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Computationally Efficient Sibship and Parentage Assignment from Multilocus Marker Data

Overview
Journal Genetics
Specialty Genetics
Date 2012 Feb 28
PMID 22367033
Citations 32
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Abstract

Quite a few methods have been proposed to infer sibship and parentage among individuals from their multilocus marker genotypes. They are all based on Mendelian laws either qualitatively (exclusion methods) or quantitatively (likelihood methods), have different optimization criteria, and use different algorithms in searching for the optimal solution. The full-likelihood method assigns sibship and parentage relationships among all sampled individuals jointly. It is by far the most accurate method, but is computationally prohibitive for large data sets with many individuals and many loci. In this article I propose a new likelihood-based method that is computationally efficient enough to handle large data sets. The method uses the sum of the log likelihoods of pairwise relationships in a configuration as the score to measure its plausibility, where log likelihoods of pairwise relationships are calculated only once and stored for repeated use. By analyzing several empirical and many simulated data sets, I show that the new method is more accurate than pairwise likelihood and exclusion-based methods, but is slightly less accurate than the full-likelihood method. However, the new method is computationally much more efficient than the full-likelihood method, and for the cases of both sexes polygamous and markers with genotyping errors, it can be several orders faster. The new method can handle a large sample with thousands of individuals and the number of markers limited only by the computer memory.

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References
1.
Thomas S, Hill W . Estimating quantitative genetic parameters using sibships reconstructed from marker data. Genetics. 2000; 155(4):1961-72. PMC: 1461185. DOI: 10.1093/genetics/155.4.1961. View

2.
McPeek M, Sun L . Statistical tests for detection of misspecified relationships by use of genome-screen data. Am J Hum Genet. 2000; 66(3):1076-94. PMC: 1288143. DOI: 10.1086/302800. View

3.
Hammond R, Bourke A, Bruford M . Mating frequency and mating system of the polygynous ant, Leptothorax acervorum. Mol Ecol. 2002; 10(11):2719-28. DOI: 10.1046/j.0962-1083.2001.01394.x. View

4.
Epstein M, Duren W, Boehnke M . Improved inference of relationship for pairs of individuals. Am J Hum Genet. 2000; 67(5):1219-31. PMC: 1288564. DOI: 10.1016/S0002-9297(07)62952-8. View

5.
Berger-Wolf T, Sheikh S, Dasgupta B, Ashley M, Caballero I, Chaovalitwongse W . Reconstructing sibling relationships in wild populations. Bioinformatics. 2007; 23(13):i49-56. DOI: 10.1093/bioinformatics/btm219. View