Optimal peeling order for pedigrees with incomplete genotypic information. (English) Zbl 1124.62071

Summary: The likelihood approach is common in linkage analysis of large extended pedigrees. Various peeling procedures, based on the conditional independence of separate parts of a pedigree, are typically used for likelihood calculations. A peeling order may significantly affect the complexity of such calculations, particularly for pedigrees with loops or when many pedigree members have unknown genotypes. Several algorithms have been proposed to address this problem for pedigrees with loops. However, the problem has not been solved for pedigrees without loops until now.
We suggest a new graph theoretic algorithm for optimal selection of peeling order in zero-loop pedigrees with incomplete genotypic information. It is especially useful when multiple likelihood calculation is needed, for example, when genetic parameters are estimated or linkage with multiple marker loci is tested. The algorithm can be easily introduced into the existing software packages for linkage analysis based on the Elston-Stewart algorithm for likelihood calculation. The algorithm was implemented in a software package PedPeel, which is freely available at http://mga.bionet.nsc.ru/nlru/.


62P10 Applications of statistics to biology and medical sciences; meta analysis
92D10 Genetics and epigenetics
05C90 Applications of graph theory
92D15 Problems related to evolution


Full Text: DOI


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