Calibrating genome wide significance by minor allele frequency across three major populations.

ABSTRACT: Conventional genome-wide association study (GWAS) thresholds, notably 5 × 10⁻⁸, were established under assumptions that may not hold across diverse populations and whole-genome sequencing (WGS) analyses. Given the complex linkage disequilibrium structure of the human genome, a single fixed threshold risks inadequate type I error control. Here, we sought to derive minor allele frequency (MAF)-specific, population-tailored significance thresholds using the Li-Ji method across European, African, and Asian cohorts from the 1000 Genomes Project. We partitioned the genome into natural linkage disequilibrium (LD) blocks defined by the LDetect database and applied rigorous quality control measures before generating LD matrices. Using the Li-Ji method-we estimated the effective number of independen

SUBMITTER: Vejandla SC 

PROVIDER: S-EPMC12586462 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature