What changed in this filing

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Item 1. Business

2025-03-31 compared with 2024-03-05 · 111 added, 164 removed, 549 unchanged (33% of the section changed)

We are a global genomics company focused on elevating the health and wellness of all people.

We are pioneers of optical genome mapping (“OGM”) for genome analysis and provide a suite of genome analysis solutions designed to 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 our OGM solutions, our nucleic acid isolation and purification solutions, our genomic analysis and interpretation software, and our clinical testing and laboratory services, we believe that we have a suite of products that will drive new discoveries, elevate health and wellness, and increase our understanding of the genome in transformative ways.

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.

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.

The Company also offers nucleic acid extraction and purification solutions using proprietary isotachophoresis ITP technology.

Through our Bionano Laboratories business, we also provide OGM-based diagnostic testing services.

We market and sell OGM systems, including the Saphyr ® system and the Stratys™ system, which deliver OGM data to enable ultra-sensitive and ultra-specific detection of all classes of structural variation (“SV”).

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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 purifications solutions.

The Ionic ® Purification system is used to extract, purify, and concentrate DNA or RNA from a variety of sample types, and is comprised of an instrument, consumables, and reagents.

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We believe the integration of OGM with data types common in the industry, such as Variant Call Format (“VCF”), and Binary Alignment Map (“BAM”), into the VIA software should accelerate and broaden our position in digital cytogenetics and comprehensive genome analysis by enabling us to simplify the assessment of clinically relevant variants in cytogenomics applications, potentially reducing interpretation time per sample and expanding our reach into the discovery and translational research markets through the combination of OGM and NGS.

Our Bionano Laboratories business provides proprietary genetic clinical testing services for individuals demonstrating clinical presentations consistent with neurodevelopmental disorders (“NDDs”), including autism spectrum disorders (“ASDs”) and other disorders of childhood development.

Their comprehensive genetic testing services include reporting for known NDD-causing genome variations, including testing for proprietary variations, and combines testing with our Proprietary Variant Index (PRISM) which uses a proprietary database of over 35,000 individuals with NDDs tested with over 60,000 tests that provides additional evidence for candidate genes associated with NDDs.

This testing is a CLIA-certified diagnostic testing service, and we have expertise in selling cytogenetic assays to physicians, providing genetic counseling services to individuals undergoing testing and their families, and contracting with third-party payors for reimbursement.

Additionally, Bionano Laboratories has developed 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, and for detecting SVs in individuals with hematologic malignancies.

As of March 1, 2024, we decided to phase out over time the offering by Bionano Laboratories of certain testing services related to NDDs, including ASDs, and other disorders of childhood development.

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.

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.

Bionano Laboratories also provides laboratory services to clinicians, scientists, pharmaceutical companies, and others who are seeking to incorporate OGM into their genomics research without the need to bring one of our OGM systems in house.

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.

Over the past year, we believe we have transformed our business from an instrument company to a provider of a full suite of genomic solutions.

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 furthered our transformation through the expansion into software solutions, made possible by our October 2021 acquisition of BioDiscovery and continued with our November 2022 acquisition of Purigen bringing their leading nucleic acid

isolation and purification technology to Bionano.

We believe that these acquisitions, along with internal investments in research and development and the build out of our commercial teams, have positioned us well to provide solutions to our customers that we believe will make OGM the standard cytogenetic technique for structural variant analysis.

Despite these transformations, as part of our cost saving initiatives we have also made a change in our 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 (as further described throughout this Annual Report).

Recent Highlights

Achievement of 2023 ELEVATE!

Bionano executed on its 2023 ELEVATE!

milestones and achieved or exceeded all publicly stated milestones outlined at the beginning of 2023.

• Reimbursement:

We submitted a dossier to Medicare seeking a local coverage determination (“LCD”) for OGM coverage.

• Clinical Studies:

We received institutional review board (IRB) approval for our hematological and solid tumor studies.

Site selection was completed, and sample enrollment commenced for our prenatal, postnatal, and hematological malignancy clinical trial studies.

Data collection for our prenatal study was completed.

We completed our postnatal study.

We had an interim publication for our prenatal and hematological malignancy studies.

We had a peer-reviewed interim publication from postnatal study.

• Expand Awareness:

We achieved an installed base of 326 OGM systems.

We conducted a pre-submission discussion with FDA in connection with the planned clearance of the Stratys™ system.

• Product Developments:

◦ Full commercial release of our high throughput OGM instrument, called the Stratys™ system was announced in early 2024.

The Stratys system is expected to enable a four-fold increase in raw data generation rate compared to the Saphyr® system and is designed for maximum lab flexibility by enabling up to 12 single access chips, accessible as they complete runs, without the need to batch multiple samples on a consumable.

◦ We released VIA software, which replaces NxClinical™ software with a simple and integrated workflow for visualization, interpretation, and reporting for OGM, microarray and next-generation sequencing (NGS) data types for enhanced contextualization across multiple variant types and accelerated time to results at a reduced cost.

◦ We released a pre-commercial version of the Ionic Purification System for isolation of DNA for OGM analysis running in the field with the full commercial launch planned for the second half of 2024.

◦ We launched an OGM laboratory developed test (LDT) for constitutional genetic disease applications through Bionano Laboratories.

Achievement of Business Milestones in 2024

• Completed full commercial release of high throughput OGM instrument, called the Stratys™ system.

The Stratys™ system is expected to enable a four-fold increase in raw data generation rate compared to the Saphyr® system and is designed for maximum lab flexibility to enable routine use in consolidating legacy cytogenetic workflows into streamlined OGM workflows.

• Released advancements in data analysis with updates to VIA ™ software, which provides a simple and integrated workflow for visualization, interpretation, and reporting for OGM, microarray and NGS data types for enhanced contextualization across multiple variant types and accelerated time to results while reducing the cost of analysis by lowering the amount of high-cost labor required.

• Released the first version of a computation solution for OGM developed in collaboration with NVIDIA, called Stratys™ Compute , which, along with a new analysis pipeline, can accelerate data analysis times compared to its predecessor, Saphyr® Compute.

Stratys Compute is a low footprint IT solution that can be deployed quickly, sitting next to a Stratys™ system in any lab, allowing labs of all sizes to adopt Stratys.

• The AMA established a category I CPT code for OGM which is a key component OGM users may take advantage of to get reimbursement from insurance companies and other third-party payers.

• The International System for Human Cytogenomic Nomenclature (ISCN) added OGM nomenclature to its 2024 guide.

• The American College of Medical Genetics (ACMG) recognized OGM as a key tool in postnatal and solid tumor applications in two publications.

Commercial Adoption of Offerings for OGM

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The OGM chip is the consumable that packages nanochannel arrays for DNA linearization.

In its current form, each OGM chip has three flowcells.

Flowcells sold refers to the units of genome mapping consumables used for analyzing one genome, purchased by customers to process optical genome mapping.

In its current form, the OGM chip can comprise - one, two or three flowcells per chip.

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.

Continued to Validate the Utility of OGM for Applications in Clinical Research with Benchmarking, Scientific Publication and Adoption

Rigorous and extensive benchmarking of our OGM systems against traditional cytogenetic methods and long read sequencing has continued and these results were published and validated in several key publications, presentations and announcements including:

• In a study published in Nature Communications, OGM was used for the evaluation of CRISPR-Cas9 edited human induced pluripotent stem cell lines in order to uncover possible pathogenic structural alterations that may limit their usefulness for stem cell therapy.

The study authors found that approximately 15% of CRISPR-Cas9 edited genomes had potentially pathogenic large chromosomal deletions at two unexpected off-target sites.

In addition to those two off-target deletions, the authors reported that OGM identified a large, unexpected deletion at the target site.

• Researchers from Augusta University published a study comparing a combined approach of OGM and a 523-gene next-generation sequencing (NGS) panel to the common approach of karyotyping and FISH with a 54-gene NGS panel for the evaluation of myeloid cancers.

OGM and the 523-gene NGS panel had an analytical concordance of 100% with karyotyping, FISH, and the 54-gene panel, and the OGM workflow also led to changes in risk assessment in 22% of myelodysplastic syndrome cases (2/9) and identified compound heterozygous events of potential clinical relevance in 20% of cases (6/30).

• A peer-reviewed publication covered an interim readout from the clinical trial designed to support establishing OGM as part of the standard of care (SOC) in diagnosis of genetic disease for postnatal patients.

The clinical trial is designed to compare OGM to the SOC, including concordance, reproducibility, technical success rate and the rate of detecting reportable findings in cases.

The study, which included 404 samples, showed OGM’s high technical performance and reproducibility across sites versus SOC analysis, with 99.5% concordance, and an overall success rate of 98.8%.

• A framework for consistent, universal OGM analysis in hematologic malignancies published by an international consortium comprising 17 different distinguished researchers.

• Publications from our clinical studies in post and pre-natal constitutional genetic disease.

• Four papers on use of OGM in blood cancer research published by MD Anderson Cancer Center, including one describing the use of OGM in the largest single cohort of 1277 hematologic malignancy samples.

• Two publications from Johns Hopkins University Medical Center outlining use of OGM in two new applications:

multiple myeloma and sarcoma.

Macroeconomic and Geopolitical Developments

We are subject to additional risks and uncertainties as a result of adverse geopolitical and macroeconomic developments, such as the ongoing conflict between Ukraine and Russia and related sanctions, the Israel-Hamas war, any effects of global pandemics, and uncertain market conditions, including inflation and supply chain disruptions, which could continue to have a material impact on our business and financial results.

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 conflicts between Ukraine and Russia and in the Middle East, related sanctions, and any effects of regional and global pandemics and uncertain market conditions, including inflation and supply chain disruptions, which, to date, have not had a material impact on our business and financial results.

For a more detailed discussion of the impacts of macroeconomic and geopolitical developments on our business, see “Management’s Discussion and Analysis of Financial Condition and Results of Operations - Macroeconomic and Geopolitical Developments.”

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The majority of software solutions on the market today have been developed with NGS as the primary application with the focus on the interpretation and reporting of single nucleotide variants (“SNVs”) instead of SVs.

predecessor of our VIA software (NxClinical) was developed with copy number variants (CNV) as the core focus and became established as an industry leading solution for interpretation and reporting of CNVs for CMA and NGS.

The predecessor of our VIA™ software (NxClinical) was developed with copy number variants (“CNV”) as the core focus and became established as an industry leading solution for interpretation and reporting of CNVs for CMA and NGS.

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.

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We highly value our relationships with third parties that enable us to provide these solutions and will continue to work with others to ensure our customers’ needs are being met.

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.

To that end, we have recently engaged in two transactions, which we believe will substantially benefit our customers and their adoption of OGM as a solution of choice for SV and CNV analysis.

In 2021 we acquired BioDiscovery and its leading NxClinical software for data analysis, and in 2022 we acquired Purigen, and its proprietary isolation and purification technology.

We believe that each of these acquisitions, together with our organic development, will significantly enhance the customer experience with OGM.

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.

To that end, in 2021 we acquired BioDiscovery and its leading NxClinical software for data analysis, and in 2022 we acquired Purigen, and its proprietary isolation and purification technology.

We believe that each of these acquisitions, together with our organic development, will substantially benefit our customers and their adoption of OGM as a solution of choice for SV and CNV analysis and significantly enhance the customer experience with OGM.

Our systems use a proprietary approach to measure genome structure and SV through OGM.

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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.

Today, VIA software is among the most comprehensive solutions for analysis and interpretation OGM data and any microarray or NGS generated data integrating CNVs, absence of heterozygosity (AOH) and loss of heterozygosity (LOH), as well as SNVs from sequencing data into a single well integrated interface that is used across the globe by renowned academic and commercial clinical laboratories.

Today, VIA software is among the most comprehensive solutions for analysis and interpretation of OGM data and any microarray or NGS generated data integrating CNVs, absence of heterozygosity (“AOH”) and loss of heterozygosity (“LOH”), as well as SNVs from sequencing data into a single well integrated interface that is used across the globe by renowned academic and commercial clinical laboratories.

Our acquisition of BioDiscovery has expanded our portfolio into providing data analysis and interpretation solutions across NGS, CMA and OGM.

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Additionally, through our VIA software, we serve the NGS and array markets directly though with an industry leading data interpretation solution for revealing more answers with delivery of copy number variants across the genome.

Our software monetization strategy for the NGS and array markets is based on a pay-per-sample model where customers running NGS and/or array today can adopt, which sets the stage for potential future OGM adoptions by these

Software is a way for us to participate directly in the NGS market while also enabling OGM data to be seamlessly integrated with NGS in one view for a comprehensive analysis, which is unique to Bionano.

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Studies are ongoing to determine the sensitivity and specificity for OGM as it relates to fragile X syndrome.

Bionano Laboratories also employs Whole Exome Sequencing, which aims to detect genome SNVs that are different from genome SVs and are not detectable by OGM.

We believe that Bionano Laboratories is uniquely positioned to develop LDT’s that can improve upon the existing SOC for diagnostic testing for NDDs.

Bionano Laboratories also

employs Whole Exome Sequencing, which aims to detect genome SNVs that are different from genome SVs and are not detectable by OGM.

We believe that Bionano Laboratories is uniquely positioned to develop LDT’s that can improve upon the existing standard of care (“SOC”) for OGM-based diagnostic testing.

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.

Bionano Laboratories plans to 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 equipment expenditure.

Bionano Laboratories is working to enable access, demonstrate excellence of the OGM workflow as a model within a CLIA setting for educational purposes, and drive advancements in product development for clinical grade testing of OGM at scale.

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We are optimizing the system with the intent it be used in an OGM workflow.

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.

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.

Software Solutions

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• 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.

Additionally, 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 March 1, 2024 has determined to phase out over time the offering of these products, including:

Additionally, 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;

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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 the three areas of the genomics market that are driving demand for the OGM systems today:

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%.

We believe there are three areas of the genomics market that are driving demand for the OGM systems today:

• Consolidation of traditional cytogenetics techniques in two applications - constitutional genetic disease and cancer.

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We believe that cell and gene therapy is an emerging market opportunity and could be up to $3.0 billion annually with the potential for approximately 2.4 million samples per year analyzed.

We believe that if our OGM-based solutions can successfully penetrate these addressable market opportunities, and should spur additional basic and translational research creating new areas where the OGM instruments and OGM data can be used to improve the standard of care and patient management.

These may include preconception, products of conception and prenatal

genetic applications, uses to advance gene editing techniques and precision medicine.

We believe that our OGM-based solutions can successfully penetrate these addressable market opportunities, and should spur additional basic and translational research creating new areas where the OGM instruments and OGM data can be used to improve the standard of care and patient management.

These may include preconception, products of conception and prenatal genetic applications, uses to advance gene editing techniques and precision medicine.

In the long term, we anticipate potential opportunities in newborn screening, population genomics, and neurological and cardiological risk assessment.

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• Accelerate broad reimbursement for OGM and establish it as the SOC in guidelines by professional medical societies.

We are investing in four multi-center clinical studies for postnatal, prenatal, hematologic malignancies and solid tumor analyses relative to SOC.

Each study is designed with an expectation for recruitment of 1,000 subjects and will assess sensitivity, specificity, reproducibility, concordance and incremental clinically relevant findings relative to SOC.

We are investing in these programs to build the necessary evidence to establish reimbursement and to pave the way for inclusion in professional society guidelines to advance SOC.

We have previously invested in 3 multicenter clinical studies for postnatal, prenatal and hematologic malignancies analyses relative to SOC.

The studies progressed and resulted in 4 multi-site peer-reviewed publications.

The programs were designed to build the necessary evidence to establish reimbursement and to pave the way for inclusion in professional society guidelines to advance SOC.

We are no longer investing in these programs.

issued a category 1 CPT code for OGM in heme malignancies (code 81195) which was priced by the Clinical Laboratory Fee Schedule (“CLFS”) and effective Jan 1, 2025.

• Support the publication of findings with OGM by our customers beyond the more than 1,300 papers published to date.

The annual number of publications featuring data generated by Bionano OGM systems has steadily increased since 2010 when the first publication appeared.

Of these 1000 peer-reviewed and pre-print papers, more than 67% were published since 2021.

We intend to continue to support and foster our customer base to help grow the number of publications featuring our systems’ data.

We believe that these publications are impactful as they cover SVs in areas of high unmet medical need, such as rare and undiagnosed pediatric diseases, neurological and muscular diseases, developmental delays and disorders, multiple leukemia, lymphoma and myelomas as well as cell and gene therapy applications.

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.

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.

We believe these publications are highly impactful as they address SVs in areas of significant unmet medical need, including rare and undiagnosed pediatric diseases, neurological and muscular disorders, developmental delays, acute and chronic leukemias, lymphomas, myelomas, and applications in cell and gene therapy.

• Continue to innovate our products and technologies.

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• Partner with industry-leading companies and laboratories to expand adoption in clinical markets.

Establish additional collaborations with customers to help drive validating studies.

Expand partnership efforts with clinical diagnostic companies to commercialize LDTs in the U.S.

We intend to e stablish additional collaborations with customers to help drive validating studies and expand partnership efforts with clinical diagnostic companies to commercialize LDTs in the U.S.

as well as LDTs and approved tests outside the U.S.

• Complement NGS with OGM in translational, applied and discovery research markets.

In addition to the three areas of the genomics market that are driving demand for the OGM systems today, we believe the combination of NGS and OGM can provide the most comprehensive and cost-effective analysis of genome variants from SNVs to whole chromosomes.

In addition to the three areas of the genomics market that we believe are driving demand for the OGM systems today, we believe the combination of NGS and OGM can provide the most comprehensive and cost-effective analysis of genome variants from SNVs to whole chromosomes.

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.

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Sales and Marketing

As of December 31, 2023, our commercial team consisted of 146 individuals in sales, sales support and marketing.

Our sales support personnel include individuals in customer solutions, field service engineers and field application specialists.

This commercial staff is primarily located in North America, Europe, and China.

Most of our sales support team is located at our headquarters in San Diego, California and some work remotely throughout North America, Europe, and China.

This commercial staff is primarily located in North America and Europe.

Most of our sales support team is located at our headquarters in San Diego, California and some work remotely throughout North America and Europe.

We sell our products through a direct sales force based in North America and Europe.

Our sales strategy involves the use of a combination of sales managers and sales representatives.

We intend to increase our sales, support, and marketing efforts in the future by continuing to expand our direct footprint in North America and Europe as well as developing a more comprehensive support network in China and India, where we believe significant market opportunities exist, as we expand our business.

We intend to focus our sales, support, and marketing efforts in order to drive utilization within our existing customer base and seek to opportunistically expand our installed base with new customers who show a commitment to adopting OGM.

We are continuing to develop our support networks in China and India, and believe significant market opportunities exist.

We sell our products through a network of distributors in the Asia-Pacific region and select other markets outside of North America and Europe.

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The role of our field application specialists is to provide on-site training and scientific technical support to prospective and existing customers.

Our field application specialists are technical experts with advanced degrees, including nine with PhDs., and generally have extensive experience in academic research and core sequencing lab experience.

Our field application specialists are technical experts with advanced degrees, including some with PhDs., and generally have extensive experience in academic research and core sequencing lab experience.

In addition, we maintain an applications lab team in San Diego, California composed of scientific experts who can transfer knowledge from the research and development team to the field application specialists.

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Because of these factors and the budget cycles of our customers, our sales cycle, the time from initial contact with a customer to our receipt of a purchase order, can often be nine to 12 months.

Bionano Laboratories primarily sells a suite of LDTs to pediatric physicians through a physician-directed “in-person” sales model.

This commercial staff is located in North America, and the sales personnel primarily work remotely in U.S.

Bionano Laboratories primarily offered a suite of LDTs to pediatric physicians through a physician-directed “in-person” sales model.

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 are targeted primarily at specialty pediatricians, including pediatric neurologists, medical geneticists, and developmental and behavioral pediatricians.

Bionano Laboratories also targets general pediatricians with large numbers of patients.

Their managed care efforts are 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.

As of March 1, 2024, we have determined to phase out over time the offering of these LDTs.

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.

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.

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 or nearly complete instruments are shipped by the manufacturer to us for final assembly and quality control testing.

Upon completion, we ship directly to our customers’ locations globally, or distributors’ locations in the case of certain systems sold in the Asia-Pacific region.

Complete instruments are shipped by the manufacturer to us for final quality control testing.

Upon completion, we ship directly to our customers’ locations globally either from our San Diego headquarters or from our third-party managed distributions center in Europe, or, in the case of certain systems sold in the Asia-Pacific region.

Installation of, and training on, our products is provided by our employees in the markets where we conduct direct sales, and by distributors in those markets where we operate with distributors.

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Although we believe that alternatives would be available for both our OGM reagents and ITP reagents, it would take time to identify and validate replacement reagents for our assay kits, which could negatively affect our ability to supply assay kits on a timely basis.

Some reagents are supplied through a single source

Some reagents are supplied through a single source supplier.

This supplier requires a sufficient notification period to allow for supply continuity and the identification and technology transfer to a new supplier in the event either party wishes to terminate the relationship.

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Manufacturing and Supply

Our manufacturing strategy is to outsource instrument and chip manufacturing and internally develop and assemble reagent kits in our own facility.

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.

Our fundamental long-term software strategy is based on our goal of making OGM ubiquitous.

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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.

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.

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.

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 intends to increase its testing capacity.

Bionano Laboratories has CLIA certification for its San Diego lab.

For diagnostic testing, Bionano Laboratories maintains contracts with a network of laboratories to perform the wet work on various non-OGM LDT tests in order to conserve capital and maintain flexibility of adjusting contract labs to seek the best-in-class/most updated technology and customer service.

As of March 1, 2024, we have determined that Bionano Laboratories will phase out over time the offering of the non-OGM LDT tests.

As of December 31, 2023, Bionano Laboratories has established contracts with four primary laboratories to perform wet lab services.

All third-party laboratories have met stringent criteria and are CLIA-certified.

Bionano Laboratories obtains raw data from contracted laboratories for select tests and then performs its own interpretation and reporting.

In addition, Bionano Laboratories’ plans to continue to offer OGM-based LDTs to be performed at its San Diego facility, four of which have been announced.

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.

During 2024, Bionano Laboratories phased out the offering of the non-OGM-based LDT tests.

Key Agreements

License Agreement with Princeton University

In January 2004, we entered into a license agreement (the Princeton License Agreement) with Princeton University (Princeton).

Pursuant to the Princeton License Agreement, we received a worldwide, exclusive right and license to, among other things, manufacture and market products or services utilizing patents and inventions related to our sample preparation, DNA imaging and genomic data analysis platform and other key technology.

We are obligated to pay Princeton an annual license maintenance fee in the mid-four digits, which can be reduced by royalties paid to Princeton during the preceding 12 month period.

We are also obligated to make royalty payments to Princeton equal to (i) a percentage in the mid-single digits of our and any of our sub-licensees’ net sales of products covered by the Princeton License Agreement and (ii) a percentage in the low-single digits of our and any of our sub-licensees’ revenue from services covered by the Princeton License Agreement.

Our royalty obligations continue on a licensed product-by-licensed product and licensed service-by-licensed service basis, in every country of the world, until the later of the last sale of a licensed product or service or the expiration of all the Princeton patent rights covering such products or services.

The term of the Princeton License Agreement will continue until all of our royalty payment obligations have expired, unless terminated earlier.

Princeton may terminate the Princeton License Agreement upon written notice in the event of our material breach of the Princeton License Agreement if such breach remains uncured for 60 days.

We may terminate the Princeton License Agreement without cause upon 60 days’ advance written notice to Princeton.

License Agreement with Stanford University

In connection with our November 2022 acquisition of Purigen, we acquired an amended and restated license agreement (the Stanford License Agreement) between Purigen and the Board of Trustees of the Leland Stanford Junior University (Stanford).

Pursuant to the Stanford License Agreement, we received a worldwide, exclusive right and license to, among other things, make, have made, use, import, offer to sell and sell certain products utilizing patents and inventions related to our ITP-based sample preparation platform.

We are obligated to pay Stanford an annual license maintenance fee in the low-five digits, which can be reduced by royalties paid to Stanford during the preceding 12 month period.

We are also obligated to make royalty payments to Stanford equal to a percentage in the low-single digits of our and any of our sub-licensees’ annual net sales of products covered by the Stanford License Agreement.

Our royalty obligations continue on a licensed product-by-licensed product basis, in every country of the world, until the later of the last sale of a licensed product or the expiration of all the Stanford patent rights covering such products.

The term of the Stanford License Agreement will continue until all of our royalty payment obligations have expired, unless terminated earlier.

Stanford may terminate the Stanford License Agreement upon written notice in the event of our material breach of the Stanford License Agreement if such breach remains uncured for 60 days.

We may terminate the Stanford License Agreement without cause upon 30 days’ advance written notice to Stanford.

Agreement for the Manufacture of Our Instruments

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The manufacturer of our instruments has no obligation to manufacture our instruments without a purchase order.

In addition, this 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 the agreement.

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 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.

Agreement for the Manufacture of Our Chip Consumables

We have engaged a single third-party manufacturer to manufacture our chip consumables used in our Saphyr system and provide engineering services to us.

This third-party has no obligation to manufacture our chip consumables without a purchase order.

The prices and fees we pay are established in our agreement with this manufacturer or determined by the manufacturer pursuant if supported by appropriate information.

Our agreement with this manufacturer automatically renews for successive one year terms unless a party notifies the other party in writing at least 30 days prior to the expiration of the then-current term.

We may terminate an order of the agreement at any time upon 30 days’ written notice.

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.

Agreements for the Manufacture of Our Chip Consumables

We have engaged multiple third-party manufacturers to manufacture our chip consumables used in our OGM systems and provide engineering services to us.

These third-parties have no obligation to manufacture our chip consumables without a purchase order.

The prices and fees we pay are established in our agreements with these manufacturers.

Our agreements with these manufacturers allow for purchases through individual purchase orders or through entering into long term commitments.

Intellectual Property

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Our core technology for nucleic acid research is related to methods and devices for non-sequencing based analysis of macromolecules such as nucleic acids.

Using this technology, long (UHMC) nucleic acids can be suitably labeled and elongated in order to ascertain structural information such as scaffold organization, copy number, and genomic repeats that is not readily obtained with current sequencing-based approaches.

We recently added a portfolio of patents and patent applications related to ITP through the Purigen acquisition, which we plan to continue to pursue and develop.

Using this technology, long (UHMW) nucleic acids can be suitably labeled and elongated in order to ascertain structural information such as scaffold organization, copy number, and genomic repeats that is not readily obtained with current sequencing-based approaches.

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.

We have secured and continue to pursue intellectual property rights globally, including rights related to isolation, purification and analysis of nucleic acid molecules, as well as innovations in the molecular biology and bioinformatics spaces.

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We sell our OGM systems on an RUO basis to CLIA certified cytogenetic laboratories, which may use the system to develop LDTs.

On October 3, 2023 FDA issued proposed regulations under which it would phase out its enforcement discretion approach to LDTs over a period of four years.

Although the proposed regulation is subject to a period of notice and comment, if finalized as proposed, we and our collaborators or customers would be required to obtain PMA approval or 510(k) clearance for certain tests by October 1, 2027.

We would also be subject to device registration and listing requirements, medical device reporting requirements and the requirements of the FDA’s Quality System Regulation.

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.

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.

Notably, implementation of the LDT final rule’s phaseout policy may be affected by the change in administrations.

We may be required to conduct clinical trials prior to continuing to sell our existing LDTs.

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That process will become more difficult and costly to complete.

Other Governmental Regulation

Other Regulatory Requirements

We are subject to laws and regulations related to the protection of the environment, the health and safety of employees and the handling, transportation and disposal of medical specimens, infectious and hazardous waste and radioactive materials.

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Postal Service and the International Air Transport Association.

We generally use third-party vendors to dispose of regulated medical waste, hazardous waste and radioactive materials that we may use during our research.

Our laboratories, and the laboratories of Bionano Laboratories, are subject to federal, state and local regulations relating to the handling and disposal of regulated medical waste, hazardous waste and biohazardous waste, including chemical, biological agents and compounds, blood and bone marrow samples and other human tissue.

Typically, we use outside vendors who are contractually obligated to comply with applicable laws and regulations to dispose of such waste.

These vendors are licensed or otherwise qualified to handle and dispose of such waste.

Laboratories that purchase certain of our OGM products and perform clinical diagnostic testing are also subject to extensive regulation under the Clinical Laboratory Improvement Amendments of 1988 (“CLIA”), requiring clinical laboratories to meet specified standards in areas such as personnel qualifications, administration, participation in proficiency testing, patient test management, quality control, quality assurance and inspections.

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There are several PLA codes on the Medicare Clinical Lab Fee Schedule (“CLFS”) for OGM-based tests as of January 1, 2024.

In June 2024 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 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.

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In Europe, coverage for molecular diagnostic testing is varied.

Countries with statutory health insurance (e.g., Germany, France, The Netherlands) tend to be more progressive in technology adoption with favorable reimbursement for molecular

diagnostic testing.

Countries with statutory health insurance (e.g., Germany, France, The Netherlands) tend to be more progressive in technology adoption with favorable reimbursement for molecular diagnostic testing.

In countries such as the United Kingdom (“UK”) with tax-based insurance, adoption and reimbursement for molecular diagnostic testing is not uniform and is influenced by local budgets.

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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.

Both of Bionano Laboratories’ facilities, one located in Salt Lake City, Utah and the other in San Diego, California are CLIA certified.

These laboratories must comply with all applicable CLIA requirements.

The Bionano Laboratories’ facility, located in San Diego, California is CLIA certified.

This laboratory must comply with all applicable CLIA requirements.

If a clinical laboratory is found to be out of compliance with CLIA standards, CMS may impose sanctions, limit or revoke the laboratory’s CLIA certificate (and prohibit the owner, operator or laboratory director from owning, operating, or directing a laboratory for two years following license revocation), a directed plan of correction, on-site monitoring, civil monetary penalties, civil actions for injunctive relief, criminal penalties, or suspension or exclusion from the Medicare and Medicaid programs.

CLIA provides that a state may adopt laboratory licensure requirements and regulations that are more stringent than those under federal law and requires compliance with such laws and regulations.

The State of Utah follows all CLIA regulations for laboratory facility and personnel requirements.

Utah does not have any additional licensure and regulations.

The State of California follows CLIA regulations for in-state laboratory facilities, but requires additional licensing requirements for laboratory personnel established by the California Department of Public Health (“CDPH”).

As of December 31, 2023, we received CAP accreditation for the San Diego facility.

We received CAP accreditation for the San Diego facility in 2023.

Additionally, certain states require clinical laboratories to obtain out-of-state licenses to test specimens from patients, or to receive orders from physicians, within those states.

Our Salt Lake City and San Diego facilities currently hold such out-of-state laboratory licenses in Pennsylvania and Maryland.

Our San Diego facility currently holds such out-of-state laboratory licenses in California, Maryland, and Pennsylvania.

HIPAA and other Privacy Laws

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Required breach notices must be made as soon as is reasonably practicable, but no later than 60 days following discovery of the breach.

Reports must be made to affected individuals and to the Secretary and, in some

cases depending on the size of the breach, they must be reported through local and national media.

Reports must be made to affected individuals and to the Secretary and, in some cases depending on the size of the breach, they must be reported through local and national media.

Breach reports can lead to investigation, enforcement and civil litigation, including class action lawsuits.

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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.

The IVDR was published in May 2017, marking the start of a five-year period of transition from the IVDD.

During the transitional period the IVDR will come into force gradually, starting with the provisions related to the designation of Notified Bodies and the ability of manufacturers to apply for new certificates under the IVDR.

The transitional period will end on 26 May 2022, the “Date of Application” of the IVDR.

From that point the IVDR will apply fully.

The IVDR was published in May 2017, marking the start of an initial five-year period of transition from the IVDD.

During the transitional period the IVDR came into force gradually, starting with the provisions related to the designation of Notified Bodies and the ability of manufacturers to apply for new certificates under the IVDR.

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 EU has also implemented the GDPR, which requires us to meet new and more stringent requirements regarding the handling of personal data about EU residents.

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Foreign Corrupt Practices Act, as amended (“FCPA”) its books and records provisions and its anti-bribery provisions.

Other Regulatory Requirements

Typically, we use outside vendors who are contractually obligated to comply with applicable laws and regulations to dispose of such waste.

These vendors are licensed or otherwise qualified to handle and dispose of such waste.

For example, the U.S.

Occupational Safety and Health Administration (“OSHA”) has established extensive requirements relating specifically to workplace safety for healthcare employers in the U.S.

This includes requirements to develop and implement multi-faceted programs to protect workers from exposure to blood-borne pathogens, including preventing or minimizing any exposure through needle stick injuries.

For purposes of transportation, some biological materials and laboratory supplies are classified as hazardous materials and are subject to regulation by one or more of the following agencies:

Department of Transportation, the U.S.

Public Health Service, the United States Postal Service, the Office of Foreign Assets Control, and the International Air Transport Association.

We generally use third-party vendors to dispose of regulated medical waste, hazardous waste and radioactive materials and contractually require them to comply with applicable laws and regulations.

Healthcare Reform

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It is possible that the ACA will be subject to judicial or Congressional challenges in the future.

It is unclear how such challenges and the healthcare reform measures of the Biden administration will impact the ACA and our business.

It is unclear how such challenges and the healthcare reform measures of the Trump administration will impact the ACA and our business.

Further, other legislative changes have been proposed and adopted since the ACA was enacted.

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will subject us to foreign regulatory requirements, which may also change over time.

We acquired Purigen in November 2022.

For a further discussion of this acquisition, please refer to Note 14 (Acquisitions), to our consolidated financial statements included in this Annual Report.

Human Capital Management

As of December 31, 2023, we had 344 employees, of which 146 work in sales, sales support and marketing, 127 work in research and development, and 71 work in general and administrative.

This is slightly higher than our expected number of employees as announced in October 2023.

Based on a continuing assessment of needs we determined that 17 employees would be needed longer than anticipated and we extended the employment of 11 employees to January 2, 2024, of four employees to varying dates in February 2024, of one employee to March 2024, and of one employee to April 2024.

Additionally, we determined that six employees would not be included in the originally planned reduction.

As of December 31, 2024, we had a total of 100 employees, 98 of whom were full-time employees and 2 of whom were part time employees.

As of December 31, 2024, of our 100 employees, 74 were located in the U.S.

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Our filings with the SEC may be accessed through the SEC’s website at www.sec.gov.

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.

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-K

Item 1. Business