Illumina Teases New Chemistry, Long Reads, Oncology, Proteomics Partnerships

By Allison Proffitt

January 11, 2022 | At the JP Morgan Healthcare Conference—being held virtually again this year—Illumina CEO Francis deSouza outlined Illumina’s record for 2021, announced several new partnerships, and teased new chemistry and new long read technologies.

deSouza gave his annual update on Illumina’s install base and user numbers. He reported more than 8,000 customers in 140 countries and reported preliminary revenue of $4.517 billion in 2021—more than half a billion dollars ahead of expectations. This growth, he said, is up 39% over 2020 and 27% from 2019.

Last year Illumina enjoyed record consumable shipments for the research and clinical markets, record NovaSeq shipments serving the high-throughput market, record NextSeq 1000/2000 shipments for the mid-throughput market, and record placements for the MiniSeq and iSeq 100 representing low-throughput platforms. The company saw a 40% growth in consumables and a 75% growth in instruments, he said, bringing the company’s cumulative install base to more than 20,000 instruments.

Technology Launches

Without giving too much detail, deSouza teased new technology to come, starting with “Chemistry X”, new SBS chemistry that comprises novel dyes, linkers, blocks, and polymerases that deSouza claims will deliver two times faster cycles times, two times longer reads, and three times greater accuracy, all on the road to the $100 genome. IP has been filed on the new chemistry, deSouza said, and the company is developing a large-scale manufacturing facility to apply the new chemistry to all future platforms.

This quarter the company is launching new bioinformatics technology—DRAGEN Graph—on its DRAGEN platform, which can support DNA, RNA, methylation, and a novel Bayesian theory approach to machine learning, enabling the fastest, lowest cost, and most accurate analysis of any platform. “Our unique parallel compute architecture enables dynamic scaling,” deSouza added, “so speed is the same for one sample or thousands.”

Finally, deSouza reported the company’s efforts to sequence the “hard-to-reach” regions of the genome by unveiling Infinity, the company new technology for highly accurate long read workflows, delivering contiguous data up to 10kb in length with 90% less DNA input “to address the final edge cases of the genome.” The Infinity long read technology is compatible with SBS chemistry and can be rapidly applied to the entire existing Illumina install based. “We have a pipeline to deliver this technology at 10x lower cost than on-market, legacy long reads,” deSouza said, and says early access launch will happen in the second half of 2022.

Market Applications

In research updates, deSouza focused on Illumina’s efforts to expand their existing clinical genomics markets in oncology, reproductive health, genetic disease, and research. “More than one billion people are now covered for genomic testing globally and we expect this number to grow to two billion by 2026. We are well-positioned to serve the clinical genomics markets with more than 4,000 clinical customers globally and 70 product approvals from 55 regulatory agencies around the world,” he said.

He announced a new partnership with Optum to accelerate large-scale demonstration of genetic utility with Optum’s newly-launched Optum Evidence Engine. Studies are underway, deSouza said, in cardiovascular disease, rare genetic disease, and oncology, with future areas of study including organ transplants, polychronic patients, and hematological cancers.

Diagnostics Partnerships

Oncology testing is a $75B market that is only 4% penetrated, deSouza believes, and opportunities for genomics lie in early detection, therapy selection, and monitoring.

GRAIL, an Illumina subsidiary that was spun out of the company in 2016 and then acquired in 2021, has Galleri, a multi-cancer early detection blood test for more than 50 cancers. “GRAIL is working closely with partners throughout healthcare to support access and utilization of Galleri,” deSouza said. “Their goal is to bring this test to as many patients as possible as soon as possible. They’re seeing early success.” deSouza promoted an upcoming GRAIL monitoring test for minimal residual disease, expected in 2023.

deSouza said that Illumina is leading the $14B therapy selection market, highlighting 11 partnerships for the Illumina TruSight oncology comprehensive test including a just-announced partnership with Boehringer Ingelheim, as well as 34 IVD development partnerships including a just-announced partnership with Agendia.

Both of these partnerships were announced today in conjunction with JP Morgan. The Boehringer Ingelheim partnership aims to accelerate the development of therapy selection and precision medicines for patients with advanced cancer. It spans current and future CDx programs, with plans to add CDx claims to an in vitro diagnostic test Illumina is developing that is based on the content of TruSight Oncology 500 (TSO 500). The first program will co-develop a CDx for a Boehringer Ingelheim investigational medicine.

The Agendia partnership will focus on new tests to enhance the care and management of breast cancer patients, utilizing the Illumina MiSeq Dx sequencing platform, expanding the range of gene panels available for solid tumor analysis. Agendia’s flagship test, MammaPrint, which is FDA- cleared and currently offered via Agendia’s central laboratory, is expected to be the first decentralized NGS-based breast cancer recurrence risk test cleared by the FDA

New Market Areas  

Illumina applications are also growing as well into infectious diseases, drug discovery, and proteomics, deSouza added. Illumina platforms have been essentially involved in pathogen surveillance throughout the Covid-19 pandemic. deSouza reported that more than 75% of published SARS-CoV-2 sequences were done on an Illumina platform. He also predicted that Illumina platforms will be fundamental to future pan-pathogen surveillance efforts.

Drug discovery, he said, is also powered by Illumina sequencing platforms as well as DRAGEN ICA (Illumina Connected Analytics, the company’s bioinformatics solution announced last year at the JP Morgan) and AI-based genome interpretation. He highlighted existing pharma customers including Amgen, Regeneron, and AstraZeneca as well as another newly-announced partnership with Nashville Biosciences, a wholly-owned subsidiary of Vanderbilt University Medical Center.

Illumina and Nashville Biosciences plan to engage a commercial alliance of pharmaceutical and biotech partners who can use the data analysis of VUMC’s extensive, high-quality biobank of approximately 250,000 de-identified human DNA samples and associated longitudinal, structured medical data, BioVU, to drive improved therapeutic development. The program will leverage Illumina’s AI capabilities, genome interpretation, and scaled analytic infrastructure to support the identification of new genomic-based drug targets.

Finally, proteomics, deSouza said, represents a more than $50B market and NGS is emerging as a leading readout for proteomics research, he said. “We are catalyzing this acceleration by supporting partners and identifying key spaces to participate,” he said, highlighted last week’s partnership announcement between SomaLogic and Illumina to co-develop a proteomic solution, “using the largest protein target set of more than 10,000 proteins and the high-throughput capabilities of Illumina’s NGS platforms,” he said. The workflow will address diseases including cardiovascular, neurodegenerative, and cancer.  “With this solution, we will accelerate proteomics onto NGS and deliver scale for the fastest growing space in the proteomics market,” deSouza said.

During the Q&A, deSouza clarified that Illumina will continue to support the whole proteomics ecosystem, but that the company saw a void in the market. “We felt in the high-throughput segment that we could bring something differentiated into the market, and if we didn’t do it, that part of the market wouldn’t develop as quickly as it could,” he explained. “We didn’t see anybody targeting that segment in a way that we thought we would. We wanted to make sure that part of the market developed as well.”