What changed in this filing

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Item 1. Business

2024-03-05 compared with 2023-03-09 · 213 added, 209 removed, 500 unchanged (46% of the section changed)

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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 market and sell the Saphyr ® system, which delivers OGM data to enable ultra-sensitive and ultra-specific detection of all classes of structural variation (SV).

The Saphyr system is used to identify structural changes in chromosomes, known as cytogenetics, and to accelerate the search for answers in genetic disease and cancer applications.

The Saphyr system is comprised of an instrument, chip consumables, reagents and software containing a suite of data analysis and visualization tools.

The Saphyr system has been shown to outperform the current gold standard methods for cytogenetics and molecular genetics including karyotyping, fluorescence in-situ hybridization (FISH), Southern blot and chromosomal microarray (CMA).

The Saphyr system has also been shown to identify structural changes in chromosomes that cannot be identified using current commercially available solutions for gene sequencing.

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”).

These systems are used to identify structural changes in chromosomes, the study of which is known as cytogenetics, and to accelerate the search for answers in genetic disease and cancer applications as well as in applications for cell and gene therapy.

The systems are comprised of an instrument, chip consumables, reagents and software containing a suite of data analysis and visualization tools.

OGM has been shown to outperform the current gold standard cytogenetic methods including karyotyping, fluorescence in-situ hybridization (“FISH”), Southern blot and chromosomal microarray (“CMA”), for the detection of SVs.

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.

Our software 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 structural variation.

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.

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 next-generation sequencing (NGS) and microarray data, and we are developing a version that we expect to be able to incorporate OGM data to make our software a more comprehensive offering for analysis of genomic data.

We believe the integration of OGM with data types common in the industry, such as Variant Call Format (VCF), and Binary Alignment Map (BAM), 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 software currently enables analysis of OGM, next-generation sequencing (NGS) and microarray data.

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.

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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.

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 our Saphyr system 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 the Saphyr system.

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.

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 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 of care for many constitutional genetic disorders and cancers.

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.

Recent Highlights

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• Reimbursement:

We applied for a category 1 Current Procedural Terminology (CPT) code for OGM.

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 study.

Site selection was completed, and enrollment commenced for our hematological study.

Data generation for our prenatal study commenced.

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 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 240 Saphyr systems.

• Planned Product Developments:

We released a pre-commercial version of NxClinical software, version 7.0, enabling OGM data analysis in the field.

We released labeling protocol 2.0 and the SP Next DNA isolation protocol.

We placed a pre-commercial version of our next-generation OGM system in the field.

Our Bionano Laboratories business launched an OGM test menu for genetic disease and hematologic malignancies.

Commercial Adoption of Offerings for Saphyr

Bionano executed on its commercialization strategy, expanded the utilization of its Saphyr system and increased the amount of Bionano data generated across the globe, driving commercial momentum.

• Grew our installed base of Saphyr systems to 240 as of December 31, 2022, an increase of approximately 46% from a total installed base of 164 as of December 31, 2021.

Installed base represents the global number of Saphyr instruments installed at end-customer locations to perform optical genome mapping.

• Sold 4,781 flowcells in the fourth quarter of 2022, an increase of approximately 49% over the 3,204 flowcells sold during the fourth quarter of 2021.

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.

Commercial Adoption of Offerings for OGM

Bionano executed on its commercialization strategy, expanded the utilization of its OGM systems and increased the amount of Bionano data generated across the globe, driving commercial momentum.

• Grew our installed base of OGM systems to 326 as of December 31, 2023, an increase of approximately 36% from a total installed base of 240 as of December 31, 2022.

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, 2023, total flowcells sold reached 26,444, an increase of approximately 72% over the 15,375 flowcells sold during the year ended December 31, 2022.

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

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

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.

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

Rigorous and extensive benchmarking of our Saphyr system 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:

• Researchers from The University of Texas MD Anderson Cancer Center published the first study to evaluate the utility of OGM for myelodysplastic syndrome (MDS) prognostication.

The publication reported that when OGM was used instead of karyotyping, 17 to 21% of study subjects had different prognostic risk scores depending on the scoring system used, and in 13% of study subjects additional pathogenic variants were revealed.

• In a study published in Blood Cancer Journal , researchers found that in 33% of MDS samples and 54% of acute myeloid leukemia (AML) samples, more clinically relevant variants were detected using OGM than were found by traditional cytogenetic methods and these variants were reported to be highly relevant to the understanding of pathogenesis of these disorders.

• Researchers from eight research institutes analyzed OGM’s utility for detection of cytogenetic abnormalities in AML samples, finding that OGM identified pathogenic variants in 12% of cases that altered European LeukemiaNet ( ELN) risk-level or identified eligibility for clinical trials.

• The first published validation study to evaluate the performance of OGM versus traditional cytogenetic techniques for the analysis of hematological neoplasms showed that OGM’s technical performance resulted in a 100% first-pass rate, with concordance to traditional methods showing a sensitivity of 98.7%, a specificity of 100%, and an accuracy of 99.2%.

• A study demonstrated the utility of OGM as part of a workflow to evaluate the quality of hypoimmunogenic induced pluripotent stem cells (iPSCs) which could be used in regenerative medicine.

This research provides scientific and practical support for OGM’s ability to detect cryptic and balanced SVs in CRISPR-edited cells, some of which were not detected by karyotyping, and which may impact the genomic integrity of iPSCs.

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%.

Macroeconomic and Geopolitical Developments

We are subject to additional risks and uncertainties as a result of adverse geopolitical and macroeconomic developments, such as any lingering effects of COVID-19, the ongoing conflict between Ukraine and Russia and related sanctions, 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 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.

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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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.

OGM enables the detection of all known classes of SVs, and we believe no methodology exists that can detect SVs more comprehensively or cost efficiently than OGM with the Saphyr system.

OGM enables the detection of all known classes of SVs, and we believe no methodology exists that can detect SVs more comprehensively or cost efficiently than our OGM systems.

We believe the traditional cytogenomic methods of detecting SVs for research and clinical applications, such as karyotyping, CMA, and FISH are antiquated and cumbersome and can only detect a small proportion of the SVs across an entire genome.

OGM is designed to offer cytogeneticists the ability to fully digitize and replace these traditional methods with one simplified, cost effective and scalable workflow using the Saphyr system.

OGM is designed to offer cytogeneticists the ability to fully digitize and replace these traditional methods with one simplified, cost effective and scalable workflow using one of our OGM systems.

We believe that DNA isolation is the critical first step in the analysis of DNA.

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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.

Our software solution, NxClinical™, was developed with CNV as the core focus and has become established as an industry leading solution for interpretation and reporting of CNVs for CMA and NGS.

To the extent we are successful in integrating OGM into our NxClinical software, we anticipate that our software will be the first software solution delivering a fully integrated interpretation capability for SVs from OGM as well as seamless integration with NGS, with the potential to enable complementary OGM and NGS workflows through one software solution.

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.

Our Solutions

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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.

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.

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

Our system uses a proprietary approach to measure genome structure and SV through OGM.

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

The OGM workflow is novel, comprehensive, scalable, cost effective and highly differentiated.

OGM data is currently generated using the Saphyr system, which directly measures sequence specific patterns (SSPs) along UHMW DNA molecules in an unbiased approach without any amplification.

OGM data is currently generated using our OGM systems, which directly measure sequence specific patterns (“SSPs”) along UHMW DNA molecules in an unbiased approach without any amplification.

Using the SSPs, software constructs a detailed physical map of the genome that accurately assigns the chromosomal location, order, orientation and quantity of sequence and in-turn, all the genome’s functional elements.

We believe OGM is capable of comprehensive, cost-effective and efficient detection of all classes of SVs and CNVs.

Today, these SVs cannot be reliably detected by genome sequencing, from existing high throughput sequencers, which is focused on identifying genomic differences involving a few base pairs or SNVs, which the Saphyr system does not identify.

We believe the Saphyr system is ideally suited to be adopted alongside the installed base of high throughput sequencers as a complement that is designed to give users the ability to see a much wider scope of genome variation, from single bases of DNA to full chromosomes.

We believe that our OGM systems are ideally suited to be adopted alongside the installed base of high throughput sequencers as a complement that is designed to give users the ability to see a much wider scope of genome variation, from single bases of DNA to full chromosomes.

OGM was built upon four key elements:

• Extremely long molecules for analysis (or UHMW DNA).

The Saphyr system is capable of analyzing single molecules that are on average approximately 250,000 base pairs in length and can be as long as millions of base pairs.

Our OGM systems are capable of analyzing single molecules that are on average approximately 250,000 base pairs in length and can be as long as millions of base pairs.

These lengths are over 1,000 times longer than the average short read length with Illumina sequencing systems and approximately 10-20 times longer than the average long read lengths with Pacific Biosciences of California (PacBio), and Oxford Nanopore systems.

We believe these long read lengths overcome the inherent challenges of genome complexity and are the key to the Saphyr system’s unprecedented sensitivity and specificity.

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.

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The pattern of labels detected on all these fragments can then be related to the pattern of sequence motif sites in a reference genome for comparison.

Changes in the pattern indicate structural variation.

Changes in the pattern indicate SV.

• Bioinformatic tools for SV analysis.

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It comprises proprietary algorithms for the construction of a structurally accurate physical map of the genome to assign structure.

maps of a test subject are then compared to a reference or other subjects in cross-mapping analysis that allows our system to detect genome wide SV, including the most complex balanced events.

The Saphyr system provides a solution for comprehensive SV analysis at a higher resolution than traditional techniques allowing for more answers that matter to be obtained in genetic disease and cancer applications.

We believe that the Saphyr system is the only product capable of detecting SVs at high sensitivity and specificity with a workflow that is cost-effective and time efficient.

Physical maps of a test subject are then compared to a reference or other subjects in cross-mapping analysis that allows our system to detect genome wide SV, including the most complex balanced events.

Our OGM systems provide solutions for comprehensive SV analysis at a higher resolution than traditional techniques allowing for more answers that matter to be obtained in genetic disease and cancer applications.

We believe that our OGM systems are the only products capable of detecting SVs at high sensitivity and specificity with a workflow that is cost-effective and time efficient.

Our customers include researchers and clinicians who seek to identify and understand the biological implications of genome variation.

We believe that the Saphyr system 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 the Saphyr system has the potential to significantly increase success rates and provide more answers across a wide range of applications in genomics.

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.

Nucleic Acid Isolation and Purification Systems

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An additional limitation of many of the traditional isolation processes is the number of cells that are required to be processed in order to obtain sufficient nucleic acid molecules for OGM analysis.

Current methodologies require upwards of 1.5 million cells in order to isolate sufficient DNA for use on the Saphyr system.

Current methodologies require upwards of 1.5 million cells in order to isolate sufficient DNA for use on an OGM system.

Our Ionic Purification system, employing ITP technology, addresses many of these deficiencies and yields high purity nucleic acid that is not denatured, dehydrated or fragmented.

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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, NxClinical software is among the most comprehensive solutions for analysis and interpretation of 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 we are working to add OGM.

These software solutions are expected to allow us to leverage and expand our network of Bionano customers and to potentially enable future adoption of OGM.

We believe integrating OGM data into the NxClinical software should substantially improve the analysis and reporting capabilities of our current Saphyr system, making OGM easier to adopt and use by our customers.

Through BioDiscovery, we can now serve the NGS and array markets directly though software with an industry leading data interpretation solution for revealing more answers with delivery of copy number variants across the genome.

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

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.

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

These software solutions are expected to allow us to leverage and expand our network of Bionano customers in ways that we believe will help accelerate the adoption of OGM.

We believe that the integration of OGM data into the VIA software can substantially improve the analysis and reporting capabilities of our current OGM systems, making OGM easier to adopt and use by our customers.

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.

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 (ACMG), the American Academy of Pediatrics (AAP), and the American Academy of Neurology (AAN), among other renowned societies.

We are actively performing research to determine whether OGM with the Saphyr system can replace CMA as the front-line test for children with developmental disorders.

As the scientific, peer-reviewed literature supports this claim, the coding entities such as CMS and the 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.

Importantly, OGM is expected to be able to detect full mutations consistent with fragile X syndrome, which is another front-line test for children, especially males, with

autism spectrum disorder and intellectual disability.

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.

We are actively performing research to determine whether OGM with an OGM system can replace CMA as the front-line test for children with developmental disorders.

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.

Importantly, OGM is expected to be able to detect full mutations consistent with fragile X syndrome, which is another front-line test for children, especially males, with autism spectrum disorder and intellectual disability.

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 (WES), which aims to detect genome SNVs that are different from genome SVs and are not detectable by OGM.

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 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 Saphyr system.

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.

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Our Commercial Offerings

The Saphyr System and Consumables

We develop and market the Saphyr system, a complete sample-to-result solution for SV analysis by OGM that empowers comprehensive genome analysis and facilitates a deeper understanding of genetic variation and function.

We believe the Saphyr system is capable of addressing the needs for SV analysis because it is:

Our OGM Systems and Consumables

We develop and market the Saphyr system and the Stratys system.

Each system is a complete sample-to-result solution for SV analysis by OGM that empowers comprehensive genome analysis and facilitates a deeper understanding of genetic variation and function.

We believe these systems are capable of addressing the needs for SV analysis because they are:

• Highly sensitive.

We believe Saphyr is the most sensitive detector of SV larger than 500 base pairs currently on the market.

We believe these systems are the most sensitive detector of SV larger than 500 base pairs currently on the market.

• Cost effective.

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• Scalable and fast.

Relative to traditional techniques, Saphyr has demonstrated up to a 75% reduction in turnaround time for analysis of acute lymphoblastic leukemia (ALL) subjects when used instead of karyotyping, FISH and MLPA.

The Saphyr Instrument

The Saphyr instrument is a single-molecule imager that includes high performance optics, automated sample loading based on machine learning algorithms and computational hardware and control software.

Relative to traditional techniques, these systems have demonstrated up to a 75% reduction in turnaround time for analysis of acute lymphoblastic leukemia (ALL) subjects when used instead of karyotyping, FISH and MLPA.

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.

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 Saphyr instruments.

The computational hardware is responsible for the secondary processing of the image data being produced on the instruments.

The Saphyr instrument is currently capable of analyzing up to 4,000 human genomes per year at 100x coverage.

At the end of 2022 we announced the placement of a pre-commercial unit that we expect to significantly increase the throughput.

The Saphyr Chip

The Saphyr Chip® is the consumable that packages the nanochannel arrays for DNA linearization.

The Stratys instrument is currently capable of analyzing up to 13,500 human genomes per year at 100x coverage.

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.

The Stratys Chip™ is the consumable that packages the nanochannel arrays for DNA linearization for use on the Stratys instrument.

In its current form, each Stratys Chip has one flow cell containing approximately 120,0000 nanochannels that are roughly 30 nanometers wide, and each flowcell can hold one unique sample.

To manufacture the arrays, we use photolithography in a semiconductor fabrication facility to print hundreds of thousands of tiny grooves on silicon wafers and then dice the wafers into individual chips.

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Saphyr Sample Prep and Labeling Kits

Our Bionano Prep™ kits and DNA labeling kits provide the reagents and protocols needed to extract and label UHMW DNA for use with the Saphyr system.

Our Bionano Prep™ kits and DNA labeling kits provide the reagents and protocols needed to extract and label UHMW DNA for use with OGM systems.

These kits are optimized for performing our genome mapping applications on a variety of sample types.

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DLS uses a single direct-labeling enzymatic reaction to attach a fluorophore to the DNA at a specific 6-base pair sequence motif, yielding approximately 16 labels per 100,000 base pairs in the human genome.

After labeling, the molecules are linearized in the Saphyr chip on the Saphyr instrument and imaged.

After labeling, the molecules are linearized in the nanochannel chips on the OGM instruments and imaged.

Through the isolation, labeling and linearization steps, the molecules maintain an average length of around 250,000 base pairs.

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Our customers use our variant annotation workflow to specifically uncover rare and sample-specific mutations.

Our hardware solution includes the Saphyr Compute Server, which provides cluster-like performance in an affordable, compact solution and the Bionano Compute Server, which expands the analytical capacity of the suite of tools.

Our hardware solution includes the Saphyr and Stratys Compute Servers, which provides cluster-like performance in an affordable, compact solution and the Bionano Compute Server, which expands the analytical capacity of the suite of tools.

With these solutions, our customers are capable of performing multiple simultaneous analyses and sustaining continuous throughput, which allows them to spend less time waiting for data, so they can focus on investigating results.

We also offer a cloud-based solution for data analysis.

Our NxClinical software is among the most comprehensive and up-to-date solutions for cytogenetics and molecular genetics, providing one solution for analysis and interpretation of all genomic variants from microarray and NGS data.

We are developing a version of NxClinical to incorporate OGM data, which is expected to become our software solution once completed.

Our VIA software is among the most comprehensive and up-to-date solutions for cytogenetics and molecular genetics, providing one solution for analysis and interpretation of all genomic variants from microarray and NGS data.

VIA evolved from our NxClinical software to incorporate OGM data and is now our primary software solution for interpretation and reporting of genomic features from OGM data.

Testing and Laboratory Services

Our Bionano Laboratories business offers OGM data to researchers seeking access to OGM data.

Bionano Laboratories intends to build a menu of LDTs using OGM solutions, and in 2022 Bionano Laboratories introduced their first two OGM-based tests, one for hematological malignancy and another for genetic disorder applications.

Additionally, Bionano Laboratories offers molecular genetic clinical testing services for individuals demonstrating clinical presentations consistent with NDDs, including ASDs and other disorders of childhood development, including:

Our Bionano Laboratories business offers OGM based RUO testing to researchers, biotech and pharmaceutical companies, and others seeking OGM data.

Bionano Laboratories also offers four OGM-based LDTs.

• 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 FSHD is a test intended for individuals suspected of having FSHD type 1;

• 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.

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:

• 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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• NextStepDx PLUS is a whole exome sequencing test designed to identify genetic variants that are associated with disorders of childhood development.

• EpiPanelDx PLUS is a genetic testing panel designed for patients who have experienced seizures, infantile spasms, encephalopathy, or febrile seizures;

• PGx test identifies over 60 alleles in 11 genes.

PGx testing is one aspect of personalized medicine and is used to aid health care providers with medications and dosage.

Market Opportunity

According to Markets and Markets, the worldwide market for genomics products and services is expected to reach approximately $54.4 billion by 2025, up from approximately $22.7 billion in 2020, representing a compound annual growth rate of 19%.

We expect to see OGM adoption in cytogenomics, discovery research and cell bioprocessing quality control (QC).

Within cytogenetics and molecular pathology, we estimate the number of cytogenetic labs on a worldwide basis (excluding India and

developing countries) to be approximately 10,000.

According to MarketsandMarkets, the worldwide market for genomics products and services is expected to reach approximately $54.4 billion by 2025, up from approximately $22.7 billion in 2020, representing a compound annual growth rate of 19%.

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.

Additionally, we estimate the number of pharmaceutical and biotech companies that are engaged in research and development of various cell therapies that rely on methods, including cytogenetics, for QC of the cell modification and manufacturing process to be approximately 1,400.

Based on these estimates, we believe the economic potential for OGM in these markets is approximately $10.0 billion annually, $3.0 billion of which we attribute to cell bioprocessing QC.

Additionally, we estimate that approximately 1,400 pharmaceutical and biotech companies are engaged in research and development of various cell therapies that rely on methods, including cytogenetics.

Based on these estimates, we believe the economic potential for OGM in these markets is approximately $10.0 billion annually, $3.0 billion of which we attribute to cell and gene therapy applications.

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 Saphyr system today:

• Consolidation of traditional cytogenetics techniques in constitutional and cancer applications.

To provide a robust clinical analysis, cytogenetic assays detect known SVs that are linked to specific diseases or therapeutic responses.

We believe the 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.

To provide a robust clinical analysis, cytogenetic assays detect SVs that are linked to specific diseases or therapeutic responses.

The technologies used for detecting SVs are expensive and involve cumbersome workflows with relatively limited ability to scale to higher volumes or more complex testing panels.

Sequencers tend not to be used for cytogenetics due to their inability to reliably detect SVs.

Cytogenetics laboratories are beginning to adopt the Saphyr system as a more effective, scalable and efficient approach to finding the SVs causative to genetic diseases and cancer.

For this segment, the Saphyr system can be used as the sole tool for providing comprehensive and accurate detection of all classes of SVs and enable clinically relevant calls without the need for any sequencing or legacy cytogenetic technology.

We estimate that approximately 10,000 cytogenetics labs exist worldwide (excluding India and developing countries).

• Combining OGM with sequencing for molecular genetics and discovery research applications.

In discovery research across patient cohorts, sequencing is primarily used to find SNVs responsible for disease or therapeutic response.

Sequencing alone, however, is significantly limited due to its inability to reveal SV.

Our Saphyr system has been expanding this market segment by complementing sequencing to expand the scope of genome variation that can be analyzed in studies to achieve a more comprehensive view of the genome .

• Cell bioprocessing QC applications.

An important part of cell bioprocessing applications is to ensure that genomic modifications did not introduce any SVs into the cell population.

As a QC step, our Saphyr system has been used by researchers to evaluate the ability of OGM to detect SVs that may impact cellular stability.

Cytogenetics laboratories are beginning to adopt OGM systems as a more effective, scalable and efficient approach to finding the SVs causative to constitutional genetic diseases and cancer.

For this segment, an OGM system can be used as the sole tool for providing comprehensive and accurate detection of all classes of SVs and enable clinically relevant calls without the need for any sequencing or legacy cytogenetic technology.

We estimate that labs analyze approximately 1.7 million constitutional genetic disease samples per year and approximately 8.3 million cancer samples per year.

• Cell and gene therapy applications.

An important part of cell and gene therapy applications is to ensure that genomic modifications did not introduce any SVs into the cell population.

Our OGM systems have been used by researchers to evaluate the ability of OGM to detect SVs that may impact cellular stability.

Several studies have been published showing the OGM can be used to evaluate cellular stability.

We believe that this is an emerging market opportunity and could be up to $3.0 billion annually.

We believe that if our OGM-based solutions can successfully penetrate these addressable market opportunities, this should spur additional basic and translational research creating new areas where the Saphyr instrument (or successor 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 population screening, newborn screening, biopharma applications in cell quality control and oncology.

We are primarily focused on driving adoption of OGM through the Saphyr system (and successor instruments).

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.

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

We are primarily focused on driving adoption of OGM through our 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 strategy to achieve this includes:

• Demonstrate that Saphyr is a superior alternative to traditional techniques in constitutional genetic disorders and hematologic malignancy applications.

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.

Optical genome mapping has demonstrated superior detection sensitivity for all classes of SVs relative to karyotyping, FISH and CMA in numerous peer-reviewed publications over the past several years and offers benefits of improved assay success rates, faster time to result and a lower total cost.

The value proposition and competitive differentiation for OGM in cytogenetics market is exceptionally strong with an immediate opportunity to digitize legacy microscope techniques (karyotyping) with a superior approach using the Saphyr system.

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

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 an accurate technique for 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.

There are over 15,000 NGS instruments installed globally and our vision is for each of these sequencers to be complemented with an OGM system to provide a more comprehensive picture of the genome for more discoveries, publications and translation into molecular genetics.

• 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.

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.

• Support the publication of findings with OGM by our customers beyond the more than 1000 papers published to date.

The annual number of publications featuring data generated by the Saphyr system and its predecessor system has steadily increased since 2010 when the first publication appeared.

Recently, the overall number of these publications has grown significantly.

For example, of the 521 peer-reviewed and pre-print papers published since 2019, 173 were published in 2022 alone.

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 our customers’ studies cover SVs in areas of high unmet medical need, such as rare and undiagnosed pediatric diseases, neurological and muscular diseases, developmental delays and disorders, prostate cancer and leukemia.

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.

• Continue to innovate our products and technologies.

We designed the Saphyr system to accommodate performance enhancements without the need for replacement of the entire instrument.

For example, hardware upgrades and new consumables are made available to purchase by customers.

We designed our OGM systems to accommodate performance enhancements without the need for replacement of the entire instrument.

For example, hardware upgrades and new consumables may be made available to purchase by customers.

We intend for these performance enhancements to be delivered on a regular basis.

In addition, we periodically make available software upgrades to customers through download at no charge.

We expect to continue developing and refining our technologies to improve the ease of use of our Saphyr system and enable our existing installed systems to meaningfully increase sample throughput and sensitivity and specificity of SV detection.

A high throughput version is currently in development is expected to significantly increase the throughput and lower the cost per sample.

Compared to the Saphyr system, which images DNA at a rate of approximately 205 Gbp per hour, the new system is expected to image nearly 820 Gbp per hour and we announced the placement of a pre-commercial beta system at a customer facility in December 2022.

In addition, we periodically make available software upgrades to customers through download.

We expect to continue developing and refining our technologies to improve the ease of use of our OGM systems and enable our existing installed systems to meaningfully increase sample throughput and sensitivity and specificity of SV detection.

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.

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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.

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.

Sales and Marketing

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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 and some work remotely throughout the U.S., 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.

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

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

Specifically, we distribute our instruments and reagents via third-party distributors in markets such as China, Japan, South Korea, Singapore, Australia, India and South Africa.

Three of our distributors are in China, one in Australia, one in Italy, one in Sweden, one in Japan, and one in South Korea.

The role of our sales managers and sales representatives is to educate customers on the advantages of Saphyr and the applications that our system makes possible.

For example, we distribute our instruments and reagents via third-party distributors in markets such as China, Japan, South Korea, Singapore, Australia, India and South Africa.

The role of our sales managers and sales representatives is to educate customers on the advantages of OGM and the applications that our systems make possible.

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 seven 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 nine 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.

The applications lab team also runs foundational scientific collaborations and proof of principle studies, which help demonstrate the value of our product offering to prospective customers.

This team also provides commercial services by running samples on Saphyr for researchers who do not have a Saphyr system of their own.

This team also provides commercial services by running samples on an OGM system for researchers who do not have an OGM system of their own.

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 Saphyr systems.

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.

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states where Bionano Laboratories has obtained insurance reimbursement.

The sales and marketing efforts are targeted primarily on specialty pediatricians, including pediatric neurologists, medical geneticists, and developmental and behavioral pediatricians.

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.

Our instruments are manufactured by a third-party medical device manufacturer.

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

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All of our chip consumables for both OGM and ITP applications are produced by third-party manufacturers at their facilities;

however, we have established procedures for a replacement manufacturer if required.

We complete final assembly and quality control assessments of our chips at our headquarters in San Diego and our facility in Pleasanton.

however, we have established procedures for replacement manufacturers if required.

We complete final assembly and quality control assessments of our chips at our headquarters in San Diego, California.

Our OGM reagents are sourced from a limited number of suppliers, including certain single source suppliers.

Our ITP reagents are sourced from a limited number of suppliers, including certain single source suppliers and also prepared in-house at our facility in Pleasanton.

Our ITP reagents are sourced from a limited number of suppliers, including certain single source suppliers and also prepared in-house at our facility in San Diego, California.

The OGM reagents include all components required to run a sample on OGM, such as capture and detector reagents, enzyme reagents and enzyme substrate.

The ITP reagents include all the components required to run a sample for isolation and purification of nucleic acid.

Although we believe that alternatives would be available, 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 supplier.

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

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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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 NxClinical 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.

Testing and Laboratory Services

Bionano Laboratories’ OGM testing is performed at our lab in San Diego, or at our partner labs in the United States and Europe.

Bionano Laboratories intends to increase its testing capacity, and expand its menu of testing.

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-

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 to its current menu, Bionano Laboratories’ plans to add OGM-based LDTs to be performed at its San Diego facility, the first two of which have been announced.

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.

Key Agreements

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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 160 issued patents or allowed applications across approximately 35 patent families that are either owned or exclusively licensed.

We have developed a global patent portfolio that includes more than 151 issued patents across approximately 39 patent families that are either owned or exclusively licensed.

The owned and licensed patent families contain issued patents and pending applications that relate to devices, systems, and methods for macromolecular analysis, isolation and purification of molecules, genetic testing, computer software systems and reflect our active and ongoing research programs.

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Optical Genome Mapping

Our OGM products are currently intended for research use only, or RUO, applications, although our customers may use our products to develop their own products that are subject to regulation by the FDA.

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.

Although most products intended for RUO are not currently subject to clearance or approval by the FDA, RUO products fall under the FDA’s jurisdiction if they are used for clinical rather than research purposes.

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The FDA classifies medical devices into one of three classes on the basis of the intended use of the device, the risk associated with the use of the device for that indication, as determined by the FDA, and on the controls deemed by the FDA to be necessary to reasonably ensure their safety and effectiveness.

Class I devices, which have the lowest level of risk associated

with them, are subject to general controls.

Class I devices, which have the lowest level of risk associated with them, are subject to general controls.

Class II devices are subject to general controls and special controls, including performance standards.

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The FDA does not consider devices to be LDTs if they are designed or manufactured completely, or partly, outside of the laboratory that offers and uses them.

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

At various times since 2006, the FDA has issued documents outlining its intent to require varying levels of FDA oversight of many types of LDTs.

Congress has also considered legislation that would change how LDTs are regulated.

It is unclear at this time if or when the FDA will finalize its plans to end enforcement discretion for LDTs, and even then, whether the new regulatory requirements are expected to be phased-in over time.

However, the FDA may decide to regulate certain LDTs on a case-by-case basis at any time.

A significant change in the way that the FDA regulates any LDTs that we, our collaborators, or our customers develop using our technology could affect our business.

If the FDA requires laboratories to undergo premarket review and comply with other applicable FDA requirements in the future, the cost and time required to commercialize an LDT will increase substantially and may reduce the financial incentive for laboratories to develop LDTs, which could reduce demand for our instruments and our other products.

In addition, if the FDA were to change the way that it regulates LDTs to require that we undergo pre-market review or comply with other applicable FDA requirements before we can sell our instruments or our other products to clinical cytogenetics laboratories, our ability to sell our instruments and other products to this addressable market would be delayed, thereby impeding our ability to penetrate this market and generate revenue from sales of our instruments and our other products.

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.

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

Europe/Rest of World Government Regulation

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and may be easier or more difficult to satisfy and are subject to change.

For example, the European Union recently published new regulations that will result in greater regulation of medical devices and IVDs.

For example, the European Union (“EU”) recently published new regulations that will result in greater regulation of medical devices and IVDs.

The IVD Regulation is significantly different from the IVD Directive that it replaces in that it will ensure that the new requirements apply uniformly and on the same schedule across the member states, including a risk-based classification system and increasing the requirements for conformity assessment.

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

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, or 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.

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.

Adverse interpretations of current CLIA regulations or future changes in CLIA regulations could have an adverse effect on sales of any affected products.

Moreover, if we decide to operate our own clinical testing laboratory with respect to our OGM products, such clinical testing would require compliance with CLIA.

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, or 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.

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 the Saphyr system and direct label and stain chemistry to create their own diagnostic tests and potentially seek reimbursement for such tests.

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.

Our customers may generate revenue for these testing services by seeking the necessary approval of their product from the FDA or CMS, along with coverage and reimbursement from third-party payors, including government health programs and private health plans.

The ability of our customers to commercialize diagnostic tests based on our technology will depend in part on the extent to which coverage and reimbursement for these tests will be available from such third-party payors.

In the U.S., molecular testing laboratories have multiple options for reimbursement coding, but we expect that the primary codes used will be the genomic sequencing procedure codes, or GSPs.

The American Medical Association, or AMA, added GSPs to its clinical laboratory fee schedule in 2015.

In addition, CMS issued a coverage determination providing for the reimbursement of next-generation sequencing for certain cancer diagnostics using an FDA-approved in vitro diagnostic test.

In the U.S., molecular pathology tests have multiple options for reimbursement coding.

Current Procedural Terminology (“CPT”) codes developed by the American Medical Association (“AMA”), can be assigned to new products through applying for either a Proprietary Laboratory Analysis (“PLA”) code or through applying for a category 1 CPT code.

IT is also an option to use an unlisted molecular pathology code such as 81479.

There are several PLA codes on the Medicare Clinical Lab Fee Schedule (“CLFS”) for OGM-based tests as of January 01, 2024.

Additionally, CMS, through its Medicare contractors, can write coverage determinations for molecular testing through their LCD process.

Private health plans often follow CMS coverage and reimbursement guidelines to a substantial degree, and it is difficult to predict what CMS will decide with respect to the coverage and reimbursement of any products or services our customers try to commercialize.

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.

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

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.

Ultimately, coverage and reimbursement of new products and services is uncertain, and whether laboratories that use our instruments to develop their own products or services will attain coverage and adequate reimbursement is unknown.

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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).

CAP accreditation for the San Diego facility is pending.

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

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 facility currently holds such out-of-state laboratory licenses in Pennsylvania and Maryland.

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

HIPAA and other Privacy Laws

The Health Insurance Portability and Accountability Act of 1996 (“HIPAA”), established comprehensive federal standards for the privacy and security of health information.

HIPAA established comprehensive federal standards for the privacy and security of health information.

The HIPAA standards apply to three types of organizations:

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The HIPAA security standards require the adoption of administrative, physical, and technical safeguards and the adoption of written security policies and procedures.

On February 17, 2009, Congress enacted Subtitle D of the Health Information Technology for Economic and Clinical Health Act, or HITECH, provisions of the American Recovery and Reinvestment Act of 2009.

On February 17, 2009, Congress enacted Subtitle D of the Health Information Technology for Economic and Clinical Health Act (“HITECH”), provisions of the American Recovery and Reinvestment Act of 2009.

HITECH expanded and strengthened HIPAA, created new targets for enforcement, imposed new penalties for noncompliance and established new breach notification requirements for Covered Entities.

Regulations implementing major provisions of HITECH were finalized on January 25, 2013 through publication of the HIPAA Omnibus Rule (the “Omnibus Rule”).

Regulations implementing major provisions of HITECH were finalized on January 25, 2013 through publication of the HIPAA Omnibus Rule.

Under HITECH's breach notification requirements, Covered Entities must report breaches of protected health information that has not been encrypted or otherwise secured in accordance with guidance from the Secretary of the U.S.

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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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The GDPR applies not only to organizations within the EU, but also applies to organizations outside of the EU that offer goods or services to EU data subjects or that process or hold personal data of EU data subjects.

Additionally, from January 1, 2021, companies have had to comply with the GDPR and also the United Kingdom GDPR (“UK GDPR”), which, together with the amended United Kingdom Data Protection Act 2018, retains the GDPR in the United Kingdom national law.

Both the GDPR and the UK GDPR regulations specify potential liabilities for certain data protection violations, and we anticipate that it will result in a greater compliance burden for us as we conduct our business in the European Union.

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.

Fines for non-compliance can range from the greater of 2% of annual global revenues or €10 million, up to the greater of 4% of annual global revenues or €20 million.

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Reimbursement and billing for diagnostic services is highly complex.

Laboratories must bill various payors, such as private third-party payors, including managed care organizations (“MCO”), and state and federal health care programs, such as Medicare and Medicaid, and each may have different billing requirements.

Laboratories must bill various payors, such as private third-party payors, including managed care organizations, and state and federal health care programs, such as Medicare and Medicaid, and each may have different billing requirements.

Additionally, the audit requirements Bionano Laboratories must meet to ensure compliance with applicable laws and regulations, as well as our internal compliance policies and procedures, add further complexity to the billing process.

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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 MCO;

• a third-party who provides coverage to the patient, such as an insurance company or managed care organization;

• a state or federal healthcare program;

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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, or EKRA, prohibits payments for referrals to recovery homes, clinical treatment facilities, and laboratories.

Further, the Eliminating Kickbacks in Recovery Act of 2018 (“EKRA”), prohibits payments for referrals to recovery homes, clinical treatment facilities, and laboratories.

EKRA’s reach extends beyond federal health care programs to include private insurance (i.e., it is an “all payor” statute).

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State and Federal Prohibitions on False Claims

The federal False Claims Act imposes liability on any person or entity that, among other things, knowingly presents, or causes to be presented, a false or fraudulent claim for payment to the federal government.

Under the False Claims Act, a person acts knowingly if he or she has actual knowledge of the information or acts in deliberate ignorance or in reckless disregard of the truth or falsity of the information.

The federal False Claims Act (“FCA”) imposes liability on any person or entity that, among other things, knowingly presents, or causes to be presented, a false or fraudulent claim for payment to the federal government.

Under the FCA, a person acts knowingly if he or she has actual knowledge of the information or acts in deliberate ignorance or in reckless disregard of the truth or falsity of the information.

Specific intent to defraud is not required.

The qui tam provisions of the False Claims Act allow a private individual to bring an action on behalf of the federal government and to share in any amounts paid by the defendant to the government in connection with the action.

The qui tam provisions of the FCA allow a private individual to bring an action on behalf of the federal government and to share in any amounts paid by the defendant to the government in connection with the action.

Penalties include payment of up to three times the actual damages sustained by the government, plus significant civil penalties, as well as possible exclusion from federal health care programs.

In addition, various states have enacted similar laws modeled after the False Claims Act 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.

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.

Civil Monetary Penalties Law

The federal Civil Monetary Penalties Law, or 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;

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;

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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 European Union (“EU”).

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” (“DoA”) of the Regulation.

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 EU has also implemented the General Data Protection Regulation, or GDPR, which requires us to meet new and more stringent requirements regarding the handling of personal data about European Union residents.

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.

In many countries outside of the United States, coverage, pricing and reimbursement approvals are also required.

We are also required to maintain accurate information on and control over sales and distributors’ activities that may fall within the purview of the Foreign Corrupt Practices Act, its books and records provisions and its anti-bribery provisions.

We are also required to maintain accurate information on and control over sales and distributors’ activities that may fall within the purview of the U.S.

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

Other Regulatory Requirements

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There have been executive, judicial and Congressional challenges to certain aspects of the ACA.

For example, President Trump signed several Executive Orders and other directives designed to delay the implementation of certain provisions of the ACA or otherwise circumvent some of the requirements for health insurance mandated by the ACA.

Concurrently, Congress considered legislation to repeal or repeal and replace all or part of the ACA.

While Congress has not passed comprehensive repeal legislation, it has enacted laws that modify certain provisions of the ACA, such as removing penalties, effective January 1, 2019, for not complying with the ACA’s individual mandate to carry health insurance.

On June 17, 2021, the U.S.

For example, on June 17, 2021, the U.S.

Supreme Court dismissed a challenge on procedural grounds that argued the ACA is unconstitutional in its entirety because the “individual mandate” was repealed by Congress.

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For example, on August 16, 2022, President Biden signed the Inflation Reduction Act into law, which among other things, extends enhanced subsidies for individuals purchasing health insurance coverage in ACA marketplaces through plan year 2025.

The IRA also eliminates the coverage gap under the Medicare Part D program beginning in 2025 by significantly lowering the beneficiary maximum out-of-pocket cost and through a newly established manufacturer discount program.

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 Clinical Laboratory Fee Schedule, or CLFS.

The Inflation Reduction Act of 2022 (“IRA”) also eliminates the coverage gap under the Medicare Part D program beginning in 2025 by significantly lowering the beneficiary maximum out-of-pocket cost and through a newly established manufacturer discount program.

PAMA requires certain laboratories performing clinical diagnostic laboratory tests to report to CMS the amounts paid by private payors for laboratory tests.

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

We acquired BioDiscovery in October 2021 and Purigen in November 2022.

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

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.

As of December 31, 2022, of our 405 employees, 342

were located in the U.S.

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, 2023, of our 344 employees, 273 were located in the U.S.

and 71 were employed outside the U.S.

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Our principal executive offices are located at 9540 Towne Centre Drive, Suite 100, San Diego, California 92121, and our telephone number is (858) 888-7600.

Our website address is www.bionanogenomics.com.

Our website address is www.bionano.com.

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.

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Available Information

Access to our Annual Report on Form 10-K, 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.bionanogenomics.com.

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.

Information in the investor section and on our website is not part of this Annual Report on Form 10-K or any of our other securities filings.

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.

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