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Open Access Research article

A genome-wide Asian genetic map and ethnic comparison: The GENDISCAN study

Young Seok Ju1, Hansoo Park1, Mi Kyeong Lee23, Jong-Il Kim12, Joohon Sung3, Sung-Il Cho3 and Jeong-Sun Seo14*

Author Affiliations

1 Department of Biochemistry and Molecular Biology, College of Medicine, Seoul National University, Seoul, Korea

2 Psoma Therapeutics, Seoul, Korea

3 Department of Epidemiology, Graduate School of Public Health and Institute of Health and Environment, Seoul National University, Seoul, Korea

4 ILCHUN Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea

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BMC Genomics 2008, 9:554  doi:10.1186/1471-2164-9-554

Published: 25 November 2008

Abstract

Background

Genetic maps provide specific positions of genetic markers, which are required for performing genetic studies. Linkage analyses of Asian families have been performed with Caucasian genetic maps, since appropriate genetic maps of Asians were not available. Different ethnic groups may have different recombination rates as a result of genomic variations, which would generate misspecification of the genetic map and reduce the power of linkage analyses.

Results

We constructed the genetic map of a Mongolian population in Asia with CRIMAP software. This new map, called the GENDISCAN map, is based on genotype data collected from 1026 individuals of 73 large Mongolian families, and includes 1790 total and 1500 observable meioses. The GENDISCAN map provides sex-averaged and sex-specific genetic positions of 1039 microsatellite markers in Kosambi centimorgans (cM) with physical positions. We also determined 95% confidence intervals of genetic distances of the adjacent marker intervals.

Genetic lengths of the whole genome, chromosomes and adjacent marker intervals are compared with those of Rutgers Map v.2, which was constructed based on Caucasian populations (Centre d'Etudes du Polymorphisme Humain (CEPH) and Icelandic families) by mapping methods identical to those of the GENDISCAN map, CRIMAP software and the Kosambi map function. Mongolians showed approximately 1.9 fewer recombinations per meiosis than Caucasians. As a result, genetic lengths of the whole genome and chromosomes of the GENDISCAN map are shorter than those of Rutgers Map v.2. Thirty-eight marker intervals differed significantly between the Mongolian and Caucasian genetic maps.

Conclusion

The new GENDISCAN map is applicable to the genetic study of Asian populations. Differences in the genetic distances between the GENDISCAN and Caucasian maps could facilitate elucidation of genomic variations between different ethnic groups.