Influence of genotyping error in linkage mapping for complex traits--an analytic study.

BMC Genetics
Jérémie J P LebrecHans C van Houwelingen

Abstract

Despite the current trend towards large epidemiological studies of unrelated individuals, linkage studies in families are still thoroughly being utilized as tools for disease gene mapping. The use of the single-nucleotide-polymorphisms (SNP) array technology in genotyping of family data has the potential to provide more informative linkage data. Nevertheless, SNP array data are not immune to genotyping error which, as has been suggested in the past, could dramatically affect the evidence for linkage especially in selective designs such as affected sib pair (ASP) designs. The influence of genotyping error on selective designs for continuous traits has not been assessed yet. We use the identity-by-descent (IBD) regression-based paradigm for linkage testing to analytically quantify the effect of simple genotyping error models under specific selection schemes for sibling pairs. We show, for example, that in extremely concordant (EC) designs, genotyping error leads to decreased power whereas it leads to increased type I error in extremely discordant (ED) designs. Perhaps surprisingly, the effect of genotyping error on inference is most severe in designs where selection is least extreme. We suggest a genomic control for genotyping er...Continue Reading

References

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Citations

Apr 11, 2014·Genetic Epidemiology·Charles Y K CheungEllen M Wijsman
Feb 5, 2010·Biometrical Journal. Biometrische Zeitschrift·Thomas A Louis, Ingo Ruczinski
Apr 28, 2011·Journal of Bioinformatics and Computational Biology·Wei-Bung Wang, Tao Jiang

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Methods Mentioned

BETA
genotyping
chip
chips

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