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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 9, Issue 4 - Dec 2011
Volume 9, Issue 3 - Sep 2011
Volume 9, Issue 2 - Jun 2011
Volume 9, Issue 1 - Mar 2011
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Trends and Directions in Personality Genetic Studies
Kim, Han-Na ; Kim, Hyung-Lae ;
Genomics & Informatics, volume 9, issue 2, 2011, Pages 45~51
DOI : 10.5808/GI.2011.9.2.45
How personality forms and whether personality genes exist are long-studied questions. Various concepts and theories have been presented for centuries. Personality is a complex trait and is developed through the interaction of genes and the environment. Twin and family studies have found that there are critical genetic and environmental components in the inheritance of personality traits, and modern advances in genetics are making it possible to identify specific variants for personality traits. Although genes that were found in studies on personality have not provided replicable association between genetic and personality variability, more and more genetic variants associated with personality traits are being discovered. Here, we present the current state of the art on genetic research in the personality field and finally list several of the recently published research highlights. First, we briefly describe the commonly used self-reported measures that define personality traits. Then, we summarize the characteristics of the candidate genes for personality traits and investigate gene variants that have been suggested to be associated with personality traits.
Genome-wide Association Study Identification of a New Genetic Locus with Susceptibility to Osteoporotic Fracture in the Korean Population
Hwang, Joo-Yeon ; Lee, Seung-Hun ; Go, Min-Jin ; Kim, Beom-Jun ; Kim, Young-Jin ; Kim, Dong-Joon ; Oh, Ji-Hee ; Koo, Hee-Jo ; Cha, My-Jung ; Lee, Min-Hye ; Yun, Ji-Young ; Yoo, Hye-Sook ; Kang, Young-Ah ; Oh, Ki-Won ; Kang, Moo-Il ; Son, Ho-Young ; Kim, Shin-Yoon ; Kim, Ghi-Su ; Han, Bok-Ghee ; Cho, Yoon-Shin ; Koh, Jung-Min ; Lee, Jong-Young ;
Genomics & Informatics, volume 9, issue 2, 2011, Pages 52~58
DOI : 10.5808/GI.2011.9.2.52
Osteoporotic fracture (OF), along with bone mineral density (BMD), is an important diagnostic parameter and a clinical predictive risk factor in the assessment of osteoporosis in the elderly population. However, a genome-wide association study (GWAS) on OF has not yet been clarified sufficiently. To identify OF-associated genetic variants and candidate genes, we conducted a GWAS in a population-based cohort (Korean Association Resource [KARE], n=1,427 [case: 288 and control: 1139]) and performed a de novo replication study in hospital-based individuals (Asan and Catholic Medical Center [ACMC], n=1,082 [case: 272 and control: 810]). In a combined meta-analysis, a newly identified genetic locus in an intergenic region at 10p11.2 (near genes FZD8 and ANKRD30A ) showed the most significant association (odd ratio [OR] = 2.00, 95% confidence interval [CI] = 1.47~2.74, p=
) in the same direction. We provide the first evidence for a common genetic variant influencing OF and genetic information for further investigation in bone metabolism.
Lack of Replication of Genetic Association with Body Mass Index Detected by Genome-wide Association Study
Lee, Hae-In ; Kim, Jae-Jung ; Park, Tae-Sung ; Kim, Kyung-A ; Lee, Jong-Eun ; Cho, Yoon-Shin ; Lee, Jong-Young ; Han, Bok-Ghee ; Lee, Jong-Keuk ;
Genomics & Informatics, volume 9, issue 2, 2011, Pages 59~63
DOI : 10.5808/GI.2011.9.2.59
Obesity provokes many serious human diseases, including various cardiovascular diseases and diabetes. Body mass index (BMI) is a highly heritable trait that is broadly used to diagnose obesity. To identify genetic loci associated with obesity in Asians, we conducted a genome-wide association study (GWAS) of a population of Korean adults (n=6,742, age 40~60 years) and detected six BMI risk loci (TNR, FAM124B, RGS12, NFE2L3, MC4R and FTO) having p<
. However, in the replication study, only melanocortin 4 receptor gene (MC4R) (rs9946888, p=
) was replicated with marginal significance (p<0.05) in the second cohort (n=5,102, age 40~60 years). This study indicates that each locus associated with BMI has very weak genetic effect.
Association of the X-linked Androgen Receptor Leu57Gln Polymorphism with Monomelic Amyotrophy
Park, Young-Mi ; Lim, Young-Min ; Kim, Dae-Seong ; Lee, Jong-Keuk ; Kim, Kwang-Kuk ;
Genomics & Informatics, volume 9, issue 2, 2011, Pages 64~68
DOI : 10.5808/GI.2011.9.2.64
Monomelic amyotrophy (MA), also known as Hirayama disease, occurs mainly in young men and manifests as weakness and wasting of the muscles of the distal upper limbs. Here, we sought to identify a genetic basis for MA. Given the predominance of MA in males, we focused on candidate neurological disease genes located on the X chromosome, selecting two X-linked candidate genes, androgen receptor (AR ) and ubiquitin-like modifier activating enzyme 1 (UBA1). Screening for genetic variants using patients' genomic DNA revealed three known genetic variants in the coding region of the AR gene: one nonsynonymous single-nucleotide polymorphism (SNP; rs78686797) encoding Leu57Gln, and two variants of polymorphic trinucleotide repeat segments that encode polyglutamine (CAG repeat; rs5902610) and polyglycine (GGC repeat; rs3138869) tracts. Notably, the Leu57Gln polymorphism was found in two patients with MA from 24 MA patients, whereas no variants were found in 142 healthy male controls. However, the numbers of CAG and GGC repeats in the AR gene were within the normal range. These data suggest that the Leu57Gln polymorphism encoded by the X-linked AR gene may contribute to the development of MA.
Identification of Genomic Differences between Hanwoo and Holstein Breeds Using the Illumina Bovine SNP50 BeadChip
Melka, Hailu Dadi ; Jeon, Eun-Kyeong ; Kim, Sang-Wook ; Han, James-Bond ; Yoon, Du-Hak ; Kim, Kwan-Suk ;
Genomics & Informatics, volume 9, issue 2, 2011, Pages 69~73
DOI : 10.5808/GI.2011.9.2.69
The use of genomic information in genomic selection programs for dairy and beef cattle breeds has become a reality in recent years. In this investigation, we analyzed single-nucleotide polymorphisms (SNPs) for Hanwoo (n=50) and Holstein (n=50) breeds using the Illumina Bovine SNP50 BeadChip to facilitate genomic selection and utilization of the Hanwoo breed in Korea. Analysis of the entire genomes showed different spectra of SNP frequencies for Hanwoo and Holstein cattle. The study revealed a highly significant (p<0.001) difference between Hanwoo and Holstein cattle in minor allele frequency (MAF). The average MAFs were
for Hanwoo and Holstein, respectively. From the total of 52,337 SNPs that were successfully identified, about 72% and 79% were polymorphic in Hanwoos and Holsteins, respectively. Polymorphic and fixed SNPs were not distributed uniformly across the chromosomes within breeds or between the two breeds. The number of fixed SNPs on all chromosomes was higher in Hanwoo cattle, reflecting the genetic uniqueness of the Hanwoo breed. In general, the rate of polymorphisms detected in these two breeds suggests that the SNPs can be used for different applications, such as whole-genome association and comparative genetic studies, and are a helpful tool in developing breed identification genetic markers.
Analysis of the Globular Nature of Proteins
Jung, Sung-Hoon ; Son, Hyeon-Seok ;
Genomics & Informatics, volume 9, issue 2, 2011, Pages 74~78
DOI : 10.5808/GI.2011.9.2.74
Numerous restraints and simplifications have been developed for methods that anticipate protein structure to reduce the colossal magnitude of possible conformational states. In this study, we investigated if globularity is a general characteristic of proteins and whether they can be applied as a valid constraint in protein structure simulations with approximated measurements (Gb-index). Unexpectedly, most of the proteins showed strong structural globularity (i.e., mode of approximately 76% similarity to the perfect globe) with only a few percent of proteins being outliers. Small proteins tended to be significantly non-globular (
=0.79) and the minimum Gb-index showed a logarithmic increase with the increase in protein size (
=0.62), strongly implying that the non-globular characteristics might be more acceptable for smaller proteins than larger ones. The strong perfect globe-like character and the relationship between small size and the loss of globular structure of a protein may imply that living organisms have mechanisms to aid folding into the globular structure to reduce irreversible aggregation. This also implies the possible mechanisms of diseases caused by protein aggregation, including some forms of trinucleotide repeat expansion-mediated diseases.
Analysis of the Structure-stability Relationship of Cold-adapted Lipase PsLip1 from Homology Modeling
Choo, Dong-Won ;
Genomics & Informatics, volume 9, issue 2, 2011, Pages 79~84
DOI : 10.5808/GI.2011.9.2.79
Two initial models of cold-adapted lipase PsLip1 have been constructed, based on homology with the bacterial lipases Chromobacterium viscosum (CvLip) and Pseudomonas cepacia (PcLip), whose X-ray structures have been solved and refined to high resolution. The mature polypeptide chains of these lipases have 84% similarity. The models of Mod1 and Mod2 have been compared with the tertiary structures of CvLip and PcLip, respectively, and analyzed in terms of stabilizing interactions. Several structural aspects that are believed to contribute to protein stability have been compared: the number of conserved salt bridges, aromatic interactions, hydrogen bonds, helix capping, and disulfide bridges. The 3-dimensional structural model of PsLip1 has been constructed in order to elucidate the structural reasons for the decreased thermostability of the enzyme in comparison with its mesophilic counterparts.
An Information-based Model for an Interactive Web Service with Agricultural Biotechnology
Kim, Chang-Kug ; Seo, Young-Joo ; Park, Dong-Suk ; Hahn, Jang-Ho ;
Genomics & Informatics, volume 9, issue 2, 2011, Pages 85~88
DOI : 10.5808/GI.2011.9.2.85
The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a biological information-based database. The major functions of the NABIC are focused on biotechnological developments for agricultural bioinformatics and providing a web-based service to construct bioinformatics workflows easily, such as protein function prediction and genome systems biology programs. The NABIC has concentrated on the functional genomics of major crops, building an integrated biotechnology database for agro-biotech information that focuses on the proteomics of major agricultural resources, such as rice, Chinese cabbage, rice Ds-tagging lines, and microorganisms.
A Clustering Tool Using Particle Swarm Optimization for DNA Chip Data
Han, Xiaoyue ; Lee, Min-Soo ;
Genomics & Informatics, volume 9, issue 2, 2011, Pages 89~91
DOI : 10.5808/GI.2011.9.2.89
DNA chips are becoming increasingly popular as a convenient way to perform vast amounts of experiments related to genes on a single chip. And the importance of analyzing the data that is provided by such DNA chips is becoming significant. A very important analysis on DNA chip data would be clustering genes to identify gene groups which have similar properties such as cancer. Clustering data for DNA chips usually deal with a large search space and has a very fuzzy characteristic. The Particle Swarm Optimization algorithm which was recently proposed is a very good candidate to solve such problems. In this paper, we propose a clustering mechanism that is based on the Particle Swarm Optimization algorithm. Our experiments show that the PSO-based clustering algorithm developed is efficient in terms of execution time for clustering DNA chip data, and thus be used to extract valuable information such as cancer related genes from DNA chip data with high cluster accuracy and in a timely manner.