Three-point appraisal of genetic linkage maps |
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Authors: | W. R. Gilks S. J. Welham J. Wang S. J. Clark G. J. King |
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Affiliation: | 1. Department of Computational and Systems Biology, Rothamsted Research, Harpenden, AL5 2JQ, UK 2. Department of Statistics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK 3. VSN International Ltd, 5 The Waterhouse, Waterhouse St, Hemel Hempstead, HP1 1ES, UK 4. Plant Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK 5. Centre for Haemato-Oncology, Institute of Cancer, Barts and the London School of Medicine and Dentistry, Charterhouse Square, London, EC1M 6BQ, UK 6. Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
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Abstract: | This paper develops a simple diagnostic for the investigation of uncertainty within genetic linkage maps using a Bayesian procedure. The method requires only the genotyping data and the proposed genetic map, and calculates the posterior probability for the possible orders of any set of three markers, accounting for the presence of genotyping error (mistyping) and for missing genotype data. The method uses a Bayesian approach to give insight into conflicts between the order in the proposed map and the genotype scores. The method can also be used to assess the accuracy of a genetic map at different genomic scales and to assess alternative potential marker orders. Simulation and two case studies were used to illustrate the method. In the first case study, the diagnostic revealed conflicts in map ordering for short inter-marker distances that were resolved at a distance of 8–12?cM, except for a set of markers at the end of the linkage group. In the second case study, the ordering did not resolve as distances increase, which could be attributed to regions of the map where many individuals were untyped. |
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