With a trio of partnership announcements this month, 10x Genomics has signaled it is looking beyond its traditional focus on research tools for academic, government, and industry customers, by expanding into clinical diagnostics through collaborations with top-tier institutions aimed at generating scientific evidence intended to develop the clinical potential of the company’s single-cell and spatial biology technologies.
10x announced clinical collaborations with two Boston-based institutions, Brigham & Women’s Hospital and Dana-Farber Cancer Institute, as well as the New York-based Cancer Research Institute. The company also committed to building its own CLIA-certified laboratory within about a year, with the goal of enabling clinical deployment of diagnostics that will come up with these kinds of collaborations.
The clinical moves hold potential for an expansion of the company’s customer base and thus more business for 10x, which is now the second largest publicly traded spatial biology company, as ranked by GEN, and a leading developer of instruments, reagents, and software used for spatial and single-cell biology.
“Over the course of the past year, we have had physicians who have been telling us, ‘If you guys offer single cell and spatial in a CLIA lab for patient testing, it would be a game changer for me to be able to send patient samples to you.’ So, the signal from the market is clearly there—there’s potential,” 10x co-founder and CEO Serge Saxonov, PhD, told GEN in an interview during the recent J.P. Morgan 44th Annual Healthcare Conference in San Francisco.
Saxonov also said his company’s expansion into clinical diagnostics was in sync with its ultimate goal of advancing human health.
“We set up the company to be really, really good at building technologies for measuring biology. How we deploy that set of capabilities was always subject to evolution and expansion,” Saxonov said. “We always knew that starting in a world of basic science and research tools makes the most sense. That’s where you’ve got the highest initial leverage to drive new science, and we’ve been very successful at that. But we always knew that ultimately there’s huge potential in terms of advancing human health more directly in terms of clinical diagnostics.”
Overlapping expansions
10x isn’t the only research tools developer that sees significant expansion potential in clinical diagnostics.
Illumina, the longtime next-generation sequencing (NGS) leader, has also expanded its competitive horizon in recent years from research use to clinical diagnostics and multiomics. Just last week, Illumina secured reimbursement from the Centers for Medicare and Medicaid Services (CMS) for its FDA-approved in vitro diagnostic (IVD) TruSight
Oncology (TSO) Comprehensive test. In May, Illumina announced an expanded clinical oncology portfolio, partnering with Pillar Biosciences to offer Illumina customers Pillar oncoReveal CDx, an IVD kit used for detecting genetic variations in 22 genes in previously diagnosed patients with solid tumors.
This year, Illumina plans to commercially release the spatial transcriptomics technology it unveiled at last year’s Advances in Genome Biology and Technology (AGBT) General Meeting—tech that will use a new multimodal analysis platform and be compatible with Illumina’s NextSeq and NovaSeq sequencers. At AGBT, Illumina highlighted researchers from St. Jude Children’s Research Hospital, the Broad Institute, and TGen who shared data on their use of Illumina’s spatial technology.
“We are expanding on the multiomics vertical and across the horizontal of the multimodal capabilities,” Steve Barnard, PhD, Illumina’s CTO, told GEN in an October interview.
Both 10x and Illumina sought to downplay the potential for head-to-head clinical-market competition in recent days, speaking instead of overlap between the companies in spatial and single-cell biology that makes them more partners than rivals.
Following the GEN interview, Saxonov and Roman Yelensky, 10x’s vice president of clinical applications, discussed the clinical expansion vis-à-vis Illumina in a LinkedIn post by Alex Dickinson, a former Illumina senior vice president who is co-founder and chairman of Ryght AI, developer of an enterprise-grade generative artificial intelligence (AI) platform for life sciences:
“Serge also told me he sees Illumina’s omics push as validation, not threat,” Dickinson wrote, with Saxonov reasoning that the market created by 10x is now so important Illumina is investing heavily in it, due to potentially infinite demand: “The potential scale of data in biology is essentially inexhaustible. AI has huge potential to transform understanding of biology, but the key thing it needs is data.”
“Competitive battle”
Concluded Dickinson: “My take from the conversation was this is the start of another great competitive battle in NGS: Illumina is coming after 10x’s omics research markets, and 10x is going after Illumina’s genomics clinical markets.”
Saxonov elaborated on 10x’s clinical push in terms of data generation days after Dickinson’s post, when GEN asked to what extent 10x viewed the clinical initiatives as a potential opportunity for giving customers an alternative to Illumina.
“From first principles, disease is driven by dysregulation of cell behavior, which means diagnostics need to measure biology at the cellular level. Some analytes, like cell-free DNA, are inherently bulk and provide valuable but different kinds of information; however, when the question is about dynamic cell states or tissue context, bulk measurements average away the underlying biology,” Saxonov replied. “That’s why we’ve spent more than a decade engineering our single-cell and spatial technologies to deliver the data quality, robustness, and scalability required for translational and clinical use, positioning them to become foundational for the next generation of diagnostics.”
Illumina noted that 10x uses Illumina NGS sequencers for its spatial or single-cell sequencing, that the vast majority of single-cell and spatial applications that use Illumina sequencing apply technologies from 10x, and that Illumina is still early into single-cell technology, having expanded into the space by acquiring Fluent BioSciences in 2024.
Yet last October, 10x joined two licensor partners in suing Illumina, accusing the sequencing giant of infringing on nine patents related to spatial biology and single-cell sequencing, in cases that were still pending. The partners were Prognosys Biosciences and Roche Sequencing Systems, the latter a potential head-on sequencing competitor after unveiling its Sequencing By Expansion (SBX) technology last year. Illumina strongly denies the claims and has promised a vigorous defense against them. (The spatial biology lawsuit is Case 1:25-cv-01286-UNA. The single-cell sequencing lawsuit, Case 1:25-cv-01287-UNA.)
“More companies are entering the clinical diagnostics market, and this trend underscores the growing patient need as well as the continued demand in the clinical market,” Illumina said through a company spokesperson. “We welcome new innovation to the market as it makes the field stronger, expands access to precision medicine options, and brings us closer to a world in which sequencing and multiomics are utilized as part of the standard of care.”
“Key” growth driver
During Illumina’s presentation at J.P. Morgan last week, CEO Jacob Thaysen, PhD, noted that clinical markets were a “key driver” of growth: “We expect clinical demand to remain as an important source of strength going forward.” Clinical customers now represent Illumina’s largest market, accounting for roughly 60% of the company’s consumables revenue; the remainder is customers in the research and applied markets.
“This scale and leadership support a durable financial profile with a high level of recurring revenue and healthy margins, allowing us to continue investments in innovations and long-term growth,” Thaysen said.
Thaysen added that Illumina was in the early stages of clinical adoption, with less than 20% of patients receiving a relevant NGS test across disease modalities. In recent years, he continued, Illumina saw a “meaningful” increase in clinical adoption across oncology and genetic and reproductive diseases, with new assay approvals, broader reimbursement, and an increase in new clinical trials.
Oncology testing accounts for ~51% of Illumina’s clinical market exposure, with genetic disease testing second at ~25% and reproductive health at ~21%. The remaining 3% is categorized as “other,” primarily consisting of infectious disease testing.
Clinical customers are increasingly adopting larger panels and greater sequencing depths to improve sensitivity and provide deeper insights for more accurate analysis, all powered by the NovaSeq X sequencing system launched in 2022, Thaysen said.
“For rare genetic diseases, many are now converting assays from exome sequencing to whole genome sequencing, which requires approximately a 15x increase in sequencing volume. These dynamics are driving clinical sequencing volume growth above 30%,” Thaysen said. “We see continued adoption of approved and emerging NGS tests in areas like early cancer detection and MRD [minimal residual disease], plus more demand for sequencing-intense assays as drivers of continued growth volume in the future.”
Conditions for expansion
Saxonov said 10x’s success in the research tools market has created conditions for expanding more directly into clinical diagnostics as well, driven by advances in single-cell and spatial technologies.
“They have become a lot more robust, scalable, and suitable for this kind of work,” Saxonov explained. “The signals have now become more and more clear, just emerging from the scientific literature, that if you use single cell or you use spatial, you will be able to see the relevant information for selecting therapies. The need is there, and it’s only growing.”
One key way 10x aims to address that perceived need is through the clinical collaborations it has announced with the three research and patient care institutions.
With Dana-Farber, 10x aims to identify biomarkers linked to treatment response by analyzing tumor samples from hundreds of patients, with an eye toward evaluating therapeutic targets and relevant tumor microenvironment features for emerging therapies in oncology—including antibody-drug conjugates (ADCs), radioligand therapies (RLTs), bispecific antibodies, immune checkpoint inhibitors, and other precision approaches.
Investigators will use 10x’s Chromium Flex single-cell assay and Xenium spatial biology platform to generate detailed molecular maps of tumors that integrate both cellular composition and spatial architecture. 10x said it also plans to partner with Dana-Farber in defining actionable biomarkers for future clinical reporting and exploring how spatial and single-cell insights, such as target expression patterns, immune contexture, or indicators of therapeutic sensitivity, could be summarized in a format designed to support oncologists’ treatment decisions.
“If you look at the landscape of oncology right now, if you look at all the therapies that are recently coming on the market, and a lot more that are set to come on the market, they’re all targeting expression markers in cells and tissues in cancer—which is in contrast to the wave of therapies that were there like 15 or so years ago when you had specific mutations in a DNA that were being targeted,” Saxonov said.
“So, all these new therapies that are coming up now are all targeting different expression markers or the tumor marker environment in some fashion. And what needs to exist now for physicians to be able to select the right therapy is a way to comprehensively measure all the different targets that are being targeted by these drugs. And that doesn’t exist now,” Saxonov added. “We feel that with our technologies, we can address that. And that’s what the collaboration with Dana-Farber is about.”
Partnering with Brigham and Women’s, CRI
10x will also partner with Brigham & Women’s Hospital to analyze peripheral blood samples from patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and giant cell arteritis (GCA), in order to uncover immune signatures associated with disease activity and therapeutic response.
Using single-cell profiling of peripheral blood, the collaboration with Brigham and Women’s aims to generate a high-resolution view of the dynamic immune signatures that drive autoimmune disease. The partners plan to enroll 1,000 patients with RA, SLE, or GCA, along with healthy controls, in a study that will follow the patients over 18 months, with blood collection during routine clinical visits.
“I think this is going to be the biggest study of its kind, which is really, really exciting. And every person we talk to, like the specialists, they are very excited about the study’s potential,” Saxonov said.
As with the Dana-Farber collaboration, 10x will make Chromium Flex available to investigators as they create detailed molecular maps of circulating immune cells over the course of disease and treatment. By pairing the profiles with longitudinal clinical data, the collaboration seeks to identify immune features that distinguish controlled disease from active inflammation, responders from non-responders, and flare from remission.
With CRI, 10x also plans to advance an AI-driven immuno-oncology initiative that is intended to develop one of the world’s most comprehensive translational immuno-oncology datasets. The multi-phase project will combine 10x’s Chromium single-cell and Xenium spatial platforms with advanced AI to build what the partners say will be one of the world’s most comprehensive translational and preclinical immuno-oncology datasets, spanning more than 20,000 samples.
10x and CRI aim to reveal how the immune system recognizes and responds to cancer and to inform smarter treatment and prevention strategies for the future. The collaboration is intended to generate approximately 3,000 samples and analyze them using 10x’s Chromium and Xenium platforms, with CRI incorporating 10x’s Chromium Flex single-cell assay, purpose-built for ultra-high-throughput studies, to profile more than 500 million cells.
Roller coaster year
10x’s stated expansion into clinical diagnostics follows a roller-coaster year in which the company saw its traditional market of academic and government customers shrink due to federal cuts in research funding. In May, 10x eliminated about 100 jobs—8% of its workforce—as part of a company effort to cut $50 million in costs and better reflect strategic priorities that include addressing the unsettled financial climate.
But on the first day of the J.P. Morgan conference, 10x had mostly better news to announce. The company released preliminary, unaudited select results for the fourth quarter that included an 11% quarter-over-quarter jump and 1% year-over-year increase in revenue, to approximately $166 million, 6% above a consensus analyst forecast cited by Jefferies.
Consumables revenue of approximately $141.7 million showed 11% growth from Q3 2025, and a 6% rise from the year-ago quarter. Instrument revenue soared 29% quarter-over-quarter to about $15.5 million, but a 36% tumble vs. Q4 2024. Consumables revenue consisted of about $100.8 million of single-cell consumables (up 9% sequentially and 3% year-over-year), and $41 million of spatial consumables revenue (up 16% sequentially and 14% year-over-year).
Instrument revenue of approximately $15.5 million represented 29% growth quarter over quarter but nosedived 36% from a year earlier. Instruments revenue consisted of about $6.1 from single cell instruments (up 24% sequentially but down 44% from Q4 2024) and $9.4 million of spatial instruments (up 32% but down 30%).
“We view the preliminary results as a directional positive for potential budget flush across the broader instruments group,” Jefferies equity analyst Tycho Peterson wrote in a research note.
Investors appear to remain bullish on 10x. The company’s stock closed Friday at $22.38, a 36% jump over the past month from $16.69 on December 24 and a 64% leap over the past six months from $13.73 on July 24.
Growth ARKK
Last week, 10x climbed 13% over three trading days from $20.52 to $23.19 on Thursday after ARK Innovation ETF (ARKK)—an exchange traded fund of ARK Investment Management (ARK Invest), the high-profile firm led by chief investment officer and portfolio manager Catherine D. (Cathie) Wood—added to its portfolio 49,000 shares of 10x, while selling 14,166 shares of Illumina.
As of January 23, ARKK held 8,913,981 shares of 10x class A stock with a market value of $206,715,219.39, accounting for 2.41% of total fund assets, the 14th largest of the fund’s 47 holdings. ARKK held 995,304 Illumina shares valued at $153,227,050.80—1.79% of total fund assets, the 19th largest of the fund’s 47 holdings.
Saxonov expressed pride in the 10x workforce’s ability to weather the rougher than expected financial storms of 2025.
“2025 had major, major upheavals in our end markets, and it was really, really challenging in a lot of ways that no one, I don’t think, really could have expected,” Saxonov said. “I’m really proud of how the team performed through it and executed, and showed lots of dedication and ingenuity in partnering with customers, managing through a really unpredictable financial landscape.”
“And yes, we ended up finishing the year what I think is with really, really nice momentum.”
The post Clinical Ambitions: 10x Expands Beyond Research with Trio of Collaborations appeared first on GEN – Genetic Engineering and Biotechnology News.
