coverage and characteristics of the affymetrix genechip human mapping 100k snp set覆盖和特征affymetrix genechip人类映射100 k snp.pdfVIP

Coverage and Characteristics of the Affymetrix GeneChip Human Mapping 100K SNP Set 1* 2 2 2,3 Dan L. Nicolae , Xiaoquan Wen , Benjamin F. Voight , Nancy J. Cox 1 Department of Statistics, The University of Chicago, Chicago, Illinois, United States of America, 2 Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America, 3 Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America Improvements in technology have made it possible to conduct genome-wide association mapping at costs within reach of academic investigators, and experiments are currently being conducted with a variety of high-throughput platforms. To provide an appropriate context for interpreting results of such studies, we summarize here results of an investigation of one of the first of these technologies to be publicly available, the Affymetrix GeneChip Human Mapping 100K set of single nucleotide polymorphisms (SNPs). In a systematic analysis of the pattern and distribution of SNPs in the Mapping 100K set, we find that SNPs in this set are undersampled from coding regions (both nonsynonymous and synonymous) and oversampled from regions outside genes, relative to SNPs in the overall HapMap database. In addition, we utilize a novel multilocus linkage disequilibrium (LD) coefficient based on information content (analogous to the information content scores commonly used for linkage mapping) that is equivalent to the familiar measure r2 in the special case of two loci. Using this approach, we are able to summarize for any subset of markers, such as the Affymetrix Mapping 100K set, the information available for association