Abstract
BackgroundGenotyping has become more cost-effective and less invasive with the use of buccal cell sampling. However, low or fragmented DNA yields from buccal cells collected using FTA cards often requires additional whole genome amplification to produce sufficient DNA for genotyping. In our case–control study of childhood leukaemia, discordance was found between genotypes derived from blood and whole genome amplified FTA buccal DNA samples. We aimed to develop a user-friendly method to correct for this genotype misclassification, as existing methods were not suitable for use in our study.MethodsDiscordance between the results of blood and buccal-derived DNA was assessed in childhood leukaemia cases who had both blood and FTA buccal samples. A method based on applying misclassification probabilities to measured data and combining results using multiple imputations, was devised to correct for error in the genotypes of control subjects, for whom only buccal samples were available, to minimize bias in the odds ratios in the case–control analysis.ResultsApplication of the correction method to synthetic datasets showed it was effective in producing correct odds ratios from data with known misclassification. Moreover, when applied to each of six bi-allelic loci, correction altered the odds ratios in the logically anticipated manner given the degree and direction of the misclassification revealed by the investigations in cases. The precision of the effect estimates decreased with decreasing size of the misclassification data set.ConclusionsBias arising from differential genotype misclassification can be reduced by correcting results using this method whenever data on concordance of genotyping results with those from a different and probably better DNA source are available.
Highlights
Genotyping has become more cost-effective and less invasive with the use of buccal cell sampling
0.91, 1.85 aa OR = Odds ratio; confidence intervals (CI) = confidence interval; a wgaDNA heterozygous result (Aa) = Heterozygous genotype; aa = Homozygous mutant genotype. a Confidence intervals based on Wald method for uncorrected estimates and percentile-based for corrected estimates. bFree of genotyping error
With Single nucleotide polymorphism (SNP) A-type error introduced into the data, the uncorrected OR was 1.82 while the corrected OR was 2.11, close to the ‘true’ result
Summary
Genotyping has become more cost-effective and less invasive with the use of buccal cell sampling. In our case–control study of childhood leukaemia, discordance was found between genotypes derived from blood and whole genome amplified FTA buccal DNA samples. We aimed to develop a user-friendly method to correct for this genotype misclassification, as existing methods were not suitable for use in our study. Because of the differential nature of the misclassification (all controls provided buccal DNA while most cases provided a blood sample) and the large number of covariates required and analyses planned, all those requiring more than one gene in a model or examination of gene-environment or gene-gene interactions, we needed a comparatively simple and easy-to-use method for addressing this issue. Clayton et al have described an ingenious method for adjusting for a similar problem of differential bias [9], which uses statistical properties of the observed data and requires no validation data; it requires large samples so could not be used in our study. It was necessary to develop a novel correction method, as described below
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