To correct for multiple testing of SNPs in linkage disequilibrium, we used an implementation of methods described by Li and Ji (2005). Similar to Nyholt (2004), their approach is based on Cheverud (2001), and involves first estimating the “effective number” of independent tests using a spectral decomposition of the correlation matrix of the SNPs, followed by an adjustment of the correlated tests using the effective number of independent tests. In our case, this number was estimated to equal 5, hence the significance level is 0.05/5 = 0.01, whereas marginal significance is 0.1/5 = 0.02. Note that this correction does not correct for testing multiple phenotypes, or fitting multiple models (see also “Limitations” in the “Discussion” section).
