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Overview of genome-wide association studies (GWAS) with permutation-based significance thresholds. (A) GWAS with classical Bonferroni significance threshold. (B) GWAS with permutation-based significance threshold, ignoring population structure by permuting the phenotype vector. (C) GWAS with permutation-based significance threshold, taking into account the population structure by permuting the genetic markers, which is equivalent to permuting the phenotype and covariance matrix.
