Bionano Genomics - Earnings Call - Q3 2025

Executive Summary

• Q3 2025 revenue was $7.367M, up 21% year over year, and above both prior quarter guidance ($6.7–$7.2M) and Wall Street consensus ($6.906M*). EPS was -$1.59 versus consensus of -$2.08*, a beat driven by higher utilization and disciplined OpEx.
• Gross margin stabilized at 46% GAAP and non-GAAP, a material improvement versus the prior year’s (139)% GAAP and 26% non-GAAP, aided by cost reductions and manufacturing efficiencies.
• Operational KPIs strengthened: record 8,390 flowcells sold (+7% YoY) and installed base reached 384 systems (+4% YoY), with consumables and software mix at 72% in Q3 (strategy pivot toward routine users).
• Guidance: full-year 2025 revenue reiterated at $26–$30M; Q4 2025 revenue guided to $7.5–$7.9M; new OGM installations now expected to surpass 25 (raised from 20–25). Management noted cash runway extended into Q3 2026 following a $10M September offering.

Consensus values marked with *; Values retrieved from S&P Global.

What Went Well and What Went Wrong

What Went Well

• Record consumables throughput: “We sold an all-time record 8,390 flow cells in the third quarter of 2025,” reflecting increased routine user utilization (+7% YoY).
• Margin expansion and cost control: non-GAAP gross margin reached 46% vs 26% last year; non-GAAP OpEx fell 40% YoY to $9.7M, signaling improved profitability profile.
• Strategic validation: “Focusing on these routine users is restoring growth in our core business,” with consumables + software sales up 15% YoY and mix at 72% of product revenue, underscoring a sustainable revenue base.

What Went Wrong

• Persistent losses and financing needs: net loss of -$8.503M and disclosure of going concern and financing risks in forward-looking statements highlight ongoing capital dependence.
• Instrument revenue remains modest: instrument revenue of $1.6M (vs $1.4M LY) as the company shifts away from aggressively expanding the installed base, limiting near-term top-line leverage from placements.
• International ramp is early-stage: only one system installed in Japan; management expects time to build local data and adoption in constitutional disorders and hematologic malignancies.

Transcript

Operator (participant)

Today, and welcome to the Bionano third quarter 2025 Earnings conference call. Today's conference is being recorded. At this time, I would like to turn the conference over to Kelly Gura from Investor Relations. Please go ahead.

Kelly Gura (VP of Investor Relations)

Thank you, Dee Dee, and good afternoon, everyone. Welcome to the Bionano third quarter 2025 financial results conference call. Leading the call today is Dr. Erik Holmlin, CEO and Principal Financial Officer of Bionano, and he is joined by Mark Adamchak, Bionano's Vice President of Accounting and Principal Accounting Officer. After market close today, Bionano issued a press release announcing its financial results for the third quarter of 2025. A copy of the release can be found on the Investor Relations page of the company's website. Certain statements made during this conference call may be forward-looking statements. Actual results may differ materially from such statements due to several factors and risks, some of which are identified in Bionano's press release and Bionano's reports filed with the SEC.

These forward-looking statements are based on information available to Bionano today, November 13, 2025, and the company assumes no obligation to update statements as circumstances change. During our call, we may reference certain non-GAAP financial measures, which we believe provide useful information for investors. Reconciliation of these measures to GAAP can be found in our press release and slide deck. An audio recording and webcast replay for today's conference call will also be available online on the company's Investor Relations page. With that, I will turn the call over to Erik.

Erik Holmlin (CEO and Principal Financial Officer)

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, our focus is on transforming pathology, which is the medical discipline that investigates disease, including its causes, developments, and effects. This transformation is from pathology's analog past to a digital future. Our digital pathology solutions include optical genome mapping systems, the Ionic 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 mapping 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 the third quarter of 2025 was $7.4 million, reflecting an increase of 21% compared to the third quarter of 2024. When adjusting for a write-down of $0.5 million 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 the third quarter of 2025, which reflects a 7% increase compared to the same period last year. We are 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 the third quarter of 2025 was 46%, which was significantly higher than the 26% non-GAAP gross margin reported for the third quarter of 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 the third quarter of 2024. We installed seven new systems and brought one back for a net increase of 384 for the installed base as of the end of the third quarter of 2025. Year to date, through September 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 the third quarter of 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 the third quarter of 2024 and those sold in this quarter. Flow cells 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 within 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 the third quarter of 2025 and 76% in the first nine months of this year, whereas in 2024, it represented 76% in the third quarter, but just 62% in the first nine months of 2024. 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 the first quarter of 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.

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 the third quarter of 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. 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 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. 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 for us. Third, multiple studies highlighting the OGM utility for analysis of the cancer biomarker chromoanagenesis were published in a book edition of Molecular Methods in Molecular Biology. Chromoanagenesis 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 chromoanasynthesis, 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 chromoanagenesis.

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 fluorescent tagging of chromatin accessibility, which is a hybrid method for highly detailed spatial analysis of chromatin assemblies. This is one of the first times that we're seeing optical genome mapping being integrated into spatial analysis. On 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. 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. 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 $26-30 million.

We expect the fourth quarter of 2025 revenues to be in the range of $7.5-$7.9 million. Given that we have reached 23 new OGM system installations in the first nine months of this year, we now expect to exceed the prior range of 20-25 systems, likely surpassing the high end of that. With that, Deedee, please go ahead and open the line for questions.

Operator (participant)

Thank you. To ask a question, please press star one one on your telephone and wait for your name to be announced. To withdraw your question, please press star one one again. Please stand by while we compile the Q&A roster. Our first question comes from Yi Chen of H.C. Wainwright. Your line is open.

Yi Chen (Managing Director)

Hi, good afternoon. Thank you for taking my question.

My first question is with respect to increasing utilization of routine among routine use customers, can you talk about what is the potential peak level of utilization for these routine use customers? How soon do you expect to help these customers achieve the peak level based on the current trend? Thanks.

Erik Holmlin (CEO and Principal Financial Officer)

Yeah, I think it's a key question, an 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. They have an abundance of samples. Those samples are distributed across multiple different indications.

The sort of 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 is really the primary mechanism of growth. 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. At the highest end of the spectrum, it is as high as 40 samples per week. 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 20s on average across all of the routine users.

And so that's what we're going to try to make happen.

Yi Chen (Managing Director)

Got it. Thank you. With respect to the Japanese market, can you tell us how many, what is the current install base in Japan? How do you think the market could ramp up in comparison to the U.S. market?

Erik Holmlin (CEO and Principal Financial Officer)

Yeah. We have really only one system installed in Japan, and it's at a laboratory of a service provider. Different academic customers, industrial customers can send samples to this laboratory, have them processed, and get data. That's what's going on. What we see is that the interest in Japan has evolved over time. Initially, when this services lab first got going, they were primarily focused on non-human applications, actually. Now, in the last couple of years, that has changed.

The evolution is much more consistent with what we see in other areas: work in genetic diseases, leukemias, and lymphomas. 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. We're seeing some of these pharma companies begin to access this service provider. There is 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, it will take some time. They're going to want to 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.

We are paying attention to all of these, and we are quite happy to see some presentations or posters, actually, at ASHG last month. Got it. With respect to operating expenses, do you expect it to remain relatively stable going forward? Yes. Yes. I think this is the range that we are intending to be in. We are in the process of putting together our detailed operating plan for next year. 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 (Managing Director)

Got it. Thank you, Erik. Yeah, you are welcome, Yi.

Operator (participant)

Thank you. I show no further questions at this time. I would like to turn it back to Erik Holmlin for closing remarks.

Erik Holmlin (CEO and Principal Financial Officer)

Great. Very good, Deedee. Thank you. Thank you to everybody who joined the call.

We look forward to updating you on our full year results next year. Thank you very much.

Operator (participant)

This concludes today's conference call. Thank you for participating, and you may now disconnect.