• Genomics & Informatics
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• v.6 no.1
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• pp.18-28
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• 2008

Single nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variations and resources for mapping complex genetic traits and disease association studies. We have constructed a linkage disequilibrium (LD) map of chromosome 22 in Korean samples and compared it with those of other populations, including Yorubans in Ibadan, Nigeria (YRI), Centre d'Etude du Polymorphisme Humain (CEPH) reference families (CEU), Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) in the HapMap database. We genotyped 4681 of 111,448 publicly available SNPs in 90 unrelated Koreans. Among genotyped SNPs, 4167 were polymorphic. Three hundred and five LD blocks were constructed to make up 18.6% (6.4 of 34.5 Mb) of chromosome 22 with 757 tagSNPs and 815 haplotypes (frequency $\geq$ 5.0%). Of 3430 common SNPs genotyped in all five populations, 514 were monomorphic in Koreans. The CHB + JPT samples have more than a 72% overlap with the monomorphic SNPs in Koreans, while the CEU + YRI samples have less than a 38% overlap. The patterns of hot spots and LD blocks were dispersed throughout chromosome 22, with some common blocks among populations, highly concordant between the three Asian samples. Analysis of the distribution of chimpanzee-derived allele frequency (DAF), a measure of genetic differentiation, Fst levels, and allele frequency difference (AFD) among Koreans and the HapMap samples showed a strong correlation between the Asians, while the CEU and YRI samples showed a very weak correlation with Korean samples. Relative distance as a quantitative measurement based upon DAF, Fst, and AFD indicated that all three Asian samples are very proximate, while CEU and YRI are significantly remote from the Asian samples. Comparative genome-wide LD studies provide useful information on the association studies of complex diseases.

• Korean Journal Plant Pathology
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• v.10 no.1
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• pp.1-6
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• 1994

Randomly chosen recombinant clones of Fusarium oxysporum were analysed to select useful probes for relatedness analysis of Fusarium oxysporum. Genomic DNA of F. oxysproum f. sp. cubense, digested with HindIII, was ligated to pUC118 and used to transform Escherichia coli strai DH5$\alpha$. Three clones were identified that hybridized to mutiple restriction fragments of some formae speciales of F. oxysporum. These probes detected repetitive sequences in HindIII or EcoRI digested DNAs. Repeated copy clone pFC46, pFC52 and pFC54 showed evident polymorphisms among ten formae speciales of this fungus. Since clone pFC 52 strongly hybridized to multiple EcoRI-digested restriction fragments of f. sp. cubense, it may be useful as a probe for analysis of other genetic characteristics of this forma specialis. The results suggest that our clones might be very useful as probes for relatedness analysis between or within formae speciales of Fusarium oxysporum.

• Archives of Pharmacal Research
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• v.26 no.6
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• pp.482-486
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• 2003

Adult periodontitis is a multifactorial disease characterized by multple genetic and environmental factors. In view of the importance of interleukin-4 (IL-4) gene as a genetic factor for adult periodontitis, we investigated the relationship between two polymorphisms (-590 C $\rightarrow$ T polymorphism and 70 bp repeat polymorphism) of the human IL-4 gene and adult periodontitis in the Korean population. Genomic DNA was extracted from white blood cells of 32 adult periodontitis patients and 150 normal controls, respectively. There were no significant differences in the allele, genotype and haplotype distributions of two polymorph isms between normal controls and adult periodontitis group. Therefore, our results suggest that IL-4 gene locus contributes little to the interindividual susceptibility for adult periodontitis in Korean population.

• Journal of Nutrition and Health
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• v.43 no.4
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• pp.357-366
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• 2010

There has been no genome-wide association study (GWAS) for macronutrient intake as a quantitative trait. To explore genetic loci associated with total calorie and macronutrient intake, genome-wide association data of autosomal single nucleotide polymorphisms (SNPs) from Korean adults were analyzed. We conducted a GWAS in 3,690 men and women aged 40 to 60 years from an urban population-based cohort. At the baseline examination (June 18, 2001 through January 29, 2003), DNA samples of the study subjects were collected and analyzed for genotyping. The information of average daily consumption of total calorie, carbohydrate, protein, and fat was obtained from a semi-quantitative food frequency questionnaire and transformed by natural logarithm for analyses after adjustment of calorie intake. Using multivariate linear regression analysis adjusted for age, sex, and height, we tested for 352,021 SNPs and found weak associations, which do not reach genome-wide association significance, with calorie and macronutrient intake. However, a number of SNPs were found to have potential associations with macronutrient intake; in particular, signals in SORBS1 and those in PRKCB1 were likely associated with carbohydrate and fat intake, respectively. We observed an inverse association between the minor allele of the SNPs in these genes and the amount of consumption of carbohydrate or fat. Our GWAS identified loci and minor alleles weakly associated with macronutrient intake. Because SORBS1 and PRKCB1 are reportedly associated with the metabolism of glucose and lipid as well as with obesity-related diseases, further investigations on biological and functional roles of polymorphism of these genes in the relation to macronutrient intake are warranted.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8227-8233
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• 2016

Background: To investigate polymorphisms in heat shock proteins A1B and A1L (HOM) and associated risk of oesophageal carcinoma in Northeast India. Materials and Methods: The study includes oesophageal cancer (ECA) patients attending general outpatient department (OPD) and endoscopic unit of Gauhati Medical College. Patients were diagnosed based on endoscopic and histopathological findings. Genomic DNA was typed for HSPA1B1267 and HSPA1L2437 SNPs using the polymerase chain reaction with restriction fragment length polymorphisms. Results: A total of 78 cases and 100 age-sex matched healthy controls were included in the study with a male: female ratio of 5:3 and a mean age of $61.4{\pm}8.5years$. Clinico-pathological evaluation showed 84% had squamous cell carcinoma and 16% were adenocarcinoma. Dysphagia grades 4 (43.5%) and 5 (37.1%) were observed by endoscopic and hispathological evaluation. The frequency of genomic variation of A1B from wild type A/A to heterozygous A/G and mutant G/G showed a positive association [chi sq=19.9, p=<0.05] and the allelic frequency also showed a significant correlation [chi sq=10.3, with cases vs. controls, OR=0.32, $p{\leq}0.05$]. The genomic variation of A1L from wild T/T to heterozygous T/C and mutant C/C were found positively associated [chi sq=7.02, p<0.05] with development of ECA. While analyzing the allelic frequency, there was no significant association [chi sq=3.19, OR=0.49, p=0.07]. Among all the risk factors, betel quid [OR=9.79, Chi square=35.0, p<0.05], tobacco [OR=2.95, chi square=10.6, p<0.05], smoking [OR=3.23, chi square=10.1, p<0.05] demonstrated significant differences between consumers vs. non consumers regarding EC development. Alcohol did not show any significant association [OR=1.34, chi square=0.69, p=0.4] independently. Conclusions: It can be concluded that the present study provides marked evidence that polymorphisms of HSP70 A1B and HSP70 A1L genes are associated with the development of ECA in a population in Northeast India, A1B having a stronger influence. Betel quid consumption was found to be a highly significant risk factor, followed by smoking and tobacco chewing. Although alcohol was not a potent risk factor independently, alcohol consumption along with tobacco, smoking and betel nut was found to contribute to development of ECA.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.17
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• pp.7413-7417
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• 2014

Background: Development of gastric cancer (GC) is a multistep process that requires alterations in the expression of oncogenes and tumor suppressor genes, occurring over several decades. The p53 tumor suppressor protein is involved in cell-cycle control, apoptosis and DNA repair. One of the most important regulators of p53 is MDM2, which acts as a negative regulator in the p53 pathway. Based on the key role of p53 and MDM2 in tumor suppression, polymorphisms that cause change in their function might affect cancer risk. We therefore elevated associations of the polymorphisms of p53 (R72P) and MDM2 (SNP309) with GC in Iran. Materials and Methods: A total of 104 patients with gastric cancer and 100 controls were recruited. Genomic DNA was extracted from fresh gastric samples. Genotyping of the p53 and MDM2 genes was performed using allele specific PCR (AS-PCR). Results: There was no significant difference between the p53 codon 72 polymorphism distribution in control and patient groups (p=0.54), but the G allele of MDM2 was found to be over-represented in patients (p=0. 01, Odds Ratio=2. 08, 95% Confidence Interval= 1.37-4.34). Conclusions: The p53 R72P seems not to be a potential risk factor for development of GC among Iranian patients, but our data suggest that MDM2 SNP309 might modify the risk related to GC.

• Journal of Animal Science and Technology
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• v.53 no.6
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• pp.511-516
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• 2011

Fas gene known to associate with intramuscular fat content in Korean cattle was selected for DNA marker development. Fas (APO-1, CD95), a member of the tumor necrosis factor (TNF) receptor superfamily, is a cell membrane protein that mediates apoptosis (programmed cell death). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers at genomic level. Of this gene to search for SNP, sequences of whole exon and 1kb range of both front and back of the gene using 24 cattle were determined by direct-sequencing methods. As a result, 16 SNPs in exon, 37 SNPs in intron and 2 SNPs in promoter region, a total of 55 SNPs were discovered. In these SNPs, thirty-one common polymorphic sites were selected considering their allele frequencies, haplotype-tagging status and Linkage Disequilibrium (LD) for genotyping in larger-scale subjects. Selected SNPs were confirmed genotype through SNaPshot method (n=274) and were examined for possible genetic association of Fas polymorphisms with carcass weight (CWT), eye muscle area (EMA), and backfat thickness (BF). So, the SNP have been identified significant g.-12T>G, g.1112T>G and g.32548T>C. These results suggest that polymorphism of Fas gene was associated with meat quality traits in Hanwoo.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3955-3961
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• 2013

Background: Defects of manganese superoxide dismutase (MnSOD) have long been implicated in generation of oxidative stress and risk susceptibility to various cancers. Two functional polymorphisms within the MnSOD gene, including the Val-9Ala of the mitochondrial targeting sequence (MTS) and the Ile58Thr of the exon-3, have been proposed to reduce its enzyme activity and antioxidant potential. Materials and Methods: A high-throughput multiplex SNaPshot$^{(R)}$ system was developed herein for simultaneous analyses of Val-9Ala and Ile58Thr in a single reaction. Genomic DNA extracted from each whole blood sample of 248 patients including 107 with cervical cancer and 141 with breast cancer and from 136 healthy women as controls was analyzed by the multiplex SNaPshot$^{(R)}$ system. Results: The Val/Val, Val/Ala genotypes and the Val allele of the MTS were predominant in patients with cervical or breast cancer as well as healthy women in Thailand. The Ile/Ile genotype and the Ile allele of the exon-3 were found in all of them whereas none of the Ile/Thr, the Thr/Thr genotypes and the Thr allele was detected. Genotypic association of both Val-9Ala and Ile58Thr polymorphisms with cervical cancer and breast cancer of these patients comparing to healthy women was not statistically significant (p<0.05). Conclusions: The Val/Val, Val/Ala genotypes and the Val allele of the MTS were found predominantly but the Ile/Ile genotype and the Ile allele of the exon-3 were detected in patients with cervical cancer, breast cancer and healthy women in Thailand. These two functional polymorphisms (Val-9Ala and Ile58Thr) in MnSOD gene did not associate with susceptibility risk of these cancer patients in Thailand.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.12
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• pp.6217-6220
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• 2012

Introduction: Up to present, EGF $61^*A$/G, TGF-${\beta}1$-$509^*T$/C and TNF-${\alpha}$-$308^*A$/G gene polymorphisms have been analysed in other cancer entities than hepatocellular carcinoma (HCC). We here investigated the frequency of these gene polymorphisms among HCC patients. Materials and Methods: A total of 73 HCC patients and 117 cancer-free healthy people were recruited at the Surgical Department of Zhongshan Hospital. Genomic DNA was isolated from peripheral blood and gene polymorphisms were analyzed by PCR-RFLP. Results: The distribution of EGF $61^*G$/G homozygotes among HCC patients was more frequent than that in the control group (24.7% vs 11.1%, OR=2.618, 95%CI=1.195-5.738). In parallel, the frequency of the "G" allele in the HCC patient group was also higher than that in the control group (45.9% vs 33.3%, OR= 1.696, 95%CI=1.110-2.592). No difference could be found for the TGF-${\beta}1$-509 and TNF-${\alpha}$-308 genotypes. Conclusion: EGF $61^*G$/G genotype and G allele are significantly increased among patients with HCC. TGF-${\beta}1$-$509^*T$/C and TNF-${\alpha}$-$308^*A$/G gene polymorphisms are not related to this cancer entity.

• Journal of Korean Medicine for Obesity Research
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• v.6 no.2
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• pp.59-73
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• 2006

Objectives: This study was conducted to investigate the effects of Uncoupling protein (UCP) polymorphisms on weight loss. We analyzed associations between polymorphisms of UCP-2, 3 and changes in percentage of obesity phenotypes (Body mass index and percent body fat) after treatment. Materials and Methods: A total of 207 Korean women (BMI over 25) were recruited from the obesity clinic in Kirin Oriental Medical Hospital (Seoul, Korea). All patients were treated with a very low calorie diet and oriental medical therapy for one month. The effect of UCP polymorphisms on changes in obesity-phenotypes were analyzed. For the genotyping of a single nucleotide polymorphism (SNPs), genomic DNA from each subject was extracted from whole blood and genotyped using the TaqMan Method. Associations between changes in percentage of obesity phenotypes (BMI and percent body fat) and UCP polymorphisms were analyzed using age-adjusted general linear model. Results and Conclusions: In this study, AG, GG type of UCP-2 -866A>G, CC, CT type of UCP-2 +4787C>T, CG, GG type of UCP-3 +2564C>G, AG, GG type of UCP-3 +3106A>G, and TC, CC type of UCP-3 +4589T>C played a role as a resistance gene to weight loss.