Comparative study of the haplotype structure and linkage disequilibrium of chromosome 1p36.2 region in the Korean and Japanese populations.
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.
Department of Human Genetics, University of Tokyo, Tokyo, Japan.
Tamao
T
Akesaka
Asan Institute for Life Science, University of Ulsan College of Medicine, Seoul, 138-736, South Korea.|Department of Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea.
Seong-Gene
SG
Lee
Department of Human Genetics, University of Tokyo, Tokyo, Japan.
Jun
J
Ohashi
Department of Human Genetics, University of Tokyo, Tokyo, Japan.
Makoto
M
Bannai
Department of Human Genetics, University of Tokyo, Tokyo, Japan.
Naoyuki
N
Tsuchiya
Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 138-736, South Korea.
Yongsook
Y
Yoon
Department of Human Genetics, University of Tokyo, Tokyo, Japan.
Katsushi
K
Tokunaga
Asan Institute for Life Science, University of Ulsan College of Medicine, Seoul, 138-736, South Korea. kysong@amc.seoul.kr.|Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 138-736, South Korea. kysong@amc.seoul.kr.
Kyuyoung
K
Song
D001483:Base Sequence; D002878:Chromosomes, Human, Pair 1 / Q000235:genetics*; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D007564:Japan; D007723:Korea; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013050:Spectrometry, Fluorescence; D016615:Telomere / Q000235:genetics; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics
C439524:TNF protein, human; D014409:Tumor Necrosis Factor-alpha