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

Ju YS, Park H, Lee MK, Kim JI, Sung J, Cho SI, Seo JS - BMC Genomics (2008)

Bottom Line: 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.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.As a result, genetic lengths of the whole genome and chromosomes of the GENDISCAN map are shorter than those of Rutgers Map v.2.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, College of Medicine, Seoul National University, Seoul, Korea. jueenome@gmail.com

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.

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Comparison of whole genome lengths between the GENDISCAN map and Rutgers Map v.2. Error bars represents the 95% confidence intervals from the paired t-tests.
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Figure 1: Comparison of whole genome lengths between the GENDISCAN map and Rutgers Map v.2. Error bars represents the 95% confidence intervals from the paired t-tests.

Mentions: The sex-averaged, female and male whole genome lengths were 3230.6 cM, 3906.0 cM and 2394.0 cM, respectively, which are 5 – 9% shorter than the respective genome lengths of Rutgers Map v.2 (Figure 1). The genetic lengths of chromosomes of the sex-averaged, female and male maps are illustrated in Figures 2, 3 and 4, respectively. All chromosomal lengths of the GENDISCAN map were shorter than those of the Rutgers Map v.2 except for male chromosomes 3 and 6, and sex-averaged chromosome 3. Paired t-tests demonstrated significant differences between the whole genome and chromosome genetic lengths (Table 2). The whole genome and chromosome 2 lengths of all three types of GENDISCAN map were significantly shorter than those of the Rutgers MAP v.2.


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

Ju YS, Park H, Lee MK, Kim JI, Sung J, Cho SI, Seo JS - BMC Genomics (2008)

Comparison of whole genome lengths between the GENDISCAN map and Rutgers Map v.2. Error bars represents the 95% confidence intervals from the paired t-tests.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2612022&req=5

Figure 1: Comparison of whole genome lengths between the GENDISCAN map and Rutgers Map v.2. Error bars represents the 95% confidence intervals from the paired t-tests.
Mentions: The sex-averaged, female and male whole genome lengths were 3230.6 cM, 3906.0 cM and 2394.0 cM, respectively, which are 5 – 9% shorter than the respective genome lengths of Rutgers Map v.2 (Figure 1). The genetic lengths of chromosomes of the sex-averaged, female and male maps are illustrated in Figures 2, 3 and 4, respectively. All chromosomal lengths of the GENDISCAN map were shorter than those of the Rutgers Map v.2 except for male chromosomes 3 and 6, and sex-averaged chromosome 3. Paired t-tests demonstrated significant differences between the whole genome and chromosome genetic lengths (Table 2). The whole genome and chromosome 2 lengths of all three types of GENDISCAN map were significantly shorter than those of the Rutgers MAP v.2.

Bottom Line: 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.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.As a result, genetic lengths of the whole genome and chromosomes of the GENDISCAN map are shorter than those of Rutgers Map v.2.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, College of Medicine, Seoul National University, Seoul, Korea. jueenome@gmail.com

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.

Show MeSH