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Open Access Research article

Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype

Kyung-Seon Kim1, Ghi-Su Kim23, Joo-Yeon Hwang1, Hye-Ja Lee1, Mi-Hyun Park1, Kwang-joong Kim1, Jongsun Jung1, Hyo-Soung Cha1, Hyoung Doo Shin4, Jong-Ho Kang5, Eui Kyun Park26, Tae-Ho Kim2, Jung-Min Hong2, Jung-Min Koh23, Bermseok Oh1, Kuchan Kimm1, Shin-Yoon Kim27* and Jong-Young Lee1*

Author Affiliations

1 Center for Genome Science, National Institute of Health, 5 Nokbun-dong, Eunpyung-gu, Seoul 122-701, Republic of Korea

2 Skeletal Diseases Genome Research Center, Kyungpook National University Hospital, 44-2, Samduk 2-ga, Jung-gu, Daegu, 700-412, Republic of Korea

3 Division of Endocrinology and Metabolism, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 138-736, Republic of Korea

4 Department of Genetic Epidemiology, SNP Genetics, Inc., Rm 1407, 14th floor, B-dong, WooLim Lion's Valley, 371-28, Gasan-dong, Geumcheon-gu, Seoul, 153-803, Republic of Korea

5 World Meridian Venture Center 10F, #60-24, Gasan-dong, Geumcheon-gu, Seoul 153-023, Republic of Korea

6 Department of Pathology and Regenerative Medicine, School of Dentistry, Kyungpook National University, 188-1 Samduk 2-ga, Jung-gu, Daegu, 700-412, Republic of Korea

7 Department of Orthopedic Surgery, Kyungpook National University School of Medicine, 50, Samduk 2-ga, Jung-gu, Daegu, 700-412, Republic of Korea

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BMC Medical Genetics 2007, 8:70  doi:10.1186/1471-2350-8-70

Published: 26 November 2007

Abstract

Background

Osteoporosis is defined as the loss of bone mineral density that leads to bone fragility with aging. Population-based case-control studies have identified polymorphisms in many candidate genes that have been associated with bone mass maintenance or osteoporotic fracture. To investigate single nucleotide polymorphisms (SNPs) that are associated with osteoporosis, we examined the genetic variation among Koreans by analyzing 81 genes according to their function in bone formation and resorption during bone remodeling.

Methods

We resequenced all the exons, splice junctions and promoter regions of candidate osteoporosis genes using 24 unrelated Korean individuals. Using the common SNPs from our study and the HapMap database, a statistical analysis of deviation in heterozygosity depicted.

Results

We identified 942 variants, including 888 SNPs, 43 insertion/deletion polymorphisms, and 11 microsatellite markers. Of the SNPs, 557 (63%) had been previously identified and 331 (37%) were newly discovered in the Korean population. When compared SNPs in the Korean population with those in HapMap database, 1% (or less) of SNPs in the Japanese and Chinese subpopulations and 20% of those in Caucasian and African subpopulations were significantly differentiated from the Hardy-Weinberg expectations. In addition, an analysis of the genetic diversity showed that there were no significant differences among Korean, Han Chinese and Japanese populations, but African and Caucasian populations were significantly differentiated in selected genes. Nevertheless, in the detailed analysis of genetic properties, the LD and Haplotype block patterns among the five sub-populations were substantially different from one another.

Conclusion

Through the resequencing of 81 osteoporosis candidate genes, 118 unknown SNPs with a minor allele frequency (MAF) > 0.05 were discovered in the Korean population. In addition, using the common SNPs between our study and HapMap, an analysis of genetic diversity and deviation in heterozygosity was performed and the polymorphisms of the above genes among the five populations were substantially differentiated from one another. Further studies of osteoporosis could utilize the polymorphisms identified in our data since they may have important implications for the selection of highly informative SNPs for future association studies.