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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 11, Issue 4 - Dec 2013
Volume 11, Issue 3 - Sep 2013
Volume 11, Issue 2 - Jun 2013
Volume 11, Issue 1 - Mar 2013
Selecting the target year
Interplay between Epigenetics and Genetics in Cancer
Choi, Jae Duk ; Lee, Jong-Soo ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 164~173
DOI : 10.5808/GI.2013.11.4.164
Genomic instability, which occurs through both genetic mechanisms (underlying inheritable phenotypic variations caused by DNA sequence-dependent alterations, such as mutation, deletion, insertion, inversion, translocation, and chromosomal aneuploidy) and epigenomic aberrations (underlying inheritable phenotypic variations caused by DNA sequence-independent alterations caused by a change of chromatin structure, such as DNA methylation and histone modifications), is known to promote tumorigenesis and tumor progression. Mechanisms involve both genomic instability and epigenomic aberrations that lose or gain the function of genes that impinge on tumor suppression/prevention or oncogenesis. Growing evidence points to an epigenome-wide disruption that involves large-scale DNA hypomethylation but specific hyper-methylation of tumor suppressor genes, large blocks of aberrant histone modifications, and abnormal miRNA expression profile. Emerging molecular details regarding the modulation of these epigenetic events in cancer are used to illustrate the alterations of epigenetic molecules, and their consequent malfunctions could contribute to cancer biology. More recently, intriguing evidence supporting that genetic and epigenetic mechanisms are not separate events in cancer has been emerging; they intertwine and take advantage of each other during tumorigenesis. In addition, we discuss the collusion between epigenetics and genetics mediated by heterochromatin protein 1, a major component of heterochromatin, in order to maintain genome integrity.
Application of Cancer Genomics to Solve Unmet Clinical Needs
Lee, Se-Hoon ; Sim, Sung Hoon ; Kim, Ji-Yeon ; Cha, SooJin ; Song, Ahnah ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 174~179
DOI : 10.5808/GI.2013.11.4.174
The large amount of data on cancer genome research has contributed to our understanding of cancer biology. Indeed, the genomics approach has a strong advantage for analyzing multi-factorial and complicated problems, such as cancer. It is time to think about the actual usage of cancer genomics in the clinical field. The clinical cancer field has lots of unmet needs in the management of cancer patients, which has been defined in the pre-genomic era. Unmet clinical needs are not well known to bioinformaticians and even non-clinician cancer scientists. A personalized approach in the clinical field will bring potential additional challenges to cancer genomics, because most data to now have been population-based rather than individualbased. We can maximize the use of cancer genomics in the clinical field if cancer scientists, bioinformaticians, and clinicians think and work together in solving unmet clinical needs. In this review, we present one imaginary case of a cancer patient, with which we can think about unmet clinical needs to solve with cancer genomics in the diagnosis, prediction of prognosis, monitoring the status of cancer, and personalized treatment decision.
Genomic Profiling of Liver Cancer
Lee, Ju-Seog ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 180~185
DOI : 10.5808/GI.2013.11.4.180
Development of liver cancers is driven largely by genomic alterations that deregulate signaling pathways, influencing growth and survival of cancer cells. Because of the hundreds or thousands of genomic/epigenomic alterations that have accumulated in the cancer genome, it is very challenging to find and test candidate genes driving tumor development and progression. Systematic studies of the liver cancer genome have become available in recent years. These studies have uncovered new potential driver genes, including those not previously known to be involved in the development of liver cancer. Novel approaches combining multiple datasets from patient tissues have created an unparalleled opportunity to uncover potential new therapeutic targets and prognostic/predictive biomarkers for personalized therapy that can improve clinical outcomes of the patients with liver cancer.
Perspectives on Clinical Informatics: Integrating Large-Scale Clinical, Genomic, and Health Information for Clinical Care
Choi, In Young ; Kim, Tae-Min ; Kim, Myung Shin ; Mun, Seong K. ; Chung, Yeun-Jun ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 186~190
DOI : 10.5808/GI.2013.11.4.186
The advances in electronic medical records (EMRs) and bioinformatics (BI) represent two significant trends in healthcare. The widespread adoption of EMR systems and the completion of the Human Genome Project developed the technologies for data acquisition, analysis, and visualization in two different domains. The massive amount of data from both clinical and biology domains is expected to provide personalized, preventive, and predictive healthcare services in the near future. The integrated use of EMR and BI data needs to consider four key informatics areas: data modeling, analytics, standardization, and privacy. Bioclinical data warehouses integrating heterogeneous patient-related clinical or omics data should be considered. The representative standardization effort by the Clinical Bioinformatics Ontology (CBO) aims to provide uniquely identified concepts to include molecular pathology terminologies. Since individual genome data are easily used to predict current and future health status, different safeguards to ensure confidentiality should be considered. In this paper, we focused on the informatics aspects of integrating the EMR community and BI community by identifying opportunities, challenges, and approaches to provide the best possible care service for our patients and the population.
A Primer for Disease Gene Prioritization Using Next-Generation Sequencing Data
Wang, Shuoguo ; Xing, Jinchuan ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 191~199
DOI : 10.5808/GI.2013.11.4.191
High-throughput next-generation sequencing (NGS) technology produces a tremendous amount of raw sequence data. The challenges for researchers are to process the raw data, to map the sequences to genome, to discover variants that are different from the reference genome, and to prioritize/rank the variants for the question of interest. The recent development of many computational algorithms and programs has vastly improved the ability to translate sequence data into valuable information for disease gene identification. However, the NGS data analysis is complex and could be overwhelming for researchers who are not familiar with the process. Here, we outline the analysis pipeline and describe some of the most commonly used principles and tools for analyzing NGS data for disease gene identification.
Review of Biological Network Data and Its Applications
Yu, Donghyeon ; Kim, MinSoo ; Xiao, Guanghua ; Hwang, Tae Hyun ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 200~210
DOI : 10.5808/GI.2013.11.4.200
Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.
Current Status, Challenges, Policies, and Bioethics of Biobanks
Kang, Byunghak ; Park, Jaesun ; Cho, Sangyun ; Lee, Meehee ; Kim, Namhee ; Min, Haesook ; Lee, Sooyoun ; Park, Ok ; Han, Bokghee ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 211~217
DOI : 10.5808/GI.2013.11.4.211
Many biobanks were established as biorepositories for biomedical research, and a number of biobanks were founded in the 1990s. The main aim of the biobank is to store and to maintain biomaterials for studying chronic disease, identifying risk factors of specific diseases, and applying personalized drug therapies. This report provides a review of biobanks, including Korean biobanks and an analysis of sample volumes, regulations, policies, and ethical issues of the biobank. Until now, the top 6 countries according to the number of large-scale biobanks are the United Kingdom, United States, Sweden, France, the Netherlands, and Italy, and there is one major National Biobank of Korea (NBK) and 17 regional biobanks in Korea. Many countries have regulations and guidelines for the biobanks, and the importance of good management of biobanks is increasing. Meanwhile, according to a first survey of 456 biobank managers in the United States, biobankers are concerned with the underuse of the samples in their repositories, which need to be advertised for researchers. Korea Biobank Network (KBN) project phase II (2013-2015) was also planned for the promotion to use biospecimens in the KBN. The KBN is continuously introducing for researchers to use biospecimens in the biobank. An accreditation process can also be introduced for biobanks to harmonize collections and encourage use of biospecimens in the biobanks. KBN is preparing an on-line application system for the distribution of biospecimens and a biobank accreditation program and is trying to harmonize the biobanks.
Introduction to International Ethical Standards Related to Genetics and Genomics
Yim, Seon-Hee ; Chung, Yeun-Jun ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 218~223
DOI : 10.5808/GI.2013.11.4.218
The rapid advances in genetic knowledge and technology raise various, sometimes unprecedented, ethical dilemmas in the scientific community as well as the public realm. To deal with these dilemmas, the international community has prepared and issued ethical standards in various formats. In this review, seven international standards regarding genetics and genomics will be briefly introduced in chronological order. Critical reflections on them will not be provided in this review, and naturally, they have their own problems and shortcomings. However, a common set of the principles expressed in them will be highlighted here, because they are still relevant, and many of them will be more relevant in the future. Some of the interesting contents will be selected and described. After that, the morality of one recent event related to whole-genome sequencing and person-identifiable genetic data will be explored based on those international standards.
Receptor for Advanced Glycation Endproducts (RAGE), Its Ligands, and Soluble RAGE: Potential Biomarkers for Diagnosis and Therapeutic Targets for Human Renal Diseases
Lee, Eun Ji ; Park, Jong Hoon ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 224~229
DOI : 10.5808/GI.2013.11.4.224
Receptor for advanced glycation endproducts (RAGE) is a multi-ligand receptor that is able to bind several different ligands, including advanced glycation endproducts, high-mobility group protein (B)1 (HMGB1), S-100 calcium-binding protein, amyloid-
-protein, Mac-1, and phosphatidylserine. Its interaction is engaged in critical cellular processes, such as inflammation, proliferation, apoptosis, autophagy, and migration, and dysregulation of RAGE and its ligands leads to the development of numerous human diseases. In this review, we summarize the signaling pathways regulated by RAGE and its ligands identified up to date and demonstrate the effects of hyper-activation of RAGE signals on human diseases, focused mainly on renal disorders. Finally, we propose that RAGE and its ligands are the potential targets for the diagnosis, monitoring, and treatment of numerous renal diseases.
Study of Modern Human Evolution via Comparative Analysis with the Neanderthal Genome
Ahmed, Musaddeque ; Liang, Ping ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 230~238
DOI : 10.5808/GI.2013.11.4.230
Many other human species appeared in evolution in the last 6 million years that have not been able to survive to modern times and are broadly known as archaic humans, as opposed to the extant modern humans. It has always been considered fascinating to compare the modern human genome with that of archaic humans to identify modern human-specific sequence variants and figure out those that made modern humans different from their predecessors or cousin species. Neanderthals are the latest humans to become extinct, and many factors made them the best representatives of archaic humans. Even though a number of comparisons have been made sporadically between Neanderthals and modern humans, mostly following a candidate gene approach, the major breakthrough took place with the sequencing of the Neanderthal genome. The initial genome-wide comparison, based on the first draft of the Neanderthal genome, has generated some interesting inferences regarding variations in functional elements that are not shared by the two species and the debated admixture question. However, there are certain other genetic elements that were not included or included at a smaller scale in those studies, and they should be compared comprehensively to better understand the molecular make-up of modern humans and their phenotypic characteristics. Besides briefly discussing the important outcomes of the comparative analyses made so far between modern humans and Neanderthals, we propose that future comparative studies may include retrotransposons, pseudogenes, and conserved non-coding regions, all of which might have played significant roles during the evolution of modern humans.
Somatic Mutaome Profile in Human Cancer Tissues
Kim, Nayoung ; Hong, Yourae ; Kwon, Doyoung ; Yoon, Sukjoon ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 239~244
DOI : 10.5808/GI.2013.11.4.239
Somatic mutation is a major cause of cancer progression and varied responses of tumors against anticancer agents. Thus, we must obtain and characterize genome-wide mutational profiles in individual cancer subtypes. The Cancer Genome Atlas database includes large amounts of sequencing and omics data generated from diverse human cancer tissues. In the present study, we integrated and analyzed the exome sequencing data from ~3,000 tissue samples and summarized the major mutant genes in each of the diverse cancer subtypes and stages. Mutations were observed in most human genes (~23,000 genes) with low frequency from an analysis of 11 major cancer subtypes. The majority of tissue samples harbored 20-80 different mutant genes, on average. Lung cancer samples showed a greater number of mutations in diverse genes than other cancer subtypes. Only a few genes were mutated with over 5% frequency in tissue samples. Interestingly, mutation frequency was generally similar between non-metastatic and metastastic samples in most cancer subtypes. Among the 12 major mutations, the TP53, USH2A, TTN, and MUC16 genes were found to be frequent in most cancer types, while BRAF, FRG1B, PBRM1, and VHL showed lineage-specific mutation patterns. The present study provides a useful resource to understand the broad spectrum of mutation frequencies in various cancer types.
Characterization of H460R, a Radioresistant Human Lung Cancer Cell Line, and Involvement of Syntrophin Beta 2 (SNTB2) in Radioresistance
Im, Chang-Nim ; Kim, Byeong Mo ; Moon, Eun-Yi ; Hong, Da-Won ; Park, Joung Whan ; Hong, Sung Hee ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 245~253
DOI : 10.5808/GI.2013.11.4.245
A radioresistant cell line was established by fractionated ionizing radiation (IR) and assessed by a clonogenic assay, flow cytometry, and Western blot analysis, as well as zymography and a wound healing assay. Microarray was performed to profile global expression and to search for differentially expressed genes (DEGs) in response to IR. H460R cells demonstrated increased cell scattering and acidic vesicular organelles compared with parental cells. Concomitantly, H460R cells showed characteristics of increased migration and matrix metalloproteinase activity. In addition, H460R cells were resistant to IR, exhibiting reduced expression levels of ionizing responsive proteins (p-p53 and
-H2AX); apoptosis-related molecules, such as cleaved poly(ADP ribose) polymerase; and endoplasmic reticulum stress-related molecules, such as glucose-regulated protein (GRP78) and C/EBP-homologous protein compared with parental cells, whereas the expression of anti-apoptotic X-linked inhibitor of apoptosis protein was increased. Among DEGs, syntrophin beta 2 (SNTB2) significantly increased in H460R cells in response to IR. Knockdown of SNTB2 by siRNA was more sensitive than the control after IR exposure in H460, H460R, and H1299 cells. Our study suggests that H460R cells have differential properties, including cell morphology, potential for metastasis, and resistance to IR, compared with parental cells. In addition, SNTB2 may play an important role in radioresistance. H460R cells could be helpful in in vitro systems for elucidating the molecular mechanisms of and discovering drugs to overcome radioresistance in lung cancer therapy.
Genetic Variations of ABCC2 Gene Associated with Adverse Drug Reactions to Valproic Acid in Korean Epileptic Patients
Yi, Ji Hyun ; Cho, Yang-Je ; Kim, Won-Joo ; Lee, Min Goo ; Lee, Ji Hyun ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 254~262
DOI : 10.5808/GI.2013.11.4.254
The multidrug resistance protein 2 (MRP2, ABCC2) gene may determine individual susceptibility to adverse drug reactions (ADRs) in the central nervous system (CNS) by limiting brain access of antiepileptic drugs, especially valproic acid (VPA). Our objective was to investigate the effect of ABCC2 polymorphisms on ADRs caused by VPA in Korean epileptic patients. We examined the association of ABCC2 single-nucleotide polymorphisms and haplotype frequencies with VPA related to adverse reactions. In addition, the association of the polymorphisms with the risk of VPA related to adverse reactions was estimated by logistic regression analysis. A total of 41 (24.4%) patients had shown VPA-related adverse reactions in CNS, and the most frequent symptom was tremor (78.0%). The patients with CNS ADRs were more likely to have the G allele (79.3% vs. 62.7%, p=0.0057) and the GG genotype (61.0% vs. 39.7%, p=0.019) at the g.-1774delG locus. The frequency of the haplotype containing g.-1774Gdel was significantly lower in the patients with CNS ADRs than without CNS ADRs (15.8% vs. 32.3%, p=0.0039). Lastly, in the multivariate logistic regression analysis, the presence of the GG genotype at the g.-1774delG locus was identified as a stronger risk factor for VPA related to ADRs (odds ratio, 8.53; 95% confidence interval, 1.04 to 70.17). We demonstrated that ABCC2 polymorphisms may influence VPA-related ADRs. The results above suggest the possible usefulness of ABCC2 gene polymorphisms as a marker for predicting response to VPA-related ADRs.
TT Mutant Homozygote of Kruppel-like Factor 5 Is a Key Factor for Increasing Basal Metabolic Rate and Resting Metabolic Rate in Korean Elementary School Children
Choi, Jung Ran ; Kwon, In-Su ; Kwon, Dae Young ; Kim, Myung-Sunny ; Lee, Myoungsook ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 263~271
DOI : 10.5808/GI.2013.11.4.263
We investigated the contribution of genetic variations of KLF5 to basal metabolic rate (BMR) and resting metabolic rate (RMR) and the inhibition of obesity in Korean children. A variation of KLF5 (rs3782933) was genotyped in 62 Korean children. Using multiple linear regression analysis, we developed a model to predict BMR in children. We divided them into several groups; normal versus overweight by body mass index (BMI) and low BMR versus high BMR by BMR. There were no differences in the distributions of alleles and genotypes between each group. The genetic variation of KLF5 gene showed a significant correlation with several clinical factors, such as BMR, muscle, low-density lipoprotein cholesterol, and insulin. Children with the TT had significantly higher BMR than those with CC (p=0.030). The highest muscle was observed in the children with TT compared with CC (p=0.032). The insulin and C-peptide values were higher in children with TT than those with CC (p=0.029 vs. p=0.004, respectively). In linear regression analysis, BMI and muscle mass were correlated with BMR, whereas insulin and C-peptide were not associated with BMR. In the high-BMR group, we observed that higher muscle, fat mass, and C-peptide affect the increase of BMR in children with TT (p < 0.001, p < 0.001, and p=0.018, respectively), while Rohrer's index could explain the usual decrease in BMR (adjust
=1.000, p < 0.001, respectively). We identified a novel association between TT of KLF5 rs3782933 and BMR in Korean children. We could make better use of the variation within KLF5 in a future clinical intervention study of obesity.
Phylogeny of Flavobacteria Group Isolated from Freshwater Using Multilocus Sequencing Analysis
Mun, Seyoung ; Lee, Jungnam ; Lee, Siwon ; Han, Kyudong ; Ahn, Tae-Young ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 272~276
DOI : 10.5808/GI.2013.11.4.272
Sequence analysis of the 16S rRNA gene has been widely used for the classification of microorganisms. However, we have been unable to clearly identify five Flavobacterium species isolated from a freshwater by using the gene as a single marker, because the evolutionary history is incomplete and the pace of DNA substitutions is relatively rapid in the bacteria. In this study, we tried to classify Flavobacterium species through multilocus sequence analysis (MLSA), which is a practical and reliable technique for the identification or classification of bacteria. The five Flavobacterium species isolated from freshwater and 37 other strains were classified based on six housekeeping genes: gyrB, dnaK, tuf, murG, atpA, and glyA. The genes were amplified by PCR and subjected to DNA sequencing. Based on the combined DNA sequence (4,412 bp) of the six housekeeping genes, we analyzed the phylogenetic relationship among the Flavobacterium species. The results indicated that MLSA, based on the six housekeeping genes, is a trustworthy method for the identification of closely related Flavobacterium species.
Forensic Body Fluid Identification by Analysis of Multiple RNA Markers Using NanoString Technology
Park, Jong-Lyul ; Park, Seong-Min ; Kim, Jeong-Hwan ; Lee, Han-Chul ; Lee, Seung-Hwan ; Woo, Kwang-Man ; Kim, Seon-Young ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 277~281
DOI : 10.5808/GI.2013.11.4.277
RNA analysis has become a reliable method of body fluid identification for forensic use. Previously, we developed a combination of four multiplex quantitative PCR (qRT-PCR) probes to discriminate four different body fluids (blood, semen, saliva, and vaginal secretion). While those makers successfully identified most body fluid samples, there were some cases of false positive and negative identification. To improve the accuracy of the identification further, we tried to use multiple markers per body fluid and adopted the NanoString nCounter system instead of a multiplex qRT-PCR system. After measuring tens of RNA markers, we evaluated the accuracy of each marker for body fluid identification. For body fluids, such as blood and semen, each body fluid-specific marker was accurate enough for perfect identification. However, for saliva and vaginal secretion, no single marker was perfect. Thus, we designed a logistic regression model with multiple markers for saliva and vaginal secretion and achieved almost perfect identification. In conclusion, the NanoString nCounter is an efficient platform for measuring multiple RNA markers per body fluid and will be useful for forensic RNA analysis.
Molecular Vibration-Activity Relationship in the Agonism of Adenosine Receptors
Chee, Hyun Keun ; Oh, S. June ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 282~288
DOI : 10.5808/GI.2013.11.4.282
The molecular vibration-activity relationship in the receptor-ligand interaction of adenosine receptors was investigated by structure similarity, molecular vibration, and hierarchical clustering in a dataset of 46 ligands of adenosine receptors. The resulting dendrogram was compared with those of another kind of fingerprint or descriptor. The dendrogram result produced by corralled intensity of molecular vibrational frequency outperformed four other analyses in the current study of adenosine receptor agonism and antagonism. The tree that was produced by clustering analysis of molecular vibration patterns showed its potential for the functional classification of adenosine receptor ligands.
hpvPDB: An Online Proteome Reserve for Human Papillomavirus
Kumar, Satish ; Jena, Lingaraja ; Daf, Sangeeta ; Mohod, Kanchan ; Goyal, Peyush ; Varma, Ashok K. ;
Genomics & Informatics, volume 11, issue 4, 2013, Pages 289~291
DOI : 10.5808/GI.2013.11.4.289
Human papillomavirus (HPV) infection is the leading cause of cancer mortality among women worldwide. The molecular understanding of HPV proteins has significant connotation for understanding their intrusion in the host and designing novel protein vaccines and anti-viral agents, etc. Genomic, proteomic, structural, and disease-related information on HPV is available on the web; yet, with trivial annotations and more so, it is not well customized for data analysis, host-pathogen interaction, strain-disease association, drug designing, and sequence analysis, etc. We attempted to design an online reserve with comprehensive information on HPV for the end users desiring the same. The Human Papillomavirus Proteome Database (hpvPDB) domiciles proteomic and genomic information on 150 HPV strains sequenced to date. Simultaneous easy expandability and retrieval of the strain-specific data, with a provision for sequence analysis and exploration potential of predicted structures, and easy access for curation and annotation through a range of search options at one platform are a few of its important features. Affluent information in this reserve could be of help for researchers involved in structural virology, cancer research, drug discovery, and vaccine design.