Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities

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Abstract

Dense single nucleotide polymorphism (SNP) panels are widely used for genome-wide association studies (GWAS). In these panels, SNPs within a genomic segment tend to be highly correlated. Thus, association studies based on testing the significance of single SNPs are not very effective, and genomic-window based tests have been proposed to address this problem. However, when the SNP density on the genotype panel is not homogeneous, genomic-window based tests can lead to the detection of spurious associations by declaring effects of genomic windows that explain a large proportion of genetic variance as significant. We propose two methods to solve this problem.

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Li, J., Wang, Z., Fernando, R., & Cheng, H. (2021). Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities. Genetics Selection Evolution, 53(1). https://doi.org/10.1186/s12711-021-00638-x

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