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Pathway Genomics Launches Hereditary Colon Cancer Test; More Tests to Come on Multiple NGS Platforms

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Pathway Genomics plans to launch a number of genetic tests in several disease areas this year that will run on different next-generation sequencing platforms.

Last month, the San Diego-based company launched its first NGS-based test, called Hereditary Colorectal Cancer DNA Insight, that assesses a patient's risk for developing diseases such as Lynch syndrome, familial adenomatous polyposis, Li-Fraumeni syndrome, juvenile polyposis, MUTYH-associated polyposis, Peutz-Jeghers syndrome, hereditary diffuse gastric cancer, and PTEN-hamartoma tumor syndrome.

The test, which analyzes DNA from a saliva sample, looks for mutations in a panel of 16 genes – MLH1, MSH2, MSH6, PMS2, EPCAM, APC, BLM, BMPR1A, CDH1, CHEK2, MDM2, MUTYH, PTEN, SMAD4, STK11, and TP53. According to the firm's website, it will not only identify known mutations but will also analyze and interpret "additional genetic changes that are clinically significant." The company also offers patients whom the test reveals carry variants of unknown significance and their families an opportunity to enroll in a "familial studies program" to further investigate those variants.

The test, which has a turnaround time of 14 to 21 days, was originally developed on the Ion Torrent PGM but now runs on either the PGM or the Ion Proton, depending on the firm's sample workload, Ardy Arianpour, Pathway's chief strategy officer, told Clinical Sequencing News.

It will likely compete with tests offered by other molecular diagnostic labs, for example Myriad's Colaris and Colaris AP tests, which analyze disease-causing mutations in a total of eight genes associated with hereditary colorectal and uterine cancer and have turnaround times of up to 21 days, or Ambry Genetics' ColoNext, which analyzes 14 genes associated with hereditary colon cancer and has a turnaround time of eight to 12 weeks.

Arianpour said that Pathway decided to develop the colorectal cancer test first because there was demand for it from its clients, the test seemed "the fastest way to get into the cancer market," and because no intellectual property was associated with it.

Last June, after the US Supreme Court struck down patents around the BRCA1 and BRCA2 genes owned by Myriad, Pathway said it would launch a Hereditary Cancer DNA Insight test in August that would test about 30 genes, including the BRCA genes, but it has not begun offering that test, and Arianpour provided no update on its launch. Myriad has sued several labs that have started offering tests that include the BRCA genes.

In the meantime, Pathway said this month that it acquired two new sequencing platforms from Illumina – the MiSeqDx, the first FDA-cleared NGS sequencing system, and the recently-launched NextSeq 500 – which will both run in its CLIA-certified and CAP-accredited laboratory. In addition, the firm already has the research-only MiSeq as well as an ABI 3730 Sanger sequencer installed.

Illumina sells two in vitro diagnostic cystic fibrosis tests for the MiSeqDx – a 139-variant assay and a clinical sequencing assay – which will be among the first that Pathway plans to offer on the platform this year.

In addition, Pathway plans to launch other tests for the MiSeqDx that are currently in development at Illumina, ranging from single-gene tests to comprehensive panels. "Whatever Illumina will have ready [for the MiSeqDx], we will be offering in 2014," Arianpour said, without providing specifics.

Being able to launch ready-made assays from Illumina helps Pathway cut down the time for internal assay development by 70 percent, he said. "You can just jump right into this with off-the-shelf products that are already approved on this instrument."

But Pathway also plans to develop its own IVD tests on the MiSeqDx in several disease areas, using Illumina's FDA-cleared MiSeqDx Universal Kit, though no specific information is available on these yet.

The company also plans to develop certain tests on the NextSeq 500. "Our primary objective is to provide physicians and their patients with accurate laboratory results in a timely manner, and the NextSeq 500 is a key factor in taking us to a new level in meeting that goal," David Becker, Pathways' CSO, said in a statement.

"Every instrument has its blind spots [and] we want to become the next-gen sequencing experts on all the platforms, so that we can utilize the right instrumentation with the right disease states," Arianpour said. "Depending on volumes and demand for the test … we will choose the sequencer that best fits our clinical reporting." The company plans to launch a variety of new genetic tests, both for single genes and gene panels, on its NGS platforms, he said.

Pathway wants to set itself apart from competitors by its clinical reporting, he said, which it has "heavily invested in" for several years. Its reports are designed to be easy to understand by both patients and physicians, even those without much training in genetics, he added.

Several other genetic tests that Pathway has been offering, which use array-based genotyping rather than next-gen sequencing, focus on disease prevention in generally healthy individuals, though they are all offered through physicians. The firm's Carrier Status DNA Insight test, for example, screens for mutations associated with more than 70 recessive genetic diseases.

The company also offers genetic tests that predict response to certain medications, and others that link genetic variants to certain traits and risks for common diseases.

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