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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 7, Issue 4 - Dec 2009
Volume 7, Issue 3 - Sep 2009
Volume 7, Issue 2 - Jun 2009
Volume 7, Issue 1 - Mar 2009
Selecting the target year
An Alternative Way of Constructing Ancestral Graphs Using Marker Allele Ages from Population Linkage Disequilibrium Information
Park, Lee-Young ;
Genomics & Informatics, volume 7, issue 1, 2009, Pages 1~12
DOI : 10.5808/GI.2009.7.1.001
An alternative way of constructing ancestral graphs, which is different from the coalescent-based approach, is proposed using population linkage disequilibrium (LD) data. The main difference from the existing method is the construction of the ancestral graphs based on variants instead of individual sequences. Therefore, the key of the proposed method is to use the order of allele ages in the graphs. Distinct from the previous age-estimation methods, allele ages are estimated from full haplotype information by examining the number of generations from the initial complete LD to the current decayed state for each two variants depending on the direction of LD decay between variants. Using a simple algorithmic procedure, an ancestral graph can be derived from the expected allele ages and current LD decay status. This method is different in many ways from previous methods, and, with further improvement, it might be a good replacement for the current approaches.
Association of Common Vitamin D Receptor Gene Variations with Fracture Risk and Bone Mineral Density in Postmenopausal Korean Population
Hwang, Joo-Yeon ; Lee, Seung Hun ; Kim, Ghi-Su ; Koh, Jung-Min ; Go, Min-Jin ; Kim, Tae-Ho ; Hong, Jung-Min ; Park, Eui-Kyun ; Kim, Shin-Yoon ; Lee, Jong-Young ;
Genomics & Informatics, volume 7, issue 1, 2009, Pages 13~19
DOI : 10.5808/GI.2009.7.1.013
Osteoporosis is characterized by impaired osteogenesis. BMD is a major determinant of bone strength. The role of the VDR gene in predisposition to primary osteoporosis has been recognized. However, population-based case-control studies have been reported controversial results for known candidate genes in an ethnically distinct group. To determine the genetic effects of VDR variants on osteoporosis and BMD, we directly sequenced the VDR gene in 24 unrelated Korean individuals and identified eighteen sequence variants. We investigated the potential involvement of eight SNPs in osteoporosis in postmenopausal women (n = 729). Two SNPs (LD) in intron 2, -5294G>C (rs2238135) and -4817G>A (rs17882443) showed the evidence of association with enhanced BMD of the femoral neck (
=0.031 for rs2238135;
= 0.019 for 17882443). Moreover, VDR -4817G>A was significantly associated with protective effect on all fracture risk (
=0.035, OR=0.2, 95% CI=
), and tended to be higher BMD values at various proximal femur sites. Therefore, we suggest that the -4817G>A may be useful genetic marker for vitamin D-related metabolism and may have an important role in the increased BMD of the proximal femur in postmenopausal Korean women.
Interaction between Smoking and the STAB2 Gene in the Severity of Rheumatoid Arthritis
Min, Jin-Young ; Min, Kyoung-Bok ; Sung, Joo-Hon ; Cho, Sung-Il ;
Genomics & Informatics, volume 7, issue 1, 2009, Pages 20~25
DOI : 10.5808/GI.2009.7.1.020
Rheumatoid arthritis (RA) is a chronic autoimmune disorder that is characterized by inflammation of the synovial tissue and deterioration of the joint and bone. A recent study reported a potential gene-environment interaction between HLA-DR and smoking. The present study investigated whether a specific gene was related to the association between smoking and the severity of RA (rheumatoid factor levels > 20 IU/ml). We used the resources of the NARAC family collection of GAW 15 databases, and 1139 subjects with RF>20 IU/ml were included in the current analysis. The linkage panel contained 5858 SNP markers, and 5744 SNPs passed quality control criteria. Linear regression analyses, using PLINK software and generalized estimating equation regression models, were used to test for associations between the SNPs and the severity of RA according to smoking groups. Two major findings were established. First, the severity of RA in smokers was associated with rs703618 (p=
), which lies in the intronic region of the stabilin 2 (STAB2) gene on chromosome 12. Second, there were significant differences in the levels of RF between 'ever smokers' and 'never smokers' according to the rs703618 genotype (G/G, A/G, A/A). We investigated whether a specific gene acts as a mediator between smoking and the severity of RA and found that the STAB2 gene could affect this relationship. Our finding indicates that smoking may mediate RA severity by affecting the expression level of a specific gene.
Bioinformatics Analysis of Hsp20 Sequences in Proteobacteria
Heine, Michelle ; Chandra, Sathees B.C. ;
Genomics & Informatics, volume 7, issue 1, 2009, Pages 26~31
DOI : 10.5808/GI.2009.7.1.026
Heat shock proteins are a class of molecular chaperones that can be found in nearly all organisms from Bacteria, Archaea and Eukarya domains. Heat shock proteins experience increased transcription during periods of heat induced osmotic stress and are involved in protein disaggregation and refolding as part of a cell's danger signaling cascade. Heat shock protein, Hsp20 is a small molecular chaperone that is approximately 20kDa in weight and is hypothesized to prevent aggregation and denaturation. Hsp20 can be found in several strains of Proteobacteria, which comprises the largest phyla of the Bacteria domain and also contains several medically significant bacterial strains. Genomic analyses were performed to determine a common evolutionary pattern among Hsp20 sequences in Proteobacteria. It was found that Hsp20 shared a common ancestor within and among the five subclasses of Proteobacteria. This is readily apparent from the amount of sequence similarities within and between Hsp20 protein sequences as well as phylogenetic analysis of sequences from proteobacterial and non-proteobacterial species.
Choosing Optimal STR Markers for Quality Assurance of Distributed Biomaterials in Biobanking
Chung, Tae-Hoon ; Lee, Hee-Jung ; Lee, Mi-Hee ; Jeon, Jae-Pil ; Kim, Ki-Sang ; Han, Bok-Ghee ;
Genomics & Informatics, volume 7, issue 1, 2009, Pages 32~37
DOI : 10.5808/GI.2009.7.1.032
The quality assurance (QA) is of utmost importance in biobanks when archived biomaterials are distributed to biomedical researchers. For sample authentication and cross-contamination detection, the two fundamental elements of QA, STR genotyping is usually utilized. However, the incorporated number of STR markers is highly redundant for biobanking purposes, resulting in time and cost inefficiency. An index to measure the cross-contamination detection capability of an STR marker, the mixture probability (MP), was developed. MP as well as other forensic parameters for STR markers was validated using STR genotyping data on 2328 normal Koreans with the commercial AmpFlSTR kit. For Koreans, 7 STR marker (D2S1338, FGA, D18S51, D8S1179, D13S317, D21S11, vWA) set was sufficient to provide discrimination power of
and cross-contamination detection probability of
. Interestingly, similar marker sets were obtained from African Americans, Caucasian Americans, and Hispanic Americans under the same level of discrimination power. Only a small subset of commonly used STR markers is sufficient for QA purposes in biobanks. A procedure for selecting optimal STR markers is outlined using STR genotyping results from normal Korean population.
EST Knowledge Integrated Systems (EKIS): An Integrated Database of EST Information for Research Application
Kim, Dae-Won ; Jung, Tae-Sung ; Choi, Young-Sang ; Nam, Seong-Hyeuk ; Kwon, Hyuk-Ryul ; Kim, Dong-Wook ; Choi, Han-Suk ; Choi, Sang-Heang ; Park, Hong-Seog ;
Genomics & Informatics, volume 7, issue 1, 2009, Pages 38~40
DOI : 10.5808/GI.2009.7.1.038
The EST Knowledge Integrated System, EKIS (http://ekis.kribb.re.kr), was established as a part of Korea's Ministry of Education, Science and Technology initiative for genome sequencing and application research of the biological model organisms (GEAR) project. The goals of the EKIS are to collect EST information from GEAR projects and make an integrated database to provide transcriptomic and metabolomic information for biological scientists. The EKIS constitutes five independent categories and several retrieval systems in each category for incorporating massive EST data from high-throughput sequencing of 65 different species. Through the EKIS database, scientists can freely access information including BLAST functional annotation as well as Genechip and pathway information for KEGG. By integrating complex data into a framework of existing EST knowledge information, the EKIS provides new insights into specialized metabolic pathway information for an applied industrial material.
An Integrated Database and Web Service for Microbial Resources at KACC
Kim, Chang-Kug ; Jeon, Young-Ah ; Cho, Gyu-Taek ; Kwon, Soon-Wo ; Kim, Yong-Hwan ; Hong, Seung-Beom ;
Genomics & Informatics, volume 7, issue 1, 2009, Pages 41~45
DOI : 10.5808/GI.2009.7.1.041
The Korean Agricultural Culture Collection (KACC) has developed a web-based system to provide an integrated database with information updates about microbial resources. This integrated database consists of 5 major functions and contains general information, which includes identification numbers, culture media composition, image information, DNA sequences, patent information, and general forms for ordering and depositing microorganisms. In 2008, KACC started providing characterization information. KACC maintains 9,801 cultures of microorganisms, including 3,296 strains of bacteria, 4,734 fungi, 784 actinomycetes, 64 yeasts, and 923 others.
A Simple Java Sequence Alignment Editing Tool for Resolving Complex Repeat Regions
Ham, Seong-Il ; Lee, Kyung-Eun ; Park, Hyun-Seok ;
Genomics & Informatics, volume 7, issue 1, 2009, Pages 46~48
DOI : 10.5808/GI.2009.7.1.046
Finishing is the most time-consuming step in sequencing, and many genome projects are left unfinished due to complex repeat regions. Here, we have developed BACContigEditor, a prototype shotgun sequence finishing tool. It is essentially an editor that visualizes assemblies of shotgun sequence fragment reads as gapped multiple alignments. The program offers some flexibility that is needed to rapidly resolve complex regions within a working session. The sole purpose of the release is to promote collaborative creation of extensible software for fragment assembly editors, foster collaborative development, and reduce barriers to initial tool development effort. We describe our software architecture and identify current challenges. The program is available under an Open Source license.
BioStore: A Repository System for Registering and Distributing Public Biology Databases
Tae, Hong-Seok ; Han, Jeong-Min ; Ahn, Bu-Young ; Park, Kie-Jung ;
Genomics & Informatics, volume 7, issue 1, 2009, Pages 49~51
DOI : 10.5808/GI.2009.7.1.049
Although abundant biology data have been accumulated in public biology databases, such as GenBank and PIR, few easy-interface services are provided for users to access or update them. We have developed a system, named BioStore, that is composed of several programs to aid users to not only access public data but also share their own data easily. The service can be used for maintaining a local database as a repository of raw data files of several public databases and distributing the data files to other users. Currently, BioStore manipulates major bio-databases and will expand to include more databases and more useful interfaces.