Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/5237
Title: Population stratification, not genotype error, causes some SNPs to depart from Hardy-Weinberg Equilibrium
Contributor(s): Zhang, Yuandan  (author); Tier, Bruce  (author)
Publication Date: 2009
Handle Link: https://hdl.handle.net/1959.11/5237
Abstract: 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.
Publication Type: Conference Publication
Conference Name: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, Australia, 28th September - 1st October 2009
Conference Details: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, Australia, 28th September - 1st October 2009
Source of Publication: Proceedings of the Eighteenth Conference of the Association for the Advancement of Animal Breeding and Genetics - Matching Genetics and the Environment a New Look at and Old Topic, p. 243-246
Publisher: AAABG: Association for the Advancement of Animal Breeding and Genetics
Place of Publication: Taringa, Australia
ISSN: 1328-3227
Field of Research (FOR): 060412 Quantitative Genetics (incl Disease and Trait Mapping Genetics)
Socio-Economic Outcome Codes: 830399 Livestock Raising not elsewhere classified
Peer Reviewed: Yes
HERDC Category Description: E1 Refereed Scholarly Conference Publication
Other Links: http://www.aaabg.org/proceedings18/files/zhang243.pdf
http://trove.nla.gov.au/work/36420775
http://aaabg.org/aaabg18/
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Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Conference Publication

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