A Simple and Fast Two-Locus Quality Control Test to Detect False Positives Due to Batch Effects in Genome-Wide Association Studies
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 simpl...
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| Language: | English |
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Wiley Subscription Services, Inc., A Wiley Company
2010
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3674525/ |
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pubmed-36745252013-06-06 A Simple and Fast Two-Locus Quality Control Test to Detect False Positives Due to Batch Effects in Genome-Wide Association Studies Lee, Sang Hong Nyholt, Dale R Macgregor, Stuart Henders, Anjali K Zondervan, Krina T Montgomery, Grant W Visscher, Peter M Original Articles 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 ∼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. Genet. Epidemiol. 34:854–862, 2010. © 2010 Wiley-Liss, Inc. Wiley Subscription Services, Inc., A Wiley Company 2010-12 2010-11-18 /pmc/articles/PMC3674525/ /pubmed/21104888 http://dx.doi.org/10.1002/gepi.20541 Text en © 2010 Wiley-Liss, Inc. http://creativecommons.org/licenses/by/2.5/ Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation. |
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Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Lee, Sang Hong Nyholt, Dale R Macgregor, Stuart Henders, Anjali K Zondervan, Krina T Montgomery, Grant W Visscher, Peter M |
| spellingShingle |
Lee, Sang Hong Nyholt, Dale R Macgregor, Stuart Henders, Anjali K Zondervan, Krina T Montgomery, Grant W Visscher, Peter M A Simple and Fast Two-Locus Quality Control Test to Detect False Positives Due to Batch Effects in Genome-Wide Association Studies |
| author_facet |
Lee, Sang Hong Nyholt, Dale R Macgregor, Stuart Henders, Anjali K Zondervan, Krina T Montgomery, Grant W Visscher, Peter M |
| author_sort |
Lee, Sang Hong |
| title |
A Simple and Fast Two-Locus Quality Control Test to Detect False Positives Due to Batch Effects in Genome-Wide Association Studies |
| title_short |
A Simple and Fast Two-Locus Quality Control Test to Detect False Positives Due to Batch Effects in Genome-Wide Association Studies |
| title_full |
A Simple and Fast Two-Locus Quality Control Test to Detect False Positives Due to Batch Effects in Genome-Wide Association Studies |
| title_fullStr |
A Simple and Fast Two-Locus Quality Control Test to Detect False Positives Due to Batch Effects in Genome-Wide Association Studies |
| title_full_unstemmed |
A Simple and Fast Two-Locus Quality Control Test to Detect False Positives Due to Batch Effects in Genome-Wide Association Studies |
| title_sort |
simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies |
| description |
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 ∼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. Genet. Epidemiol. 34:854–862, 2010. © 2010 Wiley-Liss, Inc. |
| publisher |
Wiley Subscription Services, Inc., A Wiley Company |
| publishDate |
2010 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3674525/ |
| _version_ |
1611984231866564608 |