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Identification and Characterization of Human Genes Targeted by Natural Selection
류하정,김영주,박영규,김재정,서을주,유한욱,박인숙,오범석,이종극 한국유전체학회 2008 Genomics & informatics Vol.6 No.4
The human genome has evolved as a consequence of evolutionary forces, such as natural selection. In this study, we investigated natural selection on the human genes by comparing the numbers of nonsynonymous (NS) and synonymous (S) mutations in individual genes. We initially collected all coding SNP data of all human genes from the public dbSNP. Among the human genes, we selected 3 different selection groups of genes: positively selected genes (NS/S≥3), negatively selected genes (NS/S≤1/3) and neutral selection genes (0.9 <NS/S<1.1). We characterized human genes targeted by natural selection. Negatively selected human genes were markedly associated with disease occurrence, but not positively selected genes. Interestingly, positively selected genes displayed an increase in potentially deleterious nonsynonymous SNPs with an increased frequency of tryptophan and tyrosine residues, suggesting a correlation with protective effects against human disease. Furthermore, our nonsynonymous/synonymous ratio data imply that specific human genes, such as ALMS1 and SPTBN5 genes, are differentially selected among distinct populations. We confirmed that inferences of natural selection using the NS/S ratio can be used extensively to identify functional genes selected during the evolutionary adaptation process.
Putative association of RUNX1 polymorphisms with IgE levels in a Korean population
채수천,박병래,박춘식,류하정,양윤식,이수옥,최유현,김은미,우수택,김용훈,김가경,오범석,정헌택,김규찬,신형두 생화학분자생물학회 2006 Experimental and molecular medicine Vol.38 No.5
RUNX1, a member of the runt domain gene family of transcription factors, encodes a heterodimeric transcription factor and regulates the expression of hematopoiesis and myeloid differentiation. RUNX1 has been one of the target genes for research into various autoimmune disea-ses due to its properties as a transcription factor and functional distribution for chromosomal trans-location. In an effort to identify additional gene polymorphisms in which variants have been implicated in asthma, we investigated the genetic polymorphisms in RUNX1 to evaluate it as a potential candidate gene for a host genetic study of asthma and IgE production. We identified 19 sequence variants by direct DNA sequencing in 24 individuals of which four common variants were selected for genotyping in our asthma cohort (1,055 asthmatic patients, 384 normal controls). Using logistic regression analysis for association with the risk of asthma, while controlling for age, gender, and smoking status as of asthma were detected. However, two poly-morphisms in the promoter region (-2084G> C and -1282G>A) showed a marginal association with total IgE levels (0.03 and 0.03 in recessive models, respectively). Our findings suggest that poly-morphisms in RUNX1 might be one of the genetic factors for the regulation of IgE production
홍경원,진현석,임지은,류하정,안윤진,이종영,한복기,신형두,조남한,신철,우정택,박헌국,오범석 한국유전체학회 2008 Genomics & informatics Vol.6 No.3
Protein phosphorylation at tyrosine residues is a key regulatory event that modulates insulin signal transduction. We studied the PTPN1 gene with regard to susceptibility to Korean type 2 diabetes mellitus (T2DM) and its related quantitative traits. A total of seven SNPs [g.36171G>A (rs941798), g.58166G>A (rs3787343), g.58208A>G (rs2909270), g.64840C>T (rs754118), g.69560C>G (rs6020612), g.69866G>A (rs718050), and g.69934T>G (rs3787343)] were selected based on frequency (>0.05), linkage disequilibrium (LD) status, and haplotype tagging status. We studied the seven SNPs in 483 unrelated patients with type 2 diabetes (age: 64±2.8 years, onset age: 56±8.1 years; 206 men, 277 women) and 1138 nondiabetic control subjects (age: 64±2.9; 516 men, 622 women). The SNP rs941798 had protective effects against T2DM with an odds ratio of 0.726 (C.I. 0.541∼0.975) and p-value=0.034, but none of the remaining six SNPs was associated with T2DM. Also, rs941798 was associated with blood pressure, HDL cholesterol, insulin sensitivity. rs941798 also has been associated with T2DM in previous reports of Caucasian-American and Hispanic-American populations. This is the first report that shows an association between PTPN1 and T2DM in the Korean as well as Asian population.