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Illumina CEO Discusses Pan-Cancer IVD Assay, CDx Collaborations at JP Morgan

This story has been updated to include additional comments from Illumina CEO Francis deSouza and CMO Phil Febbo.

NEW YORK – Illumina is in the process of obtaining regulatory approval for a pan-cancer genomic profiling assay in the US and Europe, which will be central to several new partnerships with pharma and genetic testing companies.

The next-generation sequencing-based clinical assay is one of several announcements Illumina CEO Francis deSouza made today at the virtual JP Morgan Healthcare Conference.

He also announced collaborations with pharma and genetic testing companies based around the assay with Bristol Myers Squibb (BMS), Kura Oncology, Merck, and Myriad Genetics. Financial details of the collaborations were not disclosed.

"Cancer is a disease of the genome and treatment will increasingly leverage NGS-based tests, from early detection and diagnoses, to therapy selection and monitoring," deSouza said. "The continued expansion of our TruSight Oncology pipeline perfectly complements our planned acquisition of multi-cancer early detection company Grail."

Illumina will also be introducing a new flowcell for the NextSeq 1000 and 2000 systems. The lower-throughput P1 will have output between 20 gigabases and 40 gigabases and will ship later this year, making it "an attractive upgrade option for MiSeq and NextSeq 550 customers," deSouza said.

And Illumina Connected Analytics, a set of multiomics discovery tools representing a synthesis of technologies acquired through the firm's purchases of Edico Genome, BlueBee, and Enancio, will launch later this month. One early customer, Taiwan's National Applied Research Laboratories, improved their bioinformatics pipeline processing by 50 times and reduced data storage by five times, deSouza said.

Illumina officials also provided preliminary fourth quarter and full-year 2020 financial results and reinstated guidance for 2021. The firm expects $950 million in total revenues for Q4, flat year over year, and adjusted EPS of $1.20, compared to $1.70 a year ago. Illumina expects total revenues of approximately $3.24 billion for 2020, down 9 percent year over year.

Illumina expects 2021 total revenues in the range of $3.79 billion to $3.88 billion, representing revenue growth of between 17 and 20 percent year over year, and adjusted EPS between $5.10 and $5.35. On average, analysts are expecting 2021 revenue of $3.95 billion. Illumina expects sequencing revenues to grow approximately 20 percent year over year; sequencing consumables revenue, approximately 20 percent; sequencing instrument revenue growth, 33 percent; and arrays revenue growth, 5 percent. In general, deSouza said the company expects a "return to normal" by the second half of 2021.

Illumina is also excited about the market for non-invasive prenatal testing (NIPT) in 2021. Recent coverage decisions could lead to a 50 percent increase in pregnancies in the US covered for NIPT and Germany will begin reimbursing for NIPT in the second half of the year. Illumina plans to have a distributable NIPT kit available in the US in 2022, deSouza said.

Regarding its pan-cancer IVD assay, Illumina Chief Medical Officer Phil Febbo said in an interview that "comprehensive genomic profiling is becoming the standard of care in the US and increasingly in Europe and places like Japan and China. In the US, the market is well served with innovators using our tech, like 

Foundation [Medicine] and Guardant [Health], but outside the US, it really requires … distributed IVDs to get that technology more available to patients." 

"Even in US, there's good data emerging that when a center adopts comprehensive genomic profiling… much more often, patients receive therapies that are found to be targetable," Febbo said. 

The comprehensive genomic profiling assay will be based on the same chemistry as the TSO 500, but will a have a different name, which hasn't been revealed yet, Febbo said. The firm has not revealed pricing, but the "price of the IVD will be adequate for a lab to internalize and run the test," Febbo said. He added that the firm expects to have a CE-marked IVD in the first half of 2021 and US Food and Drug Administration clearance in the second half of the year.

Illumina's collaboration with BMS expands on an existing collaboration started in 2018 to develop and commercialize companion diagnostics based on TSO 500. Under the terms of the collaboration, BMS will develop a microsatellite instability CDx, as well as a diagnostic based on the content of TruSight Oncology 500 for circulating tumor DNA, Illumina's first liquid biopsy assay. Both program expansions are planned for global use by BMS in its portfolio of cancer therapeutics.

Illumina's partnership with Kura Oncology is focused on building a CDx claim for HRAS mutations in head and neck squamous cell carcinomas.

The Merck and Myriad partnerships are based on the use of comprehensive genomic profiling to analyze homologous recombination repair deficiency (HRD) and the growing clinical use of PARP inhibitor drugs for patients with the HRD phenotype. Testing for HRD involves looking for "scarring" across the genome, Febbo explained. "You need test a that samples at least 1 megabase" of the genome, he said;  the TSO 500 assay samples around 1.8 megabases.  

Illumina and Merck are conducting a study focused on the expanded TruSight Oncology HRD offering. Meantime, the Myriad partnership will have time-limited exclusivity in certain markets, and the partners will develop and commercialize distributed kits for the assessment of HRD and for Myriad to expand its HRD service offerings, through a combination of TruSight Oncology content and Myriad's myChoice CDx test.

"The agreement between Myriad and Illumina combines clinically validated companion diagnostics and next-generation sequencing to advance comprehensive genomic profiling of tumor samples and drive improved outcomes for oncology patients," Myriad President and CEO Paul Diaz said in a statement.

Febbo noted that pursuing CDx partnerships would be important for getting reimbursement for the test, once it's available. "All you need is one companion diagnostic that's pan-cancer and that derisks reimbursement from Medicare for the IVD," he said.

At the close of the Nasdaq on Monday, shares of Illumina were down less than 2 percent at $372.48.