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URL: http://ihg2.helmholtz-muenchen.de/cgi-bin/mueller/webehh.pl
Proper Citation: Extended Haplotype Homozygosity (RRID:SCR_008491)
Description: THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 11, 2013. Web-based tool to explore the relationship between population frequency and extended linkage disequilibrium measured as haplotype homozygosity of observed haplotypes within a specified candidate region. Haplotype homozygosity (HH) is an effective measure of linkage disequilibrium (LD) for more than 2 markers. If we want to see, how LD breaks down with increasing distance to a specified core region, we can calculate HH in a stepwise manner as extended HH (EHH, Sabeti et al. 2002). EHH is calculated between a distance x and the specified core region for a chromosome population carrying a single core haplotype. Distance x increases stepwise to the most outlying marker. The procedure is repeated for each core haplotype. HH is evaluated as HH = sum(pi2) - 1/n / 1 - 1/n with pi being the relative haplotype frequency and n the sample size. It corrects for sampling effects (Sabatti & Risch 2002). The variance of HH is estimated according to Nei (1975). EHH estimates the level of haplotype splitting due to recombination and mutation at extended regions on both sides of a specified core region. It may be used to explore haplotype-specific LD patterns, e.g. for disease associated haplotypes. In combination with the core haplotype frequency it may also serve as an indicator of recent positive selection. Frequent core haplotypes with an unusually high long-range LD are supposed to be positively selected. The various core haplotypes can serve as internal controls. Input file: A text file consisting of a haplotype (chromosome) population
Abbreviations: Extended Haplotype Homozygosity
Resource Type: software resource
Defining Citation: PMID:14764566
Keywords: haplotype, population frequency, linkage disequilibrium, homozygosity, candidate region, haplotype homozygosity
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