More than seven years after it unsuccessfully attempted to acquire Illumina for $5.7 billion, Roche is now partnering with its erstwhile takeover target on a common goal: Advancing the use of distributable next-generation sequencing (NGS)-based testing in oncology.

Illumina and Roche on Monday said they signed a 15-year, non-exclusive collaboration agreement designed to realize NGS’ potential to transform cancer risk prediction, detection, diagnosis, treatment and monitoring. The value of the partnership—which includes in vitro diagnostic (IVD) and companion diagnostics (CDx) initiatives—was not disclosed.

Neil Gunn, MSc, PhD, president of Roche Sequencing Solutions, told GEN Edge that the first CDx the companies will partner to distribute on Illumina sequencers is Roche-owned Foundation Medicine’s FoundationOne® CDx assay, an FDA-approved comprehensive genomic profiling (CGP) test for all solid tumors that incorporates multiple companion diagnostics.

“We’ll then continue to evolve the marketplace,” Gunn said in an interview at the Westin St. Francis Hotel in San Francisco, shortly after Illumina CEO Francis deSouza announced the partnership during his presentation at the J.P. Morgan 38th Healthcare Conference.

“This field moves rapidly. There are new genes, new targets. So, we’ll develop a roadmap that allows us to continually stay market-leading in terms of the product itself, and also give us the largest access through the partnership with Illumina.”

FoundationOne CDx is a NGS-based IVD designed to detect substitutions, insertions, and deletions (indels) and copy number variations in 324 genes and select gene rearrangements, as well as genomic signatures including microsatellite instability and tumor mutational burden using DNA isolated from formalin-fixed paraffin embedded tumor tissue specimens. FoundationOne is the first FDA-approved broad CDx with Medicare coverage for qualifying patients across all solid tumors, including non-small cell lung cancer, colorectal, breast, ovarian, and melanoma.

‘We’re looking at the large gene panel of FoundationOne, as well as smaller panels which fit different market segments,” and meet National Comprehensive Cancer Network guidelines, Gunn said.

Market accessibility

“That’s what’s really exciting: New assay content, IVD, on a platform that allows really broad access to allow patients to benefit from it. We’re looking to leverage the market accessibility that Roche affords,” Gunn added. “We have a broad affiliate network around the world and have access to the diagnostic labs and customers around the world.” To that end, Gunn said, Roche will stay in touch with clinicians as well as with developers of cancer immunotherapies.

One analyst viewed the collaboration favorably: “We believe the Roche partnership represents a solid step forward in Illumina’s IVD strategy that will advance NGS-based testing in oncology care,” wrote Puneet Souda, managing director, Life Science Tools and Diagnostics with SVB Leerink, in a note to investors.

The companies have yet to establish a time frame for their initiatives, which will be affected by the time it takes to design panels, develop tests, then undergo regulatory reviews. “We will certainly accelerate it as much as we can,” said Gunn, who noted Roche’s long experience gaining approvals for numerous assays, including the first PCR liquid-based oncology assay, the cobas EGFR mutation test.

Illumina has granted Roche Sequencing rights to develop and distribute IVD assays on Illumina’s NextSeq™ 550Dx System, as well as on its future portfolio of diagnostic sequencing systems. Those include NovaSeqDx, a planned new regulatory-cleared version of the high-throughput NovaSeq system that will be designed to address growing demand for a diagnostics platform to support deeper sequencing. NovaSeqDx, is expected to be commercially available in 2022.

Roche, in turn, has agreed to develop, manufacture, and commercialize AVENIO IVD tests for both tissue and blood for use on Illumina’s NextSeq 550Dx. Illumina will continue selling the NextSeq 550Dx and core sequencing consumables. The collaboration will include both tissue-based and liquid-based assays.

“Bigger than our businesses”

“The goal of this partnership is really to improve access to patients. It is bigger than either of our businesses,” Kevin Keegan, senior director, Clinical Oncology Marketing at Illumina, told GEN Edge. “We’re looking to change the mortality curve in cancer by bringing this technology closer to the patient, and distributable IVDs are really the way to do that out into the community setting.”

Keegan noted that Illumina over recent months has launched or expanded IVD agreements with therapy selection CDx developer Qiagen and three developers of cancer monitoring tests, Adaptive Biotechnologies, ArcherDx, and Lexent Bio. The agreements give the companies non-exclusive rights to develop and commercialize diagnostic kits for use on Illumina sequencing systems.

“We feel like the combination of these partnerships enables us to cover two important segments of testing, for therapy assignment for newly-diagnosed patients and for therapeutic monitoring of patients who are in treatment,” Keegan said. “All of the assays in the pipeline now from those four companies in addition to Roche will be bringing IVD assays on to the NextSeq platform over the course of the next several years.”

Illumina is not now actively developing tests designed to screen for at-risk patients, though other companies such as GRAIL, are developing such tests for use on Illumina’s tech platform.

“The monitoring space is certainly one that we would look to develop assays in collaboration with Illumina for this partnership, taking them through to IVD, as well as the first-time diagnosis and therapy decision-making,” Gunn said.

Expanding on claims

Roche Pharma has also agreed to collaborate with Illumina on developing tests and expanding on the CDx claims on Illumina’s comprehensive pan-cancer assay TruSight Oncology 500 (TSO 500) for both existing and pipeline oncology-targeted therapies on NextSeq 550Dx.

TSO 500 is designed to identify known and emerging tumor biomarkers, using both DNA and RNA from tumor samples to identify key somatic variants underlying tumor progression, such as small DNA variants, fusions and splice variants.

As the anchor of Illumina’s oncology product portfolio, TSO 500 is designed to enable labs to adopt a comprehensive genomic profiling panel, in a decentralized testing model, leveraging accurate and reproducible results of Illumina’s diagnostic sequencing systems. When used to test for CDx claims, TSO 500 is designed to identify cancer patients globally who might benefit from targeted therapeutics.

Illumina will continue to manufacture, supply and commercialize TSO 500, and has agreed to lead the development and regulatory approval process. Roche will support future regulatory filings by the companies, in addition to the development of the claims.

“Our feeling is that it’s going to take multiple parties to drive the market forward. We think Foundation Medicine has done a tremendous job to build momentum in the market for comprehensive testing,” Keegan said. He said the launch of TSO500 and the work with Roche on expanding the companion diagnostic claims of TSO500 “will also help to push that market forward in the same way that the FoundationOne CDx test will.”

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