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Mayo Clinic Hoping to Sequence Cancer Patients More Routinely by Offering CLIA Hotspot Panel


NEW YORK (GenomeWeb) — The Mayo Clinic has launched a targeted-sequencing panel test, called CANCP, through its Department of Laboratory Medicine and Pathology's CLIA lab to guide targeted treatment for patients with solid tumors.

The test, which analyzes hotspot regions of 50 genes associated with sensitivity to a variety of genomically targeted cancer therapies, will be available to all patients at the clinic with solid tumors, as well as outside patients and physicians through the Mayo Medical Laboratories.

In some tumor subsets the panel may be performed routinely for all Mayo patients, Benjamin Kipp, the new test's lead designer, and Rob McWilliams, chair of the Genomic Tumor Board for Mayo's IM Clinic told PGx Reporter. Physician groups focused on treating specific tumor types at the clinic are in the process of deciding on guidelines and algorithms that will establish what subset of patients should be routinely profiled and under what conditions.

"[This] is really meant to bring genomics out into the larger practice, and have it be more part of the every-day version of care instead of [just for] a subset on the cutting edge," McWilliams said.

One area where all or nearly all patients might receive the panel is colorectal cancer, Kipp added, whereas in other tumor types, like lung cancer, single-gene tests may still be standard as a first-line option. For example, EGFR and ALK testing is still currently being performed with single-gene, US Food and Drug Administration-approved assays, Kipp noted. "For some [patients] we may expand beyond that if they are negative, but we at least start with those," he explained.

For those patients whom physicians believe might benefit from the larger panel, the new test will offer a more comprehensive profiling of potentially actionable cancer mutations than the lab can currently provide using single-gene tests.

"Colorectal cancer is a good example," Kipp said. "Most of the recent data suggests we should expand and test NRAS and BRAF, and other RAS [mutations] … It's known in the literature, for example, that 10 to 20 percent of patients receiving cetuximab likely have a mutation in one of those genes and won't respond."

"Other data even suggest that not only do [these patients] not respond but they actually do worse than if they didn’t get the drug at all," he added. "So, with evidence like this coming out, [doctors] are asking for larger panels both from our internal and external practice."

The new test relies on a hotspot sequencing panel from Ion Torrent, the AmpliSeq V2, which enables sequencing of regions of 50 genes that are associated with various solid tumors and with sensitivity to a number of genomically targeted drugs.

Though Mayo has already been analyzing similar panels of genes in cancer patients through it's Individualized Medicine Clinic to guide therapeutic decision making, as well as doing other clinical sequencing research under the umbrella of its Center for Individualized Medicine, the launch of this panel through the CLIA NGS lab will make such sequencing a more routine option for both internal and external physicians, McWilliams said.

"We really envision this panel as a preliminary rapid high-quality screen for the low-hanging fruit — the [mutations] we know what to do with," he said. "Then, if someone goes through this and there's not an answer, or their doctor is looking deeper," then they might be referred for further exploratory analyses through the individualized medicine clinic, he explained.

Mayo's IM Clinic currently treats a subset of patients with advanced disease and/or rare cancers recruited on a case-by-case basis. Those who could potentially receive the new 50-gene panel through the clinic's CLIA lab make up a much larger group, including newly diagnosed patients in some tumor subtypes.

Whether the panel will be used to guide first-line treatment or to choose drugs later in the treatment process would depend on the individual patient, according to McWilliams and Kipp.

"It really depends on what type of cancer we are looking at," McWilliams said. In some cancers an EGFR mutation may affect first-line therapy and our reports to physicians would be fairly clear as to what agents may be of benefit."

"Or in colorectal cancer, the presence of a KRAS mutation … that might affect first-line therapy as well," he added.

For other patients, some of whom may already have failed first-line therapy, the panel may also indicate more experimental therapies or clinical trials to which they could be matched.

McWilliams and Kipp said that through the life of the IM clinic, they have been able to collect some limited data on how using genomic testing to guide care may benefit patients over more common therapeutic strategies. Hopefully their experiences offering the 50-gene hotspot panel more broadly will also add to this knowledge.

"With the IM clinic, we have been recording clinical utility data. But it's hard to do much beyond some simple outcomes; in other words, did [testing] affect therapy and were the right drugs able to be identified? But we will be recording this with this panel too, and have talked with some trainees about doing follow up to see how this affects outcomes," McWilliams said.

"There are already established outcomes data, for instance in colorectal cancer, about the impact of BRAF and KRAS mutations. That's already known. This new panel is just making us able to do this more comprehensively and look at all the potential mutations in the genes in a more systematic way," Kipp explained. "Where it would really be beneficial to study more outcomes is with patients who have exhausted standard therapy and we are looking to direct them to Phase I trials and looking for differences in outcomes there."

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