A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies

Lee, S. H., Nyholt, D.R., Macgregor, S., Henders, A. K., Zondervan, K. T., Montgomery, G. W., & Visscher, P. M. (2010) A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies. Genetic Epidemiology, 34(8), pp. 854-862.

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The impact of erroneous genotypes having passed standard quality control (QC) can be severe in genome-wide association studies, genotype imputation, and estimation of heritability and prediction of genetic risk based on single nucleotide polymorphisms (SNP). To detect such genotyping errors, a simple two-locus QC method, based on the difference in test statistic of association between single SNPs and pairs of SNPs, was developed and applied. The proposed approach could detect many problematic SNPs with statistical significance even when standard single SNP QC analyses fail to detect them in real data. Depending on the data set used, the number of erroneous SNPs that were not filtered out by standard single SNP QC but detected by the proposed approach varied from a few hundred to thousands. Using simulated data, it was shown that the proposed method was powerful and performed better than other tested existing methods. The power of the proposed approach to detect erroneous genotypes was approximately 80% for a 3% error rate per SNP. This novel QC approach is easy to implement and computationally efficient, and can lead to a better quality of genotypes for subsequent genotype-phenotype investigations.

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6 citations in Scopus
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8 citations in Web of Science®

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ID Code: 91981
Item Type: Journal Article
Refereed: Yes
Additional Information: Lee, Sang Hong
Nyholt, Dale R
Macgregor, Stuart
Henders, Anjali K
Zondervan, Krina T
Montgomery, Grant W
Visscher, Peter M
076113/Wellcome Trust/United Kingdom
084766/Wellcome Trust/United Kingdom
085235/Wellcome Trust/United Kingdom
Research Support, Non-U.S. Gov't
2010/11/26 06:00
Genet Epidemiol. 2010 Dec;34(8):854-62. doi: 10.1002/gepi.20541.
Keywords: *Genetic Loci, Genome, Human, Genome-Wide Association Study/*methods/standards, Genotype, Humans, Models, Genetic, Polymorphism, Single Nucleotide/genetics, *Quality Control
DOI: 10.1002/gepi.20541
ISSN: 0741-0395
Divisions: Current > QUT Faculties and Divisions > Faculty of Health
Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2010 Wiley-Liss, Inc.
Deposited On: 18 Jan 2016 01:40
Last Modified: 15 Feb 2016 23:15

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