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Greenville Health System, Roswell Park Adopt Targeted Sequencing in Cancer Treatment

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The ranks of health centers utilizing next-gen sequencing in the care and treatment of cancer patients continue to swell with the recent adoption by two groups — Greenville Health System in South Carolina and the Roswell Park Cancer Institute in New York — of new targeted sequencing services for cancer patients.

GHS announced last week that it has partnered with Selah Genomics to create a new Clinical Genomics Center at its Institute for Translational Oncology Research. Out of the new center, Selah and GHS will be offering a test called PrecisionPath, using Ion Torrent's AmpliSeq panel on the PGM.

According to GHS, Selah is performing the sequencing for PrecisionPath onsite at the new center, while clinicians from ITOR are organizing the return of actionable results to ordering oncologists. The group is working to keep the test turnaround time under two weeks, and if possible, to get it down to one week from when samples come in to when results are reported, at least to physicians within GHS.

We are planning on offering this to all of our patients [as] a reflex … as part of a clinically annotated biorepository," Joe Stephenson, the medical director of ITOR, told Clinical Sequencing News.

"I think that our prevailing philosophy is that it's becoming less relevant what the site of origin of disease is and much more relevant what the molecular drivers are," he explained. "Clearly, we will still be following standard of care pathways for treatment of these patients, but that will go along with this molecular profiling, which will become part of the overall clinical summation of material used to make [treatment] decisions."

Michael Bolick, CEO of Selah Genomics, said the company recognizes that offering this testing in all cancer patients is still somewhat of a pilot initiative.

"We recognize that [payors] like [the Centers for Medicare and Medicaid Services] for example, at present would only reimburse against metastatic melanoma, colon, and lung cancer, so maybe I would describe it as a piloting program to initiate PrecisionPath across the board."

Roswell Park announced earlier this year that it had purchased six Ion Torrent sequencers — four Ion Protons and two PGMs — to integrate into its new Center for Personalized Medicine. The institute is now offering targeted sequencing for patients with lung cancer, colon cancer, and melanoma, using both the PGM with an adapted AmpliSeq panel and the Illumina MiSeq, Jeffrey Conroy, the institute's director of genomics consortium technologies, told CSN this week.

The dual sequencing instruments are used to provide appropriate validation of results, Conroy said.

"In New York State we have to validate mutations before we can report them with an independent methodology, so we are running concurrent NGS platforms to validate each other. It's in some ways a response to try to get a very quick turnaround time from when a sample comes in to when we have validated variants called," because if only one platform was used initially, followed by validation, testing would take significantly longer, he explained.

Selah's Bolick said that though the company is using the PGM for PrecisionPath at GHS, it is platform agnostic overall.

"We bring tools to the table as the project calls for it," he said. "But the PGM has been very robust and we think this is an outstanding platform for this type of clinical application."

GHS announced last week that its new center has already tested six patients with six types of cancer— non-small cell lung cancer, breast cancer, colon cancer, ovarian cancer, pancreatic cancer, and melanoma.

According to Jeremy Stuart, Selah's vice president of genomic services, the test results are being delivered in two formats. One, he said, is through the patient record, where the group will report actionable and reimbursable results — "targets like KRAS or BRAF, or other mutations that are part of the standard of care."

For results that are not considered actionable, he said, "to use more for research purposes or for steering patients toward a clinical trial, those will be in a separate database that physicians can access, but will not be part of the patient record."

Conroy said that Roswell Park's team is working on developing a sequencing report that will be integrated into patients' electronic medical records.

According to ITOR's Stephenson, the PrecisionPath panel could likely evolve over time, as new, or different, genes become more relevant in cancer treatment decision making.

Bolick said Selah is also anticipating how it may shift its methodology as costs for whole-exome and whole-genome sequencing continue to fall.

"Right now, we are drilling down to the things that can be impactful from a clinical perspective, but as quick as these tools come out, and as the bioinformatics allow us to take advantage of additional data, we plan to ride the [cost] curve into the future," he said.

"We have in place the ability to do [whole-genome sequencing], in terms of the consenting process and our biorepository," Stephenson added. "But even [then] … there will always be a smaller, more focused panel of what is actionable – so that's where we are starting."

According to Conroy, Roswell Park would also consider moving to broader sequencing methods "if it gets to the point where it is cost effective and data can be managed and reported in a way that makes sense." But, he said, "up to this point, we think a subset of genes [is] the best way to go initially."

Both centers have yet to establish a running cost for their targeted sequencing offerings, and both said settling a price point is complicated by establishing how many samples can be multiplexed together.

According to Bolick, the Selah team — in addition to developing PrecisionPath at GHS — is also negotiating potential partnerships with pharmaceutical companies to develop additional assays using the PGM for clinical trial recruitment and support.

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