• Asian-Australasian Journal of Animal Sciences
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• 제28권11호
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• pp.1545-1550
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• 2015

c-MYC (v-myelocytomatosis viral oncogene homologue) is a transcription factor that plays important role in many biological process including cell growth and differentiation, such as myogenesis and adipogenesis. In this study, we aimed to detect MYC gene polymorphisms, their genotype frequencies and to determine associations between these polymorphisms and meat quality traits in Berkshire pigs. We identified a single nucleotide polymorphism (SNP) in intron 2 of MYC gene by Sanger sequencing, i.e., g.3350G>C (rs321898326), that is only found in Berkshire pigs, but not in other breeds including Duroc, Landrace, and Yorkshire pigs that were used in this study. Genotypes of total 378 Berkshire pigs (138 sows and 240 boars) were determined using Hha I restriction enzyme digestion after polymerase chain reaction. Observed allele frequencies of GG, GC, and CC genotypes were 0.399, 0.508, and 0.093 respectively. Statistical analysis indicated that the g.3350G>C polymorphism was significantly associated with $pH_{45min}$ and cooking loss (p<0.05), suggesting that g.3350G>C SNP can be used for pre-selection of $pH_{45min}$ and cooking loss traits in Berkshire pigs.

• Asian Pacific Journal of Cancer Prevention
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• 제13권6호
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• pp.2841-2846
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• 2012

Background: Many studies have investigated the association between the MDM2 promoter SNP309 T/G polymorphism and liver cancer risk, but inconsistencies make drawwing definitive conclusions difficult. Methods: We therefore searched main databases for articles relating MDM2 SNP309 T/G polymorphism to risk of liver cancer in humans and estimated summary odds ratio (OR) with 95% confidence intervals (95% CI) to assess the possible association in a meta-analysis. Results: The main analysis revealed no significant heterogeneity, and the pooled ORs of fixed-effects were all significant (for G versus T, OR = 1.59, 95% CI 1.42-1.78; for GG versus TT, OR = 2.45, 95% CI 1.93-3.12; for GT versus TT, OR = 1.70, 95% CI 1.38-2.09; for GG versus GT, OR = 1.49, 95% CI 1.24-1.79; for GG and GT versus TT, OR = 1.95, 95% CI 1.61-2.38; for GG versus TT and GT, OR = 1.73, 95% CI 1.46-2.07). Subgroup analyses by ethnicity and sensitivity analyses both showed associations to remain significant. Conclusion: The present meta-analysis of available data showed a significant association between the MDM2 SNP309 T/G polymorphism and liver cancer risk, the MDM2 SNP309 G allele contributing to increased risk in both Asians and Caucasians in a graded, dose-dependent fashion.

• Asian Pacific Journal of Cancer Prevention
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• 제14권5호
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• pp.3213-3217
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• 2013

Background: P-glycoprotein (Pgp), encoded by the multidrug resistance 1 (MDR1) gene, is an efflux transporter which plays an important role in pharmacokinetics. The current preliminary study was designed to determine associations between a germ-line polymorphism in the MDR1 gene with differentiated thyroid carcinoma (DTC). Materials and Methods: In the current case-control study, 60 differentiated thyroid cancers (DTC)- 45 papillary TC (PTC), 9 follicular TC(FTC) and 6 well-differentiated tumors of uncertain malignant potential (WDT-UMP) were examined. Results were compared to a healthy control group (n=58) from the same population. Genomic DNA was extracted from peripheral blood with EDTA and the target gene was genotyped by real-time PCR. Results: Carriers of the variant allele of MDR1 exon 26 polymorphism were at 2.8-fold higher risk of DTC than the control group (odds ratio [OR]: 0.3805, 95% confidence interval [Cl]: 0.1597-0.9065 (p> 0.046). Conclusions: Presented results suggest that the MDR1 3435TT genotype might influence risk of development of DTC and that the CC genotype might be linked to a poor prognosis. Large-scale studies are now needed to validate this association.

• Asian Pacific Journal of Cancer Prevention
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• 제14권2호
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• pp.1093-1100
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• 2013

Background: p53 gene variants i.e. 16 bp duplication in intron 3, Arg72Pro in exon 4 and G>A in intron 6 have been reported to modulate susceptibility to various malignancies. Therefore, the present study evaluated the role of these p53 polymorphisms in oral cancer susceptibility in a population from Gujarat, West India. Method: Genotype frequencies at the three p53 loci in 110 controls and 79 oral cancer cases were determined by the PCR-RFLP method. Results: Heterozygous individuals at exon 4 showed protection from developing oral cancer. Homozygous wild and heterozygous individuals at intron 3 and those heterozygous at exon 4 in combination appeared to be at lowered risk. Furthermore, carriers of the 16 bp duplication allele at intron 3, proline allele at exon 4 and G allele at intron 6 were protected from oral cancer development. Conclusion: p53 polymorphisms, especially Arg72Pro in exon 4 could significantly modify the risk of oral cancer development in Gujarat, West Indian population.

• Clinical and Experimental Pediatrics
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• 제52권4호
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• pp.476-480
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• 2009

목 적 : 저자들은 가와사키병 환아에서 TNF-alpha 유전자의 다형성을 조사함으로써 가와사키병과 유전자 다형성의 관련 여부를 알아보고, 또한 관상동맥 병변의 발생과 연관이 있는지를 살펴보려 하였다. 방 법 : 2003년 1월부터 2007년 1월까지 가와사키병 환아 51명과 대조군 48명을 대상으로 TNF-alpha 촉진자의 단일 유전자 다형성을 살펴보았으며, 가와사키병 환아 중 관상동맥 병변이 있는 24명(관상동맥병변군)과 관상동맥 이상이 없었던 27명(정상관상동맥군)에서의 유전자 다형성을 또한 비교하였다. 말초 혈액에서 DNA를 추출하여 TNF-alpha 유전자 -308 부위의 촉진자에 위치한 2개의 단일 염기 서열 G/A에 대한 대립 유전자의 다형성을 Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) 방법으로 분석하였다. 결 과 : 가와사키병 환아군에서의 -308번 TNF-alpha 유전자의 다형성은 51명 중 9명으로 17.6%였고, 정상 대조군에서는 48명 중 3명으로 6.8%로 가와사키병 환아군에서 높았으나 통계학적으로 유의성은 없었다. 가와사키병 환아 중 관상동맥병병군 24명 중 3명인 12.5%에서 유전자 다형성이 있었고 정상관상동맥군은 27명 중 6명인 22.2%로 정상관상동맥군에서 더 높은 빈도 이었으나 통계학적으로 유의하지 않았다. 결 론 : 본 연구에서는 가와사키병 환아의 TNF-alpha의 다형성과 가와사키병의 발병과의 관련성이 통계학적으로 유의한 수준은 아니지만 가와사키병 환아에서 G/A 빈도수가 17.6%으로 대조군에서 6.8% 보다 다소 높게 나타난 결과를 얻었고 앞으로 많은 수의 환아를 대상으로 한다면 유의한 차이가 있을 것으로 생각되므로 향후 대규모의 지속적인 연구가 필요할 것이다.

• 한국환경성돌연변이발암원학회지
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• 제22권2호
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• pp.70-75
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• 2002

Gly460Trp polymorphism of a-adducin gene has been reported to be associated with hypertension in some populations, and we, therefore, attempted to replicate this finding in Korean population. There were no significant differences in allele and genotype frequencies of Gly460Trp polymorphism in Korean normotensives and hypertensives, respectively. The meta-analysis revealed that the Mantel-Haenszel estimate of the odds ratio across the studies was 1.17 (95%CI 1.04-1.31), and that there was significant evidence against homogeneity of the odds ratio among the studies included (Breslow-Day test = 27.34, df = 9, p = 0.001). Although the meta- analysis appeared in favour of association between the Gly4601tf polymorphism of $\alpha$-adducin gene and hypertension, there was the considerable heterogeneity among the studies and the evidence is also rather borderline. Further comprehensive approaches are needed to resolve this debatable issue.

• 원예과학기술지
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• 제31권1호
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• pp.72-79
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• 2013

Inactivation of the gene coding for dihydroflavonol 4-reductase (DFR) is responsible for the color difference between red and yellow onions (Allium cepa L.). Two inactive DFR-A alleles, DFR-$A^{PS}$ and DFR-$A^{DEL}$, were identified in our previous study. A functional marker was developed on the basis of the premature stop codon that inactivated the DFR-$A^{PS}$ allele. A derived cleaved amplified polymorphic sequences (dCAPS) primer was designed to detect the single nucleotide polymorphism, an A/T transition, which produced the premature stop codon. Digested PCR products clearly distinguished the homozygous and heterozygous red $F_2$ individuals. Meanwhile, to develop a molecular marker for detection of the DFR-$A^{DEL}$ allele in which entire DFR-A gene was deleted, genome walking was performed and approximately 3 kb 5' and 3' flanking sequences of the DFR-$A^R$ coding region were obtained. PCR amplification using multiple primers binding to the extended flanking regions showed that more of the extended region of the DFR-A gene was deleted in the DFR-$A^{DEL}$ allele. A dominant simple PCR marker was developed to identify the DFR-$A^{DEL}$ allele using the dissimilar 3' flanking sequences of the DFR-A gene and homologous DFR-B pseudogene. Distribution of the DFR-$A^{PS}$ and DFR-$A^{DEL}$ alleles in yellow onion cultivars bred in Korea and Japan was surveyed using molecular makers developed in this study. Results showed predominant existence of the DFR-$A^{PS}$ allele in yellow onion cultivars.

• 한국정보과학회논문지:소프트웨어및응용
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• 제32권2호
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• pp.99-107
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• 2005

본 논문에서는 단일염기변이(SNP: Single Nucleotide Polymorphism)와 같은 유전형(Rcnotype)자료에서 결측치가 발생하였을 경우 유전형 자료의 특이성을 고려해 자료 원래의 정보손실을 최소화하는 대치법인 연관불균형 기반의 대치법(linkage disequilibrium- based imputation)과 일배체형 기반의 대치법(haplotype-based imputation)을 제시한다. 이러한 결측치 대치는 실험상에서 발생하는 결측치에 의한 중요한 정보의 손실을 최소화 한다는 점에서 필요한 방법이다. 일반적으로 그동안 생물학 자료의 결측치 대치는 대부분 주형질 대치법(major allele imputation)이 활용되어왔는데 유전형 자료에서의 이 방법의 사용은 사료의 특이성으로 인하여 결측치에 대한 높은 오차율(error rate)을 보임으로서 자료의 신뢰성을 떨어뜨릴 수 있다. 본 논문에서는 유전형 자료인 단일염기변이 자료의 시뮬레이션을 통하여 기존의 주형질 대치법과 논문에서 제안된 연관불균형 기반의 대치법과 일배체형 기반의 대치법을 비교하고 그 결과를 보여 준다.

• Asian Pacific Journal of Cancer Prevention
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• 제17권7호
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• pp.3381-3384
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• 2016

Background: Hepatitis B virus (HBV) is a key factor for hepatocellular carcinoma (HCC). About 350 million people are affected by chronic infection which is related to the rapid development of liver diseases as well as hepatitis, cirrhosis and hepatocellular carcinoma. Expression of tumor necrosis factor alpha (TNF-${\alpha}$) in the liver demonstrates a major genetic polymorphism which is involved in resistance or susceptibility to chronic HBV infection. Materials and Methods: In this study, two populations were studied by the sequence specific primer-polymerase chain reaction (SSP-PCR) method: HBV cases (n=409), who were HBS-Ag+, and healthy controls (n=483). Results: The results shown that the frequency of TNF-${\alpha}$ -308 G/G genotype in healthy controls (47.2%) was significantly higher than in HBV infected patients (28%) (CI = 1.29-2.61, OR = 1.83, P = 0.0004). Also TNF-${\alpha}$ -308 A/A and A/G genotype frequencies in the healthy controls were 4.6% and 48.2% and in patient group were 19.5% and 52.5% (CI = 2.23-7.12, p: 0.0001, OR: 3.94) respectively. Conclusions: We found that among Iranian people TNF-${\alpha}$ -308A allele not only has the highest genotype frequency but also it has the highest frequency in the world population. In addition, TNF-${\alpha}$-308 G/G polymorphism was associated with HBV resistance, whereas TNF-${\alpha}$-308A (A/A or A/G) polymorphism appeared to associated with chronic HBV infection. These data suggested that among the Iranian population, the -308 G/G polymorphism of TNF-${\alpha}$ gene promoter region has the potential to influence the susceptibility to HBV infection and it may be responsible for viral antigen clearance.

• Journal of Animal Science and Technology
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• 제44권4호
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• pp.391-398
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• 2002

본 연구는 제주마집단(GroupⅠ, 제주도 축산진흥원 사육, 137두; Group II, 농가사육, 30두)과 더러브렛 품종집단(한국마사회 육성마목장, 43두)을 이용하여 SSCP를 통한 Transferrin exon 13, 15, 16의 다형현상 확인과 각 SSCP 유전자형의 염기서열을 분석하기 위하여 수행하였다. 공시재료에서 SSCP에서 관찰된 band에 의한 분석결과 대립인자는 exon 13, 15 및 16에서 각각 2개(A,B), 3개(A,B,C) 및 3개(A,B,C)가 존재하는 것으로 확인되었다. Transferrin exon 13에서 제주마와 더러브렛 집단 모두 A인자가 매우 높게 분포하고 있음이 확인되었다. exon 15에서는 그룹간의 빈도차를 확인 할 수 있었다. exon 15에서 높게 출현되고 있는 유전자형은 GroupⅠ에서 AB (0.445)형, GroupⅡ에서 AA(0.367)형, 더러브렛 품종에서는 AA(0.767) 유전자형이 가장 높은 빈도로 출현되어 제주마 집단간 또는 품종간에 빈도의 차이를 관찰할 수 있었다. exon 16에서는 GroupⅠ은 A, B, C 인자, GroupⅡ에서는 A 및 B 2종류의 인자형이 확인되었고 더러브렛 품종에서는 A인자형만 검출되었다. exon 16에서도 그룹간에 유전인자의 빈도차를 확인 할 수 있었다. 또한 exon 13, 15 및 16의 조합으로 형성된 개체의 유전자형은 전체 13종류가 출현되었고 이 조합도 그룹간 차이를 확인 할 수 있었다. SSCP 유전자형에 따른 각 인자들에 대한 염기서열을 분석한 결과 exon 13과 16에서 각 1개의 새로운 SNP가 발견되었다. 본 연구결과 제주마 transferrin exon 13, 15, 16은 더러브렛 품종에서와 같이 높은 대립인자의 다형성을 보였으며, 각 Group 간 빈도차를 확인 할 수 있었다.