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Illumina Growing Clinical and Dx Business with Submission of MiSeqDx, Two CF Assays to FDA

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This article was originally published Jan. 8.

SAN FRANCISCO — Illumina has submitted its MiSeqDx system and two cystic fibrosis assays to the US Food and Drug Administration for 510(k) clearance, company officials said this week during a presentation at the JP Morgan Healthcare conference in San Francisco.

The company said last November that it planned to submit the system and assay to the FDA (CSN 11/1/2012).

The FDA submissions are just one part of a larger strategy by Illumina to grow its clinical and diagnostic business. The company yesterday announced it had acquired Verinata Health for up to $450 million in order to tap into the growing noninvasive prenatal testing market, building on its acquisition last year of cytogenomic array firm BlueGnome (see story, this issue). This week, the company also outlined future directions for moving into the nascent but rapidly growing clinical sequencing space.

CEO Jay Flatley said that the company submitted the MiSeqDx system, a version of its MiSeq sequencer, as a platform-only submission, and also separately submitted a cystic fibrosis diagnostics assay and a carrier screening version of the CF assay, which both run on the MiSeqDx system.

For the platform-only submission, Flatley said that the company had to submit a list of specific claims around the sequencer, for instance, detailing sensitivity and specificity depending on the type of genomic content being analyzed. As an example, claims could cover its performance in regions with homopolymers and varying amounts of GC content.

Platform-only clearance would enable customers to develop their own diagnostic products for the sequencer as long as the assays fall within the cleared claims of the platform.

"This is a first submission like that," said Greg Heath, senior vice president and general manager of Illumina's Diagnostic unit, during a question and answer session following the company presentation.

"We started with a list of analytical claims [for the MiSeqDx] and over time as we gather more data, we can expand that," CEO Jay Flatley added.

The MiSeqDx system will differ from the research version of the MiSeq. The system will be manufactured differently and the company will take on a higher burden to ensure each system abides by the specified claims, Flatley said. As such, it will be sold at a higher price that has not yet been disclosed.

Additionally, the system will be "locked down," while the research-use-only MiSeq will continue to evolve over time. Flatley said that the MiSeqDx will periodically be upgraded and resubmitted to the FDA, but not as frequently as improvements are made to the MiSeq.

Aside from the system, Illumina also submitted two versions of its cystic fibrosis assay: one for diagnostic purposes and one as a carrier screen.

Flatley said that the company's CF diagnostic has an advantage over other CF tests because it sequences through the entire cystic fibrosis transmembrane conductance regulator (CFTR) gene.

Additionally, he said the company is working on other products around reproductive health, including a "more advanced carrier screening product."

In the future he sees a market for products addressing fertility, with the largest segment of the reproductive health market in newborn screening.

Flatley said that these recent submissions to the FDA were a good first step and that the company has been having "high-level discussions" with FDA officials indicating that the agency is "hungry to try and get their heads around next-generation sequencing." The FDA is "fully cognizant that this market is moving fast and that sequencing is going to be applied clinically," Flatley said.

Illumina is also reaching the clinical market via its targeted TruSight panels, which it launched last fall under its Translational and Consumer Genomics business unit (CSN 9/12/2012).

The TruSight panels are designed to be run on the MiSeq system and are sold as research-use-only products that customers can then adopt and build proprietary content around to validate for clinical use. Flatley said that already, four large reference laboratories have adopted the TruSight inherited cancer panel.

Flatley said that based on discussions with clinical customers, the company has determined that one of the key challenges around clinical sequencing has been analysis and interpretation. Last fall, the company said it was collaborating with Partners HealthCare to provide its GeneInsight Suite, which is already CLIA and HIPPA compliant and registered with the FDA, for interpretation.

This week, the company said that aside from Illumina and Partners HealthCare, other members of the network would include ARUP Laboratories, Mount Sinai Genetic Testing Laboratory, and the New York Genome Center.

These founding members will all share data and resources to improve variant annotations and genomic interpretations. Additionally, the sites will serve as initial pilots for a combined offering of the MiSeqand the GeneInsight Suite.

Looking ahead, Flatley predicted that the clinical sequencing market over the next five years will continue to be a "mix" of targeted sequencing panels, exome sequencing, and whole-genome sequencing, but that ultimately it is on an "inevitable track toward whole-genome sequencing."

Nevertheless, "sometimes people don't want extra information, even if they can get it for free," he said, either because of the interpretation or because of the added complexities of explaining variants of unknown significance.

Reimbursement will also be key toward adoption of clinical sequencing, he said, and he projected that reimbursement would be "application specific."

For instance, while there's "not a lot of progress yet on the general idea of getting sequenced and reimbursed," there has been "tremendous progress" in cases like noninvasive prenatal testing, and over the next year, reimbursement in that area should pick up even more dramatically due to the clinical and economic benefits of those tests. While Illumina has a had a few cases of being reimbursed for whole-genome sequencing, Flatley said that those were surprises and not the norm.

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