SNP identification, linkage disequilibrium, and haplotype analysis for a 200-kb genomic region in a Korean population.
Understanding patterns of linkage disequilibrium (LD) across genomes may facilitate association mapping studies to localize genetic variants influencing complex diseases, a recognition that led to the International Haplotype Mapping Project (HapMap). Divergent patterns of haplotype frequency and LD across global populations require that the HapMap database be supplemented with haplotype and LD data from additional populations. We conducted a pilot study of the LD and haplotype structure of a genomic region in a Korean population. A total of 165 SNPs were identified in a 200-kb region of 22q13.2 by direct sequencing. Unphased genotype data were generated for 76 SNPs in 90 unrelated Korean individuals. LD, haplotype diversity, and recombination rates were assessed in this region and compared with the HapMap database. The pattern of LD and haplotype frequencies of Korean samples showed a high degree of similarity with Japanese data. There was a strong correlation between high LD and low recombination frequency in this region. We found considerable similarities in local LD patterns between three Asian populations (Han Chinese, Japanese, and Korean) and the CEPH population. Haplotype frequencies were, however, significantly different between them. Our results should further the understanding of distinctive Korean genomic features and assist in designing appropriate association studies.
Kim
Kwang Joong
KJ
Center for Genome Sciences, Korean National Institute of Health, Eunpyung-Gu, Seoul 122-701, Korea.
Lee
Hye-Ja
HJ
Park
Mi-Hyun
MH
Cha
Seung-Hun
SH
Kim
Kyung-Seon
KS
Kim
Hung-Tae
HT
Kimm
Kuchan
K
Oh
Bermseok
B
Lee
Jong-Young
JY
D044466:Asian People / Q000235:genetics*; D002874:Chromosome Mapping; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D030561:Databases, Nucleic Acid; D014644:Genetic Variation; D005828:Genetics, Population; D015894:Genome, Human; D023281:Genomics; D006239:Haplotypes; D006801:Humans; D007723:Korea; D015810:Linkage Disequilibrium; D010865:Pilot Projects; D020641:Polymorphism, Single Nucleotide