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Life Tech Updates Multifaceted Clinical Strategy for Ion Torrent

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NEW YORK (GenomeWeb) – Thermo Fisher Scientific's Life Technologies plans to position its Ion Torrent products solely within the clinical market by executing licensing deals, developing its own oncology products, partnering with pharmaceutical companies, and tapping into the various clinical specialties within Thermo Fisher's diagnostics business units, Clinical Sequencing News has learned.

Earlier this month, molecular diagnostics firm VelaDx said it planned to launch clinical next-generation sequencing workflows on the Ion Torrent PGM platform that would include CE-IVD marked oncology and virology assays.

Last week, Ronnie Andrews, president of Thermo Fisher Scientific's Genetic, Medical and Applied Sciences division, told CSN that this type of licensing agreement is one part of Life Tech's clinical strategy.

"We basically have pivoted Ion completely towards the clinic, with small work still going on for the $1,000 genome," he said. "The business is in the clinic."

Andrews said that the firm is going after the clinical sequencing market on four different fronts. First, he said, it continues to work toward bringing its own products, including the PGM, through US Food and Drug Administration clearance. The company is also looking to partner with pharmaceutical companies that want to use sequencing for companion diagnostics in oncology. Also on the oncology front, Life Tech will develop its own products, including a universal CDx. For other disease areas, it is looking to partner within Thermo Fisher's diagnostics division as well as to license the rights to outside diagnostic companies to develop tests on the PGM.

The company plans to register the PGM with the FDA, as opposed to going through the 510(k) clearance process, since it will have the same intended use as Illumina's FDA-cleared MiSeqDx system. Life Tech will market that version as Ion PGM Dx and it will include the company's AmpliSeq chemistry for library prep, template kits using 200-base-pair chemistry, sample prep on the Ion One Touch 2 system, and the 318 chip. Andrews said he expects the Ion PGM Dx system to be available this fall.

Life Tech will also register the system as CE-IVD marked in Europe and will launch two CE-IVD marked oncology assays — for lung cancer and colon cancer — in the fourth quarter of this year, Andrews said. The company has been validating the assays in collaboration with around 20 pathology laboratories that are part of its OncoNetwork in Europe.

Further down the line, Andrews said that the company is looking to develop a clinical sequencing instrument that would be able to run both the chips that now run on the Ion Proton as well as the lower throughput PGM chips. Eventually, he said that the company would stop using the "P1, P2" designations and instead have an "exome chip," an "Oncomine chip," a "transcriptome chip," and so on, and those would all run on the same platform that would combine the economics of the Proton with the accuracy of the PGM's 318 chip. He declined to disclose a development timeline or provide further details on how such a system would differ from the existing PGM and Proton.

Life Tech is also aiming to work with pharmaceutical companies to develop a universal companion diagnostic test for cancer drugs. The firm's 2012 acquisition of cancer bioinformatics firm Compendia gave it access to a cloud-based tool called Oncomine which, among other things, can integrate cancer data from next-generation sequencing to correlate mutational profiles with drug response and clinical outcomes.

The company then tapped into that data to develop its Oncomine cancer panel that targets 160 cancer genes. The panel includes "all the actionable targets that exist for [drugs] that are on the market today, but also over 500 compounds in Phase II and III trials," Andrews said. Leveraging Compendia's database, the company was able to "reverse engineer the pipelines of all the major pharmaceutical companies," he added. Life Tech's Oncomine panel will also be used in the National Cancer Institute's MATCH trial, and as such, the company has been working with Mickey Williams at the National Cancer Institute and Stan Hamilton at MD Anderson to further develop and validate the panel, Andrews said.

Andrews said that as part of the MATCH trial, the company will be able to take its Oncomine panel through FDA clearance as a companion diagnostic test. "MATCH is an umbrella trial, but under each arm we'll gain enough statistical power to power a submission [of the panel as a CDx] around the various drugs," he said. "Our strategy is to work closely with pharma to play this out."

Illumina, too, hopes to develop a universal companion diagnostic test for oncology drugs. At the American Association for Cancer Research meeting in April, Illumina's Chief Medical Officer Richard Klausner said that the company has been in discussions with the FDA about developing a universal oncology CDx.

Life Tech is also looking to develop relationships with molecular diagnostic companies similar to its VelaDx partnership. Under the supply agreement with VelaDx, Life Tech manufactures and supplies the PGM for VelaDx, which in turn is responsible for bringing clinical assays through regulatory clearance. Andrews said the company is pursuing this strategy with other molecular diagnostic companies solely in fields outside of oncology.

For instance, last year it announced it would partner with Claritas Genomics to develop diagnostics for inherited diseases. Life Tech previously said that the first offering would be an inherited disease panel similar to the Ion AmpliSeq Inherited Disease Panel that is composed of 10,500 amplicons targeting 300 genes involved in more than 700 diseases.

As VelaDx's CEO Michael Tillman previously told CSN, Life Tech will manufacture the PGM, but it will be according to VelaDx's specifications. Andrews said that in essence this means that certain components of the system are "configurable" and can be optimized to suit different applications.

The PGM itself will not be custom-made for each diagnostic partner, but the chip, reagents, and software will each have slight differences, he explained. For instance, he said, the Oncomine assay will have slightly different requirements in terms of read length, accuracy, and depth of coverage than a virology assay, he said.

Partners will likely not have an exclusive license to develop specific types of assays, Andrews said.

In addition, he said that Life Tech would tap into expertise within Thermo Fisher's $3 billion diagnostic division, which specializes in key niche areas like immunology, microbiology, and anatomic pathology.

With regards to Life Tech's Claritas Genomics partnership, Andrews said that the company has shifted its focus from trying to develop a pan-inherited disease panel that would applicable across all ethnicities to more targeted panels "because of the complexity of ethnicity in mixed populations like the US and Europe."

Instead, it will focus on panels in specific disease areas like a neurodegenerative disease panel, or a childhood neurome panel, Andrews said. Claritas will launch these panels as laboratory-developed tests, and depending on the requirements, Life Tech may or may not bring them through FDA clearance.

Particularly for panels that look at rare disorders, it is challenging to accrue enough samples to statistically power a trial, Andrews said.

One area that Life Tech is not looking to develop products in is the noninvasive prenatal testing market. Andrews said that while it is working with the current NIPT companies, it does not plan to develop its own test in that market. He said that the company looked closely at the market and decided that it did not have the resources to enter both the onoclogy and NIPT markets, adding that he anticipated the market for next-gen sequencing in oncology to be $3 billion by 2018.

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