P56-M High-Throughput Genotyping of International HapMap Project Populations with Applied Biosystems TaqMan Drug Metabolism Genotyping Assays: An Automated Laboratory and Analysis Pipeline

摘要

Although high-density whole-genome SNP scans are available for association studies, the tagging SNP approach used to design many of these panels from International HapMap Project data may miss a substantial number of coding functional variations of drug metabolism enzymes (DME). In fact, more than 40 DME genes are not covered by the HapMap Project, probably due to the difficulties in assay design for these highly homologous gene families. Additionally, many of these technologies do not provide detection in a high number of known DME genes, leading to further gaps in whole-genome scans. Of the polymorphic putative functional DME variants not typed in Hap-Map, a large proportion is untagged by any combination of HapMap SNPs. Therefore, to correlate phenotypes to putative functional DME variations in pharmacogenomic studies, direct genotyping of these functional SNPs will be necessary. Applied Biosystems has developed a panel of N = 2394 TaqMan Drug Metabolism Genotyping Assays to interrogate putative functional variations in N = 220 DME genes. At the National Cancer Institute’s Core Genotyping Facility, an automated, high-throughput pipeline has been created to genotype these assays on the International HapMap Project population. DNA sample preparation and handling, assay set-up, genotype analysis, and data publishing at SNP500 Cancer Database (), have all been automated. Using a series of custom-designed methods on five Beckman Coulter Biomek FXs, a Laboratory Information Management System, and analysis software, >650,000 genotypes have been obtained and analyzed by a single person in about 8 weeks. Using this pipeline, a completion rate of >99% and no Mendelian inheritance errors were observed. Furthermore, the CGF has implemented quality-controlled, automated pipelines for sample receiving, quantification, numerous DNA handling procedures, genotyping, and analysis for all samples and studies processed.