Bionano Genomics at H.C. Wainwright: Strategic Shift to Digital Pathology

On Monday, 08 September 2025, Bionano Genomics (NASDAQ:BNGO) presented at the H.C. Wainwright 27th Annual Global Investment Conference. The company, led by CEO Erik Holmlin, highlighted its strategic transformation towards a more capital-efficient model, focusing on routine-use customers and digital pathology solutions. While the shift shows promise with new reimbursement codes and expanded product offerings, challenges remain in executing this ambitious plan.

Key Takeaways

• Bionano Genomics is transitioning to a digital pathology company with a focus on optical genome mapping (OGM).
• The American Medical Association established Category 1 CPT codes for OGM, enhancing reimbursement prospects.
• The company reported solid revenue growth in consumables and software, reiterating its annual revenue guidance.
• New system installation guidance was raised from 15-20 to 20-25 systems for 2025.
• Bionano aims to improve margins through higher sales volumes and cost reductions.

Financial Results

• Q1 and Q2 2025 revenues were within the guided range, with mid-double-digit growth in consumables and software.
• Overall consumables and software revenue grew nearly double-digits in the first half of 2025.
• Annual revenue guidance for 2025 is $26 million to $30 million.
• Q3 revenue guidance is set at $6.7 million to $7.2 million.
• Gross margin stood at 52% in Q2 2025, with non-GAAP operating expenses remaining flat.

Operational Updates

• Bionano focuses on routine-use customers to drive capital efficiency and profitability.
• Training programs and VIA software enhance customer workflow and increase consumable usage.
• Over 10,000 human clinical research genomes have been published, indicating significant adoption.
• Category 1 CPT codes for hematologic malignancies and constitutional genetic disorders were established.
• The Ionic Purification System for OGM is set for release in 2026, with 20 to 25 new system installations expected in 2025.

Future Outlook

• Bionano plans to support routine-use customers and drive utilization through training and VIA software.
• The company aims to build support for OGM reimbursement and inclusion in medical guidelines.
• Efforts to drive margins up and reduce costs are underway to improve profitability.
• Future growth catalysts include new CPT codes and software versions.

For more detailed insights, refer to the full transcript.

Full transcript - H.C. Wainwright 27th Annual Global Investment Conference:

Katherine Dagan, Associate Biotech Research Analyst, HC Wainwright: Welcome to the HC Wainwright 27th Annual Global Investment Conference. I’m Dr. Katherine Dagan, an Associate Biotech Research Analyst at the firm. I’d like to take a moment to welcome Erik Holmlin from Bionano Genomics and take it away.

Erik Holmlin, Bionano Genomics: Thank you, Katie. I want to certainly thank everybody at Wainwright for the opportunity to participate here today. This is always a great conference, and we really began a pretty significant transformation of Bionano Genomics about a year ago, and I’m happy to report on the progress that we’ve been making. Before I delve into that, I want to take some time to point out that we’re a publicly traded company, and I want to refer everybody to our filings on the SEC website and certainly take a moment to step back from the sort of day-to-day and quarter-to-quarter operations of Bionano Genomics and think about the space that we’re operating in. When we do that, we see the analog world of pathology.

You know, if you look across pathology and patient sample testing, both for diagnostic applications and for cutting-edge research, it’s really an array of multiple techniques that have been in operation in many cases for upwards of 50 years. Just take karyotyping as an example. It’s a global standard used around the world, a lot in cancer and in genetic diseases, and yet it hasn’t changed much in that period of time. In fact, there are millions and millions of samples that process through these workflows, causing a labor-intense workflow that takes a lot of time to go from sample to result and creates a lot of confusion amongst the oncologists or physicians who are managing patients. That’s because it’s an analog world, and we recognize at Bionano Genomics the opportunity to digitize the whole pathology process. Now, we can’t do that alone with our products.

Our optical genome mapping is playing a big role in transforming cytogenetics, which is something that I’ll talk a lot more about. We also have our VIA software, which is an AI-driven platform that spans across the optical genome mapping world into sequencing. We also have our Ionic Purification System for nucleic acid isolation, which fits nicely into sequencing workflows. We’re playing a big role in the transformation of pathology to digital pathology, and that’s why we think of ourselves as a digital pathology company. We pioneered optical genome mapping to be something that would really replace the legacy methods across cytogenetics. In fact, we believe we’re serving an available market of about $10 billion. It comprises roughly 10,000 labs across the world, processing about 10 million cases per year.

Right now, we’re focused in key geographies like the United States, Canada, Western Europe, and Israel, where optical genome mapping has a really strong foothold. When we look at the value proposition of optical genome mapping against some of the more traditional methods that are out there, in fact, the global standards like karyotyping, FISH, and microarrays, we can see on the one hand, those workflows are outdated. They’re antiquated, very labor-intense. When you talk to laboratories that are offering those workflows, they’ll tell you that the people who run karyotyping, for example, are retiring, and it’s more of an art than a science. It’s difficult to replace them. They’re looking for digital methods that can do the same thing but get better results. If you look at the clinical utility of traditional cytogenetic methods, it’s pretty limited.

Only about half of karyotypes, for example, come back with useful information that can be used to guide therapy. In fact, in leukemias, 50% of the time, patients who are known to have leukemia get a normal karyotype, and that really gives the oncologists nothing to work from to manage the patients. Studies have shown that as many as 20% of prognostic scores in myelodysplastic syndrome, for example, may be wrong. Those are scores that are used to treat patients or make a decision between therapeutic intervention or something like a bone marrow transplant. If that’s wrong one out of five times, that’s not good. Half of the time, you don’t get a useful answer at all. Of the 50% answers that are coming back, a fifth of those are wrong. The clinical utility of these traditional workflows is severely limited, and this is the problem that we’re attacking.

Now, optical genome mapping, on the other hand, is a faster and simpler workflow. It takes the place of three of these traditional methods. You can imagine, just from a technology workflow consolidation standpoint, optical genome mapping offers something that labs are looking for. They’re constantly under pressure to reduce costs. Workforce shortages are real things across these labs. Optical genome mapping can replace three of these workflows with one. It consistently finds more actionable variants. In an analysis, for example, compared to karyotyping, optical genome mapping will return useful information that researchers or physicians can use in their project much more commonly than the traditional methods. Importantly, recently, in June of 2024, the American Medical Association established a Category 1 CPT code to cover the use of optical genome mapping in hematologic malignancies.

This year, in June of 2025, they established a second code, this one, the second code to cover constitutional genetic disorders. Our two main application areas are covered by Category 1 CPT codes, which is a very high bar to overcome. Lastly, I want to point out that if you think about this whole space of transforming traditional pathology methods into a digital approach, you’re going to think that sequencing is going to be there. You may think, is optical genome mapping competing with sequencing? The answer is they’re not competing. In fact, they’re highly complementary. Labs run mapping and sequencing side by side, and that really improves the results that they’re seeing. Customers adopt what we call the end-to-end solution for optical genome mapping. In this sense, it’s a relatively traditional life sciences instrumentation model.

We have kits, kits for isolating nucleic acids, labeling it before it goes into the imaging chip and into the imaging instrument. We have also been in development of the Ionic Purification System for optical genome mapping. It currently serves nucleic acid isolation markets from formalin-fixed paraffin embedded tissues. That’s useful in advance of next-generation sequencing assays, for example. We’re going to release that system for optical genome mapping sometime in 2026. Customers buy the instrument. We sell the Stratus instrument, which is pictured here, as well as the Saphyr. Those are two models that customers can adopt depending on their throughput needs. We have a high-performance compute server. This is a server we developed in a collaboration with NVIDIA to incorporate their GPU chips into the server. Lastly, we have the VIA software.

VIA software is a critical component of the overall workflow, and it’s really cutting-edge compared to what any sequencing analysis platform or genome analysis platform company is selling. VIA, which stands for Variance Intelligence Applications, allows researchers to visualize, interpret, analyze, annotate, and report their findings in an incredibly streamlined workflow that’s highly automated. In the past, with traditional methods, laboratories would be delivering multiple reports to their end customers at multiple times across the analysis of the sample. VIA really streamlines that in conjunction with optical genome mapping. There is a single report with all of the information that somebody might be looking for, for example, from WHO or NCCN guidelines in relation to that specific sample. The end-to-end workflow is what customers adopt.

As I point out on this slide, parts of it serve adjacent markets like the sequencing market, the Ionic Purification System for nucleic acid isolation, and VIA software is used for analysis, interpretation, and reporting from chromosomal microarray analysis, as well as NGS. We have a product portfolio serving this pathology digitization effort that is pretty broad. Now, optical genome mapping works because its resolution across the resolution sort of continuum of genome variation analysis covers an incredibly large area. As you can see on this slide, optical genome mapping covers the resolution that has typically required three techniques: karyotyping, FISH, and microarrays. Optical genome mapping can pick up all the variants that those pick up and provide a lot more information in many cases. As you can see, it also spans a coverage gap that historically no technique has been able to analyze.

That is why we believe that optical genome mapping consistently finds more information in samples because it’s finding variants that are typically not detected. Importantly, there’s very little overlap with sequencing, some with long-read sequencing, but it lines up nicely with short-read sequencing. For a lab to get comprehensive analysis of genome variation across samples, they really only need to use mapping and sequencing, which is very powerful. You can see that the VIA software fits in nicely for analysis of large variants, and that can be from sequencing or mapping. It doesn’t matter. The Ionic Purification System marries up nicely with nucleic acid isolation from FFPE in advance of sequencing assays. That is why optical genome mapping works. When we think about the application areas that are specifically of interest to us in this cytogenetics market, the three of them are listed here. Hematologic malignancies, leukemias, lymphomas, myelomas.

This is where we have great support in the literature for the application of optical genome mapping as a faster system with higher success rates in detecting pathologic variants and a higher level of accuracy. Constitutional genetic diseases. Here you should be thinking about intellectual disability, autism spectrum disorder, other forms of developmental delays that cause for analysis in a genetics lab. Optical genome mapping can perform those. Now those two applications are covered by Category 1 CPT codes in the United States, and reimbursement is in place in many countries throughout Europe where we’re active. Other places such as Israel and the Turkish Health Ministry just introduced optical genome mapping into its systems, and physicians can order it as a clinical test there. The third area is in cell and gene therapy.

When you think about stem cell therapies or CAR-T therapies or other gene therapies, it’s important to monitor the genome integrity of the samples that you’re dealing with. That may be in the case of editing cells where you want to make sure that you don’t have off-target effects or you want to confirm on-target delivery of the therapeutic payload. Optical genome mapping can play a role in that determination. In stem cell therapy, where you’re growing successive generations of cells, you want to make sure that the starting material looks like the final material. It’s possible to verify that using optical genome mapping. These are the three areas that are driving adoption and utilization of optical genome mapping in our target geographies.

As I mentioned a year ago, we really undertook a large transformation of the company to take the focus away from aggressive growth of the installed base, which is, let’s face it, not the most capital-efficient approach to proliferating our platform, to something that’s much more capital-efficient and focuses on the existing users that we had developed at that time. We call them our routine use customers. These are customers who are buying consumables consistently on a periodic basis, repeatedly, and generating useful results, publishing their results from optical genome mapping data. These are the profitable customers. Our strategy is focused on them. We want to, of course, support and sustain them. We want to drive their utilization up. We have a number of training programs, and our VIA software is something that really enhances their workflow and speeds it up.

It makes it possible for them to process more samples. We have teams that are dedicated to training labs and using VIA software and increasing their capacity, expecting them to then utilize more consumables. We’re very focused on continuously building support needed for reimbursement of optical genome mapping, as well as the eventual inclusion of OGM into medical society recommendations and other guidelines. Lastly, we’re focused on driving margins up, reducing costs, and through higher volumes driven by sales, improving profitability. This is the strategy we’ve been executing on. You can see here is quarterly top-line revenues over an extended period of time. You can look at this chart, and you can feel the turbulence that the company has gone through. I want to focus in really on the first and second quarter of 2025. These were solid quarters, well within our guided ranges for each quarter.

We’re starting to see hopefully a return to revenue growth. You’ll notice some gray bars in some of the earlier years. Those are products that we no longer sell. We discontinued a handful of products that were just not profitable at the scale that we were providing them. That left behind our blue, what we call the core revenues, really the optical genome mapping software and ionic revenues. We’re pleased with the progress that we’ve seen so far in 2025. When we looked a little bit deeper into these numbers, specifically at consumables and software revenue, we see importantly that it’s growing, especially with our existing customers. The second quarter, we had mid-double-digit teens growth here of the combination of consumables and software selling into our existing customer base. On the half-year, you know, some growth. Getting close to double-digit growth. We expect this to continue to evolve and accelerate.

There are many catalysts in the market, such as these CPT codes, such as new versions of the software that we’ve introduced, and other efforts that we believe will drive this growth going forward. We’re happy to see that growth. One of the leading indicators of future growth are the publications. In the second quarter of 2025, we had a record number of publications for a single quarter. We have seen this trajectory continuously over the past several years, and we expect it to continue. This means customers are using the product, writing up their papers, publishing them, which means that new potential customers can see those publications and take the lead from it. Importantly, on the right-hand side, that tracks the number of published human clinical research genomes.

You can think of that as individual samples or clinical research samples. It has doubled year over year in the second quarter. Importantly, we surpassed this 10,000 genomes published mark, and it’s a substantial mark for us. You can see that we’ve done that largely in just about four years, four to five years, as that curve really starts to ramp up in 2021. These are the kinds of proof sources that enable folks to have the confidence to adopt the product and utilize it. I mentioned these Category 1 CPT codes, but this is the one that was established in June of this year, covering constitutional genetic disorders. We believe that will reduce barriers to adoption and enable folks to utilize optical genome mapping more consistently in the field.

Regarding the cost structure, on the left-hand side of this slide, you can see our non-GAAP operating expenses quarterly for the past several quarters. We woke up in 2023 and said that the cost structure that was in place at that time was not going to be sustainable. It took us some time, but we reduced costs drastically over the period of time that you see outlined here. Importantly now, because two points define a line, we have a nice flat structure over the last couple of quarters. I think that is a very positive development. Over that same period of time, our gross margin has expanded significantly. We printed 52% in the second quarter. These are the types of trends that make us believe that we have a sustainable business that’s growing. We know how to invest in and drive that growth. We need to see these trends continue.

We are very encouraged with the progress that we’ve been making. Lastly, for the remainder of 2025, we have reiterated our annual guidance of $26 million to $30 million on the top line. We raised our guidance of new systems installation. Previously, we had guided to 15 to 20 systems, but we’ve raised that to 20 to 25. Our Q3 revenue guidance that we gave on August 14th, the Q2 call, was $6.7 to $7.2 million. That would be another quarter of sequential quarterly growth if we’re able to come in within that guidance range. We’re happy with the progress that we’ve made so far this year, and we think that this really provides a solid endorsement for the strategic adjustments that we’ve made and for the stability of Bionano Genomics going forward in this significant opportunity.

I want to thank everybody for attending, those of you in person, as well as those of you on the webcast. Thank you very much.

Katherine Dagan, Associate Biotech Research Analyst, HC Wainwright: I think we’re out of time, so we’ll wrap it up there.

Erik Holmlin, Bionano Genomics: Okay, thank you.

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