ArticleBMC genetics2009
Impact of genotyping errors on the type I error rate and the power of haplotype-based association methods.
Article in BMC genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
6 citing papers in PubMed, 1 synthesis or guideline pooled it, 15 citations in OpenAlex.
- Meta-Analysis of Genetic Variants Associated With HBV Infection Susceptibility and Hepatocellular Carcinoma Risk.Journal of viral hepatitis · 2026Pooled it
- Marker genotyping error effects on genomic predictions under different genetic architectures.Molecular genetics and genomics : MGG · 2021Article
- An Analytic Solution to the Computation of Power and Sample Size for Genetic Association Studies under a Pleiotropic Mode of Inheritance.Human heredity · 2016Article
- Single-variant and multi-variant trend tests for genetic association with next-generation sequencing that are robust to sequencing error.Human heredity · 2012Article
- A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studies.Genetic epidemiology · 2010Article
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Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWe investigated the influence of genotyping errors on the type I error rate and empirical power of two haplotype based association methods applied to candidate regions. We compared the performance of the Mantel Statistic Using Haplotype Sharing and the haplotype frequency based score test with that of the Armitage trend test.Our study is based on 1000 replication of simulated case-control data settings with 500 cases and 500 controls, respectively. One of the examined markers was set to be the disease locus with a simulated odds ratio of 3. Differential and non-differential genotyping errors were introduced following a misclassification model with varying mean error rates per locus in the range of 0.2% to 15.6%.
resultsWe found that the type I error rate of all three test statistics hold the nominal significance level in the presence of non-differential genotyping errors and low error rates. For high and differential error rates, the type I error rate of all three test statistics was inflated, even when genetic markers not in Hardy-Weinberg Equilibrium were removed. The empirical power of all three association test statistics remained high at around 89% to 94% when genotyping error rates were low, but decreased to 48% to 80% for high and non-differential genotyping error rates.
conclusionCurrently realistic genotyping error rates for candidate gene analysis (mean error rate per locus of 0.2%) pose no significant problem for the type I error rate as well as the power of all three investigated test statistics.
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