Illumina at JPM: Cloud Analytics Platform, More Diagnostics Focus, Sequencing Updates To Come

By Allison Proffitt

January 11, 2021 | At the 39th Annual J.P. Morgan Healthcare Conference in San Francisco today, Illumina CEO Francis deSouza outlined Illumina’s take on the genomics market, made partnership announcements, and launched Illumina Connected Analytics, an expanding software analytics platform. deSouza did not announce any new sequencing platforms, though he teased updates coming in 2021.

The biggest new product offering was Illumina Connected Analytics (ICA), a new bioinformatics software platform that offers a direct sequencer-to-platform transfer of data onto the private Illumina cloud. There, data can be seen, read, automatically processed, analyzed, and shared securely. 

“This software solution enables population initiatives to analyze, interpret, aggregate and explore, and share multi-omic data at scale, combining the technology from our Edico, Enancio, and BlueBee acquisitions into a single, fully-integrated solution,” deSouza said.

DeSouza illustrated ICA’s benefits specifically with regard to population health projects—referring to Illumina’s recent selection as a clinical sequencing partner for Denmark. “Managing the large volumes of data generated is a bottleneck for population genomics programs,” he said.

But Illumina Connected Analytics will eventually address data analysis pain points for all Illumina customers, explained Susan Tousi, Illumina’s Chief Product Officer, in a pre-event conversation with Bio-IT World. “Data analysis continually emerges as a major bottleneck for our customers,” she said. “We’ve invested significantly—including acquisitions—to get to this very scalable platform. For us, this was designed to deal with not only the amount of data we see today in the marketplace, but the amount of data we are enabling with our continued roadmap of sequencing.”

ICA will eventually be available to the entire Illumina install base, but population genomics will take priority at the product launch January 28, 2021. “Our first focus is pop gen customers and pharma customers who have the largest need for data at scale and driving data insights,” Tousi said. To that end, high throughput customers will be the first connected to ICA—"primarily those using NextSeq and NovaSeq”—but eventually “seamless integration” will be available for the entire Illumina fleet globally, Tousi said, similar to the current connection to BaseSpace.

(BaseSpace, she said, "has its place in terms of instrument health management through our proactive utility on BaseSpace. It has a number of easy to find pipelines, and does things very simply and easily for customers... [ICA] has a much broader range of capability and flexibility and allows for much higher power data aggregation, exploration, sharing. We will be working on connecting BaseSpace and this platform more and more... BaseSpace will become a seamless integration with this platform.")

The tools available through ICA include the entire DRAGEN analysis pipeline with integrated Enanciao compression, a data science workbench with a Jupyter notebook interface—important for research customers, Tousi said, drag-and-drop analysis workflows, and a growing suite of AI and machine learning tools. deSouza mentioned two Illumina AI tools that are in development and he expects to launch in 2021: PrimateAI v2, deep learning to classify VUS and SpliceAI v2, deep learning to predict splice sites.

Tousi describes ICA as a private cloud offering that will sit above any other cloud structure. ICA will be available via a web portal or through APIs and has been, “designed with compliance and security in mind,” she said. Amazon Web Services is the launch partner, “but we intend to make it available ubiquitously,” she said. Although the pricing details have not been released, Tousi suggested it would be a subscription service. Although a main ICA feature is the direct connect to the instrument, customers will not need to have sequencers. Data can be shared with collaborators through the platform. 

While the summer’s acquisitions of BlueBee and Enancio may have pushed the ICA launch the last mile, Tousi emphasized that the product is the result of several years of internal Illumina development. “This is genomics-plus, or multi-omics data. The platform was designed for being able to operate on, store, aggregate on any ‘omics data,” she said.

Multi-Omics, SBS Chemistry Improvements

That functionality aligns well with the areas deSouza highlighted in Illumina’s market outlook. The multi-omics space is a rapidly-growing area of innovation to which Illumina sequencing is central, he said, particularly single cell sequencing, spatial analysis, and proteomics. Spatially resolved transcriptomics, “was named Nature’s 2020 Method of the Year, and companies like 10x and NanoString are making it accessible,” he said (DOI: 10.1038/s41592-020-01042-x). “These applications allow researchers to understand additional dimensions of biology and will drive demand for vast amounts of sequencing data.”

Much of that data, of course, will be generated by Illumina. deSouza reported an ongoing strong recovery from the Q2 COVID-19 slump. Research has returned to pre-COVID-19 levels, he said, and the company reported record NovaSeq shipments—the most successful sequencer in company history, a strong showing for the NextSeq 2000, which launched in January 2020, and more than 2,000 overall instrument shipments in 2020. The first half of 2021 will certainly be impacted by the ongoing pandemic, but deSouza expects business to be back to normal by the middle of 2021 and forecasts a 20% sequencing growth in 2021, 33% increase in instruments, and a 20% increase in consumables.

While no new sequencers were announced this year, deSouza emphasized the research advances Illumina has achieved in the past year. “We have now achieved the key technology breakthroughs to deliver the next order of magnitude improvement in cost as well as significant steps forward in accuracy, speed, and read length,” he said.

In terms of cost, he cited a 5x improvement in cluster density over NovaSeq v1.5 and a manufacturing process that doubles wafer yield, together reducing flow cell cost by 90%. He also reported new dyes and blocking chemistries so that sequencing by synthesis (SBS) technology now realizes a 3x increase in accuracy, 2x faster cycle times, and 2x longer reads. 

These are the technology improvements that will be needed to achieve routine population sequencing and genetic disease testing at $100 per human genome, deSouza said. The increased cluster density and larger wafers are already running in the Illumina labs, he said. “And we’ll think about what is the right form factor to bring it into the market… whether that’s an addition to NovaSeq or a new instrument. But we certainly have now the technologies available and running in our lab.”

Diagnostics Outlook

deSouza’s other area of focus and high expectations: diagnostics. The company’s acquisition of GRAIL is still pending, but deSouza foresees a strong future for GRAIL’s multi-cancer early detection test, non-invasive prenatal testing, and minimal residual disease (MRD) testing, driven in part by various favorable legislation and insurance coverage decisions. 

He also announced a portfolio of new and expanded oncology partnerships including new partnerships with Merck, Gilead, and Kura Oncology and expanded partnerships with Bristol-Myers Squibb. Each of these partnerships is centered on developing liquid or tissue diagnostics for the existing TruSight Oncology 500 (TSO 500) tests.

TSO 500 is a Research Use Only comprehensive pan-cancer assay designed to identify 523 known and emerging tumor biomarkers. TSO 500 utilizes both DNA and RNA from tumor samples to identify key somatic variants critical for cancer development and progression, such as small DNA variants, fusions, and splice variants.

Based on the content of TSO 500, Illumina will be adding an in vitro diagnostic (IVD) test to the TruSight Oncology product family. This comprehensive tumor profiling assay will have similar chemistry and analytics to TSO 500 and is currently undergoing review with regulatory authorities. It is expected to be launched in both the U.S. and Europe later this year.