• Asian Pacific Journal of Cancer Prevention
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• v.15 no.21
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• pp.9347-9353
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• 2014

Background: Excision repair crossing-complementing group 2 (ERCC2), also called xeroderma pigmentosum complementary group D (XPD), plays a crucial role in the nucleotide excision repair (NER) pathway. Previous epidemiological studies have reported associations between ERCC2 polymorphisms and non-Hodgkin lymphoma (NHL) risk, but the results have remained controversial. Materials and Methods: We conducted this meta-analysis based on eligible case-control studies to investigate the role of two ERCC2 polymorphisms (Lys751Gln and Asp312Asn) in determining susceptibility to NHL. Ten case-control studies from several electronic databases were included in our study up to August 14, 2014. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using fixed- or random-effects models to estimate the association strength. Results: The combined results based on all studies did not show any association between Lys751Gln/Asp312Asn polymorphisms and NHL risk for all genetic models. Stratified analyses by histological subtype and ethnicity did not indicate any significant association between Lys751Gln polymorphism and NHL risk. However, a significant reduced risk of NHL was found among population-based studies (Lys/Gln versus Lys/Lys: OR=0.87, 95% CI=0.77-0.99, P=0.037) but not hospital-based studies. As for Asp312Asn polymorphism, there was no evidence for the association between this polymorphism and the risk of NHL in all subgroup analyses. Conclusions: This meta-analysis suggests that there may be no association between Lys751Gln/Asp312Asn polymorphism and the risk of NHL and its two subtypes, whereas ERCC2 Lys751Gln heterozygote genotype may provide protective effects against the risk of NHL in population-based studies. Therefore, large-scale and well-designed studies are needed to clarify the effects of haplotypes, gene-gene, and gene-environment interactions on these polymorphisms and the risk of NHL and its different histological subtypes in an ethnicity specific population.

• Journal of Korean Society for Geospatial Information Science
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• v.18 no.3
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• pp.49-56
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• 2010

The Genetic Algorithm is one of the population surface modelling tool in the field of urban and environmental research based on the gridded population data. Taking the East-Hwasung area as the case, this study first builds a gridded population data based on the GIS databases as well as municipal population survey data. The study then constructs the attribute values of the explanatory variables by way of GIS tools. The regression model constructed with the same variables is also run as a comparative purpose at the same time. It is shown that the GenAlg output predicted as much consistent and meaningful coefficient estimates for the explanatory variables as the regression model, indicating that it is a very useful interdisciplinary research tool to find optimal solutions in urban problems.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2857-2861
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• 2014

More and more evidence indicates that the G801A polymorphism in the CXCL12 gene might be associated with susceptibility to breast carcinoma in humans being. However, individually published results have been inconsistent. The purpose of this meta-analysis was to investigate the association between the G801A polymorphism in the CXCL12 gene and breast carcinoma risk. A complete search strategy was done by the electronic databases including PubMed and Chinese Biomedical Literature Database. A meta-analysis including seven individual studies was carried out in order to explore the association between the G801A polymorphism in the CXCL12 gene polymorphisms and breast carcinoma. The pooled odds ratios (ORs) and their corresponding 95% confidence intervals (95%CIs) between the G801A polymorphism in the CXCL12 gene and breast carcinoma risk were assessed by the random-effects model. A significant relationship between the G801A polymorphism in the CXCL12 gene and breast carcinoma was discovered in an allelic genetic model (OR: 1.214, 95%CI: 1.085-1.358, p=0.001), a homozygote model (OR: 1.663, 95%CI: 1.240-2.232, p=0.001), a heterozygote model (OR: 1.392, 95%CI: 1.190-1.629, p=0.000), a recessive genetic model (OR: 1.407, 95%CI: 1.060-1.868, p=0.018) and a dominant genetic model (OR: 1.427, 95%CI: 1.228-1.659, p=0.000). On sub-group analysis based on ethnicity, significance was observed between the European group and the mixed group. A significant relationship was found between the G801A polymorphism in the CXCL12 gene and breast carcinoma risk. Individuals with the A allele of the G801A polymorphism in the CXCL12 gene are under a higher risk for breast carcinoma.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.18
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• pp.7941-7945
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• 2014

Catechol-O-methyltransferase (COMT) is involved in estrogen metabolism and is vital to estrogen-induced carcinogenesis, including that of ovarian cancer. Although many recent epidemiologic studies have investigated associations between the COMT rs4680 polymorphism and ovarian cancer risk, the results remain inconclusive. We therefore performed a meta-analysis to derive a more precise estimate of associations. Systematic searches of the PubMed, Embase, Web of Science, Cochrane Library, Wanfang, China National Knowledge Infrastructure, and Chinese Biomedicine databases were undertaken to retrieve eligible studies. Odds ratios (ORs) with their corresponding 95% confidence intervals (CIs) were pooled to assess the strength of the association. In total, 8 case-control studies involving 1,293 cases and 2,647 controls were included in the meta-analysis. Overall, the results showed no evidence of significant association between the COMT rs4680 polymorphism and ovarian cancer risk in any of the assessed genetic models. Subgroup analyses by ethnicity also did not reveal any significant association in any genetic model (p>0.05). In conclusion, our findings suggest that the COMT rs4680 polymorphism may not contribute to the risk of ovarian cancer.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.13
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• pp.5407-5413
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• 2015

Background: Published data regarding associations between the P275A polymorphism in the macrophage scavenger receptor 1 (MSR1) gene and prostate cancer (PCa) risk are inconclusive. The aim of this study was to comprehensively evaluate the genetic risk of P275A polymorphism in MSR1 gene for PCa. Materials and Methods: A systematic literature search was carried out in Pubmed, Medline (Ovid), Embase, CBM, CNKI, Weipu, and Wanfang databases, covering all available publications (last search was performed on Apr 27, 2015). Statistical analysis was performed using Revman 5.2 and STATA 10.1 software. Results: A total of 5,017 cases and 4,869 controls in 12 case-control studies were included in this meta-analysis. When all groups were pooled, there was no evidence that the P275A polymorphism had a significant association with PCa under dominant (OR=0.93, 95%CI=0.81-1.06, and p=0.28), co-dominant (homogeneous OR=0.97, 95%CI=0.56-1.68, and p=0.92; heterogeneous OR=0.93, 95%CI=0.74-1.15, and p=0.49), recessive (OR=1.10, 95%CI=0.65-1.87, and p=0.73), over-dominant (OR=0.93, 95%CI=0.75-1.15, and p=0.50), and allelic (OR=0.95, 95%CI=0.77-1.16, and p=0.61) genetic models. For stratified analyses by ethnicity and study design, no significant associations were found in the white race, the yellow race, the black race and mixed ethnicity, and the population-based case-control (PCC) and hospital-based case-control (HCC) studies under all genetic models. Conclusions: Based on our meta-analysis, the P275A polymorphism in the MSR1 gene is unlikely to be a risk factor for PCa.

• Journal of the Korean Association of Geographic Information Studies
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• v.13 no.3
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• pp.119-130
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• 2010

The Genetic Algorithm has been frequently applied by many researchers as one of the population surface modelling tool in estimating the regional population based on the gridded spatial system. Taking the East-Hwasung area as the case, this study first builds a gridded population data based on the KLIS and eAIS databases as well as municipal population survey data, and then constructs the attribute values of the explanatory variables by way of GIS tools. The GA model is run to maximize its fitness function measuring the correlation coefficient between the observed and predicted values of the 70 population cells. It is shown that the GA output predicted reasonably consistent and meaningful coefficient estimates for the explanatory variables of the model.

• Journal of the Institute of Electronics Engineers of Korea CI
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• v.46 no.2
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• pp.65-74
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• 2009

In optimizing the neural network structure, there are two methods of the pruning scheme and the constructive scheme. In this paper we use the pruning scheme to optimize neural network structure, and the genetic algorithm to find out its optimum node pruning. In the conventional researches, the input and hidden layers were optimized separately. On the contrary we attempted to optimize the two layers simultaneously by encoding two layers in a chromosome. The offspring networks inherit the weights from the parent. For teaming, we used the existing error back-propagation algorithm. In our experiment with various databases from UCI Machine Learning Repository, we could get the optimal performance when the network size was reduced by about $8{\sim}25%$. As a result of t-test the proposed method was shown better performance, compared with other pruning and construction methods through the cross-validation.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.95-105
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• 2005

Transposon-mediated insertional mutagenesis provides one of the most powerful tools for functional studies of genes in higher plants. This project has been performed to develop a large population of insertional mutations, and to construct databases of molecular information on Ds insertion sites in rice. Ultimate goals are to supply genetic materials and information to analyze gene function and to identify and utilize agronomically important genes for breeding purpose. Two strategies have been employed to generate the large scale of transposon population in a Japonica type rice, Dongjin Byeo; 1) genetic crosses between Ac and Ds lines and 2) plant regeneration from seeds carrying Ac and Ds. Our study showed that over 70% of regenerated plants generally carried independent Ds elements and high activity of transposition was detected only during regeneration period. Ds-flanking DNA amplified from leaf tissues of F2 and T1 (or T2) plants have been amplified via TAIL-PCR and directly sequenced. So far, over 65,000 Ds lines have been generated and over 9,500 Ds loci have been mapped on chromosomes by sequence analysis. Database of molecular information on Ds insertion sites has been constructed, and has been opened to the public and will be updated soon at http://www.niab.go.kr. Detailed functional analysis of more than 30 rice mutants has been performed. Several Ds-tagged rice genes that have been selected for functional analysis will be briefly introduced. We expect that a great deal of information and genetic resources of Ds lines would be obtained during the course of this project, which will be shared with domestic and international rice researchers. In addition to the Japonica rice, we have established the tagging system in an rice line of indica genetic background, MGRI079. MGRI079 (Indica/Japonica) was transformed with Agrobacteria carrying Ac and Ds T-DNA vectors. Among transgenic lines, we successfully identified single-copy Ds and Ac lines in MGR1079. These lines were served as ‘starter lines’ to mutagenize Indica genetic background. To achieve rapid, large scale generation of Ds transposant lines, MGR1079 transformants carrying homozygous Ac were crossed with ones with homozygous Ds, and $F_2$seeds were used for plant regeneration. In this year, over 2,000 regeneration plants were grown in the field. We are able to evaluate the tagging efficiency in the Indica genetic background in the fall.

• Genomics & Informatics
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• v.18 no.2
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• pp.14.1-14.11
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• 2020

Phenotyping is a major issue for wheat agriculture to meet the challenges of adaptation of wheat varieties to climate change and chemical input reduction in crop. The need to improve the reuse of observations and experimental data has led to the creation of reference ontologies to standardize descriptions of phenotypes and to facilitate their comparison. The scientific literature is largely under-exploited, although extremely rich in phenotype descriptions associated with cultivars and genetic information. In this paper we propose the Wheat Trait Ontology (WTO) that is suitable for the extraction and management of scientific information from scientific papers, and its combination with data from genomic and experimental databases. We describe the principles of WTO construction and show examples of WTO use for the extraction and management of phenotype descriptions obtained from scientific documents.

• Journal of Microbiology and Biotechnology
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• v.17 no.3
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• pp.408-413
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• 2007

Putrescine has a negative effect on health and is also used as an indicator of quality on meat products. We investigated the genes involved in putrescine production by Serratia liquefaciens IFI65 isolated from a spoiled Spanish dry-cured ham. We report here the genetic organization of its ornithine decarboxylase encoding region. The 5,506-bp DNA region showed the presence of three complete and two partial open reading frames. Putative functions have been assigned to several gene products by sequence comparison with proteins included in the databases. The second gene putatively coded for an ornithine decarboxylase. The functionality of this decarboxylase has been experimentally demonstrated by complementation to an E. coli defective mutant. Based on sequence comparisons of some enterobacterial ornithine decarboxylase regions, we have elaborated a hypothetical pathway for the acquisition of putrescine biosynthetic genes in some Enterobacteriaceae strains.