Applied Biosystems enters collaboration with the Core Genotyping Facility, SAIC-Frederick, a contractor for the National Cancer Institute (NCI), on a series of biomarker studies for cancer research
The NCI-funded Core Genotyping Facility will use Applied Biosystems's entire TaqMan drug metabolism genotyping assay collection to examine genetic variations in the HapMap and SNP500Cancer samples in order to validate additional cancer biomarkers.
In support of the NCI, the Core Genotyping Facility is using more than 2400 TaqMan drug metabolism genotyping assays to generate the genotypes for samples from the International HapMap project and from NCI's SNP500Cancer standard sample panel.
In addition, select assays with significant correlation from data analysis will be used to genotype individuals who participated in a pharmacogenetic study at the NCI evaluating treatment for Non-Hodgkin lymphoma.
"The objective of this study is to better understand the genetic differences associated with individual responses to cancer treatment," said Dennis Gilbert, chief scientific officer for Applied Biosystems.
"Because our TaqMan drug metabolism genotyping assays were developed using extensive computational analysis in combination with assay optimization and validation that identified novel and well-known gene variants, we believe they represent the most complete set of drug metabolism assays available to the scientific research community".
"We are pleased the SAIC-Frederick, under contract to the NCI, has selected them for this important project and are confident the assays will identify genetic variations important to various cancers for future pharmacogenetic studies and treatment guidelines".
The Core Genotyping Facility will use samples from the HapMap project, SNP500Cancer, and Human Diversity Panel as controls to evaluate the genes included in the TaqMan drug metabolism genotyping assays.
Applied Biosystems and the Core Genotyping Facility will jointly analyse the resulting genotype data, and compare resulting data with previously published genotype and/or sequencing data for the same variants and individuals.
Final data meeting concordance/Mendelian transmission thresholds will be posted on the SNP500Cancer website, displaying the observed minor allele frequency, context sequences, and assay ordering information.
The collaborators also plan to publish further findings.
The TaqMan drug metabolism genotyping assays are a collection of ready-to-use assays that detect polymorphisms within approximately 220 genes identified as phase I, phase II, and transport genes within the drug metabolism pathways.
It is believed that some polymorphisms within these genes cause differences for drug efficacy between individuals.
Other polymorphisms within these genes are believed to be associated with individuals who have a higher risk for certain diseases.
The TaqMan drug metabolism genotyping assay collection comprises more than 2400 individual assays for research purposes only.
One tube contains two allele specific TaqMan probes and a primer pair to detect individual polymorphisms.
All assays have been extensively characterised within this collection with 180 genotypes generated per assay.
Where possible, information from the common public allele websites has been mapped to individual assays.
