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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
> Journal Vol & Issue
Genomics & Informatics
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Journal DOI :
Korea Genome Organization
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Volume & Issues
Volume 8, Issue 4 - Dec 2010
Volume 8, Issue 3 - Sep 2010
Volume 8, Issue 2 - Jun 2010
Volume 8, Issue 1 - Mar 2010
Selecting the target year
Association Analysis of SERPINB5 Polymorphisms with HBV Clearance and HCC Occurrence in a Korean Population
Kim, Ja-Son Y. ; Park, Tae-Joon ; Lee, Jin-Sol ; Chun, Ji-Yong ; Bae, Joon-Seol ; Park, Byung-Lae ; Cheong, Hyun-Sub ; Lee, Hyo-Suk ; Kim, Yoon-Jun ; Shin, Hyoung-Doo ;
Genomics & Informatics, volume 8, issue 1, 2010, Pages 1~8
DOI : 10.5808/GI.2010.8.1.001
Serpin peptidase inhibitor, Clade B (ovalbumin), Member 5 (SERPINB5), also known as maspin, is a potent tumor suppressor gene. It has correlations with many tumor cells, from pancreas cancer to breast cancer, so it is possible that it may also affect liver cancer. There has also been a report that SERPINB12, a gene placed right next to SERPINB5, is expressed in liver. For this study, 32 polymorphisms were identified in SERPINB5 by direct DNA sequencing, and 11 of them were selected to be tested with a larger scale subjects. The association of the 11 SERPINB5 polymorphisms with Hepatitis B virus (HBV) clearance, hepatocellular carcinoma (HCC) occurrence and the onset age of HCC were analyzed. There were no significant associations found between 11 SERPINB5 polymorphisms and HBV clearance. In the case of HCC occurrence, one of the haplotypes (ht) showed association with HCC occurrence (OR=2.26, p=0.005,
), albeit with a low statistical power (40.8%) and haplotype frequency (0.052). Further study with a bigger sample size will be needed to clearly verify the association between ht5 and HCC occurrence.
Putative Association of ITGB1 Haplotype with the Clearance of HBV Infection
Park, Tae-Joon ; Chun, Ji-Yong ; Bae, Joon-Seol ; Kim, Ja-Son Y. ; Lee, Jin-Sol ; Pasaje, Charisse Flerida ; Park, Byung-Lae ; Cheong, Hyun-Sub ; Lee, Hyo-Suk ; Kim, Yoon-Jun ; Shin, Hyoung-Doo ;
Genomics & Informatics, volume 8, issue 1, 2010, Pages 9~18
DOI : 10.5808/GI.2010.8.1.009
Integrins are transmembrane receptor proteins that mediate cell-cell adhesion and cell-extracellular matrix (ECM) adhesion. The deregulation of cell-ECM adhesion and the abnormal expression of beta1 (
) integrins (ITGB1s) are involved in tumor development and metastasis. In the liver, the expression of integrins and ECM proteins can be a cause of hepatocellular carcinoma (HCC) development. We performed direct DNA sequencing of 24 individuals, and identified 23 sequence variants of ITGB1 polymorphisms. Among these 23 variants, 7 common variants were selected based on frequencies and linkage disequilibrium, and then genotyped in a larger-scale group of subjects (n=1,103). The genetic associations of ITGB1 polymorphisms with the clearance of HBV and HCC outcome of HBV patients were analyzed using logistic regression models and Cox relative hazard models. Although there was no significant association observed between the polymorphisms and the HCC outcome of HBV patients, the second most common haplotype (ITGB1 haplotype-2 [C-C-C-C-T-C-T]) was putatively associated with HBV clearance (OR=0.75, p=0.008 and
). The minor allele frequency (MAF) of ITGB1 haplotype -2 of the spontaneously recovered (SR) group was significantly higher than that of the chronic carrier group (CC) (freq. = 0.248 vs. 0.199). The information derived from this study could be valuable for understanding the genetic factors involved in the clearance of HBV.
Replication of the Association between Copy Number Variation on 8p23.1 and Autism by Using ASD-specific BAC Array
Woo, Jung-Hoon ; Yang, Song-Ju ; Yim, Seon-Hee ; Hu, Hae-Jin ; Shin, Myung-Ju ; Oh, Eun-Hee ; Kang, Hyun-Woong ; Park, Seon-Yang ; Chung, Yeun-Jun ;
Genomics & Informatics, volume 8, issue 1, 2010, Pages 19~27
DOI : 10.5808/GI.2010.8.1.019
To discover genetic markers for autism spectrum disorder (ASD), we previously applied genome-wide BAC array comparative genomic hybridization (array-CGH) to 28 autistic patients and 62 normal controls in Korean population, and identified that chromosomal losses on 8p23.1 and on 17p11.2 are significantly associated with autism. In this study, we developed an 8.5K ASD-specific BAC array covering 27 previously reported ASD-associated CNV loci including ours and examined whether the associations would be replicated in 8 ASD patient cell lines of four different ethnic groups and 10 Korean normal controls. As a result, a CNV-loss on 8p23.1 was found to be significantly more frequent in patients regardless of ethnicity (p<0.0001). This CNV region contains two coding genes, DEFA1 and DEFA3, which are members of DEFENSIN gene family. Two other CNVs on 17p11.2 and Xp22.31 were also distributed differently between ASDs and controls, but not significant (p=0.069 and 0.092, respectively). All the other loci did not show significant association. When these evidences are considered, the association between ASD and CNV of DEFENSIN gene seems worthy of further exploration to elucidate the pathogenesis of ASD. Validation studies with a larger sample size will be required to verify its biological implication.
Genome-wide Response of Normal WI-38 Human Fibroblast Cells to 1,763 MHz Radiofrequency Radiation
Im, Chang-Nim ; Kim, Eun-Hye ; Park, Ae-Kyung ; Park, Woong-Yang ;
Genomics & Informatics, volume 8, issue 1, 2010, Pages 28~33
DOI : 10.5808/GI.2010.8.1.028
Increased exposure of human to RF fields has raised concerns for its potential adverse effects on our health. To address the biological effects of RF radiation, we used genome wide gene expression as the indicator. We exposed normal WI-38 human fibroblast cells to 1763 MHz mobile phone RF radiation at a specific absorption rate (SAR) of 60 W/kg with an operating cooling system for 24 h. There were no alterations in cell numbers or morphology after RF exposure. Through microarray analysis, we identified no differentially expressed genes (DEGs) at the 0.05 significance level after controlling for multiple testing errors with the Benjaminiochberg false discovery rate (BH FDR) method. Meanwhile, 82 genes were differentially expressed between RF-exposed cells and controls when the significance level was set at 0.01 without correction for multiple comparisons. We found that 24 genes (0.08% of the total genes examined) were changed by more than 1.5-fold on RF exposure. However, significant enrichment of any gene set or pathway was not observed from the functional annotation analysis. From these results, we did not find any evidence that non-thermal RF radiation at a 60-W/kg SAR significantly affects cell proliferation or gene expression in WI-38 cells.
Classification of Biological Effect of 1,763 MHz Radiofrequency Radiation Based on Gene Expression Profiles
Im, Chang-Nim ; Kim, Eun-Hye ; Park, Ae-Kyung ; Park, Woong-Yang ;
Genomics & Informatics, volume 8, issue 1, 2010, Pages 34~40
DOI : 10.5808/GI.2010.8.1.034
Radiofrequency (RF) radiation might induce the transcription of a certain set of genes as other physical stresses like ionizing radiation and UV. To observe transcriptional changes upon RF radiation, we exposed WI-38, human lung fibroblast cell to 1763 MHz of mobile phone RF radiation at 60 W/kg of specific absorption rate (SAR) for 24h with or without heat control. There were no significant changes in cell numbers and morphology after exposure to RF radiation. Using quantitative RT-PCR, we checked the expression of three heat shock protein (HSP) (HSPA1A, HSPA6 and HSP105) and seven stress-related genes (TNFRSF11B, FGF2, TGFB2, ITGA2, BRIP1, EXO1, and MCM10) in RF only and RF/HS groups of RF-exposed cells. The expressions of three heat shock proteins and seven stress-related genes were selectively changed only in RF/HS groups. Based on the expression of ten genes, we could classify thermal and non-thermal effect of RF-exposure, which genes can be used as biomarkers for RF radiation exposure.
Gene Expression Analysis for Statin-induced Cytotoxicity from Rat Primary Hepatocytes
Ko, Moon-Jeong ; Ahn, Joon-Ik ; Shin, Hee-Jung ; Kim, Hye-Soo ; Chung, Hye-Joo ; Jeong, Ho-Sang ;
Genomics & Informatics, volume 8, issue 1, 2010, Pages 41~49
DOI : 10.5808/GI.2010.8.1.041
Statins are competitive inhibitors of hydroxy-3-methyl glutaryl coenzyme A (HMG-CoA) reductase and used most frequently to reduce plasma cholesterol levels and to decrease cardiovascular events. However, statins also have been reported to have undesirable side effects such as myotoxicity and hepatotoxicity associated with their intrinsic efficacy mechanisms. Clinical studies recurrently reported that statin therapy elevated the level of liver enzymes such as ALT and AST in patients suggesting possible liver toxicity due to statins. This observation has been drawn great attention since statins are the most prescribed drugs and statin-therapy was extended to a larger number of high-risk patients. Here we employed rat primary hepatocytes and microarray technique to understand underlying mechanism responsible for statin-induced liver toxicity on cell level. We isolated genes whose expressions were commonly modulated by statin treatments and examined their biological functions. It is of interest that those genes have function related to response to stress in particular immunity and defense in cells. Our study provided the basic information on cellular mechanism of statin-induced cytotoxicity and may serve for finding indicator genes of statin -induced toxicity in rat primary hepatocytes.
Effects of Mercuric Chloride on Gene Expression in NRK-52E Cells
Ahn, Joon-Ik ; Baik, Si-Yeon ; Ko, Moon-Jeong ; Shin, Hee-Jung ; Chung, Hye-Joo ; Jeong, Ho-Sang ;
Genomics & Informatics, volume 8, issue 1, 2010, Pages 50~57
DOI : 10.5808/GI.2010.8.1.050
Mercuric chloride, a model nephrotoxicant was used to elucidate time- and dose- dependent global gene expression changes associated with proximal tubular toxicity. Rat kidney cell lines NRK-52E cells were exposed for 2, 6 and 12 hours and with 3 different doses of mercuric chloride. Cell viability assay showed that mercuric chloride had toxic effects on NRK-52E cells causing 20% cell death (IC20) at
concentration. We set this IC20 as high dose concentration and 1/5 and 1/25 concentration of LC20 were used as mid and low concentration, respectively. Analyses of microarray data revealed that 738 genes were differentially expressed (more than two-fold change and p<0.05) by low concentration of mercuric chloride at least one time point in NRK-52E cells. 317 and 2,499 genes were differentially expressed at mid and high concentration of mercuric chloride, respectively. These deregulated genes showed a primary involvement with protein trafficking (CAV2, CANX, CORO1B), detoxification (GSTs) and immunity and defense (HMOX1, NQO1). Several of these genes were previously reported to be up-regulated in proximal tubule cells treated with nephrotoxicants and might be aid in promoting the predictive biomarkers for nephrotoxicity.
CpG Islands Detector: a Window-based CpG Island Search Tool
Kim, Ki-Bong ;
Genomics & Informatics, volume 8, issue 1, 2010, Pages 58~61
DOI : 10.5808/GI.2010.8.1.058
CpG is the pair of nucleotides C and G, appearing successively, in this order, along one DNA strand. It is known that due to biochemical considerations CpG is relatively rare in most DNA sequences. However, in particular subsequences, which are a few hundred to a few thousand nucleotides long, the couple CpG is more frequent. These subsequences, called CpG islands, are known to appear in biologically more significant parts of the genome. The ability to identify CpG islands along a chromosome will therefore help us spot its more significant regions of interest, such as the promoters or 'start' regions of many genes. In this respect, I developed the CpG islands search tool, CpG Islands Detector, which was implemented in JAVA to be run on any platform. The window-based graphical user interface of CpG Islands Detector may facilitate the end user to employ this tool to pinpoint CpG islands in a genomic DNA sequence. In addition, this tool can be used to highlight potential genes in genomic sequences since CpG islands are very often found in the 5' regions of vertebrate genes.