Skip to main content
. Author manuscript; available in PMC: 2021 Aug 17.
Published in final edited form as: Mol Psychiatry. 2020 Feb 17;26(6):2048–2055. doi: 10.1038/s41380-020-0670-3

Table 3.

GWAS significance thresholds for correlated genotypes and phenotypes in this data set

Methods GWAS threshold for one phenotype Effective number of phenotypic tests Family-wise threshold (alpha=0.05)
Bonferroni correction 1.16E-08 335 3.46E-11
Nyholt method for phenotypes with Bonferroni correction of genotypes 1.16E-08 286 4.06E-11
Li and Ji method for phenotypes with Bonferroni correction of genotypes 1.16E-08 122 9.51E-11
Han et al (LD in sliding window of genotypes, Li and Ji for phenotypes) 2.86E-08 122 2.34E-10
Li et al (Block wise LD of genotypes, Li and Ji for phenotypes) 5.54E-08 122 4.54E-10
Gao et al (LD of genotypes, Li and Ji for phenotypes) 4.08E-08 122 3.34E-10
Permutation of genotype (subject indices) all allele frequencies 5.29E-08 NA 8.39E-13
Permutation of genotype (subject indices) (MAF > 0.1) 5.29E-08 NA 1.93E-10
Permutation of genotype (subject indices) (SNPs with MAF ≤ 0.1) 1.51E-08 NA 8.39E-13