Single-nucleotide polymorphisms and haplotype LD analysis of the 29-kb IGF2 region on chromosome 11p15.5 in the Korean population.
OBJECTIVE
We investigated sequence variations of the 29-kb insulin-like growth factor 2 (IGF2) region in human chromosome region 11p15.5 in the Korean population. This region consists of IGF2, insulin-like growth factor 2 antisense (IGF2AS), and the insulin gene, all important candidate genes for various diseases, including cancer, obesity, diabetes, and coronary disease. While single nucleotide polymorphisms (SNPs) have been identified for this region and used in association studies, ethnic differences in genetic variation at this site have not been addressed. To date, SNPs for the entire 29-kb region in the Korean population have not been reported.


METHODS
We surveyed a population of 108 Koreans for SNPs in the 29-kb IGF2 region.


RESULTS
We identified 62 SNPs, consisting of 6 SNPs in the promoter region, 17 in the untranslated region, 19 in introns, and 20 in the intergenic region. We also analyzed linkage disequilibrium (LD) patterns and haplotypes using 36 high-frequency (> 5%)SNPs and found a well-defined LD block spanning about 13 kb that includes 8 kb of the IGF2AS gene, with two hot-spot regions flanking the LD block.


CONCLUSIONS
These SNPs may be useful as genetic markers in disease association studies in the Korean population.
Lee
Hye-Ja
HJ
Division of Structural and Functional Genome Research, National Genome Research Institute, NIH Korea, Seoul, Korea.
Kim
Kwang-Joong
KJ
Park
Mi-Hyun
MH
Kimm
Kuchan
K
Park
Chan
C
Oh
Bermseok
B
Lee
Jong-Young
JY
D000328:Adult; D044466:Asian People / Q000235:genetics; D001483:Base Sequence; D002880:Chromosomes, Human, Pair 11 / Q000235:genetics*; D017931:DNA Primers; D005260:Female; D005787:Gene Frequency; D006133:Growth Substances / Q000235:genetics*; D006239:Haplotypes; D006801:Humans; D007335:Insulin-Like Growth Factor II; D007723:Korea; D015810:Linkage Disequilibrium / Q000235:genetics*; D008297:Male; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D011506:Proteins / Q000235:genetics*
D017931:DNA Primers; D006133:Growth Substances; C035170:IGF2 protein, human; D011506:Proteins; D007335:Insulin-Like Growth Factor II