improve accuracy by correcting for linkage disequilibrium, as opposed to pruning out correlated (but possibly true independent effect) SNPs (Vilhjalmsson et al., 2015) or by relying on HaploSNPs (Bhatia et al., 2015), large shared segments in high LD that can be recoded into a regional genotype. Overall, GCTA and its extensions would be useful in describing and testing the polygenic architecture of a trait, for example response to treatment or intervention, but have limited utility in defining the specific genes or pathways involved.
