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UNM to Scale Cancer Sequencing from Panels on PGM to Exomes on Proton

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This story was originally published on Sept. 21.

The University of New Mexico Cancer Center has begun profiling patients' tumors using a targeted sequencing strategy on Life Technologies' Ion Torrent PGM and plans to offer exome sequencing on the recently launched Ion Proton system.

Jeremy Edwards, an associate professor of molecular genetics and microbiology and chemical engineering at the UNM Cancer Center, told Clinical Sequencing News that the center recently started using the Ion Ampliseq Cancer panel on patients and would begin offering exome sequencing on the Proton, potentially later this year.

So far, the center has only sequenced about a dozen patients with recurrent disease, Edwards said. The sequencing is currently not being done in a CLIA-certified setting, so any actionable results are validated with Sanger sequencing in a CLIA lab before being returned to the physician.

Edwards said the team plans to validate its targeted sequencing protocol on the PGM and move one of its four PGMs into the CLIA lab.

The Proton, which Edwards expects to receive in October, will initially be brought into the research laboratory, but the goal is to eventually acquire a second machine that will be validated for the CLIA lab.

Currently, the center is sequencing patients with late-stage recurrent disease using the AmpliSeq cancer panel. So far, most of the results have identified "bad news markers," Edwards said, rather than promising new therapies.

Edwards said that this is not too surprising since these are patients who have already failed at least one course of treatment.

"There's not a well-established standard of care for patients with recurrent disease," he said. So one of the goals is to identify a therapeutic option that has not been tried, but the "reality is that most of the time there is no drug candidate."

Additionally, Edwards said the researchers have begun sequencing archived formalin-fixed paraffin-embedded samples using the AmpliSeq Cancer panel to do retrospective studies in the hopes of identifying markers that point to therapeutic options or markers of drug resistance or response.

Proton Pilot

Edwards said that when the lab receives its Proton, the plan is to establish an exome sequencing pipeline for cancer patients. The team will initially do a pilot of about 100 patients and expand from there.

The team will focus on two types of cancer for the pilot: pediatric B-cell acute lymphocytic leukemia and rectal cancer.

Edwards said the lab decided to start with these two cancers because they disproportionately impact New Mexico. Additionally, he said the team plans to establish protocols for both adult and pediatric cases to figure out the different issues in dealing with genomic data from kids and adults.

Sequencing will not be done in a CLIA lab, so as with their targeted sequencing protocol, any actionable result will be validated with Sanger sequencing before being returned. The team will also establish a tumor board to evaluate the data and decide on what should be returned.

Edwards said he would eventually like to establish a clinical sequencing pipeline as standard of care earlier on in disease. "We want to establish this so that every pediatric B-cell ALL patient will go through this," he said.

The idea, he said, is that every patient would initially receive the same standard of care and exome sequencing would also be done on the patients. Further down the treatment line, the results of the sequencing could be used to direct individual patients into clinical trials or to guide therapy options, he said.

Edwards said that after running the pilot and moving the pipeline into the CLIA lab, he would like to eventually sequence all cancer patients. "We're getting all the details in place with these first two types of cancer, and then as soon as possible, opening it up to as many people as we have the capacity for," he said.

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