Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project.

Less than 1% of autosomal SNPs show significant Hardy-Weinberg deviations in the 1000 Genomes Project, with most linked to poor sequence quality.

• Why it matters: Accurate Hardy-Weinberg equilibrium testing is crucial for genome-wide association studies, but current methods often overlook sex differences and sequencing artifacts, risking false signals.
• What they did: Analyzing high-coverage, sex-aware genome data from 2,490 individuals across five populations, researchers applied an allele-based framework and meta-analysis to identify deviations, focusing on reliable genomic regions.
• The result: They identified 255 autosomal SNPs with true deviations, including population-specific heterozygosity patterns, and created a sequence-feature-based predictor to improve quality control in sequencing studies.