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Open Access Method

hzAnalyzer: detection, quantification, and visualization of contiguous homozygosity in high-density genotyping datasets

Todd A Johnson12, Yoshihito Niimura2, Hiroshi Tanaka3, Yusuke Nakamura4 and Tatsuhiko Tsunoda1*

Author Affiliations

1 Laboratory for Medical Informatics, Center for Genomic Medicine, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa-ken, 230-0045, Japan

2 Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan

3 Department of Bioinformatics, School of Biomedical Science, Tokyo Medical and Dental University, Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan

4 Human Genome Center, Institute of Medical Science, University of Tokyo, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan

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Genome Biology 2011, 12:R21  doi:10.1186/gb-2011-12-3-r21

Published: 11 March 2011

Abstract

The analysis of contiguous homozygosity (runs of homozygous loci) in human genotyping datasets is critical in the search for causal disease variants in monogenic disorders, studies of population history and the identification of targets of natural selection. Here, we report methods for extracting homozygous segments from high-density genotyping datasets, quantifying their local genomic structure, identifying outstanding regions within the genome and visualizing results for comparative analysis between population samples.