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Date
Thursday, November 13, 2025 at 4:30 p.m. ET
Call participants
- Chief Executive Officer — Erik Holmlin
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Takeaways
- Total Revenue -- $7.4 million in 2025, a 21% increase over 2024, with core revenue up 12% after adjusting for a $500,000 write-down in discontinued clinical services in 2024.
- Flow Cells Sold -- 8,390 units in 2025, reaching an all-time record and reflecting 7% growth year-over-year; among existing customers, flow cell purchases rose 6% year-over-year in 2025.
- Non-GAAP Gross Margin -- 46% compared to 26% in the prior year, supported by lower manufacturing costs and higher volumes.
- Non-GAAP Operating Expense -- $9.7 million, marking a 40% reduction from $16.1 million in the prior year.
- Installed Base -- Net increase of three systems for a total of 384 by quarter end; 23 new OGM systems installed year-to-date.
- Consumables and Software Revenue -- Grew 15% year-over-year in Q3 2025 and 10% year-to-date; comprised 72% of total product mix in Q3 2025 vs. 76% in Q3 2024.
- Cash Position -- $31.8 million in cash, cash equivalents, and available-for-sale securities at quarter end, of which $10.3 million is restricted.
- Public Offering -- Raised $10 million from a September equity offering, extending the company’s cash runway into 2026 or beyond depending on execution of cost initiatives.
- Revenue Guidance -- Management reiterated full-year fiscal 2025 revenue guidance of $26 million to $30 million and set Q4 fiscal 2025 outlook to $7.5 million to $7.9 million.
- Operational Strategy -- Four strategic pillars emphasized: supporting and sustaining routine users, expanding software usage, building reimbursement/guideline support, and improving profitability and scalability.
- Scientific Publications -- 97 new publications on optical genome mapping in 2025, a 10% increase versus the previous year, with a cumulative total of nearly 11,500 clinical research genomes published.
- Regulatory Progress -- CMS posted a preliminary determination for a second Category I CPT code for optical genome mapping, with a proposed reimbursement of $1,263.53.
Summary
Management signaled a business model shift prioritizing increased consumable and software usage among routine users rather than aggressive expansion of the installed base. The installed base grew modestly, with a net addition of three systems. Utilization among routine users drove most of the reported growth in flow cell sales and core recurring revenue. The company executed substantial cost containment, reducing non-GAAP operating expenses by 40% while expanding gross margins through product mix and manufacturing efficiencies. A successful public offering reinforced liquidity, and strategic investments focused on OGM reimbursement support, guideline inclusion, and global clinical adoption continue. Near-term guidance remained intact, reflecting confidence in the revised operating strategy.
- Holmlin stated, "what we see across the user landscape is that the average utilization across these routine users that are running on a regular basis is about four samples per week," but the top end reaches 40 samples, indicating substantial upside if adoption broadens.
- A single laboratory in Japan comprises the current installed base there, serving as a regional service provider. Management sees opportunity from local pharmaceutical firms and ongoing scholarly presentations from Japan.
- Non-GAAP operating expenses are expected to "remain relatively stable going forward," with planned flat spending unless justified by strategic opportunities.
- The company highlighted record presentations at the ASHG annual meeting and new published research from MD Anderson, strengthening the scientific case for OGM in cancer and rare genetic disease workflows.
- CMS’s preliminary crosswalk of the new Category I CPT code to a higher laboratory price point than microarray validates management's viewpoint that reimbursement momentum could enhance adoption.
Industry glossary
- Optical Genome Mapping (OGM): A technology enabling high-resolution, genome-wide identification of structural DNA variants using single-molecule imaging techniques.
- Flow Cell: A consumable device used within genome mapping systems for processing biological DNA samples.
- Category I CPT Code: A specific reimbursement code in the American Medical Association’s Current Procedural Terminology used for reporting established medical services for insurance payment.
- Chromoanagenesis: A catastrophic event leading to massive structural rearrangements in the genome, often implicated in cancer and other genetic disorders.
Full Conference Call Transcript
Erik Holmlin: Thank you, Kelly, and good afternoon, everyone. I'm excited to update you all on the third quarter results and key highlights as well as provide an update on our expectations for the remainder of the year. At Bionano Genomics, Inc., our focus is on transforming pathology, which is the medical discipline that investigates disease, including its causes, developments, and effects. Transformation is from pathology's analog past to a digital future. Our digital pathology solutions include optical genome mapping systems, the IONIQ system for nucleic acid isolation, and our VIA software. These solutions address significant unmet needs in cytogenetics and molecular pathology through simplification of workflows.
Over the last year, we have taken decisive steps to transform our business model away from one based in aggressively growing the installed base toward a model that's driving utilization of our solutions within a subset of our existing OGM and VIA software user base. We call this subset of users our routine users. These routine users are characterized by having an established flow of samples coming into their labs, and, therefore, we believe they can generate significant consumables and software revenues and will drive most of our revenue growth in the near term. To succeed with this strategy, we're executing against four strategic pillars.
First, we're focused on supporting and sustaining our installed base of routine OGM and VIA software users. Second, we are aiming to drive utilization through the adoption of software across the routine users of OGM, and that way, we can facilitate their menu expansion. Third, we're building support needed for optical genome mapping reimbursement and inclusion in medical society guidelines, recommendations, and different schedules for reimbursement. Fourth, we intend to improve profitability and scalability with lower costs and higher volumes. We believe our performance in the third quarter and year to date validates that focusing on these routine users is restoring growth in our core business.
At a high level this quarter, we achieved solid gross margins, remained disciplined with our operating expenses, and increased the utilization from these routine users. It's increasingly evident that optical genome solutions are providing valuable insights to our customers, and that these customers are expanding their utilization. Taking a closer look at this performance, total revenue for 2025 was $7.4 million, reflecting an increase of 21% compared to 2024. When adjusting for a write-down of $500,000 in revenues from discontinued clinical services in 2024, core revenues increased by 12% year over year in Q3 2025. We sold an all-time record 8,390 flow cells in 2025, which reflects a 7% increase compared to the same period last year.
And we're pleased with this strong growth in flow cells, again, this quarter. It reflects increased utilization within this routine use customer group. Non-GAAP gross margin for 2025 was 46%, which was significantly higher than the 26% non-GAAP gross margin reported for 2024. Third quarter 2025 non-GAAP operating expense was $9.7 million, which is a 40% reduction compared to the $16.1 million in non-GAAP operating expense in 2024. We installed seven new systems and brought one back for a net increase of three to 384 for the installed base as of the end of the third quarter of 2025. And year to date through 09/30/2025, we have installed 23 new systems.
We ended the quarter with $31.8 million in cash, cash equivalents, and available-for-sale securities, of which $10.3 million was subject to certain restrictions. In September, we completed a $10 million public offering of common stock, bolstering our balance sheet and extending our cash runway into 2026 and potentially longer depending on the execution of our growth and cost savings initiatives. Now taking a closer look at our first pillar, which is supporting the utilization across our routine user base, who repeatedly purchase and use consumables and software at higher rates. Overall, flow cells grew 7% in the quarter compared to last year, achieving this new record.
After removing the flow cells that were sold to new customers since 2024, and those sold in this quarter, closed sales sold to the remaining existing customers grew by 6% on a year-over-year basis. Flow cell purchases by existing customers in the first nine months of 2025 compared to the same customers a year ago grew by 7%. Our year-to-date performance suggests that our strategy of focusing on driving utilization with this routine user base is working, and customers are using our product at higher volumes. Now when looking at the revenue contributions from consumables and software, together these sales grew 15% on a year-over-year basis in the third quarter, and 10% year-over-year for the first nine months of 2025.
As a percentage of the total product mix, consumables and software represented 72% in 2025 and 76% in the first nine months of this year. Whereas in 2024, it represented 76% of the third quarter but just 62% in the first nine months of 2024. So this shift in product mix is also a result of our change in strategy. Beyond supporting our OGM users, we're also making good progress with our second pillar of integrating VIA into customer workflows, and upgrading our software and compute platforms to make analysis of OGM, microarray, and next-generation sequencing data easier, faster, and more accurate.
Last quarter, we announced that upgrades were released in a first wave and that we are pleased to remain on track for the full commercial release of this software in the coming months. Now moving down the P&L, to discuss our pillar of improving profitability and scalability, we have made steady progress in reducing our non-GAAP operating expenses over the last few years and we have remained disciplined with this approach throughout this year. In the third quarter, our non-GAAP operating expense was $9.7 million, and that represents a 40% year-over-year reduction.
Turning to gross margin, cost reduction along with improvements to our product manufacturing costs and volumes have enabled expansion from 22% on the non-GAAP core gross margin in 2023 to 46% non-GAAP gross margin this quarter. While we expect to see continued margin expansion over time, we believe that the levels that we have seen in the last few quarters are representative of where we will be in the near term. With the shift in product mix towards consumables and software, we see a benefit to gross margin as well. Importantly, these adjustments and improvements in cost and margin are strong indicators that we are meaningfully improving the financial profile of Bionano Genomics, Inc.
Now lastly, turning to our final emphasis on building the support needed for OGM reimbursement. Where we believe a growing number of publications illustrate the utility of OGM in cytogenetics and clinical research, as well as the number of clinical research genomes published. Taken together, we see these as positive leading indicators of future adoption of optical genome mapping. In 2025, there were 97 new publications demonstrating the value of optical genome mapping, and this represents a 10% growth over the same period the year before. And the OGM community has now published on a cumulative basis nearly 11,500 clinical research genomes.
These publications provide the support for new customers to adopt, existing customers to expand their applications, and third parties to support OGM in reimbursement and consideration for medical society recommendations and guidelines. Now looking closer at some of the key studies presented and presentations over the last few months, first, we had a strong presence at the ASHG annual meeting in Boston last month, where there were nine studies presented, including oral presentations and posters that demonstrated both growing interest in key existing geographies for optical genome mapping as well as in new regions. We were impressed to see a strong contribution from Japan.
We're excited to see this interest in optical genome mapping continue to grow on a global basis.
Erik Holmlin: Second, a new publication from the MD Anderson Cancer Center at the University of Texas which was recently published, shows how optical genome mapping can overcome key limitations of targeted RNA seq for cytogenetic investigation in acute leukemias. This paper represented the first benchmark comparison of optical genome mapping directly to RNA Seq in cancer. It supports our overall digital pathology strategy by tying OGM to methods that are commonly used in molecular pathology and represents an important expansion outside of cytogenetics. Chroma antigenesis refers to a catastrophic genomic event frequently associated with complex karyotypes and extensive clonal heterogeneity, treatment resistance, poor prognosis, and it includes events such as chromothripsis, chromoplexy, and chromoanosynthesis.
All of which play significant roles in cancer development and are hard to sort out using existing tools in cytogenetics. Optical genome mapping provides a genome-wide view of structural variations at high resolution which enables precise identification and characterization of the genome variation underpinning this chromoanogenesis. The four chapters published in this series highlight the use of optical genome mapping and the expansion into new cancer types for OGM such as multiple myeloma, and chronic lymphocytic leukemia or CLL. As well as the proliferation of novel workflows such as something new called DAM assisted fluorescence tagging of chromatin accessibility which is a hybrid method for highly detailed spatial analysis of chromatin assemblies.
And so this is one of the first times that we're seeing optical genome mapping being integrated into spatial analysis. Now in our last call, we shared that the editorial board of the American Medical Association established a second category one CPT code for optical genome mapping. This one in the evaluation of constitutional genetic disorders. And that represented another incredible milestone for the OGM community. I'm pleased to share that in mid-September, CMS posted the preliminary payment determination for this CPT code, which is based on a crosswalk to a previously established OGM code priced at $1,263.53.
Pricing at this level, which is higher than what microarray codes are priced at, is consistent with the needs of laboratories today seeking to move forward from the legacy methods. We believe this CPT code builds on the evidence that OGM can outperform these legacy methods across a number of applications and may pave the way for more routine use of OGM across oncology, and clinical genetic research communities globally. So to wrap up, I would like to provide our outlook for the remainder of the year. We are reiterating our full year 2025 revenue guidance of $26 to $30 million. We expect the 2025 revenues to be in the range of $7.5 to $7.9 million.
And given that we've reached 23 new OGM system installations in the first nine months of this year, we now expect to exceed the prior range of twenty to twenty-five systems, likely surpassing the high end of that. So with that, Didi, please go ahead and open the line for questions. Thank you.
Operator: To ask a question, you press 11 again. And our first question comes from Yi Chen of H. C. Wainwright. Your line is open.
Yi Chen: Hi. Good afternoon. Thank you for taking my question. My first question is, with respect to increasing utilization of routine use customers, can you talk about what is the potential peak level of new utilization for these continuous customers? And how soon do you expect to have these customers achieve the peak level based on the current trend? Thanks.
Erik Holmlin: Yeah. It's a key question, important topic. Thank you, Yi, for joining the call and for the question. What we feel confident about first of all, is that in general, the labs are not sample limited. So they have an abundance of samples. Those samples are distributed across multiple different indications. And so the process of expanding utilization involves the laboratories developing and validating an assay for one application. And then running that for a while, and then beginning to grow the menu by developing an assay for another research indication and so on and so forth. That's really the primary mechanism of growth.
And what we see across the user landscape is that the average utilization across these routine users that are running on a regular basis is about four samples per week. But at the highest end of the spectrum, it's as high as 40 samples per week. And so our view is that a reasonable target for us to shoot for is maybe the midpoint between the four and the 40. So getting up to in the low twenties on average across all of the routine users. And so, you know, that's what we're gonna try to make happen.
Yi Chen: Thank you. And, with respect to the Japanese market, can you talk tell us what is the current installed base in Japan? How do you think the market could ramp up in comparison to the U.S. market?
Erik Holmlin: Yeah. So we have really only one system installed in Japan, and it's at a laboratory of a service provider. And so different academic customers, industrial customers, can send samples to this laboratory, have them processed, and get data. And so that's what's going on. And what we see is that the interest in Japan has evolved over time. So initially, when this services lab first got going, they were primarily focused on nonhuman applications, actually. And now the last couple of years, that has changed. And so the evolution is much more consistent with what we see in other areas. Work in genetic diseases, leukemias, and lymphomas.
And so we would expect that market to evolve similar to what we see in the U.S. for those applications. I think that there's also a significant opportunity in Japan around cell and gene therapy development. And so we're seeing some of these pharma companies begin to access this service provider, and so there's tremendous potential in Japan. I do think for the types of clinical research applications that we're doing in other regions, such as hematologic malignancies and constitutional genetic diseases, that it will take some time. They're gonna wanna build up a kind of war chest of local data in support of optical genome mapping, but that's ongoing.
I think that the pharma can accelerate and so we're paying attention to all of these, and we're quite happy to see some presentations or posters, actually, at ASHG last month.
Yi Chen: Got it. And with respect to operating expenses, do you expect them to remain relatively stable going forward?
Erik Holmlin: Yes. Yes. I think this is the range that we're intending to be in. We're in the process of putting together our detailed operating plan for next year. And we see some areas where we might like to invest, but I think that our overall intention is to keep things as flat as we possibly can except where opportunities justify it.
Yi Chen: Got it. Thank you, Erik.
Erik Holmlin: You're welcome, Yi. Thank you.
Operator: I show no further questions at this time. I'd like to turn it back to Erik Holmlin for closing remarks.
Erik Holmlin: Great. Very good, Didi. Thank you, and thank you to everybody who joined the call. And we look forward to updating you on our full year results next year. Thank you very much.
Operator: This concludes today's conference call. Thank you for participating and you may now disconnect.