Hanchard, Neil A.; Rockett, K.; Spencer, C.; Coop, G.; Pinder, M.; Jallow, M.; Kimber, M.; McVean, G.; Mott, R.; Kwiatkowski, D.P.
Author Affiliation, Ana.
Tropical Medicine Research Institute
Screening for recently selected alleles by analysis of human haplotype similarity
The American journal of human genetics
Date of Publication
There is growing interest in the use of haplotype based methods of detecting recent selection. The authors describe a method that uses a sliding window to estimate similarity among the haplotypes associated with any given SNP allele. They used simulations of natural selection to provide estimates of the empirical power of the method to detect recently selected alleles, and found it to be comparable to the popular long range haplotype (LRH) test and more powerful than methods based on nucleotide diversity. The method was applied to a recently selected allele - the sickle mutation at the HBB locus, was found to have a signal of selection significantly stronger than simulated models both with and without strong selection. Using this method we also evaluated over 4000 SNPs on chromosome 20, indicating the applicability of the method to regional datasets.....