Abstract
Errors while genotyping are inevitable and can reduce the power to detect linkage. However, does genotyping error have the same impact on linkage results for single-nucleotide polymorphism (SNP) and microsatellite (MS) marker maps? To evaluate this question we detected genotyping errors that are consistent with Mendelian inheritance using large changes in multipoint identity-by-descent sharing in neighboring markers. Only a small fraction of Mendelian consistent errors were detectable (e.g., 18% of MS and 2.4% of SNP genotyping errors). More SNP genotyping errors are Mendelian consistent compared to MS genotyping errors, so genotyping error may have a greater impact on linkage results using SNP marker maps. We also evaluated the effect of genotyping error on the power and type I error rate using simulated nuclear families with missing parents under 0, 0.14, and 2.8% genotyping error rates. In the presence of genotyping error, we found that the power to detect a true linkage signal was greater for SNP (75%) than MS (67%) marker maps, although there were also slightly more false-positive signals using SNP marker maps (5 compared with 3 for MS). Finally, we evaluated the usefulness of accounting for genotyping error in the SNP data using a likelihood-based approach, which restores some of the power that is lost when genotyping error is introduced.
Department(s)
Mathematics
Document Type
Article
DOI
https://doi.org/10.1186/1471-2156-6-S1-S153
Rights Information
© 2005 the authors, BioMed Central Ltd. licensee. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Publication Date
12-30-2005
Recommended Citation
Thompson, Cheryl L., Dan Baechle, Qing Lu, George Mathew, Yeunjoo Song, Sudha K. Iyengar, Courtney Gray-McGuire, and Katrina AB Goddard. "Effect of genotyping error in model-free linkage analysis using microsatellite or single-nucleotide polymorphism marker maps." In BMC genetics, vol. 6, no. S1, p. S153. BioMed Central, 2005.
Journal Title
BMC Genetics
