Singular Genomics Systems - Q2 2024

Executive Summary

• Q2 revenue was $0.7M (vs. $0.4M in Q1; $0.5M in Q2’23), with 2 G4 systems shipped and the highest quarterly consumables orders to date; gross profit was -$0.2M and operating expenses declined to $22.6M, driving net loss to $21.3M.
• Management reiterated G4X timelines: first early access placements at end of Q4 2024, additional early access in early Q1 2025, and commercial launch toward end of Q2 2025; services funnel and instrument interest exceed 50 opportunities, citing unmet needs for throughput and cost per sample.
• Liquidity actions: an amended facility lease reduced long‑term lease obligations by ~$50M; a $4.5M upfront lease modification payment will make Q3 cash burn higher than Q2, but management does not expect a material impact to cash runway guidance (extending to late 2026).
• No S&P Global consensus was available for Q2’24 EPS/revenue for OMIC, so we cannot quantify beats/misses versus Street estimates (S&P Global data unavailable).

What Went Well and What Went Wrong

• What Went Well

  • Consistent progress on G4X with strong customer interest; management: “We’re on track to do our first early access later this year… and… a commercial launch towards the end of Q2 next year.”
  • Improved G4 fleet metrics and monetization: system uptime averaged 95% and annualized consumables pull‑through was ~$60,000 in Q2, roughly double Q1; Q2 delivered the highest quarterly consumables orders and shipments to date.
  • Cost discipline and balance sheet optimization: operating expenses fell to $22.6M from $27.5M YoY; lease amendment reduced long‑term obligations by ~$50M and supports development/commercialization focus for G4X.

• What Went Wrong

  • Gross margin remained negative (-$0.2M), reflecting discounted G4 instrument pricing, reagent rental placements, and higher support costs, partially offset by better consumables margins.
  • Sequential reagent rental placements stepped down (5 in Q1 to 1 in Q2) as resources shift to G4X; the company is prioritizing maintaining existing sequencer customers and spatial conversion over expanding sequencer‑only placements.
  • Near‑term cash burn: Q2 cash burn was ~$17.5M; Q3 burn will be higher due to a $4.5M lease modification payment (though runway guidance to late 2026 is unchanged).

Transcript

Operator (participant)

Greetings. Welcome to the Singular Genomics Second Quarter and Business update call. At this time, all participants are in a listen-only mode. A question-and-answer session will follow the formal presentation. If anyone should require operator assistance during the conference, please press star zero on your telephone keypad. Please note, this conference is being recorded. I will now turn the conference over to your host, Philip Taylor.

Philip Taylor (Head of Investor Relations)

Thank you, operator. Presenting today are Singular Genomics Founder, Chair, and Chief Executive Officer, Drew Spaventa, and the company's Chief Financial Officer, Dalen Meeter. Earlier today, Singular Genomics released financial results for the three months ended June 30, 2024. A copy of the press release is available on the company's website. Before we begin, I'd like to inform you that comments and responses to your questions during today's call reflect management's views as of today, Tuesday, August 13, 2024 only, and will include forward-looking statements and opinion statements, including predictions, estimates, plans, expectations, and other information related to our financial and operating results, plans, and strategies. Actual results may differ materially from those expressed or implied by these statements as a result of certain risks and uncertainties.

These risks and uncertainties are more fully described in our press release issued earlier today and in our filings with the Securities and Exchange Commission, including our most recent Form 10-Q and 10-K filings, and the Form 8-K filed with today's press release. Our SEC filings can be found on our website or on the SEC's website. Investors are cautioned not to place undue reliance on forward-looking statements. We disclaim any obligation to update or revise these forward-looking statements. Please note that this conference call will be available for audio replay on our website at investor.singulargenomics.com in the Presentation and Events section. With that, I will now turn the call over to CEO Drew Spaventa.

Drew Spaventa (Founder, Chair and CEO)

Good afternoon, and welcome to Singular Genomics' second quarter 2024 earnings call. Q2 was a busy and productive quarter for our team. In Q2, we progressed development of the G4X spatial sequencer, initiated our first spatial technology access services projects, and added to our spatial pipeline of customers interested in services, collaborations, and G4X instruments. We will focus our call on the following areas: 1, revisiting our strategy following the pivot to spatial sequencing earlier this year. 2, a summary of the second quarter results. And 3, an update on the development of the G4X spatial sequencer and our spatial services. We announced a strategy shift in February at AGBT, when we unveiled the G4X spatial sequencer. The G4X is being developed to offer readouts of targeted transcripts, targeted proteins, and a fluorescent H&E stain, all in the same tissue section.

In addition, its novel capabilities will include Direct-Seq, which is the sequencing of RNA in situ and has the potential to open new areas of scientific discovery. This combination of readout modalities will offer significantly higher throughput than any spatial profiling technologies currently on market. We continue to be encouraged by discussions with spatial experts and prospective customers. Spatial biology is quickly growing in many customer segments, and throughput is a significant limitation. We believe the G4X will be uniquely suited to address these pain points and has the potential to accelerate growth in the spatial market. The business setup is encouraging in that we plan to deliver cost savings to our customers while supporting a high-margin, sustainable business.

In addition to the exciting development work to get G4X to market, we are focused on supporting our existing G4 customers, most of which we believe will benefit from our move to spatial and are poised to become G4X customers. Supporting and continuing to improve their G4 sequencing experience is paramount to our offering a second product into an existing customer base. The G4 and G4X share the same platform, which will allow for a streamlined upgrade process for existing G4 customers. Our strategy with existing G4 customers is to continue to improve their experience and facilitate higher usage with the G4 sequencer as we prepare them to convert to spatial sequencing when the G4X becomes available. We are seeing improved reliability and usage across the existing installed base. System uptime has been averaging 95% during the quarter.

Average annualized consumable pull-through for the installed base was approximately $60,000 in Q2, which is roughly double Q1. In addition, we recently initiated the rollout of our V2 System Upgrade Package, which will include system performance and feature enhancements to further improve the reliability and usage of the system as we continue to prepare for conversion to spatial sequencing on the G4X. Now, let's move into the second quarter results. We shipped 2 G4 instruments during the quarter and generated $0.7 million in revenue. Of these shipments, 1 was an academic core lab and 1 was to a commercial lab. One of the most important focus areas for us is to maintain our emphasis on supporting existing customers. We continue to see improvements in system utilization and consumables pull-through. Q2 was our highest quarterly total yet for consumable orders and shipments.

Now, let's turn to an update on our development of G4X. In R&D, we are advancing work on instrument method development, expanding the compatible tissue types, and improving protocol performance for combined readout modalities. Our internal focus is centered around developing the G4X platform and optimizing the spatial sequencing methods and protocols. Our planned initial G4X kit offering will be our V1 Immuno-Oncology panel with 300 genes, 12 proteins, and the ability to customize content. We are excited about the technology as we have continued to progress the development of capabilities and methods. In services, we continue to see growing interest in the funnel of service projects as part of the G4X Spatial Sequencing Technology Access Services program that was launched in the second quarter.

Our strategy in services is twofold: to learn from running initial customer samples in order to accelerate product development and generate customers that will buy the instrument and consumables when available. Our initial focus in services is our V1 Immuno-Oncology Panel. The project submissions in our service funnel make it clear that a lower target plex, higher sample throughput offering is addressing an unmet need in the market. Several months ago, we opened a G4X Spatial Research Grant Award Program, which was well received by prospective customers and researchers from some of the top institutions across the world. We received over 50 applications from institutions interested in using the G4X in various applications, including cancer research, the study of autoimmune diseases, chronic disease research, cardiovascular and liver diseases, vaccine development, and neuroscience.

We look forward to sharing more information about the award recipients and our collaborations with these institutions to bring forward these exciting demonstrations of G4X applications later this year. Lastly, we are planning for our G4X Early Access Program, which we intend to deliver late this year. This will include a select number of customers with early access to the G4X. The purpose of early access is to both learn and incorporate feedback for broader commercial launch, as well as to generate demand. Now I'll turn it over to Dalen to go through the details of our second quarter financial results.

Dalen Meeter (CFO)

Thank you, Drew. Revenue for the second quarter of 2024 was approximately $0.7 million, predominantly made up of $0.4 million from revenue recognized on consumable sales and $0.3 million from revenue recognized on one capital purchase instrument placement during the quarter. Gross profit was -$0.2 million in the second quarter of 2024, compared to -$0.1 million in the second quarter of 2023. Our gross margin was negative due to discounts on G4 instrument sales, our use of the reagent rental and other non-capital purchase models, and higher costs associated with the support of system placements, partially offset by higher margins on increased consumable sales. Operating expenses for the second quarter of 2024 totaled $22.6 million, compared to $27.5 million in the second quarter of 2023.

These totals included non-cash stock-based compensation expense of $2.2 million in Q2 2024 and $2.8 million in Q2 2023. The year-over-year decrease was primarily driven by a non-cash expense in Q2 2023, related to a one-time adjustment in the carrying value of property, plant, and equipment, and decreases in employee compensation costs due to reduced headcount. Net loss in the second quarter of 2024 was $21.3 million, or $8.57, compared to $25.6 million, or $10.58 per share in the second quarter of 2023. The weighted average share count for the second quarter of 2024, used to calculate net loss per share, was approximately 2.5 million. Ending cash, cash equivalents, and short-term investments, excluding restricted cash, totaled $133.2 million.

Cash burn for the second quarter was approximately $17.5 million, which was sequentially lower than the previous quarter, driven by the timing of cost savings measures implemented. Lastly, I wanted to take a moment to comment on the lease amendment that was announced last week. I'm pleased to note that we successfully amended a long-term lease obligation, rightsizing our facilities footprint to better align with our operational needs. This move not only optimizes our space utilization, but it also reduces our long-term lease obligations by approximately $50 million. This amendment will enhance our longer-term financial flexibility, allowing us to focus more resources on development and commercialization of the G4X. The amendment included a one-time upfront lease modification payment of $4.5 million, which was paid upon execution of the agreement.

As such, we expect our Q3 2024 cash burn to be higher than the second quarter. We do not expect the lease modification payment to have a material impact on our previous comments around cash runway extending to late 2026. Back to you, Drew.

Drew Spaventa (Founder, Chair and CEO)

Thank you, Dalen. I want to thank all our employees for their hard work and dedication over the last quarter. We are excited by the level of interest from early collaborators and prospective customers, as evidenced by the growth of inbound inquiries around our technology access services and research collaborations and growth in the sales funnel. The G4X's designed ability to read transcripts, proteins, and a fluorescent H&E stain at scale will provide a unique solution in an exciting, high-growth market. Where other spatial solutions in the market are pushing up on target plex, we see an unmet need for lower target plex and higher sample throughput. We look forward to updating you on our progress through the rest of the year. Now, let's open it up for questions. Operator?

Operator (participant)

Thank you. At this time, we will be conducting a question-and-answer session. If you would like to ask a question, please press star one on your telephone keypad. A confirmation tone will indicate your line is in the question queue. You may press star two if you'd like to remove your question from the queue. For participants using speaker equipment, it may be necessary to pick up your handset before pressing the star keys. One moment, please, while we poll for questions. Once again, please press star one if you have a question or a comment. And the first question is from Dan Brennan with TD Cowen. Please proceed.

Dan Brennan (Senior Analyst)

Great. Thanks, guys. Thanks for congrats on the quarter here and continued progress. Maybe could you start off with just, you know, timelines? I think you reiterated them just now, but just kind of walk through a little bit about early access and then about commercial launch. I think last quarter, you guys were discussing in and around Q2. Just, can you guys confirm, are we still thinking of the same kind of timelines right now?

Drew Spaventa (Founder, Chair and CEO)

Hey, Dan, thanks for the questions. Yeah, I'll start off with timelines. We're just starting services now, and in the midst of a few very exciting projects. We're on track to do our first early access later this year, probably end of Q4. And then we'll sequentially roll other early access sites in through the first part of Q1. And at this point, we are on track. We are planning to have a commercial launch towards the end of Q2 next year.

Dan Brennan (Senior Analyst)

Great. And then could you just speak to, you know, both, I guess, the, you know, pathway to the commercial specs, which you guys reiterated, and then as you've had more customers kind of evaluating the product right now, just kind of walk through some of the experiences. I know you spoke about some of the Dana-Farber and Harvard, I think, on the last call, but just kind of, you know, how is the interest level? Just, you know, a little more granularity on, on, you know, that front. And then the funnel, I think the last time we talked about maybe dozens of customers, I know it's not a firm kind of backlog, if you will, but just speak to kind of the interest level, if you can, as well.

Drew Spaventa (Founder, Chair and CEO)

Absolutely. So, you know, we feel like we've really hit on something here, based on the response that we've gotten, both from services and from people interested in buying a system or partnering to set up services of their own. I think that will be something unique for spatial in the G4X that was different from G4, in that a lot of the customers we're talking with, whether they're a large core lab or a CRO or a major oncology medical center, they are very direct, and one of the biggest issues they have is throughput for spatial and cost per sample, and that's exactly what we're addressing. The feedback that we get is, you know, relates to very positive directional information on the scope of the product.

And what I mean by that is, you know, we're targeting 300 genes, which is, you know, less transcripts than, than most of the other spatial platforms, at least at this point, and about 12 proteins. And what most people have said is that's more than enough on the transcripts and the proteins. You know, 300 genes, and a lot of times it's less than 10 proteins people wanna look at. But if you can do that in combination, the same section, and you can do that at a lower sample, cost point and more samples per run, that's exactly what they need. So we're really seeing that across the board, in a number of different settings and applications.

I think one other thing that is worth mentioning, if we segment the customer type into three buckets, in sequencing, you know, we have about 30 instruments out right now. The majority of those are in academic settings. There are two other segments that the G4X applies to that was a little bit different when we started talking with prospective customers, and one is CROs, or contract research organizations, that are providing services in a large part to pharma. And the other is gonna be major medical centers, places where there's high-throughput core labs that right now are doing, you know, pathology or looking at proteins and doing tumor microarrays. And that's another area where the cost and the throughput is prohibitive right now from scaling.

A lot of these places say things like, you know, "We have 40 or 50,000 samples a year we wanna run, and we run less than 10," and that's really a symptom of cost and throughput. So, it's really encouraging. On the funnel side of things, both on the instrument side and the services, we have over 50 at this point, and it's kind of pointless to really count more than 50. What we're doing right now is trying to prioritize what are the projects that don't require customization, or what are the projects that we can do as a pilot now that have larger batches of work to come behind them, and we're just trying to prioritize based on those factors, on the services side.

And then on the commercial side, I think we still have some time to think about that. We're still, again, you know, not launching this until Q2, so, you know, very much it's just, you know, put our head down and get the product developed in a place where it's robust and usable for external parties. And in the meantime, try to advance services projects that we think have a long tail of work or could create a customer that buys an instrument down the road.

Dan Brennan (Senior Analyst)

Maybe I'll sneak one final one in. Just in terms of from here to the G4X and then the full commercial launch, like, what are the biggest kind of technical or product development or manufacturing issues that... I mean, I'm sure there's a lot on your plate, but just wondering the level of confidence in kind of hitting these timelines and what needs to happen between now and then. Thanks, guys.

Drew Spaventa (Founder, Chair and CEO)

Thanks, Dan. Yeah, you know, a lot of it is optimizing the protocols to be as high quality as possible across all different tissue types. We're initially launching with 6 different tissue types, and you know, tissue can be variable depending on how it was stored or how it was treated, and we're still understanding you know, a lot about how our immuno-oncology panels of genes and proteins work across different tissue types that were stored in different conditions. So that's one part of it. The other part of it is really optimizing the workflow to try and simplify it where we can and make it as user-friendly as possible.

The workflow right now is similar to what's done with other spatial instruments, in that there's a couple days of pipetting, some overnight incubations, things like that, before it's run on the sequencer. And we're trying to just understand each and every part of that to make sure that the requirements and the user instructions are clear and the protocol is robust, so that we have, you know, consistency in results. And outside of that, there's all of the activities related to, you know, transferring, you know, the product into manufacturing, thinking about scaling it up, the informatics. I mean, there's a lot to it, but it, it's all, you know, right now, the work's being done with, you know, the experience of going through the G4.

So I'd say we've all, you know, been through this, you know, once a year ago, and I think we're eyes wide open, and we do plan to stay on schedule. So hopefully that answers your question.

Dan Brennan (Senior Analyst)

Great. Thanks, guys.

Operator (participant)

Once again, if you have a question or a comment, please press star one. The next question comes from Matt Sykes with Goldman Sachs. Please proceed.

Matt Sykes (Research Analyst)

Hey, good afternoon, Drew and Dalen. Thanks for taking my questions. Maybe just first, the step-down in reagent rental placements from, from the last quarter, I think you did 5 last quarter, it was 1 this quarter. Should we think about that more as a function of the shift in resources to G4X and less so about sort of the demand environment?

Drew Spaventa (Founder, Chair and CEO)

Yeah, you know, our strategy right now is to maintain the existing network of customers and prepare them for a conversion. We're not actively trying to push and expand new systems for sequencing only. We're really focused on developing the G4X platform, maintaining and, you know, frankly, selling instruments at a higher ASP than the sequencer itself. So, it is part of the strategy, really is maintain existing and, you know, we aren't saying we won't put any sequencers out, but that's not our priority right now. Our priority is maintaining and getting spatial customers, you know, in the queue to buy the more expensive combined system next year.

Matt Sykes (Research Analyst)

Got it. And then of the G4s that you have installed now with those customers, do a majority of them have interest in spatial as well? Like, do you feel like that's a pretty good conversion rate you could get out of the existing installed base, or are there some that, you know, weren't going to be doing spatial?

Drew Spaventa (Founder, Chair and CEO)

Yeah, so about two-thirds of them have said directly there's interest and, you know, we assume, you know, fewer than two-thirds will initially convert, just to be conservative. But, you know, we have line of sight to, you know, a good number of initial customers go converting probably very early in the product being launched. So the answer, the short answer is yes, we think the majority of the existing customers will convert into a spatial customer.

Matt Sykes (Research Analyst)

Got it. And just one more. The Spatial Sequencing Technology Access Services, that program, could you maybe talk about just sort of the costs you're incurring on that? And is it... I'm assuming it's within Dalen, the forecast of sort of cash runway and everything like that.

Dalen Meeter (CFO)

Hey, Matt. Excuse me. This is Dalen. Yeah, that's right. The costs, you know, that we're incurring related to the Spatial Services lab are baked into kind of the directional commentary around cash runway. Just to give you a sense, you know, we've got an internal lab that, you know, we've earmarked, you know, several G4X systems specifically for services, and we have, you know, a small number of lab personnel that kind of do double duty internal work, but then also work on the services projects that come in as well. But all of that, you know, internal cost is baked into what we've talked about previously in terms of cash burn.

Matt Sykes (Research Analyst)

Got it. Thanks very much.

Drew Spaventa (Founder, Chair and CEO)

Thanks, Matt.

Operator (participant)

Okay, we have no further questions in queue. I'd like to turn the call back to management for any closing remarks.

Drew Spaventa (Founder, Chair and CEO)

No further closing remarks from here. Thank you, everyone, for listening. Look forward to updating you on future calls. Thank you.

Operator (participant)

Thank you. This concludes today's conference, and you may disconnect your lines at this time. Thank you for your participation.