Determining the appropriate significance threshold for a genome wide association study, usually based on the –log10(p-value), is important to minimize the chance of finding false positive associated SNP. So far, there is little consensus in the field of pig breeding on the appropriate threshold and the best approach to correct for false positives when using sequence information. Therefore this study aimed to compare different adjustments of significance thresholds and genomic control in order to minimize the occurrence of false positives for QTL detection in a pig breeding population using medium and high density SNP panels or imputed whole genome sequence data. From our results, we recommend to perform genomic control of each chromosome independently and to use a significance threshold based on the Bonferroni correction with the total number of SNPs since it takes into account the increase in number of SNP better than accounting for independent chromosomal segments, even though the underlying assumption seems to be too conservative. Keywords: GWAS, false positives, Bonferroni correction, permutation testing, genomic control

Sanne van den Berg, Jérémie Vandenplas, Fred A van Eeuwijk, Marcos S Lopes, Roel F Veerkamp

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Theory to Application 3, , 994, 2018
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