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

Yuandan Zhang; Bruce Tier

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

Yuandan Zhang
, Bruce Tier

Animal Genetics and Breeding Unit

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	Alex Safari, Bill Pattie, Barrie Restall
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	243-246
Volume	18
ISBN (Print)	9780646521039
Publication status	Published - 2009
Event	AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics - Barossa Valley, Australia Duration: 27 Sept 2009 → 2 Oct 2009

Conference

Conference	AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics
City	Barossa Valley, Australia
Period	27/09/09 → 2/10/09

Keywords

Quantitative Genetics (incl Disease and Trait Mapping Genetics)

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

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Zhang, Y., & Tier, B. (2009). Population stratification, not genotype error, causes some SNPs to depart from Hardy-Weinberg Equilibrium. In A. Safari, B. Pattie, & B. Restall (Eds.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 18, pp. 243-246). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/5237

Zhang, Yuandan ; Tier, Bruce. / Population stratification, not genotype error, causes some SNPs to depart from Hardy-Weinberg Equilibrium. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / Alex Safari ; Bill Pattie ; Barrie Restall. Vol. 18 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2009. pp. 243-246

@inproceedings{4c19e43babc347a88b8b0daf3773d713,

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

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.",

keywords = "Quantitative Genetics (incl Disease and Trait Mapping Genetics)",

author = "Yuandan Zhang and Bruce Tier",

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editor = "Alex Safari and Bill Pattie and Barrie Restall",

booktitle = "Proceedings of the Association for the Advancement of Animal Breeding and Genetics",

publisher = "Association for the Advancement of Animal Breeding and Genetics (AAABG)",

note = "AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics ; Conference date: 27-09-2009 Through 02-10-2009",

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Zhang, Y & Tier, B 2009, Population stratification, not genotype error, causes some SNPs to depart from Hardy-Weinberg Equilibrium. in A Safari, B Pattie & B Restall (eds), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 18, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 243-246, AAABG 2009: 18th Conference of the Association for the Advancement of Animal Breeding and Genetics, Barossa Valley, Australia, 27/09/09. <https://hdl.handle.net/1959.11/5237>

Population stratification, not genotype error, causes some SNPs to depart from Hardy-Weinberg Equilibrium. / Zhang, Yuandan; Tier, Bruce.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / Alex Safari; Bill Pattie; Barrie Restall. Vol. 18 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2009. p. 243-246.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AB - 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.

KW - Quantitative Genetics (incl Disease and Trait Mapping Genetics)

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BT - Proceedings of the Association for the Advancement of Animal Breeding and Genetics

A2 - Safari, Alex

A2 - Pattie, Bill

A2 - Restall, Barrie

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

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Zhang Y, Tier B. Population stratification, not genotype error, causes some SNPs to depart from Hardy-Weinberg Equilibrium. In Safari A, Pattie B, Restall B, editors, Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 18. Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG). 2009. p. 243-246

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

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