The Extent of Linkage Disequilibrium and Haplotype Sharing Around a Polymorphic Site

The Extent of Linkage Disequilibrium and Haplotype Sharing Around a Polymorphic Site

Hideki Innan^a,b and Magnus Nordborg^a
^a Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-1340
^b Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, Texas 77030

Corresponding author: Hideki Innan, School of Public Health, University of Texas Health Science Center, 1200 Hermann Pressler, Houston, TX 77030., hinnan{at}sph.uth.tmc.edu (E-mail)

Communicating editor: J. HEIN

Various expressions related to the length of a conserved haplotypearound a polymorphism of known frequency are derived. We obtainexact expressions for the probability that no recombinationhas occurred in a sample or subsample. We obtain an approximationfor the probability that no recombination that could give riseto a detectable recombination event (through the four-gametetest) has occurred. The probabilities can be used to obtainapproximate distributions for the length of variously definedhaplotypes around a polymorphic site. The implications of ourresults for data analysis, and in particular for detecting selection,are discussed.

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