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Operator
Good day, and welcome to the Bionano fourth quarter 2024 earnings conference call. Today's conference is being recorded. At this time, I would like to turn the conference over to David Holmes from Investor Relations. Please go ahead.
David Holmes - Investor Relations Officer
Thank you, operator, and good afternoon, everyone. Welcome to the Bionano fourth quarter 2024 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 today, Bionano issued a press release announcing its financial results for the fourth quarter 2024.
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, including statements about Bionano's revenue outlook, margins, profitability, cash runway, cost savings initiatives and commercialization and product plans.
Such statements are based on current expectations, and there can be no assurances that the results contemplated in these statements will be realized. Actual results may differ materially from such statements due to a several factors, including risks 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, March 31, 2025, and the company assumes no obligation to update statements as circumstances change. In addition, to supplement Bionano's financial results reported in accordance with US generally accepted accounting principles, or GAAP, the company reports certain non-GAAP financial measures.
A description of these non-GAAP financial measures as well as a reconciliation to the nearest GAAP financial measures are included at the end of the company's earnings release issued earlier today, which has been posted on the Investor Relations page of the company's website.
These non-GAAP financial measures are not meant to be considered in isolation or as a substitute for comparable GAAP measures, should be read in conjunction with the company's consolidated financial statements prepared in accordance with GAAP, and have no standardized meaning prescribed by GAAP and are not prepared under any comprehensive set of accounting rules or principles.
An audio recording and webcast replay from today's conference call will also be available online on the company's Investor Relations page. With that, I would like to turn the call over to Erik.
R. Erik Holmlin - President, Chief Executive Officer, Director
Thank you, David, and good afternoon, everyone. I'm pleased to provide you with an update on the fourth quarter of 2024 as well as the full year 2024. While we continue to find ourselves in unprecedented times in our industry, our core business based on sales of instruments, consumables, software and optical genome mapping services is progressing well.
I'd like to start-off by taking everyone through our results for the quarter. Total revenue for the fourth quarter of 2024 was $8.2 million, a decrease of 24% compared to the fourth quarter of 2023, which included $2 million from discontinued clinical services compared to no revenues from such clinical services in Q4 2024.
GAAP gross margin for the fourth quarter of 2024 was 42%, which is significantly higher than the 23% GAAP gross margin reported in the fourth quarter of 2023. Non-GAAP gross margin for Q4 2024 was also 42% compared to 24% for the fourth quarter of 2023. Fourth quarter 2024 GAAP operating expense was $15.4 million compared to $27.4 million in the fourth quarter of 2023.
The year-over-year decrease was primarily due to a decrease in the fair value of contingent consideration of Purigen milestones and importantly, reduced headcount-related expense attributed to the cost savings initiatives that have been outlined in our Q2 2023 and Q3 2023 earnings releases. Fourth quarter 2024 non-GAAP operating expense was $10.6 million compared to $26.6 million in the fourth quarter of 2023.
Cash, cash equivalents and available-for-sale securities as of December 31, 2024, were $20.9 million, of which $11.4 million was subject to certain restrictions. We raised net proceeds of $3.6 million from ATM sales during the fourth quarter of 2024. Additionally, we modified the terms of our senior secured convertible debentures, among other things, which include -- which deferred the $1 million December 2024 amortization payment and reduced the monthly payments from January 2025 to July 2025 by 50%.
And we completed a $10 million registered direct offering in January 2025, along with raising net proceeds of $3.2 million through ATM sales during the first quarter of 2025. We now believe our cash runway extends into the first quarter of 2026.
Product revenues, instruments, consumables and software for the full year was $27 million, an increase of 1% compared to $26.7 million in 2023, despite a reduction in instrument sales of nearly $2 million. Consumables sales were $12.8 million, an increase of 14% from $11.2 million in 2023, and software sales for the full year were $6.2 million, an increase of 11% from $5.6 million in 2023.
Sales in the Americas region were up 9% in 2024 and sales in the Europe, Middle East and Africa region were up 10% in 2024 compared to 2023. We sold 30,307 nanochannel array flow cells during 2024, including 8,058 in the fourth quarter, which represents a 15% increase over the 26,444 flow cells sold in the full year of 2023, and an increase of 1% over the 7,980 flow cells sold in the fourth quarter of 2023. Full year 2024 GAAP gross margin was 1%, which is down from 26% in 2023, but that was after a series of onetime noncash adjustments.
Non-GAAP gross margin for the full year of 2024 was 35%, which is up from 28% in 2023. Finally, full year 2024 GAAP operating expense was $104.4 million and non-GAAP operating expense for the full year of 2024 was $68.9 million. The tremendous progress across the business absolutely reflects the heroic and stellar efforts of our associates whom we affectionately call transformers for the impact they are making around the world. They have our most heartfelt and sincere thanks for these incredible contributions. I would like to use the remainder of the call to discuss the plan going forward.
We believe that along with other companies in the life sciences and tools industry, we are in a period of recalibration in how the market will embrace novel technologies like ours for medical research. Keep in mind, our major economic engine is optical genome mapping or OGM for short.
OGM is used to transform the cytogenetic workflow in four key areas: hematologic malignancies, constitutional genetic disorders, solid tumors and cell and gene therapy. Applications of optical genome mapping in solid tumors are emerging and relatively novel to our list, but publications from users are demonstrating the utility. And so we now see them as a key driver alongside the other three going forward.
Now in September of 2024, we implemented a shift in our go-to-market strategy that moved away from the relatively heavy spending on growing the optical genome mapping installed base through customer acquisition toward a focus on conserving cash and concentrating on those customers who use their Saphyr and Stratys systems routinely in cytogenomics.
This strategy has four key pillars, which are to support and sustain the installed base of these routine optical genome mapping and importantly, via software users, to drive utilization and increase it through the adoption of via software across our routine optical genome mapping user sites, which we believe will facilitate menu expansion, to continue building the support needed for optical genome mapping reimbursement and inclusion in medical society recommendations and guidelines and to improve profitability and scalability with lowering costs and increasing sales volumes.
The first pillar is critical. What we see is consistent growth of consumable sales even as our focus has turned away from aggressively adding new customers and new instruments. The reason for this pattern is that a core group of users, approximately 118 customers account for more than 80% of consumables purchases and growth that we've seen over the previous two years.
These customers are primarily in the United States, Canada, Europe and Israel, and this group tends to use optical genome mapping routinely as an alternative to traditional cytogenetic methods, meaning they have a steady flow of samples to run that is not solely dependent on grant or project funding.
These routine users are where we concentrate our efforts, which is more cost effective for us. And on average, they generate a higher rate of revenues per customer compared to others that are not in that routine use group.
We expect this routine use group to grow over time and to expand its use of optical genome mapping consumables and therefore, be the primary driver of the expansion of the menu of applications of optical genome mapping to promote revenue growth. We have an ability to encourage this growth by enabling the customers to use our VIA software, which streamlines their workflows and increases their capacity to run more samples.
VIA software is used by 133 customers for analysis of non-OGM data types and provides a significant source of revenues. VIA has now been installed at over 160 OGM customers, which is up from just 40 at the end of 2023. This expansion in VIA installations creates the opportunity for us to get them proficient in using VIA, which we believe will increase their productivity and potentially be a source of consumables revenue growth on a per site basis.
Now to continue building the support needed for optical genome mapping reimbursement and drive inclusion in medical society recommendations and guidelines, we need to remain active in encouraging and supporting where possible, the publication of OGM data. Publications have continued to increase impressively, including 19% growth in 2024 of total publications and 39% growth of publications in combined clinical research and cell and gene therapy.
We have also seen an ongoing increase in published clinical research genomes, which we believe reflects the expanding adoption and use of OGM and in turn, has the potential to influence people and agencies responsible for reimbursement and guidelines showing this critical mass of adoption and utilization.
We have already seen what we believe is a benefit to these publications with the decision by the American Medical Association to establish a category one CPT code for OGM use in hematologic malignancies. This CPT code became effective on January 1 of this year. And to our knowledge, it's being used.
Lastly, our focus must remain on a disciplined approach to keep cost down, we have been successful in reducing costs and maintaining the momentum in the business, and we are seeing benefits in another key area, which is our gross margin.
Over the past eight quarters, we have seen non-GAAP gross margin increase from 22% in the first quarter of 2023 to 42% in the fourth quarter of 2024. We do expect ongoing volatility in margin going forward. And for that reason, we won't be providing guidance on margin at this time, but we are encouraged with what we are seeing.
To wrap up, I would like to provide our outlook on 2025. With our key strategic pillars as the underpinning of our streamlined business focus, we expect full year revenues for 2025 to be in the range of $29 million to $32 million.
First quarter revenues for 2025 are expected to be in the range of $6.2 million to $6.3 million, and we expect to install 15 to 20 new optical genome mapping systems, primarily at routine use sites, including at existing customer sites as well as adding new customers that fit into this routine use group.
With that, operator, please go ahead and open the line for questions.
Operator
(Operator Instructions) Sung Ji Nam, Scotiabank.
Sung Ji Nam - Analyst
Hi, thanks for taking the questions. Erik, in terms of guidance, based on kind of what you guys are providing, it kind of implies flattish growth year-over-year. Obviously, you talked about the strategic prioritization that the company has gone under. And so would you have a sense of kind of what the core revenue growth is contemplated in terms of your guidance for '25?
R. Erik Holmlin - President, Chief Executive Officer, Director
Yes, it's all core now. So 29.1% core going to 29% to 32%.
Sung Ji Nam - Analyst
Okay. Got it. And then just curious about whether there are Saphyr trade-ins taking place as well? Or just as we look at the installed base, should we expect continued placements of Stratys? Just trying to understand kind of what the net-net installed base could look like.
R. Erik Holmlin - President, Chief Executive Officer, Director
Yes. I want to sort of start working with you and others to undertake a shift in our focus. And for the first time, we've actually really dug into this installed base. And we're really going to focus on these routine use customers, of which there are 118 exiting 2024. And I think over time, we're going to see that group expand.
And if -- if we will, I think, continue to report installed base of optical genome mapping systems, but we're not going to guide to it partly for the reason that you've said, which is that there could be trade-ins, there could be different things happening at customer sites that might be like a net zero.
And so we don't want that to reflect negatively upon us. So we're going to talk about what we expect to install going forward. And we're going to spend a lot more time talking about this routine use customer group, the 118 right now. And then we hope to get into some metrics like their revenue per customer, which you can already get at that because these customers account for about 80% of consumables revenues.
And so that's right around $10 million spread across 118 customers. And so you can see that revenue per customer is in that $85,000 to $90,000 per customer range. And we think that, that's the important thing to pay attention to. And one last comment in this rather long answer is that another reason not to focus on the number of systems installed at their site is that some customers have brought in systems that they don't use on purpose. They are backup systems.
And so we don't want to skew the revenue per system. We want to focus on revenue per customer.
Sung Ji Nam - Analyst
That makes sense. And then lastly, just on the Stratys compute, which you launched in collaboration with NVIDIA. Just kind of curious kind of what the early feedback has been and also how you expect that to drive continued utilization for the -- your core customers?
R. Erik Holmlin - President, Chief Executive Officer, Director
Yes. I mean it's positive for us. And I would say that, in general, kind of where we're at with Stratys compute is that it's compatible with the Stratys system, so something that Stratys sites use. Saphyr customers can get comparable performance by using multiple of the Saphyr computes.
But we have in our pipeline updates, software updates that will be rolled out to the Stratys compute to really continue to improve its speed. And it's going to be one of the sort of like circles that we go through.
Customers who are using it, they always want more speed, that's fine. We're going to give them more speed, but then we're going to train them on VIA and they're going to start running more samples. They're going to need more speed. So we hope to have a process of being able to continuously update and advance our software over time to provide those levels of acceleration.
Sung Ji Nam - Analyst
Thank you so much, Eric.
R. Erik Holmlin - President, Chief Executive Officer, Director
Welcome, Sang ji.
Operator
Jason McCarthy, Maxim Group.
Michael Okunewitch - Analyst
Hey guys, this is Michael Okunewitch on the line for Jason. Thank you so much for taking my question today.
R. Erik Holmlin - President, Chief Executive Officer, Director
Hi, Michael.
Michael Okunewitch - Analyst
Yes. Just I guess, on the focus with customer acquisition, you did mention you're not looking to aggressively seek customer acquisition now with the expense reduction complete. But are there any areas that you do plan to continue looking at acquiring new customers that may be lower cost of acquisition or higher utilization where they may go right into that 118 group of routine users?
R. Erik Holmlin - President, Chief Executive Officer, Director
Yes. I mean I think that we will see growth of this routine user group to add new customers and that -- that will happen in our target geographies, certainly in Europe. But in the US, if you think about it, we've only just gotten started with these routine user sites and the effectiveness of the CPT code as of January 1, we believe, has the potential to be a catalyst for sites coming on board. And so we're prepared. We have the inventory.
We have everything we need to support these sites. And our sort of sales and marketing strategy there is going to be more around leveraging the amazing data that are being published and of course, the success that these routine use sites are having and are talking about at conferences. So we will be adding sites and we're only going to be adding ones where the customer acquisition cost is acceptable for the investment that both us and the customer make.
Michael Okunewitch - Analyst
All right. Thank you. And then just looking at the category one CPT code, obviously, that's been a goal for a while, good progress. Is that something that's application specific? Or could this be applied across any use of OGM?
R. Erik Holmlin - President, Chief Executive Officer, Director
It has some specificity to it. So it's specific to the use of optical genome mapping in hematologic malignancies. But that's a very, very, very large category. But it would not apply, for example, to the use of optical genome mapping for constitutional genetic disorders, for example.
And what we know is that a lot of sites that are using OGM for that application either have a PLA code, which they use or they bill for optical genome mapping as a reflex to normal test that they get by standard of care, and that seems to be a reasonably effective path for them.
And hopefully, over time, there will be a CPT code for that application as well.
Michael Okunewitch - Analyst
Thank you. And then one last one for me, and I'll hop back into the queue. But I just wanted to see if you could provide a bit more color on that second pillar you talked about, driving utilization through software adoption. And specifically, just if you could go into the mechanics of how VIA adoption could support increased utilization and what the interplay is there with menu expansion?
R. Erik Holmlin - President, Chief Executive Officer, Director
Yes. So VIA automates a number of steps that a user follows to take their post data generation and even the sort of primary analytical step of generating variant calls. After that step, in a pre-VIA world, it was necessary for a user to essentially manually curate the list of variants by comparing it to what was known in the literature comparing variants on the list to what medical societies may have recommended for that type of research analysis in that particular indication, let's say, they're working in AML or CML or something of that nature. They'd want to be guided by what's out there in the literature. Well, VIA for that sort of research automates that process.
So it takes a pretty extensive manual curation process and completely automates it. It not only automates that curation, but then generates a report. After the curation was done manually, there would need to be a process of quite literally copying and pasting from Excel into a report format, but VIA automates that. So automated curation, automated reporting. And I can tell you that there are tens of variants that need to be come through on virtually every sample.
And so by automating those steps, it means that the labs can get through that much more quickly. If they're going through these samples more quickly, they can run more per unit time. And what we know about sites is, let's say they decide to adopt for hematologic malignancy, let's say, they're doing AML, which is a very common anchor assay.
They have a lot of samples for other indications. And so they will -- they would love to be able to add additional indications and by streamlining the process, it will give them the capacity that they require.
Michael Okunewitch - Analyst
All right, thank you. I really appreciate the additional insights there. Thank you very much for taking my question. Congrats on all the progress, guys.
R. Erik Holmlin - President, Chief Executive Officer, Director
Thank you, Michael.
Operator
Mark Massaro, BTIG.
Unidentified Participant
This is Vivien on for Mark. So I heard your comments on the shift towards focusing utilization of your existing installed base. Could you just share some color on how the strategy is playing out? I heard you on the $85,000 to $90,000 rev per customer metric. I understand it's early days, but do you see room for further expansion there? Or do you think you're kind of saturated there? Thanks.
R. Erik Holmlin - President, Chief Executive Officer, Director
Sure. Thank you, Vivien, and thank you for the question. So in undertaking this shift and just thinking about all of the metrics that we cited, 9% growth year-over-year in the Americas, 10% in Europe, 14% in consumables growth overall. This progress took place with kind of a Bionano idiosyncratic backdrop of massive shift in how we were operating as a company. And so at the end of 2023, December 31, 2023, I think we reported 344 employees.
December 31, 2024, we reported 100 employees. And so over the course of this past year, we had let's just say, a lot of change happening. And I'm mentioning all of these things because I want to say, despite all of that, consumable sales grew by 14%. Then when you look at what drove that growth, you can see if you looked at one of the slides that we presented, that growth was in this group of so-called routine users. And -- and those are the ones that we decided to focus on.
So what we believe is that the strategy has fallen into place effectively and is working. And we couldn't be happier with the adoption that we are seeing and the utilization that's happening. And generally speaking, and I'm not -- I don't want to guide, but at least internally, we do believe that, there is substantial room across that entire routine use group for that average to go up significantly.
We want to be cautious about talking about how quickly, but it doesn't have to go up by a lot to make a significant dent in the overall profitability for the company, for example. And so we believe that, that is going to happen, and it's kind of what our long-term plans are based on, and it's why we are focused on all of these initiatives in the pillars to really expand utilization at every routine use site.
Unidentified Participant
Perfect. That's great color. And then maybe just switching gears, just on the reimbursement front, could you share if ODM appeared on the Medicare clinical lab fee schedule as planned? And then just any other updated timing we should be aware of on the LCD front?
R. Erik Holmlin - President, Chief Executive Officer, Director
Yes. So certainly on time, January 1, 2025. It was -- it's effective. I think that, that listing was made public in November of 2024. And the rate was consistent with what CMS initially priced it at.
What I would say is that, that rate, it's around $1,300 that, that rate is consistent with some Proprietary Laboratory Analyte or PLA codes for OGM. It's also consistent with PLA codes for constitutional genetic disorders. There are, however, PLA codes for hematologic malignancies that are priced higher.
And so I think that I would say that, the effectiveness that happened on January 1 this year is consistent with what preliminary pricing was at. I do believe, and I don't want to set an expectation, but it's not unreasonable to believe that there could be a reconsideration of the price over time.
And it's my understanding that some customers seeking consideration. We have to be cognizant of the fact that these processes, which are happening at CMS, which is part of the human health services agency are probably undergoing some transition. So we don't know the expediency with which these things will happen here in 2025. But I would say everything happened as expected, and there is the potential that pricing might increase over time.
Unidentified Participant
Okay. Great. And if I could just squeeze in one more and then I'll hop back in the queue. I think you highlighted heme and solid tumorsing, rare disease and a few other applications among your users. Just any particular areas of strength that you're seeing in the routine user group?
I think you alluded to some menu expansion as well. So could you just touch on what other applications you're thinking about in the pipeline there? Thanks.
R. Erik Holmlin - President, Chief Executive Officer, Director
Yes. I would say -- so the answer to your question unequivocally is hematologic malignancies. This is the primary application that sites are adopting OGM for. And we've narrowed our target geographies somewhat. But across the globe within these target geographies, that is the primary pull from customers.
And the reason for it is that they are reliant upon karyotyping, which has been around for 50 years and fluorescence in situ hybridization or FISH, which is a targeted methodology and simply leaves too much information on the table for them to reliably conduct their research and manage the cases that they're looking at.
And so optical genome mapping is now really a proven alternative to these techniques, and we are aware of several sites which have completely walked away from karyotyping and FISH and rely entirely on optical genome mapping. So that is, for sure, the primary driver of adoption.
A very healthy second is constitutional genetic disorders, and we saw a beautiful paper published recently by the Greenwood Genetic Center, which is really the leading site for many novel technologies and applications in genetic analysis for constitutional genetic disorders and their publication was on neural tube defects, so-called NTDs.
And what it really highlighted was that optical genome mapping could just go very far beyond what existing cytogenetic methods could do in terms of identifying likely drivers of that defect, but not only going beyond it, but also complementing very nicely what sequencing does.
And so we see this adoption for constitutional genetic disorders as a good second place. Solid tumor is emerging, but solid tumor, as is a substantial creates a substantial flow of samples. And so it's a big economic opportunity for us. And cell and gene therapy is also just getting started, but pharmaceutical companies are using optical genome mapping to analyze their modified cells or stem cells to look at things like genome integrity and on and off-target effects that are introduced by the gene editing apparatus. And so we have a good list of indications or applications that customers would adopt for.
We clearly know which is the primary one. And then menu expansion exists within each of these groups. So think about cell and gene therapy, you've got stem cells, you've got CRISPR-Cas9, you've got CAR-T. Within constitutional genetic disorders, we talked about the birth defects, but you have intellectual disability, developmental delay and a variety of applications there, which users can validate one after the other. And then across hematological malignancies, you've got leukemias, lymphomas, myelomas and then solid tumors, lung, colon, breast, prostate, et cetera.
So that's how we see menu expansion progressing within each of these application areas.
Unidentified Participant
Okay, perfect. Thanks so much for taking the question there. Thank.
Operator
And that does conclude today's Q&A session. I would like to go ahead and turn the call back over to Erik for closing remarks. Please go ahead.
R. Erik Holmlin - President, Chief Executive Officer, Director
Okay. Well, thank you, Lisa, and thank you to everyone who joined and for following along, and we look forward to updating you in the not-too-distant future on our progress in the first quarter here in 2025. So thank you very much.
Operator
This ends today's conference call. Thank you for joining. You may now disconnect.