Seer, Inc. (NASDAQ:SEER) Q3 2025 Earnings Call Transcript

Seer, Inc. (NASDAQ:SEER) Q3 2025 Earnings Call Transcript November 6, 2025

Seer, Inc. misses on earnings expectations. Reported EPS is $-0.32 EPS, expectations were $-0.31.

Operator: Good day, and welcome to the Seer Third Quarter 2025 Earnings Conference Call. [Operator Instructions] Please note this event is being recorded. I would now like to turn the conference over to Kelly Gura of Investor Relations. Please go ahead.

Kelly Gura: Thank you. Earlier today, Seer released financial results for the quarter ended September 30, 2025. If you’ve not received this news release or if you’d like to be added to the company’s distribution list, please send an e-mail to investor@seer.bio. In addition, during today’s conference call, we will be referencing a slide presentation that can be accessed on the Events and Presentations section of Seer’s Investor Relations website. Joining me today from Seer is Omid Farokhzad, Chief Executive Officer and Chair of the Board; and David Horn, Chief Financial Officer and President. Before we begin, I’d like to remind you that management will make statements during this call that are forward-looking statements within the meaning of federal securities laws.

These statements involve material risks and uncertainties that could cause actual results or events to materially differ than those anticipated. Additional information regarding these risks and uncertainties appears in the section titled Forward-Looking Statements in the press release Seer issued today. For a more complete listing description, please see the Risk Factors section of the company’s quarterly report on Form 10-Q for the quarter ended September 30, 2025, and in its other filings with the Securities and Exchange Commission. Except as required by law, Seer disclaims any intention or obligation to update or revise any financial projections or forward-looking statements, whether because of new information, future events or otherwise.

This conference call contains time-sensitive information and is accurate only as of the live broadcast, November 6, 2025. With that, I would like to turn the call over to Omid.

Omid Farokhzad: Thanks, Kelly, and thank you, everyone, for joining us this afternoon. I will begin our call today by providing updates on our business, and I will then turn the call over to David to provide more detail on our financial results for the third quarter of 2025 as well as our outlook for the full year. Starting on Slide 3. During the third quarter, our team continued to execute with discipline to advance the reach and impact of our platform. We saw a record number of third-party publications, demonstrating the value of the Proteograph and further validating its performance across a range of applications. As more customers generate data on the Proteograph, it is becoming increasingly clear that this technology is unlocking new biological insights that were previously not possible.

Beyond publications, we delivered our third consecutive quarter of strong instrument shipments, reflecting continued demand for the Proteograph. In fact, in the first 9 months of 2025, we have shipped just under 3x as many instruments as we did in all of 2024, representing a significant step-up in our installed base. We ended the third quarter with $4.1 million of revenue, representing 2% year-over-year growth and a strong balance sheet of approximately $251 million in cash, cash equivalents and investments. As of September 30, we have repurchased approximately $22 million of our Class A common shares under our $25 million share repurchase program that was authorized in May 2024, reducing our net total shares outstanding by approximately 14%.

It’s been an especially challenging year with shifting government policies around tariffs and research funding causing uncertainty and capital spending constraints on our customers. The government shutdown has yet another headwind to these customers, escalating their uncertainty around budgets and availability of funding. That said, I’m even more confident in the value proposition of the Proteograph than ever before as more customers are adopting our platform for their studies and the growing evidence from their work is revealing biological insight that will advance our understanding of health and disease in ways previously not possible. Now I’d like to walk through our recent progress in our core initiatives of validating our platform, enhancing access, driving innovation and enabling larger core studies in more detail.

Starting with product innovation on Slide 4. Over the last 3 years, Seer has helped redefine deep unbiased proteomics by enabling researchers to move from small-scale exploratory studies of a few dozen samples to now conducting large population scale studies involving tens of thousands of samples. Previously, these studies were only possible using targeted proteomics approaches that inherently are not able to address the complexity of the proteome and are prone to erroneous epitope effects because of the millions of protein variants that exist at the population level. Our Proteograph ONE Assay and SP200 Automation Instrument launched in June represent a true step change for Seer and the proteomics field. As a reminder, the Proteograph ONE more than doubled throughput to over 1,000 samples per week, improves precision and reduces run time by roughly 30% compared to Proteograph XT.

Customer feedback has been overwhelmingly positive, and we’re seeing both strong demand and utilization in the first few months following the launch. For example, of all the instruments shipped this year through September 30, almost 2/3 were SP200s, even though this instrument was only launched in late May. Moving on to Slide 5. This incredible performance is translating into tangible momentum. Multiple customers have initiated large-scale studies, including the 20,000 sample population study with Korea University and the 10,000 sample project in collaboration with Discovery Life Sciences. In addition, we’re having an increasing number of conversations with other large biobanks about how they can access the Proteograph technology to run large cohorts.

These initiatives exemplify how our technology is enabling deep unbiased proteomics research at scale, and we expect they will be an important catalyst for future revenue growth. Building on this momentum, I’m pleased to share that after a rigorous evaluation of a number of commercially available proteomics technologies, the Proteograph has been selected for use in a large multiomic study funded by the NIH. A study of this size, especially in the face of ongoing NIH budget uncertainty demonstrates how deep unbiased proteomics is critical to advancing research on human health and disease. We’re proud that Seer has been chosen to provide proteomic solution for this important initiative. Turning to Slide 6. As I mentioned earlier, validation of our technology continues to grow with 66 customer publications, preprints and reviews to date, many in high-impact journals.

Nearly half of these were published this year, reflecting the increasing momentum and visibility of our technology within the scientific community. Notably, in the third quarter alone, we achieved a new record of 13 publications and preprints highlighting the accelerating adoption and impact of the Proteograph Product Suite. One study I’d like to highlight this quarter comes from the Genes & Health cohort, a large-scale genomics initiative studying British, South Asian populations. This population has a high rate of parental relatedness, which increases the chance of homozygous genetic abnormalities, meaning it increases the chance of receiving the same loss of function mutations of given genes from each parent. The result is that the individual will lack functional copies of a specific gene and in essence, represents a genetic knockout of that specific gene.

In this study, doctors Claudia Langenberg and Maik Pietzner from Queen Mary University used the Proteograph to explore how these natural gene knockouts affect protein expression and disease biology. Among 1,500 individuals that they analyzed, nearly 200 individuals harbor these rare loss of function protein knockouts. Importantly, the Proteograph uniquely detected 11 such variants where the corresponding protein was completely absent in affected individuals but present in everyone else. In contrast, the complete absence was not detected for any protein knockout by 2 affinity-based proteomic technologies that were also used in the same study. The study then linked specific genetic variants to rare disease phenotypes and even identified new potential disease-causing proteins not observable by affinity-based methods.

This work underscores how the Proteograph Product Suite isn’t just measuring proteins, it’s revealing human biology at an entirely new scale and resolution. The ability to directly connect genetic variation to proteomic signatures is opening a new window into disease mechanism with enormous potential for precision medicine and therapeutic discovery. When we first introduced the Proteograph, our team partnered closely with early adopters to generate foundational data and publications that validated this technology and demonstrated its potential. Over time, that dynamic has evolved significantly. And today, the majority of publications are being produced independently by our customers, reflecting growing confidence and adoption of the platform.

Researchers are now uncovering unique and differentiated biological insights across areas such as metabolic health and aging, and we’re seeing increasing momentum as our customers expand their work into the clinical space. It’s incredibly rewarding to see these years of investments come to fruition. While we continue to see pressure on CapEx budgets and elongated sales cycles, especially in light of the government shutdown and its impact on NIH funding for the outright purchase of new instruments, we believe the tailwinds are starting to take effect. The flywheel is turning and the pace of external evidence and validation continues to accelerate. We’re excited to see increased awareness of the Proteograph within the genomic community as these researchers ramp up their work in proteomics after seeing the power of the Proteograph.

The Proteograph is a critical component of multiomic translational studies and enables profiling of protein isoform-specific biomarkers. As human genetics research increasingly moves from sequence to function, proteomics is becoming an essential complement to genomics in understanding disease biology and accelerating precision medicine. This is clearly exemplified by the level of interest in proteomics at the most recent American Society of Human Genetics Conference in Boston last month. Seer had a strong presence at the conference and our technology was represented in several scientific presentations. Multiple customers demonstrated how the Proteograph can translate genomic data into biological and clinical insights and 2 of these prominent researchers gave talks in our collab session.

Turning to Slide 7. Notably, Dr. Gloria Sheynkman, Assistant Professor at the University of Virginia School of Medicine, discussed how proteomic profiling identified isoform-specific biomarkers, predicting survival differences in idiopathic pulmonary fibrosis or IPF patients, pointing to new avenues for biomarker development in complex disease. In summary, Dr. Sheynkman is setting the potential role that plasma protein isoforms play in associating with IPF patient survival to discover isoform-specific biomarkers for IPF survival. While her data analysis is continuing, the early biological insights are extremely encouraging with only 30 patient samples, 15 from stable patients and 15 from sicker patients. From an 800 sample cohort, Dr. Sheynkman was able to identify and determine 2 protein isoforms that were preferentially expressed in a sicker patient population relative to the stable patient population using the Proteograph Product Suite.

When she looked at these markers at the protein group level, there were no significant difference between these 2 populations. This highlights the critical role that protein isoforms may play in disease and the need for researchers to have peptide level resolution to gain important biological insights. We’re especially pleased with this insight since Dr. Sheynkman was awarded a Seer Insights Grant last year. This type of study is exactly why we set up the Insights Grant Program, and we look forward to continuing to work with Dr. Sheynkman and her study progresses. We’re looking forward to attending the Human Proteome Organization World Congress next week in Toronto, where several posters and data will be presented, highlighting the power of the Proteograph.

Now moving to Slide 8 to take a closer look at our progress with accelerating access to the Proteograph Product Suite. As I mentioned earlier, we were pleased to see another strong quarter for instrument shipment, particularly in the current macroeconomic environment, reflecting a consistent trend from the first half of the year. In the first 9 months of the year, we have shipped just under 3x as many instruments as we did in all of 2024. Within the instrument shipment this year, a little more than half were part of our Strategic Instrument Placement Program, or SIPP, and the remainder were outright purchases of the instruments. We implemented SIPP so that capital constrained customers, particularly in the current macroeconomic environment, would be able to leverage their available operating budgets and access our technology.

We believe our traction this year is a testament to how important these initiatives are to driving adoption of the Proteograph. Beyond SIPP, we continue to see demand for our Seer Technology Access Center, or STAC, which also lowers the barrier for adoption of the Proteograph Product Suite. STAC allows the Proteograph user to run samples in their own lab and have Seer run the mass spec or alternatively provide end-to-end services from sample to proteomics data and analysis. In Q3, more than 2/3 of our instrument shipments were acquired by customers who had previously accessed the STAC. Looking ahead, we expect the percentage to fluctuate in any given quarter. We continue to see interest in a broad and diverse set of use cases and I look forward to serving more customers as they generate deep unbiased proteomics data for their studies.

We’re pleased that this initiative is bringing in new customers to access our technology and ultimately driving increased instrument adoption. Our expanded partnership with Thermo Fisher Scientific to market and sell the Proteograph Product Suite alongside the Orbitrap, Astral mass spectrometer continues to progress well, and we received our first joint sale from this partnership in the third quarter. We continue to work closely with Thermo Fisher to pursue numerous opportunities from individual customer accounts to large population scale studies. We look forward to this partnership driving additional adoption of the Proteograph Product Suite with time. Last year, we launched our 2024 Seer Insights Grant Program aimed to support innovative and collaborative researchers who require access to comprehensive unbiased proteomic insights to advance scientific discovery.

We repeated the Insights Grant Program in 2025 and received 88 applications, which is more than twice as many as last year. We recently notified the winners of the grants and look forward to seeing the results of their innovative studies. Given this incredibly strong demand, I’m pleased to share that we have launched an additional 2025 Seer Insights Grant Program focused specifically on translational researchers and their projects. With continued strong interest in the additional program, we received numerous new applications from a variety of prominent institutions. We recently closed the application period and the winner has been selected. We look forward to providing participants in the 2025 Insights Grant Program with an opportunity to present their findings at a prominent scientific conference in 2026.

My conviction in the potential of the Proteograph is stronger than ever. We believe that Proteograph is the only technology capable of delivering the depth, scale and reproducibility that is needed to explore biology and undertake deep unbiased population scale proteomics. Our team is continuing to deliver on our mission to push the boundaries of what’s possible in proteomics. With that, I will now turn the call over to David.

David Horn: Thanks, Omid. Turning to Slide 9. Total revenue for the third quarter of 2025 was $4.1 million, representing an increase of 2% compared to $4 million in the third quarter of 2024. It was primarily due to higher product and service revenue. Revenue recognized primarily consisted of sales of Proteograph instruments, consumable kits and service revenue. Product revenue for the third quarter of 2025 was $2.8 million and consisted of sales of Proteograph instruments and consumable kits. We were pleased by the continued traction we saw in terms of instrument shipments and the purchase of consumable kits in the third quarter despite the continued pressure we are seeing on CapEx budget and elongated sales cycles for the outright purchase of new instruments.

Service revenue was $1.2 million for the third quarter of 2025, including $300,000 of related party revenue and primarily consisted of revenue related to STAC service projects. We remain encouraged by the strong customer interest in running projects through STAC, particularly as more users gain access to Proteograph data. And as Omid mentioned, more than 2/3 of our instrument shipments in the third quarter were acquired by customers who had previously accessed STAC. Other revenue was $152,000 for the third quarter of 2025 and consisted of lease and shipping revenue. Total gross profit was $2.1 million for the third quarter of 2025, representing a gross margin of 51% compared to $1.9 million in the third quarter of 2024, representing a gross margin of 48%.

Gross margins were driven by higher consumable and service revenue in the third quarter of 2025. We continue to expect variability in our gross margin on a quarter-by-quarter basis as the proportion of instrument consumable and service revenue fluctuates in any given quarter. At scale, we continue to believe our long-term gross margins will be in the range of 70% to 75%. Total operating expenses for the third quarter of 2025 were $21.5 million, including $3.5 million of stock-based compensation, a decrease of 18% compared to $26.3 million, including $6.1 million of stock-based compensation in the third quarter of 2024. Research and development expenses for the third quarter of 2025 were $10.8 million, a decrease of 17% compared to $13 million in the third quarter of 2024.

The decrease in R&D expenses were primarily due to decreases in stock-based compensation and allocated costs. Selling, general and administrative expenses for the third quarter of 2025 were $10.7 million, a decrease of 20% compared to $13.3 million in the third quarter of 2024. The decrease in SG&A expenses was primarily due to a decrease in stock-based compensation and business expenses. Net loss for the third quarter of 2025 was $18.2 million compared to $21.3 million in the third quarter of 2024. Free cash flow loss, defined as net cash used in operating activities in the period less purchases of property and equipment in the period was approximately $35.1 million for the 9 months ended September 30, 2025. In addition, we continued our share repurchase activities in the third quarter of 2025 since we continue to believe that there is a significant dislocation in our share price.

In the third quarter, we repurchased approximately 1 million Class A common shares at an average price of $1.99 per share. Since the beginning of our repurchase program in May 2024 through September 30, 2025, we have repurchased approximately 11.7 million Class A common shares at a VWAP of $1.87 per share, utilizing approximately $21.9 million of our $25 million share repurchase program authorization. As a result, we have reduced our net total shares outstanding by approximately 14%. We ended the quarter with approximately $251 million in cash, cash equivalents and investments. Importantly, we believe that with our current cash, cash equivalents and investments on hand, we have sufficient capital to reach cash flow breakeven. Turning now to our outlook for the year on Slide 10.

We continue to expect revenue to be in the range of $17 million to $18 million for 2025, representing growth of 24% at the midpoint over the full year 2024. Embedded in this range is the assumption that our customers will continue to face headwinds from budget constraints and ongoing uncertainty around government funding, particularly related to the NIH. Given these near-term macro pressures are likely to continue weighing on our market visibility through year-end, we anticipate our full year revenue will likely be in the lower half of our guidance range. We did not factor in any additional impact from the government shutdown. If the shutdown were to continue for a second month or so, then this may delay grant funding and potentially impact some instrument and consumable shipments in the fourth quarter.

At this point, I would like to turn the call back to Omid for closing comments.

Omid Farokhzad: Thank you, David. Moving on to Slide 11. I’m encouraged by the traction we saw in the third quarter as exemplified by a strong quarter of instrument shipment, a record number of peer-reviewed publications and growing number of large-scale studies powered by the Proteograph. Together, these achievements highlight the growing adoption of our technology and reinforce our leadership in enabling deep unbiased proteomics at scale. I’m proud of our team’s execution as we advance the reach and impact of the Proteograph Product Suite. With that, we will now open it up for questions. Operator?

Q&A Session

Operator: [Operator Instructions] And our first question comes from Dan Brennan from TD Cowen.

William Ruby: This is William on for Dan. I start out, just wondering if you could provide — I know you talked about the partnership with Thermo on the call, I was wondering if you provide a little bit more update on that partnership and just if that’s expected to be a material revenue driver next year. And then just over the last few quarters, you highlighted a number of large studies using the Proteograph platform. Just wondering if you could talk about the potential for more of these studies in the future? And what are the barriers to doing larger sample size products in the future?

Omid Farokhzad: David, why don’t you take the Thermo question, and I’ll take the larger study question.

David Horn: Thanks, William. Appreciate the question. Yes, the Thermo partnership is going well. As we said on the call, we landed our first joint opportunity. We actually closed 2 different opportunities with Thermo during the quarter. So that was great. There continues to be a pipeline of opportunities that we’re pursuing jointly. Again, they’re looking to find accounts where they can sell Astrals and a lot of their customers are interested in also doing high-throughput proteomics in which we play a role, so they can offer the package solution. So it’s been a very good partnership, not only that, but we’re also working with Thermo to pursue some of these joint large biobank opportunities as well. We’re working with them on one right now, and we’re in discussions with others.

So it’s been a great partnership. They’re a fantastic partner. And we continue to expect good things as we move into 2026 from that partnership, both on individual account wins, but also some larger biobank projects. And with that, I’ll turn it over to Omid to talk about some of those studies.

Omid Farokhzad: And then regarding the question about the — what does it take to do these large-scale studies? I mean I think it’s worth just taking a step back of where were we and how did we get here. Mass spec has always been considered a gold standard for doing proteomics work. It’s just that before Seer, mass spec approaches did not scale. And in fact, if you wanted to do deep proteomics, meaning you wanted to look at a large number of proteins in a sample, the workflow to process those samples was so complicated that a very deep proteomic study usually would be limited to tens of samples. So that was the state-of-the-art in mass spec proteomics prior to the introduction of the Proteograph Product Suite. Since then, with the innovation that we’ve had and most recently, we launched Proteograph ONE together with the SP200 Automation Instrument and together with the Proteograph Analysis Suite, or PAS, that lets the customer go from mass spec data to insight.

It is now possible to do very large-scale studies, tens of thousands of samples or even hundreds of thousands of samples and to do it at the depth of thousands of proteins, approaching 10,000 proteins per sample. With that then comes the customers, the biobanks now have a choice. They can use their samples in their biobank to do proteomic using conventional targeted approaches, which is historically what they’ve done. I mean we’ve seen large-scale studies get published with the SomaScan with the Olink platform. But increasingly, those same biobanks are approaching us and asking us what would it take to do 10,000, 100,000, 600,000, 500,000, million samples. And the answer is, the existing technologies absolutely makes it possible to do those types of studies.

And the velocity and cost and the ease the reproducibility, those are all becoming so relatively comparable to the alternative that the customers now have an absolute choice of doing one or the other. And of course, everyone recognizes that the mass spec is the gold standard. And in many ways, if you have the data set from targeted approaches paired with the mass spec approaches, it’s extremely complementary and very powerful. So the first half of the year, and David mentioned, we did the 20,000 sample study with Korea University. We did a 10,000 sample study with Discovery Life Sciences, another biobank study involving Thermo Fisher and some colleagues that we have not announced yet. And we’re in multiple discussions with other biobank doing studies that are much, much larger.

And my prediction, by the way, is that, the first study of 100,000 sample using mass spec is right around the corner, probably in 2026. And so, I’m super excited about the biological insight that’s going to come from these types of studies, these very large-scale studies.

William Ruby: Got it. If I could just ask one more? Just wondering if you could just speak to the trends you’re seeing among academic customers now that we’re well into the new fiscal year, has spending gotten better or worse? And do you expect — I guess you’re talking about what the government shutdown impact would be, but just wondering kind of trends on academic.

Omid Farokhzad: Yes. Maybe I’ll start off, and I’ll have David add additional layers of information to it. I mean, look, this has been an interesting year because of a lot of challenges that we’ve had in terms of policies, the macroeconomic picture. And so, there have been uncertainties both in biopharma and CapEx spending and academics and there are uncertainties about the grant, especially also in the government sector. And so, we have been dealing with this since the beginning of the year. And that — despite of that headwind, what has been constructive for us is that the tailwind for us has been getting stronger. Customer publications are robust and increasing at a high velocity. This quarter, we saw 13 customer publications, which was a record for us.

And I think that momentum is continuing. And by the way, it isn’t just the number of publications. It’s the magnitude of what these publications means. So if you look at the papers that are coming from Claudia Langenberg’s group or the [indiscernible] Group, the biological insight that they’re revealing using this platform and large-scale mass spec-based proteomics, deep mass spec-based proteomics is very differentiated to what was possible. So that tailwind is helping us. Now, of course, the government shutdown happened outside of the Q3 window. But we saw almost a pause to academic spending. And of course, government, they have no choice because government shut down. Most recently at a conference — at the ACT conference, it was a very light presence in that conference.

And I think part of it is because of this guarded demeanor that the shutdown has layered on top of an already complex macroeconomic picture that we’ve been dealing with. So the headwinds have been very strong. In fact, this last month, even stronger — but the tailwind also is strong and they continue to get stronger. So I’m very, very bullish and optimistic about what’s ahead. But boy, does it seem like it’s a bumpy road. And when you think you have a break, another challenge comes in front of you that was an unforeseen one. David, I’m not sure if you want to add anything in addition to that.

David Horn: Yes. No, the only thing I would add is, again, I think we — to kind of echo Omid, it is encouraging that we see increasing interest from academics. Just to give you a stat for revenue year-to-date, the first 9 months of the year, about 40% of our revenue was from academic and government customers. That’s a higher percentage than last year. So academics are applying for their grants. They’re getting their grants. They’re spending money with us. But as Omid said, it’s just super challenging when a lot of that source for some of that funding, i.e., the NIH is essentially shut down right now. And so, it just creates more uncertainty. And even if people do have money, they are pushing the pause button a little bit while they wait to see what’s going to happen. So great interest from that academic and government, and we’re very bullish long-term, but we just have to kind of get through these near-term challenges that are beyond our control right now.

Omid Farokhzad: And let me just add one more layer of information to this, which is I alluded to it in our prepared remarks. We’ll elaborate on it in the very near-term. There was a very large consortium of scientists that got a very, very large multi-tens of millions NIH grant and that’s a multiomic study. And they did a very thorough investigation in terms of the proteomic platform that would be used for that multi-institutional consortium. And I was very, very proud that Seer was selected for that. So when I say that the tailwind is getting stronger for us, this is an example of that. But it’s also been extremely challenging given the broader picture that both David and I alluded to.

Operator: There are no more questions in the queue. This concludes our question-and-answer session. The conference has now concluded. Thank you for attending today’s presentation. You may now disconnect.