ArticleGenetic epidemiology2005
Detection of genotyping errors and pseudo-SNPs via deviations from Hardy-Weinberg equilibrium.
Article in Genetic epidemiology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers, 2 of them syntheses that pooled it.
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Who cites it
50 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Pooled it
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- Effect of genotyping errors on linkage map construction based on repeated chip analysis of two recombinant inbred line populations in wheat (Triticum aestivum L.).BMC plant biology · 2024Article
- Evaluation of the MC3R gene pertaining to body weight and height regulation and puberty development.Scientific reports · 2023Article
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- Asymptotic tests for Hardy-Weinberg equilibrium in hexaploids.Horticulture research · 2022Article
- A network algorithm for the X chromosomal exact test for Hardy-Weinberg equilibrium with multiple alleles.Molecular ecology resources · 2021Article
- Identification of genes and gene expression associated with dispersal capacity in the mountain pine beetle,PeerJ · 2021Article
- Strong association of tissue inhibitor of metalloproteinase (TIMP)-2 and -3 promoter single nucleotide polymorphisms with risk of colorectal cancer in ethnic Kashmiri population - a case control study.Bioscience reports · 2019Article
- On the testing of Hardy-Weinberg proportions and equality of allele frequencies in males and females at biallelic genetic markers.Genetic epidemiology · 2018Article
- An exome sequencing based approach for genome-wide association studies in the dog.Scientific reports · 2017Article
- A genome-wide study of Hardy-Weinberg equilibrium with next generation sequence data.Human genetics · 2017Article
- Fitting Proportional Odds Model to Case-Control data with Incorporating Hardy-Weinberg Equilibrium.Scientific reports · 2015Article
- Exceptional longevity and muscle and fitness related genotypes: a functional in vitro analysis and case-control association replication study with SNPs THRH rs7832552, IL6 rs1800795, and ACSL1 rs6552828.Frontiers in aging neuroscience · 2015Article
- PTK2 rs7460 and rs7843014 polymorphisms and exceptional longevity: a functional replication study.Rejuvenation research · 2014Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
Genotype error can greatly reduce the power of a genetic study. For family data, genotype error can be assessed by examining marker data for non-Mendelian inconsistencies, closely linked markers for double recombination events, and consistency of duplicate genotypes. For case-control data, duplicate samples are genotyped, and controls are tested for deviations from Hardy-Weinberg equilibrium (HWE). Duplicate samples can provide accurate estimates of genotyping error rates, unless systematic genotyping errors have occurred. Although genotyping errors can cause deviations from HWE, these deviations are usually small, and the power to detect them is low except for high rates of genotyping error and/or large sample sizes. An additional problem is that even when deviations from HWE are detected for marker loci, without additional experimentation it is not possible to unequivocally implicate genotyping error as the cause. The power and sample sizes necessary to detect deviations from HWE for single-nucleotide polymorphism (SNP) data are examined for a variety of genotyping error and pseudo-SNP models. For the majority of genotyping models examined, the power is poor to detect deviations from HWE. For example, for 1,000 controls, if an allele with a frequency of 0.1 fails to amplify for 28% of the heterozygous genotypes producing a sample error rate of 0.05, the power is 0.51 to detect a deviation from HWE at an alpha level of 0.05. On the other hand, the detection of deviations from HWE for pseudo-SNPs (paralogous and ectopic sequence variants) for the majority of models examined produces a power of >0.8 for sample sizes as small as 50 individuals.
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