Positive results in association studies are associated with departure from Hardy-Weinberg equilibrium: hint for genotyping error?

Abstract

Case-control studies have been widely used to test for association between DNA sequence variants and complex diseases. The premise of genetic association studies is that the increased allele or genotype frequencies in cases compared with controls implicates sequence variants that either increase risk to a disease or are in strong linkage disequilibrium (LD) with a disease-causal mutation. However, many other factors can also lead to an observed difference in allele or genotype frequencies between cases and controls. While much attention has been devoted to the potential impact of incomparability between cases and controls in terms of sources of cases and controls, environmental exposures, and genetic background (population stratification), there is a clear lack of comprehension of the impact of genotyping error on the results of association studies. The accuracy and precision of genotyping becomes more critical in case-control studies of complex diseases because:(1) the effect of a specific risk allele under study is usually small, therefore even a low frequency of genotyping error may lead to a false positive or false negative finding; (2) no Mendelian inheritance check can be performed due to lack of family genotype data; (3) a large number of genotypes are usually generated. However, the degree of genotyping error in case-control studies remains unclear, due to the lack of direct measures of this type of error.To indirectly assess the prevalence and magnitude of genotyping error in case-control studies, we systematically reviewed reported association studies from PUBMED and performed Hardy-Weinberg equilibrium (HWE) tests in control subjects for each reported single nucleotide polymorphism (SNP). A significant difference between the observed and expected genotype frequencies under HWE may indicate genotyping error, because the conditions of HWE are generally applicable to the control subjects in any well-designed study population, i.e. (1) mating takes place at random with respect to genotype, (2) allelic frequencies are the same in males and females, and (3) mutation, selection, and migration are negligible. Although exceptions to the conditions of HWE may explain deviation, it is critical that investigators recognize the need to perform a test of HWE, and then evaluate the reason(s) for any observed deviation.We searched for articles with the keywords "association genotyp* genetic case control", and limited the search to articles in English, with human subjects, and 2000 publication date. The search yielded 157 articles, which we then limited to the 101 articles available among 1,721 journals received at the Wake Forest Baptist Medical Center Coy C. Carpenter Library. We disregarded 26 articles that did not include SNPs. This search and selection scheme resulted in a total of 75 articles describing 133 SNPs (the list of these articles is at www.wfubmc.edu/genomics). It is worth noting that limiting journals to our local library could bias toward higher profile journals and our findings may not be representat...

Hardy–Weinberg equilibrium in genetic association studies: an empirical evaluation of reporting, deviations, and power

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Fetal hemoglobin in sickle cell anemia: genetic determinants of response to hydroxyurea

“…Hardy-Weinberg equilibrium was determined before analysis and was performed for quality control purposes rather than to evaluate if the genotypes met Mendelian expectation because all members of our study population have sickle cell disease. [43][44][45][46][47][48] SNPs that had more than 25% missing genotypes or less than 5% minor allele frequency were not considered in the analysis. This resulted in 280 SNPs being tested for association.…”

Association of methylenetetrahydrofolate reductase (MTHFR) polymorphisms with genetic susceptibility to gastric cancer: a meta-analysis

“…In three studies (Kim et al 2005;Shen et al 2005;Lacasana et al 2005) investigating the C677T polymorphism, and in two studies (Stolzenberg et al 2003;Miao et al 2002) of the A1298C polymorphism, the distribution of the genotypes in control groups was not in Hardy-Weinberg equilibrium (P<0.05), indicating genotyping errors and/or population stratification (Zintzaras and Hadjigeorgiou 2004;Xu et al 2002). Therefore, a sensitivity analysis was carried out for these studies.…”