A high-throughput SNP typing system for genome-wide association studies

摘要

SNPs are useful markers for identifying genes responsible for and/or associated with common diseases, and for directing personalized medical care. Furthermore, because they are so frequent in the genome and can be genotyped quite easily, SNPs can serve as markers for a whole genome association study. However, one of the most difficult issues to be solved for whole-genome association studies using SNPs is reduction of the amount of genomic DNA for genotyping. The presently available technologies require too much genomic DNA to be practical. To overcome this problem, we combined the Invader assay with multiplex PCR performed in the presence of Taq polymerase antibody as well as a novel 384-well card system that reduces the reaction volume. We amplified 96 genomic DNA fragments simultaneously in a single tube, and analyzed each SNP using the Invader assay. Since we used 10-20 nanograms of genomic DNA as a template for multiplex PCR, the amount needed to assay one SNP was only 0.1-0.2 nanograms. Our results strongly indicate the feasibility of undertaking genome-wide association studies using blood samples of only 5-10 milliliters. Using these technologies, which allow us to perform as many as 450,000 typings in one day, our system should let us identify the genes responsible for many diseases and/or pharmacological responsiveness.