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SAIC-Frederick to Use TaqMan Collection to Genotype Cancer Samples, Create Reference Database

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Applied Biosystems and the Core Genotyping Facility at SAIC-Frederick, a contractor for the National Cancer Institute, are jointly validating drug-metabolizing enzyme biomarkers in samples from the HapMap Project and the SNP500Cancer panel using ABI's TaqMan DME assays.

"The objective of this study is to better understand the genetic differences associated with individual responses to cancer treatment," ABI CSO Dennis Gilbert, said in a company statement.

ABI plans to create at least two reference datasets from the project for its clinical research market. The first will stem from 290 samples coming from the HapMap project, and the second dataset will come from testing on 100-200 clinical samples from the NCI's SNP500Cancer standard sample panel, Tom Harkins, senior product manager for TaqMan assays, told Pharmacogenomics Reporter this week.

SAIC-Frederick will also use a number of assays to genotype individuals from a study evaluating treatment for Non-Hodgkin's lymphoma.

The company also analyzed linkage disequilibrium among 1,840 SNPs in 203 drug-metabolizing enzyme genes to investigate the feasibility of using LD to guide assay development, according to an ABI poster presented this week at the American Association for Cancer Research meeting in Washington, DC.

The SNP500Cancer website will feature data meeting quality thresholds, along with minor allele frequencies, context sequences, and assay ordering information.

The effort does not yet have a name. "We're waiting for another completion of the preliminary analysis," said Harkins. "There are about three or four different ways the project could go," he said.

The company is about 90 percent finished with the HapMap samples, Harkins said.

"We see this, for Applied Biosystems, as a first step into the clinical continuum," he said.

He declined to be more specific about whether ABI planned to use the study to help ease itself into molecular diagnostics.

— Chris Womack ([email protected])

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