comprehensive survey of snps in the affymetrix exon array using the 1000 genomes dataset全面调查的snp affymetrix外显子数组使用1000基因组数据集.pdfVIP

Comprehensive Survey of SNPs in the Affymetrix Exon Array Using the 1000 Genomes Dataset 1. 2. 2 1,3 Eric R. Gamazon , Wei Zhang , M. Eileen Dolan , Nancy J. Cox * 1 Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America, 2 Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America, 3 Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America Abstract Microarray gene expression data has been used in genome-wide association studies to allow researchers to study gene regulation as well as other complex phenotypes including disease risks and drug response. To reach scientifically sound conclusions from these studies, however, it is necessary to get reliable summarization of gene expression intensities. Among various factors that could affect expression profiling using a microarray platform, single nucleotide polymorphisms (SNPs) in target mRNA may lead to reduced signal intensity measurements and result in spurious results. The recently released 1000 Genomes Project dataset provides an opportunity to evaluate the distribution of both known and novel SNPs in the International HapMap Project lymphoblastoid cell lines (LCLs). We mapped the 1000 Genomes Project genotypic data to the Affymetrix GeneChip Human Exon 1.0ST array (exon array), which had been used in our previous studies and for which gene expression data had been made publicly available. We also evaluated the potential impact of these SNPs on the differentially spliced probesets we had identified previously. Though