At Genomes Unzipped, Jeff Barrett gives a how-to on determining whether a genome-wide association study is "a landmark finding or a dud." Five factors to take into consideration, he says, are sample size, quality control, confounders, replication, and biology. "The biggest challenge to successfully carrying out a GWAS is getting good, clean genotype data. Pay close attention not only to the standard QC metrics ... but also to whether extra attention was focused on the genotypes of the most associated SNPs," he writes. In general, he adds that "you should be suspicious" if the study contained fewer than 1,000 cases and controls.
A GWAS Cheat Sheet
Jul 20, 2010