Bionano Genomics at Canaccord Conference: Mapping a New Path

On Wednesday, 13 August 2025, Bionano Genomics (NASDAQ:BNGO) presented at Canaccord Genuity’s 45th Annual Growth Conference, outlining strategic shifts and financial updates. The company emphasized its optical genome mapping (OGM) technology, aiming to replace traditional methods in genetic analysis. While Bionano faces financial challenges, it remains optimistic about its technological value and market potential.

Key Takeaways

• Bionano is focusing on expanding the use of its existing OGM platforms, Saphyr and Stratus, rather than placing new systems.
• Gross margins have improved significantly, rising from 22% in 2023 to 46% recently.
• The company aims to achieve $26 million to $30 million in revenue this year.
• Bionano has a cash flow runway until February 2026 and is exploring financing options.
• Adoption of CPT codes is expected to drive OGM’s wider acceptance and reimbursement.

Financial Results

• Gross margin improvements are attributed to cost reductions and increased volumes.
• Over $100 million in non-GAAP operating expenses have been cut in recent quarters.
• Revenue guidance for the year is set between $26 million and $30 million.
• Concerns about cash balance contribute to the company’s low market capitalization.
• Financing strategies include public equity, debt management, and cost structure optimization.

Operational Updates

• Around 20 Stratus systems have been deployed, mainly with high-volume users.
• The Via software enhances the analysis of OGM and NGS data through AI.
• Training is provided to existing users to boost internal capacity and utilization.
• Established business presence in Europe with existing reimbursement policies.
• Potential commercialization in China with a registered Saphyr system.

Future Outlook

• Bionano expects to exceed its guidance of 20 new system placements this year.
• Investment in customer success and support is planned to increase utilization.
• Positive changes are anticipated in the US reimbursement landscape with CPT code adjustments.
• Focus remains on markets in the US, Canada, Western Europe, and Israel.
• Financing exploration includes a shelf registration.

Q&A Highlights

• Shift towards clinical and pharmaceutical routine users due to predictable revenue.
• CPT codes are crucial for OGM’s adoption and reimbursement.
• Reimbursement of OGM tests is expected to boost consumables revenue.
• Oncologists at MD Anderson use OGM reports for leukemia treatment decisions.

For more detailed insights, please refer to the full transcript below.

Full transcript - Canaccord Genuity’s 45th Annual Growth Conference:

Kyle Mixon, Analyst, Canaccord: Hi, welcome to the Canaccord Growth Conference. I’m Kyle Mixon and cover life science tools and diagnostics for Canaccord. Pleased to really have this fireside chat with Bionano Genomics here with us today. Bionano offers optical genome mapping technologies for genome analysis, which we’ll learn more about today. So with us from the company we have Eric Holman, CEO.

Thanks Eric for joining us today, appreciate it. So this is a growth conference, you’re a growth oriented company. Maybe not everyone knows the story super well, we’ll just go through an overview of Bionano.

Eric Holman, CEO, Bionano Genomics: Yeah sure. I appreciate it. I appreciate the invitation Kyle. And you know, your work is really well done. And you know, everybody on my team loves reading your reports and what you’re covering.

So you’re doing a great job. What I would say is that when you think about Bionano, we are a traditional life sciences instrumentation company in that we offer a platform for genome analysis. But we really don’t wanna be thought of as a traditional life sciences instrumentation company, because what we do is look at the applications that customers use when they adopt our platform. And across this landscape of human analysis in genomics, actually there’s a long history of clinical testing that’s been going on in pathology, cytogenetics. Molecular pathology is newer, but there’s tons of anatomic and clinical pathology.

And this is where our proprietary platform, Optical Genome Mapping, is really making inroads, and what we’re focused on is transforming those workflows. So if you look at cytogenetics, for example, karyotyping is the gold standard across the world in hematological malignancies. Every leukemia, lymphoma, myeloma, there is an attempt to karyotype. Now half of the time, that result comes back normal karyotype, but the sample is being analyzed in the first place because the oncologist knows they have leukemia. And so this is a workflow we think we can digitize and completely transform.

In addition to karyotyping, there’s something called FISH, or fluorescence in situ hybridization. And optical genome mapping does what karyotyping and FISH do in leukemias and lymphomas. Then microarrays, which have been the first line standard in genetic disease analysis, optical genome mapping can replace that as well. And so, OGM for short, is consolidating these three legacy methods into one digital platform, and publications are now showing that it not only is faster, so karyotyping takes four weeks, mapping takes four days, but it’s much more accurate. So, better results, and so instead of getting 50% of your samples coming back normal karyotype, there are studies that are published that show that that number can be as high as eighty five percent with mapping.

So, we have a very focused end user application. It’s transforming this cytogenetic workflow within pathology.

Kyle Mixon, Analyst, Canaccord: Great, so you have a multi billion dollar opportunity. You wanna just walk through the different segments as see them?

Eric Holman, CEO, Bionano Genomics: Yeah, I think that there’s a couple of key elements here. Number one is for optical genome mapping as a workflow, certainly within this hematologic malignancies, leukemias, lymphomas, then across genetic diseases. So, think of your developmental delays, intellectual disability, autism spectrum disorder. Any of these sort of like situations where a child is missing a milestone, it’s indicated to be looking at some form of a genetic analysis, and so mapping can be used there. We call that Constitutional Genetic Disorders.

But a third area, and a really important one, is in pharmaceutical R and D. So, cell and gene therapies, CAR T, various gene therapies, stem cell therapies, all require some sort of genetic analysis in order to confirm that on target effects have been put in place, and that there are no off target effects. And so, what we see is a lot of adoption within pharmaceutical companies to use optical genome mapping as an alternative there as well. And so, that’s another significant opportunity for mapping outside of the clinical research pathology segment. Got it.

And then

Kyle Mixon, Analyst, Canaccord: in terms of your, like your products, so you had the Sapphire for for years, was the main platform for the for ODM. And then I think like early last year you announced the Stratus, was like the next gen kind of platform, four fold increase in I think the throughput. So, talk about how that kind of ramp has gone, recognizing there’s been some macro constraints and stuff.

Eric Holman, CEO, Bionano Genomics: Yes. The macro environment has been an interesting one to navigate. And so, what, you know, sort of historical progress has been led by the Saphyr system, which is really the first mapping platform for at scale utilization. It’s the one that we broke into these indications with. There’s the majority of publications are you know, based on data that were generated with the Saphyr system, and what we recognized was that higher volume labs, reference laboratories, would need higher throughput in order to really adopt optical genome mapping in a routine and industrial way.

So, we developed the Stratus. It’s based on the same core technology. It uses the same proprietary consumable, which linearizes DNA and enables detection of structural variations. The Stratus, as you mentioned, has about four times the throughput of the Sapphire, and we offer those together in the market today. And so, have seen, I think, excellent adoption.

There’s right around 20 Stratus systems in the field today, and they’re all being used by high volume users, and typically the customers that are coming on board with Bionano and mapping tend to be those higher volume users. It’s really found its place with people that are running routine clinical research applications. But, we’re still selling the Sapphire system. It’s proving to be maybe an entry model for some labs. So, the two of them go together, and what links all of this together is our software.

And so, we’ve developed something called the Via software. Via stands for Variant Intelligence Applications, and what’s really great about Via is that for the optical genome mapping workflow, it uses AI to completely automate the whole process from interpretation, annotation, analysis, and reporting. So, the laboratory, which historically would be delivering multiple reports to an end user at multiple stages, different times, now gives one single consolidated report, which they customize and develop on their own, but they’re able to build it around various guidelines, such as the NCCN guidelines. So it’s an incredibly streamlined workflow. And VIA not only allows for the analysis of optical genome mapping data, but you can look at microarray data on it, and next generation sequencing data.

So, you can analyze structural variations from NGS as well. And so, in addition to our sales of optical genome mapping systems, we also sell the software. So, those are the two products that are really driving the growth of the company going forward.

Kyle Mixon, Analyst, Canaccord: Got it. So given maybe like the placements and the shipments of the, you know, instruments maybe has slowed down or like will be slow going forward, how has like the utilization per instrument kind of trended? Especially when you compare Stratus to, you know, Sapphire?

Eric Holman, CEO, Bionano Genomics: Yeah, I think certainly our highest volume users, we have more than one customer, so I guess that’s multiple customers that are actually running close to a million dollars a year in consumables. You know, across the 150 or so routine users, those are relatively rare. But, what we’re seeing is that a lot of customers coming in and running at higher volumes, and some of those are Stratus customers. Others are customers that have built a network of Saphyr systems to work together to generate the pull through. But, our focus, you know, as times got tight for equity financing, and the pressure was on to reduce operating expenses, we’ve taken over a $100,000,000 of non GAAP opex, you know, out of the P and L over the last several quarters.

So, we’re burning substantially less cash. Those actions and others have enabled us through the end of the first quarter, we report the second quarter tomorrow, but through the end of the first quarter have enabled us to take gross margin from about 22% in the ’23. We reported 46% last quarter. We expect that trend to continue. That’s related to cost reductions and volumes, but we have focused our company on really addressing mostly our existing routine users, training them on our software, so that they have a higher internal capacity, and can run more.

And what we’re seeing is, you know, we’re starting to look at sort of same customer consumables purchases, and it’s growing. And so, we’ll have more to say about that actually in the earnings call, but you know, we saw good growth, you know, so far with this group, and we understand strategically how to work with customers, and have them expand their menu. So, the key to growth and utilization is somebody may adopt optical genome mapping to analyze, you know, ALL, for example. And then, once they have validated a workflow for ALL, then they can bring CLL, CML, and they can, you know, bring other indications on. Some run constitutional genetic disease analyses, like FSHD is a common one, common genetic test that people will bring on.

And so, growing that menu expands consumables revenues on a per customer basis, and obviously, customer profitability. We’re not using our capital for customer acquisition, and so, I think we’re much more capital efficient, and we’re seeing the growth. So, it’s good overall, and the margin is way up, so that’s very positive.

Kyle Mixon, Analyst, Canaccord: Yep. So you’re talking about a lot of clinical applications. Are you seeing that the clinical customers, let’s say, kind of start at a lower utilization or like a pull through metric and that grows and that’s, you know, becomes even more recurring whereas the academic guys might be a lot early on, but like, might be a bit more lumpy, or like, stop kind of short at some point.

Eric Holman, CEO, Bionano Genomics: Yes. It’s very lumpy on the academic basic research side, and you know, that’s driven by, they get a grant, they run some samples. Sometimes those grants are enormous, and so they might run, you know, 500 samples, and that’s great. But then, the same post doc that was running the samples buckles down and analyzes them, and so, you know, that continuity or routine use pattern isn’t always there. And so, you know, since we sell a RUO product, we tend not to say clinical customers, but we refer to them as routine users.

And that’s the same in pharma. It may not be a clinical end use, but it’s still a routine user. And those applications are much more consistent, predictable, and you know, higher volume overall. And, you know, that really is That is the dream overall, is to build that customer base. And so, I think if you look at the history of Bionano, and you’ve been following us for a while, optical genome mapping we’ve known has incredible capabilities, and we’ve had to feel our way through to find exactly where it was going to make the biggest impact, and I think we’ve done that, and so that’s why we’re seeing this adoption.

Now, at the front end of your question, you said, you were talking kinda like, what is the ramp look like, utilization ramp, for one of these routine users? And they tend to offer the technology in a validated environment. So, we sell them an RUO product. They bring it in, they themselves develop an assay on it, let’s say a laboratory developed test, for example. They will develop an LDT, and they’ll start running samples, and then they expand that menu, so then they develop a second LDT, and a third LDT.

We have some labs now that are running multiple LDTs on Sapphire or Stratus.

Kyle Mixon, Analyst, Canaccord: Got it. Yes, so on that note, you know, it has been for years, for five years at least, you’ve been kind of working towards that goal of having, you know, OGM LDTs, OGM tests out there, like commercialized almost. So, I think you had some recent news about category one CPT code. Can you just talk about that, as well as next steps for reimbursement for OGM?

Eric Holman, CEO, Bionano Genomics: Yes. So, you go to a lab and you say, listen, this is gonna be a great technology. You’re gonna wanna use it to replace your karyotyping and phish, and of course, they’re getting paid for those. And so, they’re interested in, well, will I get paid for OGM? And, know, historically, that’s been, well, you know, maybe you could, get some grant funding, maybe you can use your institutional funding, but last year, in June, so in 2024 in June, the AMA established a category one CPT code for using OGM in leukemias and lymphomas, hematologic malignancies.

And then, in June, the AMA established a CPT code for using it in these constitutional genetic disorders. And so, really our entire, you know, routine use portfolio is covered by a category one CPT code. And category one is, you know, an incredibly high bar. And so, we’ve been able to pass that. And, you know, anecdotally, we hear from labs that they are getting paid at the CMS rate, or whatever rate it is that they’re contracted, which is always related to the CMS rate.

And, you know, we expect there to be coverage decisions coming out over time related to OGM. But, one of the things that’s, I think, a little bit easier with OGM compared to other, you know, novel solutions in the space is that this is just a different mousetrap. Labs are already processing these samples to get this information. We’re not asking a physician to do something they aren’t always doing. Those labs are not asking an insurance company to pay for something that they’re not always paying for.

So, the category one CPT code is a tremendous leap forward for OGM.

Kyle Mixon, Analyst, Canaccord: So the thought is that your customers will get reimbursed or paid for tests, like that are developed on your platform, therefore you will get consumables revenue as that becomes a recurring kind of test for that.

Eric Holman, CEO, Bionano Genomics: That’s right. That’s right. So, a barrier to adoption for them is economic. Will they be able to overcome the opportunity cost of not using something that they would otherwise get paid for? And our belief is that the CPT code is filling that gap, and you know, that is really one of the final remaining gaps to increasingly widespread adoption.

Kyle Mixon, Analyst, Canaccord: So, what else remains from the clinical side of things? Yeah, I mean, I

Eric Holman, CEO, Bionano Genomics: think that, you know, we have certainly reached a certain tier where we’ve addressed a lot of the really like existential questions, like, without this, I simply cannot move forward. I believe that all of those are set aside, and by the way, we have tremendous adoption across Europe. Europe is a little bit more evolved when it comes to healthcare reimbursement policy. And, you know, so what we’ve seen there is that they’ve been getting paid for their OGM for a while. They need to continue to jump through hoops, so Europe is a very solid and established OGM business for this routine use.

We’re at this level where we’ve overcome these major barriers, and so now, you know, methodologic tweaks that allow for menu expansion, and a lot of that gets done by current customers. For example, multiple myeloma is a notoriously difficult sample type to work with in cytogenetics, because it typically does not grow in culture. And one of our users, but, you know, the number of affected cells in a given sample is usually very low, and so, it hasn’t met our commercial criteria for QC of the sample, and one of our users in France actually published a paper demonstrating that they could reduce that input requirement by a factor of two, and now they run multiple myeloma on a routine basis, and we’re seeing this sort of adoption happen in other places. So, there remain hurdles here and there. A major update that we recently released was to our software, which took the workflow for analysis, interpretation, reporting in constitutional genetic diseases, and fully automated that.

We had, you know, the first release of the Via software only addressed that need in hematological malignancies, but we now have released that for constitutional genetic disorders. So, you know, innovation that we can do that continuously streamlines, and simplifies the workflow, expands the utility, is the thing that we’re focused on, and we’re getting help from the existing customer base, which is nice.

Kyle Mixon, Analyst, Canaccord: Got it. So given, you know, cash is like so precious, and you have tried to like get OpEx down and get the burn down, and kind of set up a path to profitability. How are you going to invest going forward? Is it more on the pushing boxes out there side of things? Or, you know, kind of beefing up or improving the system and the software to enable like, you know, expanded applications.

Eric Holman, CEO, Bionano Genomics: Yeah, I think that, you know, if we look across, you know, the sort of OpEx line in the company, the area that is kind of two x at least any other area is, you know, what we would call like customer success, customer support, and really focused on making sure customers understand the workflow, can perform it at a high level, and you know, increase their utilization based on that training and support. So, that’s the area of greatest investment for us, which is sort of the opposite side of getting more boxes out there. And so, we really have, explicitly, we have said to, you know, the market that we’re not, I mean the stock market, but to the end user market that we are not going to be out there driving new system placements like we had in the past, that we are gonna focus on our existing users. And interestingly, when we said that on conference calls, we have large organized networks of users in three or four different geographic regions. You know, they were alarmed because, you know, the lab up the street from them is excited to get OGM, a Sapphire, a Stratus, their friend, their colleague, their mentor, and we assured them that we will continue to put systems out, and so we set guidance to do up to 20 systems this year, and I can tell you just through our, through Q one, we haven’t reported Q two yet, but just based on what Q one looked like, we’ll exceed that number.

So, we have a healthy expansion of new systems, but instead of doing 80 to a 100, we’re doing, you know, 20 or so, thereabouts. But, these are all to routine users that will pull through a high volume of consumables.

Kyle Mixon, Analyst, Canaccord: Okay. Great. So at the moment, your revenue guidance for the year is 26 to $30,000,000. It is like a year over year decrease, but given the changes, like, it makes sense. You know, you you’re gonna have an update tomorrow.

You might have you might, like, adjust that range or increase decrease it. But when you think, like, qualitatively about the path forward on in The US academic side of things given the NIH kinda news flow, The international side of things whether it be EMEA or Asia, APAC, know, and the kind of the clinical world as well. What are just some, you know, the puts and takes that we should be thinking about going forward? What could likely, you know, impact your performance, without giving any numbers?

Eric Holman, CEO, Bionano Genomics: Yeah, sure. I mean, think that overall, we find ourselves in a, you know, reasonably safe zone. We do see it. We were at a conference last week, think, in Houston, the Cancer Genomics Consortium Conference taking place in Houston. We have a big presence at MD Anderson, so we spend a lot of time with them.

And they indicated that even though their primary focus as MD Anderson is treating patients, they do see impacts of the uncertainty around funding, and it is affecting things for them. But, oncologists at MD Anderson will not treat their leukemia patients, we understand. This is being told to us anecdotally, without an OGM report. Right? So, they’re relying on it.

Oncology patients are not going anywhere. So, that seems to be a very consistent and stable place for us to be. Somewhat insulated from, you know, NIH uncertainty. Europe is stable, and we’re not seeing any of those kinds of pressures. There are different pressures there in Europe, certainly.

But, you know, that’s relatively stable. You know, China was big for us for a while in the academic research market. That has slowed down, but there’s tremendous potential there. We have a partner who has gotten a version of the Saphyr system registered with the National Medical Products Administration or NMPA there, and we’re working through how they might commercialize OGM there. And so, I think that there’s upside potential there.

In you know, Middle East, so we have a very significant presence in Turkey, and the Turkish Health Ministry in the last, you know, forty five days just, you know, placed optical genome mapping into its, you know, registry of clinical tests, so a physician can order it there, and you know, so we see a lot of growth potential there, as well as across The Middle East. Our focus directly is on United States, Canada, Western Europe, and we also have a big business in Israel. So, I would say that overall, there’s quite a bit of upside there, and we’re at a stable place with growth potential here in The US.

Kyle Mixon, Analyst, Canaccord: Alright, and then on your cash flow perspective. So, you have cash flow only until in 02/2026, I guess, so that’s, it’s not, you know, extremely long. What are some of your options to extend that, I guess, as you think?

Eric Holman, CEO, Bionano Genomics: Yeah, mean I think that like any public company, we have a variety of vehicles that are available to us, know, including, you know, shelf registration that we have an s three shelf, but you know, we can finance on other platforms in the public equity markets. You know, we have a debt, know, sort of on the books now, on the balance sheet now, and you know, there could be some things that we might do with that debt to release additional cash. And so, yes, I think that we’re, you know, at a level of, you know, cash reserves, which mean that management should focus on finding ways to replenish those. I think we’ll need to raise equity capital, but I think with the new expense and cost structures, these improvements in gross margin, our capital needs, I mean, they are a fraction of what they have been in the last several years, which is great. I think we put that capital to good use.

We figured out where our proprietary products could be adopted for routine use, both optical genome mapping systems and software, and now we can drive those forward to get to cash flow break even.

Kyle Mixon, Analyst, Canaccord: Got it. Okay. Well, finally, let’s wrap up with a couple of questions in one. So first, you know what are some attributes let’s say that you know, people under appreciate or under, know, don’t exactly like expect from a Bionano, let’s say. Then as you think about next year, you know, are you going to surprise people?

Eric Holman, CEO, Bionano Genomics: Yeah, mean I think that, you know, I’m the CEO of the company. I check the stock every once in a while, and you know, I look at our market capitalization, and it’s one third of our revenues. So we’re traded at a multiple of point three x, you know. And to me that reflects, you know, certain attitudes around our cash balance, but also a true under appreciation of what our potential is. One of the things that we’ll hear in an investor meeting very common is, wait a minute, this isn’t sequencing, and I’m thinking like, that’s the epiphany.

You got it. Like, there’s a lot of sequencers out there. By the way, they’re kind of struggling. We’re something that’s in that space, but adds completely unique value with tremendous upside. So, I think people are missing that.

You know, a year from now, I think that what we’re gonna see is a lot of progress on the reimbursement landscape here in The United States. So, we’ll see a lot more traction with third party payers in a way that, you know, is really systematic. Right now, it’s a little bit more anecdotal based on the CPT code. That seems to be working. And, you know, there’s the potential that prices could change for these CPT codes in the positive direction, but I’m not making that prediction, but, you know, that would be cool to see.

You know, we’re we’re aware that customers have been asking CMS to take the pricing up. So, let’s see what happens there.

Kyle Mixon, Analyst, Canaccord: And the price right now is?

Eric Holman, CEO, Bionano Genomics: It’s around $1,263.

Kyle Mixon, Analyst, Canaccord: Got it. Okay. Alright. Awesome. Good way to end.

Thanks a lot, Eric.

Eric Holman, CEO, Bionano Genomics: Yeah. Appreciate it. Thank you. Thanks, Kyle.

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