Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome

Mizuno, H., Atwal, G. S., Wang, H., Levine, A. J., Vazquez, A. (April 2010) Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome. BMC Genet, 11. p. 27. ISSN 1471-2156 (Electronic) 1471-2156 (Linking)

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URL: https://www.ncbi.nlm.nih.gov/pubmed/20416085
DOI: 10.1186/1471-2156-11-27

Abstract

BACKGROUND: The creation of a coherent genomic map of recent selection is one of the greatest challenges towards a better understanding of human evolution and the identification of functional genetic variants. Several methods have been proposed to detect linkage disequilibrium (LD), which is indicative of natural selection, from genome-wide profiles of common genetic variations but are designed for large regions. RESULTS: To find population-specific LD within small regions, we have devised an entropy-based method that utilizes differences in haplotype frequency between populations. The method has the advantages of incorporating multilocus association, conciliation with low allele frequencies, and independence from allele polarity, which are ideal for short haplotype analysis. The comparison of HapMap SNPs data from African and Caucasian populations with a median resolution size of ~23 kb gave us novel candidates as well as known selection targets. Enrichment analysis for the yielded genes showed associations with diverse diseases such as cardiovascular, immunological, neurological, and skeletal and muscular diseases. A possible scenario for a selective force is discussed. In addition, we have developed a web interface (ENIGMA, available at http://gibk21.bse.kyutech.ac.jp/ENIGMA/index.html), which allows researchers to query their regions of interest for population-specific LD. CONCLUSION: The haplotype entropy method is powerful for detecting population-specific LD embedded in short regions and should contribute to further studies aiming to decipher the evolutionary histories of modern humans.

Item Type: Paper
Uncontrolled Keywords: genomic map functional genetic variants linkage disequilibrium ENIGMA evolutionary histories of modern humans
Subjects: diseases & disorders
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > annotation > map annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > SNP
CSHL Authors:
Communities: CSHL labs > Atwal lab
Depositing User: CSHL Librarian
Date: 23 April 2010
Date Deposited: 03 Oct 2011 15:38
Last Modified: 19 Dec 2016 21:42
PMCID: PMC2873552
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15486

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