Go to the main menu
Skip to content
Go to bottom
REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
> Journal Vol & Issue
Genomics & Informatics
Journal Basic Information
Journal DOI :
Korea Genome Organization
Editor in Chief :
Volume & Issues
Volume 5, Issue 4 - Dec 2007
Volume 5, Issue 3 - Sep 2007
Volume 5, Issue 2 - Jun 2007
Volume 5, Issue 1 - Mar 2007
Selecting the target year
Pharmacogenomics in Drug Discovery and Development
Ahn, Chul ;
Genomics & Informatics, volume 5, issue 2, 2007, Pages 41~45
Pharmacogenomics is the study that examines how genetic variations affect the ways in which people respond to drugs. The ways people respond to drugs are complex traits that are influenced by many different genes. Pharmacogenomics intends to develop rational means of optimizing drug therapy, with respect to the patients' genotype, to maximize efficacy with minimal adverse drug reactions. Pharmacogenomics has the potential to revolutionize the practice of medicine, and promises to usher in an area of personalized medicine, in which drugs and drug combinations are optimized for each individual's unique genetic makeup. Indeed, pharmacogenomics is exploited as an essential step for target discovery and drug development in the pharmaceutical industry. The goal of the personalized medicine is to get the right dose of the right drug to the right patient at the right time. In this article, we will review the use of pharmacogenomics in drug discovery and development.
Molecular Imaging in the Age of Genomic Medicine
Byun, Jong-Hoe ;
Genomics & Informatics, volume 5, issue 2, 2007, Pages 46~55
The convergence of molecular and genetic disciplines with non-invasive imaging technologies has provided an opportunity for earlier detection of disease processes which begin with molecular and cellular abnormalities. This emerging field, known as molecular imaging, is a relatively new discipline that has been rapidly developed over the past decade. It endeavors to construct a visual representation, characterization, and quantification of biological processes at the molecular and cellular level within living organisms. One of the goals of molecular imaging is to translate our expanding knowledge of molecular biology and genomic sciences into good patient care. The practice of molecular imaging is still largely experimental, and only limited clinical success has been achieved. However, it is anticipated that molecular imaging will move increasingly out of the research laboratory and into the clinic over the next decade. Non-invasive in vivo molecular imaging makes use of nuclear, magnetic resonance, and in vivo optical imaging systems. Recently, an interest in Positron Emission Tomography (PET) has been revived, and along with optical imaging systems PET is assuming new, important roles in molecular genetic imaging studies. Current PET molecular imaging strategies mostly rely on the detection of probe accumulation directly related to the physiology or the level of reporter gene expression. PET imaging of both endogenous and exogenous gene expression can be achieved in animals using reporter constructs and radio-labeled probes. As increasing numbers of genetic markers become available for imaging targets, it is anticipated that a better understanding of genomics will contribute to the advancement of the molecular genetic imaging field. In this report, the principles of non-invasive molecular genetic imaging, its applications and future directions are discussed.
Genetic Analysis of TGFA, MTHFR, and IFR6 in Korean Patients Affected by Nonsyndromic Cleft Lip with or without Cleft Palate (CL/P)
Park, Jung-Young ; Yoo, Han-Wook ; Kim, Young-Ho ;
Genomics & Informatics, volume 5, issue 2, 2007, Pages 56~60
Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common craniofacial birth defect that is the result of a mixture of genetic and environmental factors. While studies have identified a number of different candidate genes and loci for the etiology of CL/P, the results have not been consistent among different ethnic groups. To study the genetic association of the candidate genes in Korean patients affected by CL/P, we genotyped 97 nonsyndromic CL/P patients and 100 control individuals using single nucleotide polymorphic markers at the MTHFR, TGFA, and IRF6 genes. We report that the T3827C marker at TGFA showed significant association with nonsyndromic CL/P, but all the other markers tested were not significantly associated with nonsyndromic CL/P in Korean patients.
Controlling Linkage Disequilibrium in Association Tests: Revisiting APOE Association in Alzheimer's Disease
Park, Lee-Young ;
Genomics & Informatics, volume 5, issue 2, 2007, Pages 61~67
The allele frequencies of markers as well as linkage disequilibrium (LD) can be changed in cases due to the LD between markers and the disease allele, exhibiting spurious associations of markers. To identify the true association, classical statistical tests for dealing with confounders have been applied to draw a conclusion as to whether the association of variants comes from LD with the known disease allele. However, a more direct test considering LD using estimated haplotype frequencies may be more efficient. The null hypothesis is that the different allele frequencies of a variant between cases and controls come solely from the increased disease allele frequency and the LD relationship with the disease allele. The haplotype frequencies of controls are estimated using the expectation maximization (EM) algorithm from the genotype data. The estimated frequencies are applied to calculate the expected haplotype frequencies in cases corresponding to the increase or decrease of the causative or protective alleles. The suggested method was applied to previously published data, and several APOE variants showed association with Alzheimer's disease independent from the APOE
variant, rs429358, regardless of LD showing significant simulated p-values. The test results support the possibility that there may be more than one common disease variant in a locus.
A Statistical Analysis of SNPs, In-Dels, and Their Flanking Sequences in Human Genomic Regions
Shin, Seung-Wook ; Kim, Young-Joo ; Kim, Byung-Dong ;
Genomics & Informatics, volume 5, issue 2, 2007, Pages 68~76
Due to the increasing interest in SNPs and mutational hot spots for disease traits, it is becoming more important to define and understand the relationship between SNPs and their flanking sequences. To study the effects of flanking sequences on SNPs, statistical approaches are necessary to assess bias in SNP data. In this study we mainly applied Markov chains for SNP sequences, particularly those located in intronic regions, and for analysis of in-del data. All of the pertaining sequences showed a significant tendency to generate particular SNP types. Most sequences flanking SNPs had lower complexities than average sequences, and some of them were associated with microsatellites. Moreover, many Alu repeats were found in the flanking sequences. We observed an elevated frequency of single-base-pair repeat-like sequences, mirror repeats, and palindromes in the SNP flanking sequence data. Alu repeats are hypothesized to be associated with C-to-T transition mutations or A-to-I RNA editing. In particular, the in-del data revealed an association between particular changes such as palindromes or mirror repeats. Results indicate that the mechanism of induction of in-del transitions is probably very different from that which is responsible for other SNPs. From a statistical perspective, frequent DNA lesions in some regions probably have effects on the occurrence of SNPs.
Serotonin (5-HT) Receptor Subtypes Mediate Regulation of Neuromodulin Secretion in Rat Hypothalamic Neurons
Chin, Chur ; Kim, Seong-Il ;
Genomics & Informatics, volume 5, issue 2, 2007, Pages 77~82
Serotonin (5-HT), the endogenous nonselective 5-HT receptor agonist, activates the inositol-1,4,5-triphosphate/calcium
signaling pathway and exerts both stimulatory and inhibitory actions on cAMP production and neuromodulin secretion in rat hypothalamic neurons. Specific mRNA transcripts for 5-HT1A, 5-HT2C and 5-HT4 were identified in rat hypothalamic neurons. These experiments were supported by combined techniques such as cAMP and a
assays in order to elucidate the associated receptors and signaling pathways. The cAMP production and neuromodulin release were profoundly inhibited during the activation of the Gi-coupled 5-HT1A receptor. Treatment with a selective agonist to activate the Gq-coupled 5-HT2C receptor stimulated InsP3 production and caused
release from the sarcoplasmic reticulum. Selective activation of the Gs-coupled 5-HT4 receptor also stimulated cAMP production, and caused an increase in neuromodulin secretion. These findings demonstrate the ability of 5-HT receptor subtypes expressed in neurons to induce neuromodulin production. This leads to the activation of single or multiple G-proteins which regulate the
and adenyl cyclase / cAMP signaling pathways.
A DNA Microarray LIMS System for Integral Genomic Analysis of Multi-Platform Microarrays
Cho, Mi-Kyung ; Kang, Jason Jong-ho ; Park, Hyun-Seok ;
Genomics & Informatics, volume 5, issue 2, 2007, Pages 83~87
The analysis of DNA microarray data is a rapidly evolving area of bioinformatics, and various types of microarray are emerging as some of the most exciting technologies for use in biological and clinical research. In recent years, microarray technology has been utilized in various applications such as the profiling of mRNAs, assessment of DNA copy number, genotyping, and detection of methylated sequences. However, the analysis of these heterogeneous microarray platform experiments does not need to be performed separately. Rather, these platforms can be co-analyzed in combination, for cross-validation. There are a number of separate laboratory information management systems (LIMS) that individually address some of the needs for each platform. However, to our knowledge there are no unified LIMS systems capable of organizing all of the information regarding multi-platform microarray experiments, while additionally integrating this information with tools to perform the analysis. In order to address these requirements, we developed a web-based LIMS system that provides an integrated framework for storing and analyzing microarray information generated by the various platforms. This system enables an easy integration of modules that transform, analyze and/or visualize multi-platform microarray data.
RepWeb: A Web-Based Search Tool for Repeat-Related Literatures
Woo, Tae-Ha ; Kim, Young-Uk ; Kwon, Je-Keun ; Seo, Jung-Min ;
Genomics & Informatics, volume 5, issue 2, 2007, Pages 88~91
Repetitive sequences such as SINE, LINE, and LTR elements form a major part of eukaryotic genomes. A literature search tool that summarizes the information contained within repeat elements would provide biologists in the field of genomics with a useful tool for analyzing genomic sequence features. We developed a java program designed to make literature access easier by using two search engines simultaneously. RepWeb is a web-based search system that provides a user friendly interface for searching the reference data and journals for information related to repeat elements by using the search engines, Google Scholar and PubMed, simultaneously. It provides an interface that displays the repeat element- related biological information, and includes useful functions such as the production of a repeat tree, clickable links to PubMed and Google Scholar, exporting, and sorting a field into date, author, journal and title.