More recently, attention has shifted from gene-centric studies to genomewide scans of anonymous SNPs. In this context the International HapMap Consortium [2005] used permutation tests of high density genotypes in 10 genomic regions to estimate an “effective number of independent tests” of 150 per 500 kbp. Scaling up to a 3 Gb genome suggests a significance threshold of 5.5 × 10−8 for two–sided tests of SNPs. The only threshold that has to date been rigorously applied to more than one scan is that of the WTCCC [2007]. Assuming 106 independent regions of the genome, 10 disease–causing genes and average power 50% to detect an associated gene, posterior odds of 10:1 in favour of association would be achieved by a nominal P–value of 5 × 10−7.
