• Korean Journal of Biological Psychiatry
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• v.13 no.4
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• pp.267-272
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• 2006

Objectives : Schizophrenia is a clinically heterogenous disease with a strong genetic component. Many studies have suggested that brain-derived neurotrophic factor(BDNF) is involved in the pathophysiology of schizophrenia. This study was performed to determine whether there is an association between BDNF Val66Met polymorphism and schizophrenia. Methods : To identify any genetic predisposition to schizophrenia, we investigated the BDNF Val66Met polymorphism in 106 patients with schizophrenia and 147 normal controls with PCR-RFLP method. Statistical analyses were used to test the association between and BDNF Val66Met genotype and Schizophrenia. Results : No association was found between BDNF Val66Met polymorphism and schizophrenia. No significant differences were found comparing the BDNF genotype distributions according to the age of onset, the number of admission and familial loading in schizophrenia. Conclusion : This result indicates that BDNF Val66Met polymorphism is not associated with schizophrenia. However, further studies with a large number of subjects are needed to confirm whether the BDNF gene is related to schizophrenia.

• Journal of Plant Biotechnology
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• v.42 no.4
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• pp.290-297
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• 2015

Based on the place of its origin, pear tree (Pyrus spp.) is largely divided into European pears (P. communis, cultivated mainly in Europe and the U.S.) and Asian pears (P. pyrifolia, P. bretschneideri, and P. ussuriensis, distributed and grown in East Asian countries including China, Japan, and Korea). Most pear trees have 17 chromosomes (diploidy, 2n=2x=34). Their genetic studies and precise cultivar breeding are highly restricted by conditions such as self-incompatibility controlled by S-locus and juvenility as one major character of fruit crops. Genetic studies on Pyrus have been promoted by the development of various molecular markers. These markers are being utilized actively in various genetic studies, including genetic relationship analysis, genetic mapping, and QTL analysis. In addition, research on pear genetic linkage maps has been extended to studies for the identification of QTL for target traits such as disease resistance and genetic loci of useful traits. NGS technology has radically reduced sequencing expenses based on massive parallel reactions to enable high-capacity and high-efficiency. NGS based genome analyses have been completed for Chinese pear 'Danshansuli' and European pear 'Bartlett'. In Korea, GWAS for agricultural valuable traits such as floral structure, ripening, and total soluble contents have been conducted through resequencing. GBS has been performed for 'Whangkeumbae', 'Cheongsilri', and 'Minibae'.

• Biomedical Science Letters
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• v.24 no.3
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• pp.221-229
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• 2018

Trichophyton rubrum is one of the well-known pathogenic fungi and causes dermatophytosis and cutaneous mycosis in human world widely. However, there are not an available sequence type (ST) classification methods and previous studies for T. rubrum until now. Therefore, currently, molecular biological tools using their DNA sequences are used for genotype identification and classification. In the present study, in order to characterize the genetic diversity and the phylogenetic relation of T. rubrum clinical isolates, five different housekeeping genes, such as actin (ACT), calmodulin (CAL), RNA polymerase II (RPB2), superoxide dismutase 2 (SOD2), and ${\beta}$-tubulin (BT2) were analyzed using by multilocus sequence typing (MLST). Also, DNA sequence analysis was performed to examine the differences between the sequences of Trichophyton strains and the identified genetic variations sequence. As a result, most of the sequences were shown to have highly matched rates in their housekeeping genes. However, genetic variations were found on three different positions of ${\beta}$-tubulin gene and were shown to have changed from $C{\rightarrow}G$ (1766), $G{\rightarrow}T$ (1876), and $C{\rightarrow}A$ (1886). To confirm the association with T. rubrum inheritance, a phylogenetic tree analysis was performed. It was classified as four clusters, but there was little significant correlation. Even so, MLST analysis is believed to be helpful for determining the genetic variations of T. rubrum in cases where there is more large-scale data accumulation. In conclusion, the present study demonstrated the first MLST analysis of T. rubrum in Korea and explored the possibility that MLST could be a useful tool for studying the epidemiology and evolution of T. rubrum through further studies.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.5
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• pp.2193-2197
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• 2012

Background: Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in the metabolism of folate, and the role of MTHFR C677T polymorphism in cervical carcinogenesis is still controversial. Method: We performed a meta-analysis of all relevant case-control studies that examined any association between the C677T polymorphism and cervical cancer risk. We estimated summary odds ratios (ORs) with their confidence intervals (CIs) to assess links. Results: Finally, 10 studies with a total of 2113 cervical cancer cases and 2804 controls were included. Results from this meta-analysis showed that significantly elevated cervical cancer risk was associated with the MTHFR T allele in the Asian population under conditions of two genetic comparison models (for TT vs. CC, OR = 1.37, 95%CI 1.00-1.87, P = 0.050; for TT vs. TC+CC: OR = 1.34, 95%CI 1.01-1.77, P = 0.039). However, there was no obvious association between the MTHFR C677T polymorphism and cervical cancer risk in the other populations. Conclusion: The MTHFR C677T polymorphism is associated with cervical cancer risk in Asians, while any possible link in the Caucasian population needs further studies.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.11
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• pp.1548-1551
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• 2005

The leptin, an anti-obesity protein, is a hormone protein expressed and secreted mainly from adipocyte tissue, and involved in regulation of body weight, food intake and energy metabolism. In an effort to discover polymorphism(s) in genes whose variant(s) might be implicated in phenotypic traits of growth, we have sequenced exons and their boundaries of leptin gene including 1,000 bp upstream of promoter region with twenty-four unrelated Korean cattle. Fifty-seven sequence variants were identified: fourteen in 5' flanking region, twenty-seven in introns, eight in exons, and eight in 3' flanking region. By pair-wise linkage analysis among polymorphisms, ten sets of SNPs were in absolute linkage disequilibrium (LD) (|D'| = 1 and $r^2$ = 1). Among variants identified, thirty-six SNPs were newly identified, and twenty-one SNPs, which were reported in other breeds, were also confirmed in Korean cattle. The allele frequencies of variants were quite different among breeds. The information from SNPs of bovine leptin gene could be useful for further genetic studies of this gene.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.7
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• pp.3247-3252
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• 2014

Background: Genetic factors have been shown to play an important role in the development of cancers. However, individual studies may fail to completely demonstrate complicated genetic relationships because of small sample size. Therefore, we performed a meta-analysis to evaluate the association of E-selectin Ser128Arg (S128R) with cancer risk. Materials and Methods: A literature search in PubMed, Embase, Web of Science, Science Direct, SpringerLink, EBSCO, Wanfang, and Chinese National Knowledge Infrastructure databases was carried out to identify studies of the association between E-selectin S128R polymorphism and cancer risk. The odds ratio (OR) with 95% confidence intervals (95%CIs) were used to assess the strength of association. Results: A total of eight studies involving 1,675 cancer cases and 2,285 controls were included in the meta-analysis. In overall populations, S128R polymorphism seemed to be associated with cancer risk (Arg allele vs Ser allele: OR=1.65, 95%CI =1.33-2.04, p<0.01; Arg/Arg+Arg/Ser vs Ser/Ser: OR=1.87, 95%CI =1.48-2.36, p<0.01; Arg/Ser vs Ser/Ser: OR=1.80, 95%CI =1.51-2.14, p<0.01). Similarly, subgroup analysis by ethnicity and source of control also revealed that this polymorphism was related to cancer risk. Conclusions: Our meta-analysis revealed that there was association between the E-selectin S128R polymorphism and the risk of cancer. Further large and well-designed studies are needed to confirm this association.

• The Korean Journal of Applied Statistics
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• v.23 no.5
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• pp.845-855
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• 2010

Extensively used case-control designs in medical studies can also be powerful and efficient for family association studies as long as an analysis method is developed for the evaluation of association between candidate genes and disease. Traditional Cochran-Armitage trend test is devised for independent subjects data, and to apply this trend test to the biologically related siblings one has to take into account the covariance among related family members in order to maintain the correct type I error rate. We propose a more powerful trend test by introducing weights that reflect the number of affected siblings in families for the evaluation of the association of genetic markers related to the disease. An application of our method to a sample family data, in addition to a small-scale simulation, is presented to compare the weighted and unweighted trend tests.

• Genomics & Informatics
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• v.5 no.4
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• pp.168-173
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• 2007

In previous nuclear genomic association studies, Random Forests (RF), one of several up-to-date machine learning methods, has been used successfully to generate evidence of association of genetic polymorphisms with diseases or other phenotypes. Compared with traditional statistical analytic methods, such as chi-square tests or logistic regression models, the RF method has advantages in handling large numbers of predictor variables and examining gene-gene interactions without a specific model. Here, we applied the RF method to find the association between mitochondrial single nucleotide polymorphisms (mtSNPs) and diabetes risk. The results from a chi-square test validated the usage of RF for association studies using mtDNA. Indexes of important variables such as the Gini index and mean decrease in accuracy index performed well compared with chi-square tests in favor of finding mtSNPs associated with a real disease example, type 2 diabetes.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.16
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• pp.6709-6714
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• 2014

The rs2273535 polymorphism in the AURKA gene had proven to be associated with breast carcinoma susceptibility. Nevertheless, the results of different studies remain contradictory. A meta-analysis covering 28, 789 subjects from eleven different studies was here carried out in order to investigate the association in detail. The random effects model was used to analyze the pooled odds ratios (ORs) and their corresponding 95% confidence intervals (95% CIs). A significant relationship between the rs2273535 polymorphism and breast tumors was found in an allelic genetic model (OR: 1.076, 95% CI: 1.004-1.153, p=0.040, $P_{heterogeneity}$=0.002). No significant association was detected in a homozygote model (OR: 1.186, 95% CI: 0.990-1.423, P=0.065, $P_{heterogeneity}$=0.002), a heterozygote model (OR: 1.016, 95% CI: 0.959-1.076, p=0.064, $P_{heterogeneity}$=0.000), a dominant genetic model (OR: 1.147, 95% CI: 0.992-1.325, p=0.217, $P_{heterogeneity}$=0.294) and a recessive genetic model (OR: 1.093, 95% CI: 0.878-1.361, p=0.425, $P_{heterogeneity}$=0.707). A significant relationship between the rs2273535 polymorphism in the AURKA gene and breast tumor in Asian group was found in an allelic genetic model (OR: 1.124, 95% CI: 1.003-1.29, p=0.044, $P_{heterogeneity}$=0.034), a homozygote model (OR: 1.229, 95% CI: 1.038-1.455, p=0.016, $P_{heterogeneity}$=0.266) and a recessive genetic model (OR: 1.227, 95% CI: 1.001-1.504, p=0.049, $P_{heterogeneity}$=0.006). A significant association was thus observed between the rs2273535 polymorphism in the AURKA gene and breast cancer risk. Individuals with the rs2273535 polymorphism in the AURKA gene have a higher risk of breast cancer in Asian populations, but not in Caucasians.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.sup3
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• pp.323-335
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• 2016

Breast cancer risk assessment has developed during years and evaluation of genetic factor affecting risk of breast cancer is an important component of this risk assessment. The aim of this meta-analysis was to investigate the role of XRCC1 polymorphisms (Arg194Trp, Arg280His and Arg399Gln) in risk of breast cancer among different population and categories of menopausal status.PubMed, Medline, Web of Science, and PubMed Central were systematically searched to identify studies evaluating association between breast cancer and XRCC1 gene polymorphisms (Arg194Trp, Arg280His and Arg399Gln). Two authors independently extracted required information. Odds Ratios were pooled for four genetic inheritance models using both fixed and the DerSimonian and Laird random-effect models. Egger's test and contour-enhanced funnel plot was used to evaluate publication bias and small study effect. Additional subgroup analysis was performed for menopausal status, ethnicity, and source of controls. After evaluation and applying inclusion criteria on extracted studies, fifty three studies were included in this meta-analysis. For polymorphisms of Arg194Trp and Arg280His, no significant association was observed in all genetic models. Arg194Trp had a protective effect in post-menopausal status only in homozygote model (OR=0.57 [0.37-0.88]). Arg399Gln showed significant association with breast cancer in homozygote (OR=1.21 [1.10-1.34]), dominant (OR=1.09 [1.03-1.15]) and recessive (OR=1.21 [1.09- 1.35]) genetic models. Arg399Gln was associated with higher risk in post-menopausal status for homozygote and heterozygote models. Our findings suggest that XRCC1 gene polymorphisms modify breast cancer risk in different populations and different categories of menopausal status.