.
During 2024, Bionano Laboratories phased out the offering of certain testing services for individuals demonstrating clinical presentations 8 Table of Contents consistent with neurodevelopmental disorders (“NDDs”), including autism spectrum disorders (“ASDs”) and other disorders of childhood development, and during 2025 phased out the offering of OGM-based LDT tests for hematological malignancies and pre- and postnatal constitutional genetic disorders.
Testing and Laboratory Services Bionano Laboratories’ OGM testing is performed at our lab in San Diego, California, or at our partner labs in the United States and Europe. Bionano Laboratories’ San Diego lab is CLIA accredited and CAP certified. For diagnostic testing, Bionano Laboratories offers OGM-based LDTs for postnatal, prenatal and hematological malignancy applications performed at its San Diego facility.
Testing and Laboratory Services Bionano Laboratories’ OGM testing is performed at our lab in San Diego, California, or at our partner labs in the United States and Europe. Bionano Laboratories’ San Diego lab is CLIA accredited and CAP certified.
Starting with UHMW DNA purified using the appropriate Bionano Prep kit, fluorescent labels are attached to specific sequence motifs. The result is uniquely identifiable genome-specific label patterns that enable de novo map assembly, anchoring sequencing contigs and discovery of SVs as small as 500 base pairs to up to chromosome arm lengths.
The result is uniquely identifiable genome-specific label patterns that enable de novo map assembly, anchoring sequencing contigs and discovery of SVs as small as 500 base pairs to up to chromosome arm lengths.
Below are discussions concerning government regulation of our Optical Genome Mapping, or OGM, products and services and, separately, the Diagnostic Services performed by Bionano Laboratories. Optical Genome Mapping Our OGM products are currently intended for RUO applications, although our customers may use our products to develop their own products that are subject to regulation by the FDA.
Optical Genome Mapping Our OGM products are currently intended for RUO applications, although our customers may use our products to develop their own products that are subject to regulation by the FDA.
The FDA is supposed to make a SE determination within 90 days of FDA’s receipt of the 510(k), but it often takes longer if the FDA requests additional information.
The FDA is supposed to make a SE determination within 90 days of FDA’s receipt of the 510(k), but it often takes longer if the FDA requests additional information. Most 510(k)s do not require supporting data from clinical trials, but the FDA may request such data.
In addition, we can participate directly in the NGS and array markets for genetic disease and cancer applications independent of OGM using a monetization model with a pay-per-sample VIA™ software offering.
We believe that simplified data interpretation and a seamless integration with NGS and array data to provide the most compressive genome analysis will increase utilization. In addition, we can participate directly in the NGS and array markets for genetic disease and cancer applications independent of OGM using a monetization model with a pay-per-sample VIA software offering.
Coverage and Reimbursement Currently, our OGM products are for research use only, but clinical laboratories may acquire our instrumentation through a capital purchase or capital lease and use of an OGM system and direct label and stain chemistry to create their own diagnostic tests and potentially seek reimbursement for such tests.
Currently, our OGM systems are for RUO, but clinical laboratories may acquire our instrumentation through a capital purchase or capital lease and use the OGM system and direct label stain chemistry to create their own potentially reimbursable products, such as laboratory developed tests for in vitro diagnostics.
If, in the future, we operate our own clinical laboratory to perform clinical diagnostic testing with respect to our OGM products, such activities would become subject to the Health Insurance Portability and Accountability Act of 1996 (“HIPAA”), and its corresponding regulations, as well as additional federal and state laws that impose a variety of fraud and abuse prohibitions on healthcare providers, including clinical laboratories.
If, in the future, we operate our own clinical laboratory to perform clinical diagnostic testing with respect to our OGM products, such activities would become subject to the Health Insurance Portability and Accountability Act of 1996 (“HIPAA”), and its corresponding regulations, as well as additional federal and state laws that impose a variety of fraud and abuse prohibitions on healthcare providers, including clinical laboratories. 27 Table of Contents Coverage and Reimbursement Currently, our OGM products are for research use only, but clinical laboratories may acquire our instrumentation through a capital purchase or capital lease and use of an OGM system and direct label and stain chemistry to create their own diagnostic tests and potentially seek reimbursement for such tests.
Other factors that complicate billing include: • variability in coverage and information requirements among various payors; • patient financial assistance programs; • missing, incomplete or inaccurate billing information provided by ordering physicians; • billings to payors with whom we do not have contracts; • disputes with payors as to which party is responsible for payment; and • disputes with payors as to the appropriate level of reimbursement.
Other factors that complicate billing include: • variability in coverage and information requirements among various payors; • patient financial assistance programs; • missing, incomplete or inaccurate billing information provided by ordering physicians; • billings to payors with whom we do not have contracts; • disputes with payors as to which party is responsible for payment; and • disputes with payors as to the appropriate level of reimbursement. 30 Table of Contents Depending on the reimbursement arrangement and applicable law, the party that reimburses us for our services may be: • a third-party who provides coverage to the patient, such as an insurance company or managed care organization; • a state or federal healthcare program; or • the patient.
Our Bionano Laboratories business has developed and provides several OGM-based laboratory developed tests (“LDTs”) for facioscapulohumeral muscular dystrophy type 1 (“FSHD1”), which is a progressive disorder that primarily affects the muscles of the face, shoulder blades (scapula), upper arms, and lower legs, for detecting SVs in individuals with hematologic malignancies, and for detecting SVs in pre- and post-natal samples, through its OGM-Dx™ testing services.
Our Bionano Laboratories business has developed and provides an OGM-based LDT for facioscapulohumeral muscular dystrophy type 1 (“FSHD1”), which is a progressive disorder that primarily affects the muscles of the face, shoulder blades (scapula), upper arms, and lower legs.
The Ionic ® Purification System We acquired the Ionic® Purification system through our November 2022 acquisition of Purigen. The Ionic® Purification system uses a proprietary ITP method to isolate and purify nucleic acid molecules. The technology was initially developed at Stanford University and intellectual property from that development was exclusively licensed to Purigen.
The Ionic Purification system uses a proprietary ITP method to isolate and purify nucleic acid molecules. The technology was initially developed at Stanford University and intellectual property from that development was exclusively licensed to Purigen. The technology was further developed and commercialized by Purigen. The system includes an instrument, consumable and reagents necessary to process samples.
We sell our OGM systems on an RUO basis to CLIA certified cytogenetic laboratories, which may use the system to develop LDTs. 21 Table of Contents On May 6, 2024, the FDA published a final rule on the regulation of LDTs which amends the FDA’s regulations to make explicit that LDTs are IVDs and regulated as devices under the FDCA.
On May 6, 2024, the FDA published a final rule on the regulation of LDTs which amends the FDA’s regulations to make explicit that LDTs are IVDs and regulated as devices under the FDCA.
Although OGM is our primary focus, the Ionic® Purification system has a current customer base of non-OGM users that use the system to isolate and purify nucleic acid molecules from sample types including formalin-fixed, paraffin-embedded (“FFPE”) sample, tissue, cells, and viral. We anticipate continuing to support and expanding this customer base.
We believe the addition of the Ionic Purification system to the OGM workflow will provide a more efficient yield of DNA at higher quality than can be achieved with current processes. 13 Table of Contents Although OGM is our primary focus, the Ionic Purification system has a current customer base of non-OGM users that use the system to isolate and purify nucleic acid molecules from sample types including formalin-fixed, paraffin-embedded (“FFPE”) sample, tissue, cells, and viral.
Our kits and protocols enable the extraction of UHMW DNA from a variety of sample types including human or animal tissue and tumors, plant tissue, cell lines, bone marrow aspirates and human blood. Our labeling reagents are optimized for applications on our genome mapping systems.
The resulting purified DNA is up to millions of base pairs long and optimal for use with our systems. Our kits and protocols enable the extraction of UHMW DNA from a variety of sample types including human or animal tissue and tumors, plant tissue, cell lines, bone marrow aspirates and human blood.
Information contained in, or that can be accessed through, our website is not incorporated by reference into this Annual Report, and you should not consider information on our website to be part of this Annual Report. Our design logo, “Bionano,” and our other registered and common law trade names, trademarks and service marks are the property of Bionano Genomics, Inc.
Information contained in, or that can be accessed through, our website is not incorporated by reference into this Annual Report, and you should not consider information on our website to be part of this Annual Report.
Available Information Access to our Annual Report, quarterly reports on Form 10-Q, current reports on Form 8-K, and amendments to these reports filed with or furnished to the SEC, may be obtained through the investor section of our website at http://www.bionano.com. We do not charge for access to and viewing of these reports.
Our design logo, “Bionano,” and our other registered and common law trade names, trademarks and service marks are the property of Bionano Genomics, Inc. 34 Table of Contents Available Information Access to our Annual Report, quarterly reports on Form 10-Q, current reports on Form 8-K, and amendments to these reports filed with or furnished to the SEC, may be obtained through the investor section of our website at http://www.bionano.com.
We believe that our OGM systems can replace more traditional cytogenetic tools which are expensive, slow and labor-intense, with an advanced solution designed to simplify workflow, reduce cost, and increase assay success rates. We believe our OGM systems have the potential to significantly increase success rates and provide more answers across a wide range of applications in genomics.
Our customers include researchers and clinicians who seek to identify and understand the biological implications of genome variation. We believe that our OGM systems can replace more traditional cytogenetic tools which are expensive, slow and labor-intense, with an advanced solution designed to simplify workflow, reduce cost, and increase assay success rates.
The sales process typically involves numerous interactions and demonstrations with multiple people within an organization. Some potential customers conduct in-depth evaluations of the system including having us run experiments on in-house OGM systems. In addition, in most countries, sales to academic or governmental institutions require participation in a tender process involving preparation of extensive documentation and a lengthy review process.
Our systems are relatively new to the life science marketplace and require a capital investment by our customers. The sales process typically involves numerous interactions and demonstrations with multiple people within an organization. Some potential customers conduct in-depth evaluations of the system including having us run experiments on in-house OGM systems.
Our goal is to streamline SV identification and enable new research in genomics to allow greater insight into their role in human health in ways that have not been possible with any other current research and diagnostic technologies.
Our goal is to streamline SV identification and enable new research in genomics to allow greater insight into their role in human health in ways that have not been possible with any other current research and diagnostic technologies. 19 Table of Contents Our strategy to achieve this goal includes: • Demonstrate that our OGM systems are a superior alternative to traditional techniques in constitutional genetic disorders and hematologic malignancy applications.
This commercial staff was located in North America, and the sales personnel primarily worked remotely in U.S. states where Bionano Laboratories has obtained insurance reimbursement. The sales and marketing efforts were targeted primarily at specialty pediatricians, including pediatric neurologists, medical geneticists, and developmental and behavioral pediatricians. Bionano Laboratories also targeted general pediatricians with large numbers of patients.
The sales and marketing efforts were targeted primarily at specialty pediatricians, including pediatric neurologists, medical geneticists, and developmental and behavioral pediatricians. Bionano Laboratories also targeted general pediatricians with large numbers of patients.
Most 510(k)s do not require supporting data from clinical trials, but the FDA may request such data. 20 Table of Contents Premarket Approval Pathway A PMA must be submitted if a new device cannot be cleared through the 510(k) process. The PMA process is generally more complex, costly and time consuming than the 510(k) process.
Premarket Approval Pathway A PMA must be submitted if a new device cannot be cleared through the 510(k) process. The PMA process is generally more complex, costly and time consuming than the 510(k) process.
We believe there are additional potential future market opportunities for OGM including newborn screening, population genomics, and neurological and cardiological risk assessment which are not included in our estimates above.
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.

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Item 1C. Cybersecurity

Cybersecurity — threats and controls disclosure

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Biggest changeFor example, the security and compliance team works with management to prioritize our risk management processes and mitigate cybersecurity threats that are more likely to lead to a material impact to our business, and evaluates material risks from cybersecurity threats and reports to the audit committee of the board of directors (“Audit Committee”), which evaluates our overall enterprise risk.
Biggest changeFor example, the security and compliance team works with management to prioritize our risk management processes and mitigate cybersecurity threats that are more likely to lead to a material impact to our business, and evaluates material risks from cybersecurity threats and reports to the audit committee of the board of directors (“Audit Committee”), which evaluates our overall enterprise risk. 99 Table of Contents We use third-party service providers to assist us from time to time to identify, assess, and manage material risks from cybersecurity threats, including for example professional services firms including outside legal counsel, cybersecurity consultants, penetration testing firms, cybersecurity software providers, managed cybersecurity service providers and threat intelligence service providers.
CYBERSECURITY Risk management and strategy We have implemented and maintain various information security processes designed to identify, assess and manage material risks from cybersecurity threats to our critical computer networks, third party hosted services, communications systems, hardware and software, and our critical data, including intellectual property, confidential information that is proprietary, strategic or competitive in nature, and customer data that use to provide services for our customers (“Information Systems and Data”).
CY BERSECURITY Risk management and strategy We have implemented and maintain various information security processes designed to identify, assess and manage material risks from cybersecurity threats to our critical computer networks, third party hosted services, communications systems, hardware and software, and our critical data, including intellectual property, confidential information that is proprietary, strategic or competitive in nature, and customer data that use to provide services for our customers (“Information Systems and Data”).
The Audit Committee receives periodic reports concerning the Company’s significant cybersecurity threats and risk and the processes the Company has implemented to address them. The Audit Committee also receives various reports, summaries or presentations related to cybersecurity threats, risk and mitigation. 72 Table of Contents
The Audit Committee receives periodic reports concerning the Company’s significant cybersecurity threats and risk and the processes the Company has implemented to address them. The Audit Committee also receives various reports, summaries or presentations related to cybersecurity threats, risk and mitigation. 100 Table of Contents
IT security leadership, the PFO, CEO and GC work with the Company’s incident response team to help the Company mitigate and 71 Table of Contents remediate cybersecurity incidents of which they are notified. In addition, the Company’s incident response plan includes reporting to the Audit Committee for certain cybersecurity incidents.
IT security leadership, the PFO, CEO and GC work with the Company’s incident response team to help the Company mitigate and remediate cybersecurity incidents of which they are notified. In addition, the Company’s incident response plan includes reporting to the Audit Committee for certain cybersecurity incidents.
We have not experienced a cybersecurity incident that would materially affect the company’s business strategy, results of operations or financial position. For a description of the risks from cybersecurity threats that may materially affect the Company and how they may do so, see our risk factors under Part 1. Item 1A.
We have not experienced any cybersecurity incidents that have materially affected, or are reasonably likely to materially affect, the Company’s business, results of operations or financial condition. For a description of the risks from cybersecurity threats that may materially affect the Company and how they may do so, see our risk factors under Part 1. Item 1A.
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We use third-party service providers to assist us from time to time to identify, assess, and manage material risks from cybersecurity threats, including for example professional services firms including outside legal counsel, cybersecurity consultants, penetration testing firms, cybersecurity software providers, managed cybersecurity service providers and threat intelligence service providers.

Item 2. Properties

Properties — owned and leased real estate

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Biggest changeITEM 2. PROPERTIES We lease an aggregate of approximately 41,101 square feet of office, laboratory, and manufacturing space in two buildings at our headquarters in San Diego, California, with the lease for all rented space expiring December 31, 2025.
Biggest changeITEM 2. PR OPERTIES We lease an aggregate of approximately 24,494 square feet of office, laboratory, and manufacturing space in one building at our headquarters in San Diego, California, with the lease originally expiring on December 31, 2025, and later amended to December 31, 2030.
In October 2021, through the acquisition of BioDiscovery, we obtained a finance lease for approximately 4,786 square feet of office space in El Segundo, California that expires in February 2041.
In October 2021, through the acquisition of BioDiscovery, we obtained a finance lease for approximately 4,786 square feet of office space in El Segundo, California that expires in February 2041. We believe our properties are sufficient to satisfy our current needs.
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In December 2021, we executed a new lease for approximately 11,978 additional square feet of office and laboratory space in San Diego, California that expires in January 2026.
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In January 2022, we executed an amendment to our headquarters lease for a new unit adding an additional 5,278 square feet of office and laboratory space in San Diego, California that expires in January 2026.
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In August 2020, through the acquisition of Lineagen we obtained a lease for approximately 9,710 square feet of office space in Salt Lake City, Utah under a non-cancelable operating lease that was to expire December 2026. We conducted part of our Bionano Laboratories business at this property.
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In connection with the Company’s restructuring initiatives, the Company entered into a lease termination agreement on February 28, 2024 with the landlord for the facility in Salt Lake City. The Company continued to lease the property through the end of June 2024.
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In November 2022, through the acquisition of Purigen, we obtained an operating lease for approximately 16,165 square feet of office and laboratory space in Pleasanton, California that was to expire in July 2027. In January 2025, the Company entered into a lease termination agreement with the landlord for the facility in Pleasanton, California.
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The Company continued to lease the property through the end of January 2025. We believe our properties are sufficient to satisfy our current needs.

Item 3. Legal Proceedings

Legal Proceedings — active lawsuits and investigations

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Biggest changeITEM 3. LEGAL PROCEEDINGS We are not currently a party to any material legal proceedings and we are not aware of any pending or threatened legal proceedings against us that could reasonably be expected to have a material adverse effect on our business, financial condition or results of operations. ITEM 4. MINE SAFETY DISCLOSURES Not applicable. PART II
Biggest changeITEM 3. LEG AL PROCEEDINGS We are not currently a party to any material legal proceedings and we are not aware of any pending or threatened legal proceedings against us that could reasonably be expected to have a material adverse effect on our business, financial condition or results of operations.

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