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Fox Chase Debuts CancerCode-45 Test Based on Adapted Ion Torrent AmpliSeq Panel

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The Fox Chase Cancer Center has begun offering targeted sequencing to inform cancer treatment using an adaptation of Life Technologies' Ion Torrent AmpliSeq Cancer Panel via its CLIA-certified laboratory.

The center is calling the service CancerCode-45, after the 45 genes that the test interrogates, Jeff Boyd, executive director of Fox Chase's Cancer Genome Institute, told Clinical Sequencing News this week.

The full AmpliSeq panel covers 190 amplicons in 46 cancer genes that are either commonly somatically mutated or known to be responsible for inherited forms of cancer.

After initially planning to offer whole-exome and transcriptome sequencing on the SOLiD platform, the FCCC decided in late 2011 to switch to using the AmpliSeq panel on its Ion Torrent PGMs (CSN 12/21/2011).

In choosing to go with a more targeted approach, Fox Chase hoped to be able to offer a test focusing more narrowly on the most clinically actionable genes, and which could be offered with a shorter turnaround time and at lower cost.

According to Boyd, the center spent a year putting its own spin on the AmpliSeq panel, using the Ion Torrent 318 chip.

"It's the chip with the greatest real estate that they make currently," Boyd said. "So we use it to look at two patients. We put tumor DNA for each patient in replicate and blood DNA for each patient in replicate, then we have a number of controls built in for sensitivity, specificity, and accuracy."

"We are not just putting tumor DNA from as many people as we can in an attempt to get higher throughput," he explained. "I'm not aware of others in the CLIA setting using the chip the way we are in terms of replicate samples and control samples and blood samples — hence the trademark."

Boyd also said that while validating and optimizing the approach to using the panel over the last year, the FCCC team also decided to remove one gene, JAK2, from its analysis because it didn't perform reliably.

According to Boyd, the center obtained CLIA certification for the test and its platform in October of last year.

"We had to work through a number of limitations of the test out of the box," he said, "And we worked closely with Ion Torrent to modify the test over the period of about a year and shared the data we generated for our CLIA validation with them. I think it's fair to say it was a mutually beneficial collaboration."

The FCCC has announced that CancerCode-45 will have a turnaround time of about 20 working days to a reported result. Boyd said the center is charging $3,000 for the service and that it is taking "all comers" with solid tumors.

"What we are seeing every day in the scientific literature is that some of these commonly mutated genes in one cancer are found more rarely in other solid tumors as well," he said. "So instead of ordering BRAF in melanoma and EGFR in lung cancer, we now have the ability to look at these genes potentially in any cancer patient."

Boyd said the test service "opened for business" right around the holidays, and the center is currently working through its first handful of samples.

Looking forward, Boyd said it's not clear yet what the group's testing volume might look like. Overall, he said the team hopes that they will be testing hundreds, if not thousands of patients a year, whether with the present iteration of the service, or a future version.

Currently the test is not reimbursed by insurance companies, but the FCCC is "working diligently with [payors] to try to get there as soon as we can," he said.

Boyd said the center is currently running the service on two PGMs. "We'll see how that goes, and based on volume I think its fair to say once we get comfortable with various tumor types in the clinical setting [that] we can perhaps begin to eliminate some control samples on the chip and put four patients on a chip instead of two."

"Then of course there's the whole issue of what's next," he added. "AmpliSeq has a limited lifespan as does some of the hardware that supports it … So we are already thinking in terms of version two."

According to Boyd, that version could involve anything from custom panels to whole exomes and transcriptomes using Ion Torrent's upcoming Ion Proton instrument.

Boyd said the team is working with Ion Torrent on potential updates to the AmpliSeq panel.

"We are also thinking about adding additional platforms to look at things like copy number variations that AmpliSeq doesn't do," he said, "and weighing that against reverting back to the original strategy of whole exomes and transcriptomes."

"Now that the technology has changed dramatically over the past few years, and the price point has dropped dramatically, we think it's likely that within two years we're looking at using the [Proton] to do whole-exome, whole-transcriptome sequencing for the same cost we have now on a 45-gene panel."

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