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Genetics, Vol. 178, 2123-2132, April 2008, Copyright © 2008
doi:10.1534/genetics.107.084624

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Estimation of Pairwise Identity by Descent From Dense Genetic Marker Data in a Population Sample of Haplotypes

Sharon R. Browning1

Department of Statistics, The University of Auckland, Auckland 1142, New Zealand

1 Address for correspondence: Department of Statistics, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
E-mail: s.browning{at}auckland.ac.nz

I present a new approach for calculating probabilities of identity by descent for pairs of haplotypes. The approach is based on a joint hidden Markov model for haplotype frequencies and identity by descent (IBD). This model allows for linkage disequilibrium, and the method can be applied to very dense marker data. The method has high power for detecting IBD tracts of genetic length of 1 cM, with the use of sufficiently dense markers. This enables detection of pairwise IBD between haplotypes from individuals whose most recent common ancestor lived up to 50 generations ago.






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Copyright © 2008 by the Genetics Society of America.