Illumina at JPM: Multi-Omics, Constellation, Partnerships
By Allison Proffitt
January 16, 2025 | Jacob Thaysen gave Illumina’s annual presentation at the 43rd Annual J.P. Morgan Healthcare Conference on Tuesday, outlining Illumina’s early 2024 results and the vision for the future. “Today, Illumina is operating from a position of global strength,” Thaysen said. “In 2024 alone, more than 480 petabases of data was generated on our sequencers. That is equivalent to approximately and impressively 5 million whole genomes.”
But Illumina is not focusing only on building sequencers and sequencing genomes. Thaysen outlined an M&A and partnership strategy focused on expanding the company’s addressable markets.
Transitions and Growth
It’s been a year of significant transition for the sequencing company. Thaysen took over at CEO in September 2023, making this his second J.P. Morgan Healthcare Conference presentation on behalf of Illumina. In April 2024, activist investor Carl Icahn gave up his seat on the Illumina board. The company then announced several new executives including Ankur Dhingra as CFO and Jakob Wedel as Chief Strategy and Corporate Development Officer in April 2024; and Everett Cunningham as Chief Commercial Officer in June 2024. Illumina’s general counsel position is currently open, and the company finalized the divesture of Grail mid-year as well.
Thaysen’s goal for Illumina is “return to growth” he said, with “high single-digit” growth percentages being the aim by 2027. In 2025, he reported, Illumina achieved low single-digit percentage range: “’24 was a solid initial step, and ’25 will bring us even closer to these goals. While we remain well on track, ’27 is not the end of the journey. We’re just getting started.”
For the core sequencing business, the MiSeq i100 series that Illumina announced last October began shipping in December, Thaysen said, with 70 placements before the end of the year. “Customers are excited to expand their applications with faster answers, and some are even planning to use the MiSeq i100 to test experiments before running them at scale on the NovaSeq X,” he said.
For NovaSeq X, the high-throughput platform Illumina launched in October 2022, Thaysen reported exceptional growth for NovaSeq X instrument sales—placing 91 sequencers in the fourth quarter alone—though he joked during Q&A that the 2025 outlook would not likely be “91x4”. By the second half of 2025, Thaysen predicts that 75% of Illumina’s high-throughput sequencing and 50% of high-throughput consumables revenue will come from the X platform. “As more sequencing volume moves to the X, the impact of the reduced pricing lessens, and we expect to see a higher portion of the volume translate into true revenue growth,” he predicted.
Multi-Omics Mission
But Thaysen is looking beyond the core sequencing business. In August, Thaysen gave a strategy update with a multi-omics focus: “Over the next three years, we will bring to market impressive new innovations that will redefine the genome and drive significant, deeper biological insights through multiomics,” he said in a press release. He echoed that committment yesterday.
The NovaSeq X “serves as a platform of the future for multi-omics,” Thaysen said. Last week, the company announced software updates to elevate sequencing performance and advance data quality. New NovaSeq X 25B 100- and 200-cycle kits began shipping in December, which will be key enablers of multiomic applications, including the Illumina Single-Cell 3' RNA Prep (Illumina Single Cell Prep), now available under Illumina's brand following the company's July 2024 acquisition of Fluent.
Proteomics is a particularly exciting area of focus, Thaysen said. Illumina’s new proteomics solution—jointly developed with Standard BioTools—will launch the first half of this year, he said. “Illumina’s protein solution provides a true, complete, end-to-end market solution for proteomics with easier automated workflow than other on-market products,” Thaysen said. “With 9,000 protein panel, this is the largest, orthogonal, validated NGS proteomics platform in the industry.” The panel outperforms other NGS proteomics products on both precision and reproducibility, he said. “This is not only impressive, but essential for identifying clinically relevant targets and insights,” he added.
Illumina also announced a pilot proteomics program with UK Biobank to analyze 50,000 UK Biobank samples in collaboration with deCODE Genetics, Standard BioTools, Tecan, GSK, Johnson & Johnson, and Novartis. The pilot program will use Illumina's upcoming proteomics assay, Illumina Protein Prep, with SOMAmer technology, a next-generation sequencing (NGS) based solution that will help scale access to proteomic insights.
Illumina’s constellation mapped read technology, presented at ASHG 2024 with Broad Clinical Labs, is also an area of focus, Thaysen said. The constellation technology seeks to eliminate library prep while maintaining the accuracy, depth of coverage, and scalability of standard SBS and adding the phasing, enhanced mapability, and improved structural variant detection often associated with long-read methods, the company says. The first commercially available product based on constellation technology is slated for the first half of 2026 and will leverage existing NovaSeq X Systems to create an accessible, cost-effective solution for comprehensive human WGS.
Software and analytics are other areas of growth, Thaysen said. “All Illumina solutions are supported by Illumina’s advanced software stack that customers can use for integrated workflows across a range of multi-omics applications,” he said. And Illumina is partnering to expand capabilities there. On Monday, NVIDIA’s Kimberly Powell, VP of Healthcare, announced a partnership to between NVIDIA and Illumina. Now, in addition to its own efforts, Illumina will look to expand its customer offerings with models developed by the NVIDIA Biology Foundation Model Research Team and partners. Customers will also be able to leverage these models with their own proprietary datasets to improve the performance for biologically relevant tasks of interest, such as cell state or gene transcription prediction.
Illumina’s success at sequencing has created a data volume problem. “No human can actually sit in front of their computer and [analyze their data] with an Excel sheet,” Thaysen said. “AI is going to be tremendously important to do so, and that’s really where the relationship with NVIDIA is going to be powerful… I think we will all sit here in a few years and think back and see this as the starting of a new era.”