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The impact of genotyping error on family-based analysis of quantitative traits

Summary: ARTICLE
The impact of genotyping error on family-based
analysis of quantitative traits
Gonc╦alo R Abecasis1
, Stacey S Cherny1
and Lon R Cardon*,1
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Errors in genotyping can substantially influence the power to detect linkage using affected sib-pairs, but it is
not clear what effect such errors have on quantitative trait analyses. Here we use Monte Carlo simulation to
examine the influence of genotyping error on multipoint vs two-point analysis, variable map density, locus
effect size and allele frequency in quantitative trait linkage and association studies of sib-pairs. The analyses
are conducted using variance components methods. We contrast the effects of error on quantitative trait
analyses with those on the affected sib-pair design. The results indicate that genotyping error influences
linkage studies of affected sib pairs more severely than studies of quantitative traits in unselected sibs. In
situations of modest effect size, 5% genotyping error eliminates all supporting evidence for linkage to a true
susceptibility locus in affected pairs, but may only result in a loss of 15% of linkage information in random
pairs. Multipoint analysis does not suffer substantially more than two-point analysis; for moderate error rates
(55%), multipoint analysis with error is more powerful than two-point with no error. Map density does not
appear to be an important factor for linkage analysis. QTL association analyses of common alleles are


Source: Abecasis, Goncalo - Department of Biostatistics, University of Michigan


Collections: Biology and Medicine; Mathematics