Thursday, July 29, 2010

VCU's MDx Lab May Debut Next-Gen Sequencing in One Year

The molecular diagnostics lab at Virginia Commonwealth University is about a year away from using a next-gen sequencing platform on clinical samples, according to its director.

Andrea Ferreira-Gonzalez, who is also chair of the school's Division of Molecular Diagnostics, Department of Pathology, said the lab is "working with" Illumina, and is testing certain clinical applications of the Roche 454 FLX platform installed at VCU's DNA Core Facilities.

Speaking after her presentation at this year's AACC annual meeting, held here this week, she said her lab is researching Illumina's Genome Analyzer for targeted re-sequencing applications by studying 50 genes linked to cardiomyopathy.

She also said the lab is using Roche 454's pyrosequencing-based instrument to genotype infectious diseases, noting she is keen on the platform "because you can sequence longer fragments" of DNA.

Saying her lab is "still working on issues like quality control," Ferreira-Gonzalez said she thinks it will begin running patient samples on the machines in one year — "with luck."

She noted that "we can use next-generation sequencers to perform whole-genome scans in the laboratory today, but we have nowhere to store" the data such machines are notorious for yielding.

The lab, based in VCU's Richmond, Va., campus, currently uses a pair of capillary electrophoresis platforms — an ABI 310 and 3100 — which she said can be used to confirm mutations detected by other methods and are the "gold standard" for mutation detection and histocompatibility typing (though she did quip that the 310 "belongs in a museum").

"DNA sequencing is undergoing a revolution … [but the 310 and 3100] are bread-and-butter technologies that we use every day," she said during her presentation.

Ferreira-Gonzalez also said she predicts that third-generation sequencers will make their way into clinical labs in three to five years.

"The technology is moving very fast, and I think it's going to take some time for us to catch up," she said.

Greg Tsongalis, director of the molecular pathology lab at Dartmouth College's Hitchcock Medical Center, agreed. Tsongalis, who presented at the same session, told me after Ferreira-Gonzalez's talk that his own lab isn't ready to invest in a second-generation sequencer because technologies continue to evolve.

"You don't want to spend that kind of money if something better may be around the corner," he said.

By Kirell Lakhman
Genome Web

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