Zhang, Yuandan

Tier, Bruce

2009

Large scale whole genome scans generate massive amounts of genotype data. It is essential to check genotype integrity and identify genotype errors prior to association analysis. Departure from Hardy-Weinberg Equilibrium has been adopted as one of the main methods to identify genotype errors. However population stratification also causes departure from Hardy-Weinberg Equilibrium, which is a disadvantage of this approach. This study used 2 sets of SNP genotypes to show that after basic editing using Call Rate and minor allele frequency, up to 13% of SNPs departed from Hardy-Weinberg Equilibrium (HWD) and about one third of these HWD SNPs could be falsely identified as genotype errors, were attributable to population subdivision (eg herd of origin, cohort) for one dataset and corresponding numbers for the second dataset are 21% and 16%, respectively. This approach can avoid improper culling of a considerable proportion of SNPs.

Proceedings of the Association for the Advancement of Animal Breeding and Genetics, v.18, p. 243-246

9780646521039

1328-3227

https://hdl.handle.net/1959.11/5237

Association for the Advancement of Animal Breeding and Genetics (AAABG)

Population stratification, not genotype error, causes some SNPs to depart from Hardy-Weinberg Equilibrium

Conference Publication

Publication