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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Genomics & Informatics
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Korea Genome Organization
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Volume & Issues
Volume 6, Issue 4 - Dec 2008
Volume 6, Issue 3 - Sep 2008
Volume 6, Issue 2 - Jun 2008
Volume 6, Issue 1 - Mar 2008
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Copy Number Variations in the Human Genome: Potential Source for Individual Diversity and Disease Association Studies
Kim, Tae-Min ; Yim, Seon-Hee ; Chung, Yeun-Jun ;
Genomics & Informatics, volume 6, issue 1, 2008, Pages 1~7
DOI : 10.5808/GI.2008.6.1.001
The widespread presence of large-scale genomic variations, termed copy number variation (CNVs), has been recently recognized in phenotypically normal individuals. Judging by the growing number of reports on CNVs, it is now evident that these variants contribute significantly to genetic diversity in the human genome. Like single nucleotide polymorphisms (SNPs), CNVs are expected to serve as potential biomarkers for disease susceptibility or drug responses. However, the technical and practical concerns still remain to be tackled. In this review, we examine the current status of CNV DBs and research, including the ongoing efforts of CNV screening in the human genome. We also discuss the characteristics of platforms that are available at the moment and suggest the potential of CNVs in clinical research and application.
Genome-wide Linkage Study for Plasma HDL Cholesterol Level in an Isolated Population of Mongolia
Park, Han-Soo ; Kim, Jong-Il ; Cho, Sung-Il ; Sung, Joo-Hon ; Kim, Hyung-Lae ; Ju, Young-Seok ; Bayasgalan, Gombojav ; Lee, Mi-Kyeong ; Seo, Jeong-Sun ;
Genomics & Informatics, volume 6, issue 1, 2008, Pages 8~13
DOI : 10.5808/GI.2008.6.1.008
High-density lipoprotein (HDL) whose primary role is to transport cholesterol from peripheral tissues to the liver, is associated with the incidence of coronary heart disease. We analyzed HDL cholesterol levels in a genetically isolated population of extended Mongolian families. A total of 1002 individuals (54.5% women) from 95 families were enrolled. After genotyping by use of 1000 microsatellite markers, we performed a genome-wide linkage search with variance component analysis. The estimated heritability of HDL cholesterol was 0.45, revealing that HDL cholesterol was under significant genetic influence. We found peak evidence of linkage (LOD score=1.88) for HDL cholesterol level on chromosome 6 (nearest marker D6S1660) and potential evidences for linkage on chromosomes 1, 12 and 19 with the LOD scores of 1.32, 1.44 and 1.14, respectively. These results should pave the way for the discovery of the relevant genes by fine mapping and association analysis.
Inbreeding Coefficients in Two Isolated Mongolian Populations - GENDISCAN Study
Sung, Joo-Hon ; Lee, Mi-Kyeong ; Seo, Jeong-Sun ;
Genomics & Informatics, volume 6, issue 1, 2008, Pages 14~17
DOI : 10.5808/GI.2008.6.1.014
GENDISCAN study (Gene Discovery for Complex traits in Asian population of Northeast area) was designed to incorporate methodologies which enhance the power to identify genetic variations underlying complex disorders. Use of population isolates as the target population is a unique feather of this study. However, population isolates may have hidden inbreeding structures which can affect the validity of the study. To understand how this issue may affect results of GENDISCAN, we estimated inbreeding coefficients in two study populations in Mongolia. We analyzed the status of Hardy-Weinberg Equilibrium (HWE), polymorphism information contents (PIC), heterozygosity, allelic diversity, and inbreeding coefficients, using 317 and 1,044 STR (short tandem repeat) markers in Orkhontuul and Dashbalbar populations. HWE assumptions were generally met in most markers (88.6% and 94.2% respectively), and single marker PIC ranged between 0.2 and 0.9. Inbreeding coefficients were estimated to be 0.0023 and 0.0021, which are small enough to assure that conventional genetic analysis would work without any specific modification. We concluded that the population isolates used in GENDISCAN study would not present significant inflation of type I errors from inbreeding effects in its gene discovery analysis.
Chromosome 22 LD Map Comparison between Korean and Other Populations
Lee, Jong-Eun ; Jang, Hye-Yoon ; Kim, Sook ; Yoo, Yeon-Kyeong ; Hwang, Jung-Joo ; Jun, Hyo-Jung ; Lee, Kyu-Sang ; Son, Ok-Kyung ; Yang, Jun-Mo ; Ahn, Kwang-Sung ; Kim, Eug-Ene ; Lee, Hye-Won ; Song, Kyu-Young ; Kim, Hie-Lim ; Lee, Seong-Gene ; Yoon, Yong-Sook ; Kimm, Ku-Chan ; Han, Bok-Ghee ; Oh, Berm-Seok ; Kim, Chang-Bae ; Jin, Hoon ; Choi, Kyoung-O. ; Kang, Hyo-Jin ; Kim, Young-J. ;
Genomics & Informatics, volume 6, issue 1, 2008, Pages 18~28
DOI : 10.5808/GI.2008.6.1.018
Single nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variations and resources for mapping complex genetic traits and disease association studies. We have constructed a linkage disequilibrium (LD) map of chromosome 22 in Korean samples and compared it with those of other populations, including Yorubans in Ibadan, Nigeria (YRI), Centre d'Etude du Polymorphisme Humain (CEPH) reference families (CEU), Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) in the HapMap database. We genotyped 4681 of 111,448 publicly available SNPs in 90 unrelated Koreans. Among genotyped SNPs, 4167 were polymorphic. Three hundred and five LD blocks were constructed to make up 18.6% (6.4 of 34.5 Mb) of chromosome 22 with 757 tagSNPs and 815 haplotypes (frequency
5.0%). Of 3430 common SNPs genotyped in all five populations, 514 were monomorphic in Koreans. The CHB + JPT samples have more than a 72% overlap with the monomorphic SNPs in Koreans, while the CEU + YRI samples have less than a 38% overlap. The patterns of hot spots and LD blocks were dispersed throughout chromosome 22, with some common blocks among populations, highly concordant between the three Asian samples. Analysis of the distribution of chimpanzee-derived allele frequency (DAF), a measure of genetic differentiation, Fst levels, and allele frequency difference (AFD) among Koreans and the HapMap samples showed a strong correlation between the Asians, while the CEU and YRI samples showed a very weak correlation with Korean samples. Relative distance as a quantitative measurement based upon DAF, Fst, and AFD indicated that all three Asian samples are very proximate, while CEU and YRI are significantly remote from the Asian samples. Comparative genome-wide LD studies provide useful information on the association studies of complex diseases.
Functional Haplotype Frequencies of the Interleukin-1B Promoter in the Korean Population
Lee, Kyung-A ;
Genomics & Informatics, volume 6, issue 1, 2008, Pages 29~31
DOI : 10.5808/GI.2008.6.1.029
Single nucleotide polymorphisms (SNPs) in the promoter region of the IL-1B (interleukin-1) gene have been implicated in a variety of diseases that have an inflammatory component. However, there has been significant heterogeneity among study results, especially between Caucasian and Asian populations. Recently, it has been reported that SNPs in the IL-1B gene affect transcription, according to haplotype context, and genetic association studies may be more informative if functional SNP haplotypes of population are analyzed. Therefore, we estimated the distribution of IL-1B promoter haplotypes in 433 Koreans using the three major functional IL-1B promoter SNPs (IL-1B -1464, -511, and -31) and compared the results with those in Caucasians. The difference in IL-1B promoter haplotype frequency between Korean and Caucasian populations was statistically significant. The potentially more inflammatory haplotypes had higher frequencies in Koreans when compared with Caucasians. These Korean haplotype data will be useful for future association studies between IL-1B SNPs and disease risk.
Functional Prediction of Imprinted Genes in Chicken Based on a Mammalian Comparative Expression Network
Kim, Hyo-Young ; Moon, Sun-Jin ; Kim, Hee-Bal ;
Genomics & Informatics, volume 6, issue 1, 2008, Pages 32~35
DOI : 10.5808/GI.2008.6.1.032
Little evidence supports the existence of imprinted genes in chicken. Imprinted genes are thought to be intimately connected with the acquisition of parental resources in mammals; thus, the predicted lack of this type of gene in chicken is not surprising, given that they leave their offspring to their own heritance after conception. In this study, we identified several imprinted genes and their orthologs in human, mouse, and zebrafish, including 30 previously identified human and mouse imprinted genes. Next, using the HomoloGene database, we identified six orthologous genes in human, mouse, and chicken; however, no orthologs were identified for SLC22A18, and mouse Ppp1r9a was not included in the HomoloGene database. Thus, from our analysis, four candidate chicken imprinted genes (IGF2, UBE3A, PHLDA2, and GRB10) were identified. To expand our analysis, zebrafish was included, but no probe ID for UBE3A exists in this species. Thus, ultimately, three candidate imprinted genes (IGF2, PHLDA2, and GRB10) in chicken were identified. GRB10 was not significant in chicken and zebrafish based on the Wilcoxon-Mann-Whitney test, whereas a weak correlation between PHLDA2 in chicken and human was identified from the Spearman's rank correlation coefficient. Significant associations between human, mouse, chicken, and zebrafish were found for IGF2 and GRB10 using the Friedman's test. Based on our results, IGF2, PHLDA2, and GRB10 are candidate imprinted genes in chicken. Importantly, the strongest candidate was PHLDA2.
Differential Expressions of Apoptosis-related Genes in Lung Cancer Cell Lines Determine the Responsiveness to Ionizing Radiation
Lee, Su-Yeon ; Choi, Moon-Kyung ; Lim, Jung-Min ; Wu, Hong-Gyun ; Kim, Ju-Han ; Park, Woong-Yang ;
Genomics & Informatics, volume 6, issue 1, 2008, Pages 36~43
DOI : 10.5808/GI.2008.6.1.036
Radiotherapy would be the choice of treatment for human cancers, because of high cost-effectiveness. However, a certain population of patients shows a resistance to radiotherapy and recurrence. In an effort to increase the efficacy of radiotherapy, many efforts were driven to find the genes causing the unresponsiveness to ionizing radiation. In this paper, we compared the gene expression profiles of two lung cancer cell lines, H460 and H1299, which showed differential responses to ionizing radiations. Each cell were irradiated at 2 Gy, and harvested after 0, 2, 4, 8, 12 and 24 hours to examine the expressions. Two-way ANOVA analysis on time-series experiments of two cells could select 2863 genes differentially expressed upon ionizing radiation among 32,321 genes in microarray (p<0.05). We classified these genes into 21 clusters by SOM clustering according to the interaction between cell types and time. Two SOM clusters were enriched with apoptosis-related genes in pathway analysis. One cluster contained higher levels of phosphatidyl inositol 3-phosphate kinase (PI3K) subunits in H1299, radio-resistant cells than H460, radiosensitive cells. TRAIL receptors were expressed in H460 cells while the decoy receptor for TRAIL was expressed in H1299 cells. From these results, we could characterize the differential responsiveness to ionizing radiation according to their differential expressions of apoptosis-related genes, which might be the candidates to increase the power of radiotherapy.
Sequence Analysis and Potential Action of Eukaryotic Type Protein Kinase from Streptomyces coelicolor A3(2)
Roy, Daisy R. ; Chandra, Sathees B.C. ;
Genomics & Informatics, volume 6, issue 1, 2008, Pages 44~49
DOI : 10.5808/GI.2008.6.1.044
Protein kinase C (PKC) is a family of kinases involved in the transduction of cellular signals that promote lipid hydrolysis. PKC plays a pivotal role in mediating cellular responses to extracellular stimuli involved in proliferation, differentiation and apoptosis. Comparative analysis of the PKC-
isozymes of 200 recently sequenced microbial genomes was carried out using variety of bioinformatics tools. Diversity and evolution of PKC was determined by sequence alignment. The ser/thr protein kinases of Streptomyces coelicolor A3 (2), is the only bacteria to show sequence alignment score greater than 30% with all the three PKC isotypes in the sequence alignment. S.coelicolor is the subject of our interest because it is notable for the production of pharmaceutically useful compounds including anti-tumor agents, immunosupressants and over two-thirds of all natural antibiotics currently available. The comparative analysis of three human isotypes of PKC and Serine/threonine protein kinase of S.coelicolor was carried out and possible mechanism of action of PKC was derived. Our analysis indicates that Serine/ threonine protein kinase from S. coelicolor can be a good candidate for potent anti-tumor agent. The presence of three representative isotypes of the PKC super family in this organism helps us to understand the mechanism of PKC from evolutionary perspective.
Refactoring the Code for Visualizing Protein Database Information in a 3D Viewer for Software Reusability
Chun, Yoo-Jin ; Ham, Seong-Il ; Yang, San-Duk ; Rhie, Arang ; Park, Hyun-Seok ;
Genomics & Informatics, volume 6, issue 1, 2008, Pages 50~53
DOI : 10.5808/GI.2008.6.1.050
We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC) model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.
GTVseq: A Web-based Genotyping Tool for Viral Sequences
Shin, Jae-Min ; Park, Ho-Eun ; Ahn, Yong-Ju ; Cho, Doo-Ho ; Kim, Ji-Han ; Kee, Mee-Kyung ; Kim, Sung-Soon ; Lee, Joo-Shil ; Kim, Sang-Soo ;
Genomics & Informatics, volume 6, issue 1, 2008, Pages 54~58
DOI : 10.5808/GI.2008.6.1.054
Genotyping Tool for Viral SEQuences (GTVseq) provides scientists with the genotype information on the viral genome sequences including HIV-1, HIV-2, HBV, HCV, HTLV-1, HTLV-2, poliovirus, enterovirus, flavivirus, Hantavirus, and rotavirus. GTVseq produces alternative and additive genotype information for the query viral sequences based on two different, but related, scoring methods. The genotype information produced is reported in a graphical manner for the reference genotype matches and each graphical output is linked to the detailed sequence alignments between the query and the matched reference sequences. GTVseq also reports the potential 'repeats' and/or 'recombination' sequence region in a separated window. GTVseq does not replace completely other well-known genotyping tools such as NCBI's virus sequence genotyping tool (http://www.ncbi. nlm.nih.gov/projects/genotyping/formpage.cgi), but provides additional information useful in the confirmation or for further investigation of the genotype(s) for the newly isolated viral sequences.