@article{TEXTUAL,
      recid = {8219},
      author = {Nicolae, Dan L. and Wen, Xiaoquan and Voight, Benjamin F.  and Cox, Nancy J.},
      title = {Coverage and Characteristics of the Affymetrix GeneChip  Human Mapping 100K SNP Set},
      journal = {PLOS Genetics},
      address = {2006-05-05},
      number = {TEXTUAL},
      abstract = {<p>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 <em>r</em><sup>2</sup>  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 mapping in that subset, relative to the  information available in the full set of markers included  in the HapMap, and highlight circumstances in which this  multilocus measure of LD provides substantial additional  insight about the haplotype structure in a region over  pairwise measures of LD.</p>},
      url = {http://knowledge.uchicago.edu/record/8219},
}