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Illumina 'Optimistic' About Speedy FDA Clearance of MiSeq; Pitches Companion Dx Program to Pharmas

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After being inspected by the US Food and Drug Administration two weeks ago, Illumina hopes its MiSeq sequencer will be cleared by the agency within the next several months, according to a company official.

While Illumina is waiting for the FDA's decision, it has applied the CE mark for expanded uses of the MiSeqDx in Europe, where it launched a CE-marked MiSeqDx with two cystic fibrosis assays this past summer (CSN 7/3/2013).

Marking its transition from a pure research tools company to one with a growing diagnostics branch, the company has also begun to market its services for companion diagnostics development to potential pharma partners.

Late last year, Illumina submitted a diagnostic version of its MiSeq platform, called MiSeqDx, as well as two cystic fibrosis assays to the FDA for 510(k) clearance (CSN 1/9/2013).

The submission has three components: the MiSeq in conjunction with a cystic fibrosis genotyping test, where most of the sequence except for the variants of interest is masked; the MiSeq with a cystic fibrosis diagnostic assay, where the entire gene is analyzed; and an "open" MiSeq platform with chemistry and software but no assay, which will allow customers to develop their own IVD assays more easily.

According to Nitin Udar, who leads Illumina's diagnostic assay program, the company was inspected by the FDA the week before last and is now awaiting clearance from the agency, which he said concluded its inspection "with no observations."

"I cannot speak for the FDA, but we are very optimistic that it is going to happen very soon – hopefully this quarter, or next quarter," said Udar, who spoke at Hanson Wade's NGS for Cancer Drug Development conference in Boston last week.

As the first company to submit a next-generation sequencing platform to the FDA, Illumina has been collaborating closely with the agency, he said, educating it about the technology and conducting several pre-IVD meetings.

In Europe, Illumina appears to be one step ahead already. After CE-marking the MiSeqDx for use with the cystic fibrosis tests this past summer, the company said last week that is has "declared conformity with the requirement of the [EU] IVD directive and has applied the CE mark to expand the use of the MiSeqDx system in clinical laboratories."

Clinical labs in Europe can now develop their own diagnostic tests on a CE-marked MiSeqDx, using the MiSeqDx Universal Kit, which includes reagents for library prep, index primers, and sequencing consumables to develop amplicon assays. Illumina said the new kit will start shipping in November in several European countries that require the CE mark.

At last week's conference, which was attended by several dozen scientists, many from pharmaceutical companies, Udar also touted a partnership program for companion diagnostics development that Illumina is now offering.

Under a partnership with a pharmaceutical company, Illumina would design and develop the assay and manufacture its components, following a strict product development process where every step is documented, he said. For running the assay as part of a clinical trial, the firm would partner with a clinical research organization, since its own CLIA labs currently do not offer this as a service. "Both Illumina, the CRO, and the pharma partner would have a steering committee that overlooks this entire operation," he said.

Once clinical utility for the assay has been established and its targets have been locked down, "then Illumina will develop an IVD assay and submit that to the FDA on its own," he said, in parallel with the drug submission by the pharma partner.

Utar said Illumina would make a strong clinical partner because it has access to and continues to improve new technology and software; has a "strong assay development team;" has two CLIA laboratories and a network of CLIA partners; offers a global presence and distribution channels; and now has experience with regulatory agencies and in developing IVD assays.

Next-gen sequencing would be suitable for developing companion diagnostics, he said, which require researchers to look at large targets at first, but then to lock down the assay to only a few variants that have an association with a drug. "You can do that easily [with an NGS panel] – there are several different ways you can mask the results," he said. It could be either achieved by analyzing only the data of interest and masking the remaining sequence, or by analyzing the entire sequence and only reporting the variants of interest. An alternative, he said, would be to re-design the assay.

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