• Genomics & Informatics
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• v.20 no.2
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• pp.16.1-16.12
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• 2022

Various methodologies for the genetic analysis of longitudinal data have been proposed and applied to data from large-scale genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with traits of interest and to detect SNP-time interactions. We recently proposed a grid-based Bayesian mixed model for longitudinal genetic data and showed that our Bayesian method increased the statistical power compared to the corresponding univariate method and well detected SNP-time interactions. In this paper, we further analyze longitudinal obesity-related traits such as body mass index, hip circumference, waist circumference, and waist-hip ratio from Korea Association Resource data to evaluate the proposed Bayesian method. We first conducted GWAS analyses of cross-sectional traits and combined the results of GWAS analyses through a meta-analysis based on a trajectory model and a random-effects model. We then applied our Bayesian method to a subset of SNPs selected by meta-analysis to further discover SNPs associated with traits of interest and SNP-time interactions. The proposed Bayesian method identified several novel SNPs associated with longitudinal obesity-related traits, and almost 25% of the identified SNPs had significant p-values for SNP-time interactions.

• Korean Journal of Agricultural Science
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• v.45 no.2
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• pp.238-247
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• 2018

The overall consumption of meat is increasing as the level of national income increases. The end weight is a trait closely associated with dressed meat. Genome-wide association study (GWAS) is an effective method of analyzing genetic variation and gene identification associated with a number of natural alternative traits because it can detect variations. So this paper did a GWAS analysis to identity the location on the genome related to the end weight in purebred landrace pigs and to explore the relevant candidate gene. This study identified a significant single nucleotide poly morphism (SNP) marker in chromosome 6 (ASGA0029422, $p=1.22{\times}10^{-6}$). Adhesion G protein-coupled receptor L2 (ADGRL2) was found to be the candidate gene at the identified SNP marker location. ADGRL2 genes have been found to be associated with cell development in relation to the external and internal environment of a cell. In addition, genotype and statistical analyses were done on nine variations on the exon of ADGRL2. The results show that the SNP marker (ASGA0029422, $p=1.32{\times}10^{-6}$) was significant, but the significance of the nine variations on the ADGRL2 exon was not verified. However, by performing further experiments and functional studies on other SNPs showing possible genetic ADGRL-Exon mutations, objects with high associations of high-end weights can be selected.

• BMB Reports
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• v.46 no.8
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• pp.416-421
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• 2013

Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/].

• Korean Journal of Fisheries and Aquatic Sciences
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• v.56 no.4
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• pp.411-418
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• 2023

Genome wide association studies (GWAS) identify genetic loci associated with quantitative traits in genomic selection. Although several studies have compared performance of various algorithms, no study compares them in olive flounder Paralichthys olivaceus. This study compared the GWAS results of four mixed linear model (MLM) algorithms and one Fixed and random model Circulating Probability Unification (FarmCPU) algorithm in olive flounder. Considering gender and genetic association matrices as fixed and random effects, the MLM had stable performance without inflation for λ_GC (genomic inflation factor) of -log₁₀P. The FarmCPU algorithm had some appropriate λ_GC of -log₁₀P, and an upward tail was identified in quantile-quantile plots. Therefore, the models were suitable for detecting genetic variants associated with olive flounder growth traits. Moreover, significant genotypes appeared several times at chromosome 22, around which quantitative trait loci are expected to exist. Finally, in both models, some of the most genetic variants were found in genes related to growth traits, confirming their reliability. These results will be helpful when applied to the genomic selection of olive flounder growth traits in the future.

• Communications for Statistical Applications and Methods
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• v.16 no.6
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• pp.915-923
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• 2009

The gene which is related in the disease of the human has been searched among numerous genes in GWA(Genome-Wide Association) research. However, most current statistical methods used to detect gene-gene interactions in disease association studies cannot be easily applied to handle the whole genome association study(GWAS) due to heavy computing. Therefore SNPHarvester is developed to find the main gene group among numerous genes. This research finds the superior gene groups which are related with the economic traits of the Korean beef cattle, not that of human, among sets of SNPs by using SNPHarvester, and also finds the superior genotypes which can enhance various qualities of Korean beef among SNP groups.

• Genomics & Informatics
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• v.6 no.1
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• pp.1-7
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• 2008

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.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.3
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• pp.303-309
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• 2014

The increasing importance of meat quality has implications for animal breeding programs. Research has revealed much about the genetic background of pigs, and many studies have revealed the importance of various genetic factors. Since meat quality is a complex trait which is affected by many factors, consideration of the overall phenotype is very useful to study meat quality. For integrating the phenotypes, we used principle component analysis (PCA). The significant SNPs refer to results of the GRAMMAR method against PC1, PC2 and PC3 of 14 meat quality traits of 181 Duroc pigs. The Genome-wide association study (GWAS) found 26 potential SNPs affecting various meat quality traits. The loci identified are located in or near 23 genes. The SNPs associated with meat quality are in or near five genes (ANK1, BMP6, SHH, PIP4K2A, and FOXN2) and have been reported previously. Twenty-five of the significant SNPs also located in meat quality-related QTL regions, these result supported the QTL effect indirectly. Each single gene typically affects multiple traits. Therefore, it is a useful approach to use integrated traits for the various traits at the same time. This innovative approach using integrated traits could be applied on other GWAS of complex-traits including meat-quality, and the results will contribute to improving meat-quality of pork.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.158-158
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• 2017

The purpose of this study was to identify the candidate genes involved in selenium content in brown rice. Rice (Oryza sativa L.) was important crop including diverse functional substance such as carbohydrate, protein, lysine and tocopherol, mineral. Especially, selenium as nutritionally important minerals, it was known to activate the immune system, antioxidant effect and inhibition of carcinogenesis. Also recommended daily requirements of the United States and the United Kingdom were 55 to 90 ug for selenium. Therefore, selenium content in brown rice of core-set were analyzed by using ICP-MS (Inductively Coupled Plasma Mass Spectrometer) and GWAS (Genome Wide Association Study) was conducted to search for candidate genes in this study. The new natural variants identified through haplotyping analysis would be useful to develop new rice varieties with improved storage ability of the valuable mineral through the future molecular breeding.

• BMB Reports
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• v.47 no.6
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• pp.348-353
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• 2014

The speed of sound (SOS) value is an indicator of bone mineral density (BMD). Previous genome-wide association (GWA) studies have identified a number of genes, whose variations may affect BMD levels. However, their biological implications have been elusive. We re-analyzed the GWA study dataset for the SOS values in skeletal sites of 4,659 Korean women, using a gene-set analysis software, GSA-SNP. We identified 10 common representative GO terms, and 17 candidate genes between these two traits (PGS < 0.05). Implication of these GO terms and genes in the bone mechanism is well supported by the literature survey. Interestingly, the significance levels of some member genes were inversely related, in several gene-sets that were shared between two skeletal sites. This implies that biological process, rather than SNP or gene, is the substantial unit of genetic association for SOS in bone. In conclusion, our findings may provide new insights into the biological mechanisms for BMD.

• Tuberculosis and Respiratory Diseases
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• v.76 no.3
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• pp.105-113
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• 2014

From January 2012 up until March 2013, many articles with huge clinical importance in asthma were published based on large numbered clinical trials or meta-analysis. The main subjects of these studies were the new therapeutic plan based on the asthma phenotype or efficacy along with the safety issues regarding the current treatment guidelines. For efficacy and safety issues, inhaled corticosteroid tapering strategy or continued long-acting beta agonists use was the major concern. As new therapeutic trials, monoclonal antibodies or macrolide antibiotics based on inflammatory phenotypes have been under investigation, with promising preliminary results. There were other issues on the disease susceptibility or genetic background of asthma, particularly for the "severe asthma" phenotype. In the era of genome and pharmacogenetics, there have been extensive studies to identify susceptible candidate genes based on the results of genome wide association studies (GWAS). However, for severe asthma, which is where most of the mortality or medical costs develop, it is very unclear. Moreover, there have been some efforts to find important genetic information in order to predict the possible disease progression, but with few significant results up until now. In conclusion, there are new on-going aspects in the phenotypic classification of asthma and therapeutic strategy according to the phenotypic variations. With more pharmacogenomic information and clear identification of the "severe asthma" group even before disease progression from GWAS data, more adequate and individualized therapeutic strategy could be realized in the future.