Genome-Wide Association Studies: Present Status and Future Directions Judy H. Cho  Gastroenterology  Volume 138, Issue 5, Pages 1668-1672.e1 (May 2010) DOI: 10.1053/j.gastro.2010.03.028 Copyright © 2010 AGA Institute Terms and Conditions

Figure 1 Selection of SNPs to include in GWAS genotyping platforms. Depicted are 5 adjacent SNPs (SNPs 1–5) that have been phased to depict haplotypes (closely linked markers inherited together; for autosomal chromosomes, each individual will have paternal and maternal haplotypes). The more common (1) and less common (2) alleles can be designated at each SNP. SNPs 1 and 4 are in complete linkage disequilibrium (ie, correlated) with each other (SNP group *); similarly SNPs 2, 3, and 5 are also completely correlated (SNP group ‡). Therefore, only 2 markers (ie, one each from SNP group * and ‡) would need to be genotyped to capture the variation from all 5 markers. The HapMap project, by genotyping trios (both parents and child; defines phasing patterns) from various population groups has defined linkage disequilibrium patterns throughout the genome; this has made possible efficient, parsimonious selection of SNPs to include in GWAS genotyping platforms. Gastroenterology 2010 138, 1668-1672.e1DOI: (10.1053/j.gastro.2010.03.028) Copyright © 2010 AGA Institute Terms and Conditions