Aggregating single nucleotide polymorphisms improves filtering for false-positive associations postimputation.

ABSTRACT: Imputation causes bias in P-values in downstream genome-wide association studies. Imputation quality measures such as IMPUTE info are used to discriminate between false and true associations. However, implementing a high threshold often discards true associations, while a low threshold preserves false associations. This poses a challenge, especially for studies genotyped with SNP arrays. In practice, association signals register as spikes of low P-values for SNPs in close proximity owing to linkage disequilibrium, but postimputation filtering is conducted on SNPs independently. We simulated 1536 small case-control studies on the human chromosome 19 both to quantify the introduced bias and to evaluate postimputation filtering. The established IMPUTE info thresholds 0.3 and 0.8 were compared

SUBMITTER: Stahl K 

PROVIDER: S-EPMC12060241 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature