• Asian Pacific Journal of Cancer Prevention
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• v.17 no.4
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• pp.2093-2097
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• 2016

Background: HCV is a major global health problem. IL-27 is a member of the IL-6/IL-12 cytokine family with a broad range of anti-inflammatory properties. Recent studies highlighted the effect of a SNP in the IL-27 promoter region on modulating the progression of infectious diseases and individual responses to therapy. Aim of the work: The present study investigated the potential role of (-964 A/G) SNP in the promoter region of IL-27p28 gene (alleles rs153109) on the outcome of HCV infection among genotype 4a infected patients. Materials and Methods: HCV genotyping confirmed that all of the HCV-infected patients had genotype 4a infection. Genomic DNA was extracted from 111 patients with chronic HCV infection, 42 spontaneous resolvers (SR) and 16 healthy controls. IL- 27p28.rs153109 genotyping was assessed using PCR-RFLP then confirmed by DNA sequencing. Results: The frequency of IL-27-p28.rs153109AA, AG, and GG genotypes among chronically infected subjects were 74.8 %, 25.2%, and 0% while among the SR, they were 57.1%, 35.7%, and 7.14%, respectively. Our data show the unique presence of G/G genotype in the SR group (3 patients; 7.14%). Moreover, the "G" allele frequencies among chronic and resolved subjects were 12.6% and 25.0%, respectively (p=0.0136). Importantly, subjects with the GG genotype were more likely to clear their HCV infection than those with the AA genotype (p=0.0118). Conclusions: HCV genotype 4a subjects with the IL-27-p28.rs153109 A/G and G/G genotype were more likely to clear their HCV infection. Therefore, we propose IL- 27p28.rs153109SNPas a genetic biomarker for predicting HCV infection outcome.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.2
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• pp.957-961
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• 2014

Purpose: With regard to the protective effect of vitamin D against colorectal cancer (CRC), we evaluated genetic variants that might influence vitamin D metabolism: vitamin D receptor (VDR), vitamin D binding protein (GC), vitamin D 25-hydroxylase (CYP2R1), and vitamin D 25-hydroxy 1-alpha hydroxylase (CYP27B1). Materials and Methods: A total of 657 subjects, including 303 cases with CRC and 354 controls were enrolled in this case-control study. All 657 were genotyped for the four gene variants using PCR-RFLP methods. Results: In this study, no significant difference was observed for VDR (rs2238136), GC (rs4588), CYP2R1 (rs12794714), and CYP27B1 (rs3782130) gene variants in either genotype or allele frequencies between the cases with CRC and the controls and this lack of difference remained even after adjustment for age, BMI, sex, smoking status, NSAID use, and family history of CRC. Furthermore, no evidence for effect modification of the variants and CRC by BMI, sex, or tumor site was observed. Conclusions: Our findings do not support a role for VDR, GC, and CYP27B1 genes in CRC risk in our Iranian population. Another interesting finding, which to our knowledge has not been reported previously, was the lack of association with the CYP2R1 gene polymorphism. Nonetheless, our findings require confirmation and possible roles of vitamin D metabolism-related genes in carcinogenesis need to be further investigated.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.5
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• pp.3229-3235
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• 2013

Background: Many breast cancers are caused by certain rare and familial mutations in the high or moderate penetrance genes BRCA1, BRCA2 and CHEK2. The aim of this study was to examine the allele and genotype frequencies of seven mutations in BRCA1, BRCA2 and CHEK2 genes in breast cancer patients and to investigate their isolated and combined associations with breast cancer risk. Methods: We genotyped seven mutations in BRCA1, BRCA2 and CHEK2 genes and then analyzed single variations and haplotype associations in 106 breast cancer patients and 80 healthy controls. Results: We found significant associations in the analyses of CHEK2- 1100delC (p=0.001) and BRCA1-5382insC (p=0.021) mutations in breast cancer patients compared to controls. The highest risk was observed among breast cancer patients carrying both CHEK2-1100delC and BRCA2- Met784Val mutations (OR=0.093; 95%CI 0.021-0.423; p=0.001). We identified one previously undescribed BRCA2 and a CHEK2 four-marker haplotype of A-C-G-C which was overrepresented ($X^2$=7.655; p=0.0057) in the patient group compared to controls. Conclusion: In this study, we identified a previously undescribed BRCA2 and CHEK2 A-C-G-C haplotype in association with the breast cancer in our population. Our results further suggest that the CHEK2-1100delC mutation in combination with BRCA2-Met784Val may lead to an unexpected high risk which needs to be confirmed in larger cohorts in order to better understand their role in the development and prognosis of breast cancer.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.2
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• pp.153-159
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• 2006

A 2,656 bp fragment of chicken ghrelin gene was cloned and SNPs were detected by PCR-RFLP and Allele Specific PCR (ASP) in 12 Chinese indigenous chicken breeds and a commercial chicken population. The results showed that there were 23 base variations and an amino acid change ($Gln{\rightarrow}Arg$) in cloned chicken ghrelin gene. Three SNPs were confirmed in 13 populations and associations between this gene and growth traits of Tibetan chicken (TC) and Recessive White chicken (RW) were investigated. The results of haplotype analysis revealed that 26 haplotype genotypes were composed of eight haplotypes. The results of $x^2$ tests indicated that there were significant differences between genotypes or haplotype genotype frequencies in some of the breeds or sexes at 0.05 or 0.01 levels. The results of ANOVA revealed that there were significant differences between genotypes or haplotype genotypes on some growth traits of TC and RW chicken breeds at 0.05 or 0.01 levels. Multiple comparisons showed that there were significant associations between genotype CT at site 71 and some growth traits of two chicken breeds and between genotype AG at site 1,215 and body weight at 16 wk of two chicken breeds, and there was a significant association between haplotype genotype CAA/CAG and body weight and shank girth at 16 wk of two chicken breeds.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.9
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• pp.5011-5016
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• 2013

Background: Several epidemiological studies have shown associations between colorectal cancer (CRC) risk and type 2 diabetes and obesity. Any effects would be expected to be mediated through the insulin pathway. Therefore it is possible that variants of genes encoding components of the insulin pathway play roles in CRC susceptibility. In this study, we hypothesized that polymorphisms in the genes involving the insulin pathway are associated with risk of CRC. Materials and Methods: The associations of four single nucleotide polymorphisms (SNPs) in IGF-I (rs6214), IGFBP-3 (rs3110697), INSR (rs1052371), and IRS2 (rs2289046) genes with the risk of CRC were evaluated using a case-control design with 167 CRC cases and 277 controls by the PCR-RFLP method. Results: Overall, we observed no significant difference in genotype and allele frequencies between the cases and controls for the IGF-I, IGFBP-3, INSR, IRS2 gene variants and CRC before or after adjusting for confounders (age, BMI, sex, and smoking status). However, we observed that the IRS2 (rs2289046) GG genotype compared with AA+AG genotypes has a protective effect for CRC in normal weight subjects (p=0.035, OR=0.259, 95%CI= 0.074-0.907). Conclusions: These findings do not support plausible associations between polymorphic variations in IGF-I, IGFBP-3, INSR, IRS2 genes and risk of CRC. However, the evidence for a link between the IRS2 (rs2289046) variant and risk of CRC dependent on the BMI of the subjects, requires confirmation in subsequent studies with greater sample size.

• Journal of Animal Science and Technology
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• v.52 no.5
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• pp.357-366
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• 2010

The emergence of next-generation sequencing technologies has lead to application of new computational and statistical methodologies that allow incorporating genetic information from entire genomes of many individuals composing the population. For example, using single-nucleotide polymorphisms (SNP) obtained from whole genome amplification platforms such as the Ilummina BovineSNP50 chip, many researchers are actively engaged in the genetic evaluation of cattle livestock using whole genome relationship analyses. In this study, we estimated the genomic relationship matrix (GRM) and compared it with one computed using a pedigree relationship matrix (PRM) using a population of Hanwoo. This project is a preliminary study that will eventually include future work on genomic selection and prediction. Data used in this study were obtained from 187 blood samples consisting of the progeny of 20 young bulls collected after parentage testing from the Hanwoo improvement center, National Agriculture Cooperative Federation as well as 103 blood samples from the progeny of 12 proven bulls collected from farms around the Kyong-buk area in South Korea. The data set was divided into two cases for analysis. In the first case missing genotypes were included. In the second case missing genotypes were excluded. The effect of missing genotypes on the accuracy of genomic relationship estimation was investigated. Estimation of relationships using genomic information was also carried out chromosome by chromosome for whole genomic SNP markers based on the regression method using allele frequencies across loci. The average correlation coefficient and standard deviation between relationships using pedigree information and chromosomal genomic information using data which was verified using a parentage test andeliminated missing genotypes was $0.81{\pm}0.04$ and their correlation coefficient when using whole genomic information was 0.98, which was higher. Variation in relationships between non-inbred half sibs was $0.22{\pm}0.17$ on chromosomal and $0.22{\pm}0.04$ on whole genomic SNP markers. The variations were larger and unusual values were observed when non-parentage test data were included. So, relationship matrix by genomic information can be useful for genetic evaluation of animal breeding.

• Journal of Korean Medicine for Obesity Research
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• v.4 no.1
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• pp.1-11
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• 2004

Objectives: The effects of peroxisome proliferator-activated receptor ${\gamma}2\;(PPAR{\gamma}2)$ Pro12Ala (P12A) polymorphism on body mass index (BMI) and type 2 diabetes are well documented; however, until now, only a few studies have evaluated the effects of this polymorphism on body fat distribution. This study was conducted to elucidate the effects of this polymorphism on computed tomography (CT)-measured body fat distribution and other obesity-related parameters in Korean female subjects. Methods & Results: The frequencies of $PPAR{\gamma}2$ genotypes were: PP type, 93.0%; PA type, 6.8%; and AA type, 0.2%. The frequency of the A allele was 0.035. Body weight (P .012), BMI (P .012), and waist-to-hip ratio (WHR) (P .001) were significantly higher in subjects with PA/AA compared with subjects with PP. When body composition was analyzed by bioimpedance analysis, lean body mass and body water content were similar between the 2 groups. However, body fat mass (P .003) and body fat percent (P .025) were significantly higher in subjects with PA/AA compared with subjects with PP. Among overweight subjects with BMI of greater than 25, PA/AA was associated with significantly higher abdominal subcutaneous fat (P .000), abdominal visceral fat (P .031), and subcutaneous upper and lower thigh adipose tissue (P .010 and .013). However, among lean subjects with BMI of less than 25, no significant differences associated with $PPAR{\gamma}2$ genotype were found, suggesting that the fat-accumulating effects of the PA/AA genotype were evident only among overweight subjects, but not among lean subjects. When serum lipid profiles, glucose, and liver function indicators were compared among overweight subjects, no significant difference associated with $PPAR{\gamma}2$ genotype was found. Changes in body weight, BMI, WHR, and body fat mass were measured among overweight subjects who finished a 1-month weight lose program of a hypocaloric diet and exercise; no significant differences associated with $PPAR{\gamma}2$ genotype were found. Conclusions: The results of this study suggest that the $PPAR{\gamma}2$ PA/AA genotype is associated with increased subcutaneous and visceral fat areas in overweight Korean female subjects, but does not significantly affect serum biochemical parameters and outcomes of weight loss programs.

• Journal of Life Science
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• v.14 no.4
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• pp.696-701
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• 2004

The present study was carried out to investigate the redcell types of horse breeds. A total of 210 horses (73 Korean native horses, 118 crossbreed horses, and 19 Mongolian horses) were tested a redcell types by serological procedure, and their phenotypes and gene frequencies were estimated. The blood groups phenotypes observed with highest frequency were Aa (27.4%, 63.6%, 63.2%), Ca (97.3%, 94.9%, 89.5%), K- (97.3%, 99.2%, 84.2%), Pa (39.7%, 44.9%, 42.1%), and Ua (71.2%, 70.3%, 63.2%) in the Korean native horse, crossbreed horse, and Mongolian horse, respectively. In the D system and Q system, phenotypes observed with highest frequency were Dbcm/dghm (12.3%), Dbcm/cgm (14.4%), Dcgm/dghm (15.8%), and Qc (56.2%), Qabc (36.4%), Qc (31.6%) in the Korean native horse, crossbreed horse, and Mongolian horse, respectively Alleles observed with highest frequency were A- (0.287), Ca(0.827), Ddghm (0.226), K- (0.985), Pa (0.358), Qc (0.494), U-(0.529) in the Korean native horse, Aa (0.529), Ca (0.776), Dbcm (0.306), K- (0.995), P- (0.531), Q- (0.504), U- (0.548) in crossbreed horse, and Aa (0.421), Ca (0.895), Ddghm (0.421), K- (0.842), Pa (0.447), Qc (0.448), Ua (0.632) in Mongolian horse. Dcfgk and D- alleles were not detected in these horses. These results present basic information for estimating the genetic relationships between the Korean native horse, and developing a system for parentage verification and individual identification in these horses.

• Sleep Medicine and Psychophysiology
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• v.15 no.1
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• pp.39-43
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• 2008

Objectives: The pathophysiology of restless legs syndrome (RLS) is not obvious, but many promising theories involve dopaminergic deficiency and genetic causes. The RLS is presumed to occur more frequently among schizophrenic patients who take antipsychotics, most of which blocks the dopamine receptors. This study aimed to investigate whether dopamine transporter gene (DAT1) 40 base pair (bp) variable number of tandem repeat (VNTR) polymorphism is associated with the antipsychotic-induced RLS in schizophrenia. Methods: We determined the diagnosis of RLS among the 190 Korean schizophrenic patients by the diagnostic criteria of the International Restless Legs Syndrome Study Group (IRLSSG). Genotyping was performed for the 40bp VNTR in DAT1 gene using polymerase chain reaction. Results: We separated the schizophrenic patients into 44 patients with RLS and 146 patients without RLS. The genotype and allele frequencies did not differ significantly between two groups. Conclusions: These results suggest that DAT1 gene 40bp VNTR is not associated with the antipsychotic-induced RLS in schizophrenia. To confirm these results, larger-scale association study is needed in the future.

• Journal of Life Science
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• v.18 no.4
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• pp.427-434
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• 2008

Osteonecrosis of the femoral head (ONFH) is a multifactorial disease and certain individuals are more at risk or may be predisposed to it. An altered lipid metabolism is one of the major risk factors for osteonecrosis, especially corticosteroid therapy and alcoholism. 3-hydroxy-3-methylglutaryl coenzyme A. (HMG-CoA) reductase inhibitors, stalin used as lipid-clearing agent, have been known to decrease the risk of osteonecrosis in patients receiving steroids and affect coagulation and fibrinolysis. Therefore we evaluated the association of HMG-CoA reductase gene polymorphisms and haplotypes between osteonecrosis patients and normal controls. We directly sequenced the HMG-CoA reductase gene in 24 Korean individuals, and identified five sequence variants. Four SNPs (-6933C>T, -6045T>G, +12673G>A, and +18128C>T) were selected and genotyped in 349 male ONFH patients and 300 male control subjects. The genotypes, allele frequencies, and haplotypes of the polymorphisms in the total patients as well as in the subgroup by etiology were not significantly different from those in the control group. In addition, no significant differences between each genotype of the polymorphisms and plasma lipid level could be found in the control group. These results suggest that the polymorphisms and haplotypes of HMG-CoA reductase gene are unlikely to be associated with a susceptibility to ONFH.