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Illumina's Pharma Deals Aim to Bring Universal MiSeqDx-based CDx through FDA Clearance

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NEW YORK (GenomeWeb) – Illumina said this week that it is collaborating with pharmaceutical companies AstraZeneca, Janssen Biotech, and Sanofi to develop a next-generation sequencing-based panel to serve as a universal companion diagnostic.

The company told Clinical Sequencing News that it would leverage its US Food and Drug Administration-cleared MiSeqDx system to develop an oncology test kit that includes the NGS system, bioinformatics capabilities, and reagents necessary to target single nucleotide variants, indels, copy number variants, and gene fusions.

Earlier this year, Illumina struck a deal with Amgen to develop an NGS-based companion diagnostic test for its colorectal cancer drug Vectibix (panitumumab), which it also plans to bring through FDA approval. Illumina's Senior Product Manager of Oncology, Naomi O'Grady, told CSN that the recent pharma agreement will not impact the deal with Amgen. "The work we're doing with Amgen will be complementary to the claims we're trying to achieve on our system and with our technology to also support the work with our universal oncology test," she said.

Bringing the universal oncology panel through FDA clearance will not require substantial changes to the core sequencing technology, O'Grady said. Rather, the company aims to expand on MiSeqDx's indications for clinical use in oncology. The system received FDA clearance last year in conjunction with two cystic fibrosis assays as well as a universal assay. A key difference in using the MiSeqDx for oncology purposes is that it will need to be cleared for use on formalin-fixed paraffin-embedded tissue, O'Grady said. Currently, it is cleared only for targeted sequencing of DNA from whole blood. Its use also must be expanded to include the detection of somatic, rather than germline, variants.

In addition, O'Grady said that Illumina would be looking to develop targeted library prep methods and bioinformatics pipelines "tailored specifically for the variants requested by our pharma partners."

She declined to disclose how many genes would be included on the test, but noted that the pharmaceutical companies would drive its content. According to Illumina, there are an estimated 800 oncology drugs in development, many of which are designed to target specific mutations.

The test will be able to detect SNVs, indels, copy number changes, and gene fusions and will include not only a DNA component, but also an RNA component, O'Grady said. The DNA and RNA assays will not be separate tests, but rather "parallel reactions" that are part of a complete kit.

Initially, the test will be developed for the pharmaceutical companies Illumina is working with to enable their drug registration trials, O'Grady said. And, as the companies achieve regulatory approval for the drug/CDx combination, Illumina will market the test to molecular pathology labs in the areas where that drug would be marketed, she said.

In order to bring the test through FDA clearance, Illumina will be working closely with its team at Myraqa, a regulatory and quality consulting firm that it acquired last month.

Illumina also hopes to work with the FDA to implement a different process for bringing the multi-analyte test through approval. In the current companion diagnostic paradigm, "each diagnostic system is designed with the needs of a specific drug in mind," Mya Thomae, vice president of regulatory affairs at Illumina, told CSN. But because Illumina and its pharma partners are looking to develop one test for multiple biomarkers, "we'll be working with FDA to ideally find a pathway that allows us to take the system through just once and then provide follow-up submissions to update intended use statements or add new content as new markers are identified."

At the American Association for Cancer Research meeting in San Diego earlier this year, the FDA's Director of Personalized Medicine, Elizabeth Mansfield, said that the FDA is open to such multi-analyte tests, but that for such a test to pass regulatory muster, there must be standards.

Illumina plans to address the issue of standards for clinical sequencing with its actionable genome consortium, a collaborative effort between the firm, major cancer centers, and other leaders in the oncology field to develop clinical sequencing standards. O'Grady said that Illumina would talk about its progress in this area soon.

She noted that the pharmaceutical collaboration will "create the ability to standardize testing in a decentralized way," and as such, clinical standards like the ones that will be defined by the actionable genome consortium will be necessary.

"Having a single test that's available in the regions where pharma is looking to offer drugs, really enables a unified test platform with standardized performance," she added.

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