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Offering AmpliSeq V2 Panel through CLIA Lab, Mayo Pushes More Routine Cancer Sequencing


NEW YORK (GenomeWeb) — The Mayo Clinic last week announced that it will offer a test based on Ion Torrent's AmpliSeq V2 cancer hotspot panel through its CLIA-certified Next-Generation Sequencing Lab, a move that the clinic expects will routinize use of the 50-gene panel in the care of patients with a variety of solid tumors.

The AmpliSeq panel test, called CANCP, joins just one other NGS test, a 17-gene hereditary colon cancer assay, offered through the CLIA lab to Mayo physicians and to providers worldwide through the clinic's Mayo Medical Laboratories.

Although Mayo Clinic has been performing panel-based clinical sequencing on cancer patients previously through its Individualized Medicine Clinic, offering the AmpliSeq hotspot panel now directly through the clinic's CLIA lab is intended to push such testing out of the experimental realm and into the standard of care.

Benjamin Kipp, the new test's lead designer, and Rob McWilliams, chair of the Genomic Tumor Board for Mayo's IM Clinic, told Clinical Sequencing News that hotspot sequencing was much more on the cutting edge when the IM clinic first opened. Now that leading edge has moved more toward exomes, transcriptome sequencing, and other broad pathway analyses leaving hotspot sequencing a prime candidate for more routine clinical use.

"It's been an evolution," McWilliams said. "A year and a half ago, [our] IM Clinic was really one of the first places people were getting panel testing. Now we are trying to bring panel testing into the larger clinic as part of routine oncology care."

"For the IM Clinic to still be the cutting edge, it's going to be doing deeper looks at the exome and transcriptome and exploring other omics testing … while this panel is more about navigating a patient within the standard of care and picking off the small percentage of patients with a particular druggable mutation by comprehensively screening [them]," he said.

Many centers have adopted the AmpliSeq panel, either in the context of clinical sequencing research programs, or as a commercially available laboratory test.

According to Kipp and McWilliams, the Mayo lab adopted AmpliSeq over other targeted cancer sequencing panels because the group appreciated its efficiency. "We like this panel because we can use less DNA than you can with some of the other panels and a lot of the specimens we receive are small biopsies, metastatic blocks, those types of things, so that's an advantage for us," Kipp said.

He added that Mayo is performing the panel a little differently than many others, sequencing simultaneously using both the Ion Torrent and Illumina's MiSeq.

"We actually run an orthogonal NGS assay. We take the [AmpliSeq] V2 cancer primers, get a PCR product, and then we run that product both on the MiSeq and the Ion Torrent so we have orthogonal confirmation," he said. "That decreases turnaround time and assures us that we have high accuracy as well."

In its reports back to physicians, the lab lists any alterations detected after they have been appropriately vetted. "Some of the more basic alterations can be signed out without the need of [significant expert review], but if there are more questionable findings, we get the whole team together to discuss," Kipp said.

The test report also includes interpretation of the therapeutic implications of any discovered actionable mutations.

According to Kipp and McWilliams, Mayo's clinical NGS lab will not perform the panel for every single solid tumor patient, but it may run the test routinely for specific subgroups of solid tumors.

Decisions about who to sequence and how to decide whether to use the hotspot panel for each individual are being made by the clinic's 12 tumor-specific groups.

"Its an option for all patients, but not all the tumor groups have said that they want to do it for all of their patients," McWilliams said.

"For colorectal cancer, for example, that group is saying they want to do the 50-gene panel on everyone, but for other malignancies it may not be as broadly applicable," he explained.

Whether the panel will be used to guide first-line treatment or later in the treatment process will also depend on the patient.

"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 said.

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.

Though the team has validated the 50-gene test for use in the Mayo CLIA NGS lab, that does not mean they are wedded permanently to their current technology or strategy, Kipp said. Moving forward the lab intends to keep abreast of new technologies and would consider making changes in the future.

The Mayo clinic wasn't able to provide an estimate of how many patients have received the new panel yet, but said a "very conservative" turnaround time for the test is about 12 days.