sample size of 9,000) to detect a locus with an odds ratio of ≥1.2, compared to 88% with the complete set of SNPs (9,240 is the largest discovery sample size used in GWAS of MD [Ripke et al., 2013b]). In other words, differences in coverage between chips do not translate into big differences in power. Furthermore, imputation (Howie et al., 2009) using the very high density of variants available from the 1000 Genomes Project (Abecasis et al., 2010), has further extended the scope of genotyping arrays to interrogate millions of ungenotyped variants. In short, failure of GWAS to detect common variants (MAF > 5%) conferring risk to MD is unlikely to be due to insufficient information about these variants from genotyping arrays.
