Illumina Expands Portfolio of Precision Medicine Cancer Tests

Sequencing giant Illumina is expanding its cancer testing portfolio with four new or expanded partnerships announced at the virtual JP Morgan Healthcare Conference this week.

Expanding on its agreement to acquire liquid biopsy biotech Grail for $8 billion last year, Illumina will collaborate with Bristol Myers Squibb, Merck, Kura Oncology and Myriad Genetics to develop new precision cancer tests.

Illumina has developed the TruSight Oncology 500 (TSO 500) assay uses DNA and RNA from tumors and can identify 523 cancer biomarkers. The company is developing an in vitro diagnostic test based on the TruSight Oncology 500 assay that is currently being evaluated by regulatory authorities. Illumina hopes to launch this test in the U.S. and Europe later in the year.

“We believe that the way to do efficient cancer testing is really the CGP approach,” Alex Aravanis, MD, PhD, Illumina Chief Tehcnology Officer and Senior Vice President, told GEN, referring to comprehensive genomic profiling. He noted that the number of oncology therapies that have molecular markers required for prescribing stood at 55 and growing.

“A comprehensive approach here is to do nearly all the genes implicated in cancer in a single test. Having one test that allows you to do all or a large number of them is really the way to get the most access for patients,” Aravanis said. “For many of these tests, it may only be 1% or 2% of lung cancer patients that are eligible. And then if that test isn’t done as an individual test, they may not get access to it. So we think there’s a tremendous efficiency to a comprehensive approach.”

The CGP approach, he added, better enables testing for key signatures that require the testing of several genes, such as homologous recombination repair  deficiency (HRD) and tumor mutational burden (TMB).

The new deals announced at the JP Morgan event, the value of which were not disclosed, will expand on and use data from the TruSight assay and allow additional companion diagnostics to be developed.

Illumina already has a partnership with Bristol Myers Squibb that started in 2018. The expanded collaboration will involve development of a companion diagnostic to detect microsatellite instability and a liquid-biopsy based diagnostic.

Kura Oncology is developing a precision medicine for head and neck cancers with HRAS mutations called tipifarnib, which is nearing approval. The collaboration with Illumina will aim to develop a companion diagnostic to be used to detect the presence of HRAS mutations.

Myriad Genetics has developed a test called myChoice that assesses whether cancer patients have homologous recombination DNA repair deficiency (HRD), something that can impact the success of PARP inhibitor therapy.

The companion diagnostic has a European CE mark and also has Japanese regulatory approval. Illumina will partner with Myriad to develop a kit-based version of the myChoice test for additional international markets.

“The growing use of PARP inhibitor therapeutics to broader populations of patients with HRD is paramount in our work with Myriad Genetics as the future of healthcare looks to molecular-based testing to improve patient outcomes through standardized, best in class testing,” said Phil Febbo, M.D., Chief Medical Officer of Illumina.

Lynparza is a PARP inhibitor, used to treat cancers with BRCA1 or BRCA2 hereditary mutations including some breast, ovarian and prostate cancers. It was jointly developed and commercialized by Merck and AstraZeneca

Merck is partnering with Illumina in the HRD space and are working together to research and improve TruSight Oncology’s detection capacity in this area.

“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,” said Illumina CEO, Francis deSouza. “The continued expansion of our TruSight Oncology pipeline complements our planned acquisition of multi-cancer early detection company GRAIL.”

$100 Genome Update

During a question-and-answer “breakout” session following his formal presentation at JP Morgan, deSouza said several technology breakthroughs will enable Illumina to eventually deliver on its long-expressed commitment to drive the cost of sequencing down to a $100 genome.

Illumina’s breakthroughs, he said, include 5x higher cluster density than NovaSeq version 1.5 kits; yielding 5x the data from the same flow cell area. The company has also developed a flow cell manufacturing process using 300-millimeter wafers, doubling its wafer yield. Combined, both innovations are projected to reduce flow cell cost by 90%.

deSouza said Illumina has also made fundamental improvements to its sequencing by synthesis (SBS) technology, including new dies and blocking chemistries. The enhancements enable 3x higher accuracy, 2x faster cycle times and 2x longer reads.

“We certainly have now the technologies available and running in our labs,” deSouza said “We’ll think about what is the right form factor to bring it into the market. We haven’t announced that yet, whether it’s in addition to NovaSeq or a new instrument.”

Two years ago, deSouza told J.P. Morgan attendees that Illumina viewed the development of a $100 genome as a multi-year process combining engineering work—which he said was now in progress—with customer demand. deSouza’s predecessor Jay Flatley and Illumina electrified the 2014 J.P., Morgan conference by announcing the $1,000 genome.

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