• Journal of Korean Neurosurgical Society
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• v.46 no.4
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• pp.385-388
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• 2009

Objective : We analyzed the methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) gene promoter in World Health Organization (WHO) grade III gliomas in association with other molecular markers to evaluate their prevalence. Methods : The samples of a total of 36 newly WHO grade III glioma patients including 19 anaplastic oligodendrogliomas (AO), 7 anaplastic oligoastrocytomas (AOA), and 10 anaplastic astrocytomas (AA) were analyzed. The methylation status of the MGMT gene promoter was confirmed by methylation-specific polymerase chain reaction. The 1p/19q chromosomal deletion status and EGFR amplification were assessed by Fluorescence In-Situ Hybridization. MGMT, EGFR, EGFRvlll, and p53 expression were analyzed by immunohistochemical staining. Results : The MGMT gene promoter was methylated in 32 (88.9%) and unmethylated in 4 (11.2%) Among them, all of the AO and AOA had methylated MGMT gene promoter without exception. Significant associations between MGMT gene promoter hypermethylation and 1p/19q deletion was observed (p=0.003). Other molecular markers failed to show significant associations between MGMT gene promoter statuses. Conclusion : There was extensive epigenetic silencing of MGMT gene in high grade gliomas with oligodendroglial component. Together with frequent 1p/19q co-deletion in oligodendroglial tumors, this may add plausible explanations supporting the relative favorable prognosis in oligodendroglial tumors compared with pure astrocytic tumors.

• Journal of the Korean Society of Radiology
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• v.81 no.3
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• pp.632-643
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• 2020

Purpose To investigate the correlation between magnetic resonance (MR) image-based radiomics features and the genomic features of breast cancer by focusing on biomolecular intrinsic subtypes and gene expression profiles based on risk scores. Materials and Methods We used the publicly available datasets from the Cancer Genome Atlas and the Cancer Imaging Archive to extract the radiomics features of 122 breast cancers on MR images. Furthermore, PAM50 intrinsic subtypes were classified and their risk scores were determined from gene expression profiles. The relationship between radiomics features and biomolecular characteristics was analyzed. A penalized generalized regression analysis was performed to build prediction models. Results The PAM50 subtype demonstrated a statistically significant association with the maximum 2D diameter (p = 0.0189), degree of correlation (p = 0.0386), and inverse difference moment normalized (p = 0.0337). Among risk score systems, GGI and GENE70 shared 8 correlated radiomic features (p = 0.0008-0.0492) that were statistically significant. Although the maximum 2D diameter was most significantly correlated to both score systems (p = 0.0139, and p = 0.0008), the overall degree of correlation of the prediction models was weak with the highest correlation coefficient of GENE70 being 0.2171. Conclusion Maximum 2D diameter, degree of correlation, and inverse difference moment normalized demonstrated significant relationships with the PAM50 intrinsic subtypes along with gene expression profile-based risk scores such as GENE70, despite weak correlations.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.12
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• pp.4851-4856
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• 2014

Background: Glutathione S-transferase M1 (GSTM1) have been reported to be associated with hepatocellular carcinoma. However, the effect of the GSTMl null genotype was divergent in the literature and we therefore performed the present meta-analysis to explore the relationship in detail. Materials and Metbods: Reported studies were searched from 1990 to March 1, 2014 in PubMed and Wanfang Med Online. The total odds oatio (OR) and 95% CI were calculated and analyzed by Review Manager 5.1 and STATE 12. Results: Total OR was calculated from 26 articles with 3,769 cases and 5,517 controls and the association proved significant (OR [95%CI]=1.50 [1.25, 1.80], P<0.05) in the Chinese population. However, there was no significant association between hepatocellular carcinoma risk among subjects carrying the GSTM1 null genotype (OR [95%CI]=1.20 [0.88-1.64], P=0.24) in subgroups of publication in English and in Indian populations (OR [95%CI]=1.80 [0.80-4.20], P=0.15). Conclusions: The GSTM1 deletion polymorphism might not have a significant effect on the susceptibility of hepatocellular carcinoma overall.

• Genomics & Informatics
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• v.4 no.3
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• pp.110-117
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• 2006

In microarray technology, many diverse experimental features can cause biases including RNA sources, microarray production or different platforms, diverse sample processing and various experiment protocols. These systematic effects cause a substantial obstacle in the analysis of microarray data. When such data sets derived from different experimental processes were used, the analysis result was almost inconsistent and it is not reliable. Therefore, one of the most pressing challenges in the microarray field is how to combine data that comes from two different groups. As the novel trial to integrate two data sets with batch effect, we simply applied standardization to microarray data before the significant gene selection. In the gene selection step, we used new defined measure that considers the distance between a gene and an ideal gene as well as the between-slide and within-slide variations. Also we discussed the association of biological functions and different expression patterns in selected discriminative gene set. As a result, we could confirm that batch effect was minimized by standardization and the selected genes from the standardized data included various expression pattems and the significant biological functions.

• Molecular & Cellular Toxicology
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• v.1 no.4
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• pp.281-283
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• 2005

Extraction of biologically meaningful data and their validation are very important for toxicogenomics study because it deals with huge amount of heterogeneous data. BINGO is an annotation mining tool for biological interpretation of gene groups. Several statistical modeling approaches using Gene Ontology (GO) have been employed in many programs for that purpose. The statistical methodologies are useful in investigating the most significant GO attributes in a gene group, but the coherence of the resultant GO attributes over the entire group is rarely assessed. BINGO complements the statistical methods with graph-theoretic measures using the GO directed acyclic graph (DAG) structure. In addition, BINGO visualizes the consistency of a gene group more intuitively with a group-based GO subgraph. The input group can be any interesting list of genes or gene products regardless of its generation process if the group is built under a functional congruency hypothesis such as gene clusters from DNA microarray analysis.

• Genomics & Informatics
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• v.18 no.4
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• pp.41.1-41.8
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• 2020

We provide an algorithm for the construction and analysis of autocorrelation (information) functions of gene nucleotide sequences. As a measure of correlation between discrete random variables, we use normalized mutual information. The information functions are indicative of the degree of structuredness of gene sequences. We construct the information functions for selected gene sequences. We find a significant difference between information functions of genes of different types. We hypothesize that the features of information functions of gene nucleotide sequences are related to phenotypes of these genes.

• Journal of Acupuncture Research
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• v.21 no.2
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• pp.103-113
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• 2004

Objective : This study was designed to investigate the relation between the angiotensin converting enzyme(ACE) gene polymorphism and Facial nerve palsy in the Korean population. Methods : This sudy was carried out on 117 Facial nerve palsy patients who were treated in the department of acupuncture & moxibustion, Hospital of Oriental medical college, Kyung-Hee University and 135 healthy control subjects. Blood samples from all subjects were obtaind for DNA extraction. The extracted DNA was amplified by polymerase chain reaction(PCR). PCR products were visualized by 2% agarose gel electrophoresis. Results : The sub-genotypes of ACE gene were II homozygotes, ID heterozygotes, DD homozygotes. While the distribution of ACE polymorphism in control subjects was 33%, 43%, 24%, the distribution of it in Facial nerve palsy patients was 32%, 50%, 18%(II, ID, DD). Thus, there was no significant different between the control and Facial nerve palsy groups. Conclusions : we conclude that there is no significant association between ACE gene polymorphism and Facial nerve palsy in Korean population. However, the findings of this study need to be confirmed in more patients and further studies. Additional epidemiologically based studies of the effects and relationship between ACE or other genes and lifestyles with regard to Facial nerve palsy is required.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7215-7219
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• 2013

Background: Variation in metabolic genes is regarded as an important factor in processes leading to cancer. However, the effect of GSTT1 null genotype is divergent in the form of lung cancer. Methods: Studies were conducted at different research databases from 1990 to 2013 and the total odds ratio (OR) and 95% confidence interval (CI) were calculated for lung cancer. Review Manager 5.2 and STATE 12 are employed. Results: Total OR value is calculated from 17 articles with 2,118 cases and 2,915 controls. We discovered no significant increase in lung cancer risk among subjects carrying GSTT1 null genotype [OR = 1.15; 95% CI 0.97-1.36] in this meta-analysis. Conclusion: The GSTT1 deletion polymorphism does not have a significant effect on the susceptibility to lung cancer overall in China.

• Mycobiology
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• v.46 no.4
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• pp.361-369
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• 2018

The rice blast fungus, Magnaporthe oryzae, is an important pathogen of rice plants. It is well known that genes encoded in the genome have different evolutionary histories that are related to their functions. Phylostratigraphy is a method that correlates the evolutionary origin of genes with evolutionary transitions. Here we applied phylostratigraphy to partition total gene content of M. oryzae into distinct classes (phylostrata), which we designated PS1 to PS7, based on estimation of their emergence time. Genes in individual phylostrata did not show significant biases in their global distribution among seven chromosomes, but at the local level, clustering of genes belonging to the same phylostratum was observed. Our phylostrata-wide analysis of genes revealed that genes in the same phylostratum tend to be similar in many physical and functional characteristics such as gene length and structure, GC contents, codon adaptation index, and level of transcription, which correlates with biological functions in evolutionary context. We also found that a significant proportion of genes in the genome are orphans, for which no orthologs can be detected in the database. Among them, we narrowed down to seven orphan genes having transcriptional and translational evidences, and showed that one of them is implicated in asexual reproduction and virulence, suggesting ongoing evolution in this fungus through lineage-specific genes. Our results provide genomic basis for linking functions of pathogenicity factors and gene emergence time.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.276-276
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• 2022

Wheat is one of the most widely grown food crops worldwide. Extreme precipitation and wind disturbances increased due to the abnormal climate, which resulted in increased lodging. Introduction of dwarf genes in wheat significantly increased lodging resistance and productivity in wheat breeding. In this study, we performed the genotyping of dwarfing genes between 'Keumkang' and 'Komac 5' ('Keumkang' mutant). In addition, we investigated the relationship between plant height and several phenotypic characters using F₂ segregation populations derived from crosses between the two varieties. There was no significant difference in phenotypic characters between the two varieties except for plant height. In the genotyping analysis using dwarfing genes, mutations of two dwarfing gene were found to be induced between the two varieties. The four genotypes of the F₂ populations from a crossing between 'Keumkang' and 'Komac 5' were used to compare and evaluate the effects of two dwarfing genes. Plants with two single mutant dwarfing gene and double mutant dwarfing gene revealed reduced plant heights than control plants by 4.5%, 6.9%, and 33.2%, respectively. The phenotype analysis showed that double mutant dwarfing gene affected wheat stem growth as the length decreases from the second node, resulting in decreased plant height. However, there were no significant differences in the agronomic traits between mutant plants and control plant. These results may provide novel information about the effect of double mutant dwarfing gene on plant height, and may help improve lodging tolerance and wheat yield.