Third, we drop SNPs in genomic regions containing SNPs that are outliers with respect to their effect-size estimates. Because the effect sizes of these SNPs appear to have a different variance-covariance matrix than the rest of the genome, including these regions would likely lead to the biases and inefficiencies that can occur when the homogeneous-Ω assumption is violated. In our empirical application, in the GWAS of NEUR, the effect sizes of SNPs in a region of chromosome 8 that tag an inversion polymorphism have been found to be strongly inflated relative to the effects estimated for SNPs in all other regions of the genome.10,11 Therefore, we omit SNPs in chromosome 8 between base-pair positions 7,962,590 and 11,962,591 (Supplementary Table 10).
