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Open Access Methodology article

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

Hideaki Mizuno123*, Gurinder Atwal4, Haijian Wang15, Arnold J Levine16 and Alexei Vazquez67

Author Affiliations

1 The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, USA

2 Pharmaceutical Technology Department, Chugai Pharmaceutical Co. Ltd., Kamakura, Kanagawa, Japan

3 Department of Biosciences and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan

4 Quantitative biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA

5 Laboratory of Systems Biology, Fudan University, Shanghai, PR China

6 The Cancer Institute of New Jersey, New Brunswick, New Jersey, USA

7 Department of Radiation Oncology, UMDNJ-Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA

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BMC Genetics 2010, 11:27  doi:10.1186/1471-2156-11-27

Published: 23 April 2010



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.


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 webcite), which allows researchers to query their regions of interest for population-specific LD.


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.