Comparative study of the haplotype structure and linkage disequilibrium of chromosome 1p36.2 region in the Korean and Japanese populations

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• 作者：Tamao Akesaka ; Seong-Gene Lee ; Jun Ohashi ; Makoto Bannai ; Naoyuki Tsuchiya ; Yongsook Yoon ; Katsushi Tokunaga and Kyuyoung Song
• 关键词：Chromosome 1p36.2 ; LD ; Haplotype ; Korean ; Japanese
• 刊名：Journal of Human Genetics
• 出版年：2004
• 出版时间：November 2004
• 年：2004
• 卷：49
• 期：11
• 页码：603-609
• 全文大小：548 KB
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Biomedicine
  Human Genetics
  Molecular Medicine
  Cancer Research
  Cell Biology
  Immunology
  Neurosciences
  
• 出版者：Springer Japan
• ISSN：1435-232X

文摘

The patterns of linkage disequilibrium (LD) in the human genome provide important information for disease gene mapping. LDs may vary depending on chromosomal regions and populations. We have compared LD and haplotypes defined by SNPs in the chromosome 1p36.2 region of the Korean and Japanese populations. Fifty-eight SNPs in about 418 kb ranging from tumor necrosis factor receptor 2 (TNFR2:TNFRSF1B) to procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD) gene were examined in 96 healthy Koreans and Japanese each by direct sequencing and fluorescence correlation spectroscopy combined with the PCR-sequence specific primer method (PCR-SSP-FCS), respectively. Upon pair-wise LD analysis, a total of 25 and 16 out of 58 SNPs greater than MAF 10% were included in LD blocks, encompassing almost 81 kb and 55 kb in total, in Koreans and Japanese, respectively. Both similarities and differences were observed in LD strength and haplotype frequencies between the populations. Considerable similarities were observed in the telomeric region where a long-range block of approximately 80 kb including three genes was found to have strong LDs in both Koreans and Japanese. Significant difference in LD strength was present near the TNFR2 region between the Japanese and Korean populations.