Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

ABSTRACT: 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

SUBMITTER: Nicolae DL 

PROVIDER: S-EPMC1456318 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature