• Genomics & Informatics
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• v.17 no.4
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• pp.48.1-48.6
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• 2019

Over the last decade, genome-wide association studies (GWASs) have provided an unprecedented amount of genetic variations that are associated with various phenotypes. However, previous GWAS were mostly conducted in European populations, and these biased results for non-Europeans may result in a significant reduction in risk prediction for non-Europeans. An issue with the early GWAS was the winner's curse problem, which led to misleading results when constructing the polygenic risk scores (PRS). Therefore, more non-European population-based studies are needed to validate reported variants and improve genetic risk assessment across diverse populations. In this study, we validated 422 variants independently associated with glycemic indexes, liver enzymes, and type 2 diabetes in 125,872 samples from a Korean population, and further validated the results by assessing publicly available summary statistics from European GWAS (n = 898,130). Among the 422 independently associated variants, 284, 320, and 361 variants were replicated in Koreans, Europeans, and either one of the two populations. In addition, the effect sizes for Koreans and Europeans were moderately correlated (r = 0.33-0.68). However, 61 variants were not replicated in both Koreans and Europeans. Our findings provide valuable information on effect sizes and statistical significance, which is essential to improve the assessment of disease risk using PRS analysis.

• Mycobiology
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• v.29 no.2
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• pp.80-84
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• 2001

Nine species of genus Ganoderma different in cultural characteristics each other were separated by histo-anatomical differences. Differences among the species and geographic distribution of G. lucidum were also analyzed to provide the criteria for the classification of Korean cultivation or wild type strains. Korean cultivation and wild type strains were quiet different from other species as well as Taiwan and North American G. lucidum strains in histo-anatomical traits of Ganoderma. Pore color of Korean G. lucidum strains was less brown than those of Taiwan and North American strains. Shapes of pores were round or circular in Korean strains but ellipsoidal or angular in Taiwan or North American strains. Pore numbers of Korean strains were more than those($4{\sim}6/mm$) of Taiwan or North American strains. Hardness of the pileus of Korean strains was much more than that of Taiwan or North American strains. Such characteristics of Korean strains were different from those of other species of Ganoderma. Korean G. lucidum strains could be classified into the other group because they had many different traits in growth characteristics of fruiting bodies and histo-anatomical characteristics from those of Taiwan or North American G. lucidum and other species of G. lucidum complex.

• Genomics & Informatics
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• v.20 no.2
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• pp.17.1-17.11
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• 2022

Genetic associations have been quantified using a number of statistical measures. Entropy-based mutual information may be one of the more direct ways of estimating the association, in the sense that it does not depend on the parametrization. For this purpose, both the entropy and conditional entropy of the phenotype distribution should be obtained. Quantitative traits, however, do not usually allow an exact evaluation of entropy. The estimation of entropy needs a probability density function, which can be approximated by kernel density estimation. We have investigated the proper sequence of procedures for combining the kernel density estimation and entropy estimation with a probability density function in order to calculate mutual information. Genotypes and their interactions were constructed to set the conditions for conditional entropy. Extensive simulation data created using three types of generating functions were analyzed using two different kernels as well as two types of multifactor dimensionality reduction and another probability density approximation method called m-spacing. The statistical power in terms of correct detection rates was compared. Using kernels was found to be most useful when the trait distributions were more complex than simple normal or gamma distributions. A full-scale genomic dataset was explored to identify associations using the 2-h oral glucose tolerance test results and γ-glutamyl transpeptidase levels as phenotypes. Clearly distinguishable single-nucleotide polymorphisms (SNPs) and interacting SNP pairs associated with these phenotypes were found and listed with empirical p-values.

• Journal of Distribution Science
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• v.21 no.11
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• pp.67-75
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• 2023

Purpose: The study is focused on understanding consumer behaviour related to credit card use in retail payment or identifying factors that influence risk perception. Research design, data and methodology: Based on data collecting from structured self-administered questionnaires of 247 Vietnamese bank account payers, this study uses the Cronbach alpha analysis, the factor analyses, the structural equation modeling to assess the research's measurement model and structural model with the presence of knowledge, propensity to trust, self-efficacy, risk perception, intended use and their complex, intertwined relationships. Results: The results reveal that customer's perceived risk, which is affected by their self-efficacy and propensity to trust, negatively impact on their intended use of credit cards in retail payment. However, there is no evidence of the significant influence of consumer knowledge on how they assess potential losses of credit card. Conclusions: These findings provide a better understanding of consumer risk perception, its antecedents and consequence in a direction of credit card adoption. Bank managers or marketers should focus on increasing the information about credit cards and issues related to credit card use in retail payment, promoting mechanisms to encourage customers to participate in the credit card experience.

• Biomedical Science Letters
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• v.18 no.2
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• pp.87-95
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• 2012

Hypertension is a complex disease that results from the interaction of genetic and environmental influences and heritability is influenced by about one-third to one-half. However, the specific genetic variants determining risk for hypertension are still largely unknown. Here, we performed association analysis to elucidate the possible relations of genetic polymorphisms in ESR1 gene with blood pressure traits. By examining genotype data of a total of 3,804 women in the Korean Association REsource (KARE) study, we discovered the ESR1 gene polymorphisms are associated with blood pressure and hypertension. The highest significant polymorphisms were rs2982571 (${\beta}=-1.56$, $P=6.8{\times}10^{-3}$) with systolic blood pressure (SBP), rs9322335 (${\beta}=-0.61$, P=0.013) with diastolic blood pressure (DBP), and rs851985 (OR=0.78, CI: 0.65~0.94, $P=8.6{\times}10^{-3}$) with hypertension. In the 5 SNPs (rs2982571, rs851985, rs851983, rs851981, and rs851980), their ${\beta}$-values in SBP and/or DBP showed consistent trends with the odds ratios (ORs) of hypertension, and these 5 SNPs were composed with one LD block. Consequently, we found statistically significant SNPs in ESR1 gene that are associated with both blood pressure and hypertension traits. These results suggested that the individuals with the minor alleles of the 5 SNPs in the ESR1 gene may be less susceptible to the development of hypertension in the Korean women.

• Journal of the Korea Society of Computer and Information
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• v.17 no.11
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• pp.141-148
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• 2012

The advance of technologies for human genome makes it possible that the analysis of association between genetic variants and diseases and the application of the results to predict risk or susceptibility to them. Many of those studies carried out in case-control study. For quantitative traits, statistical analysis methods are applied to find single nucleotide polymorphisms (SNP) relevant to the diseases and consider them one by one. In this study, we presented methods to select informative single nucleotide polymorphisms and predict risk for quantitative traits and compared their performance. We adopted two SNP selection methods: one considering single SNP only and the other of all possible pairs of SNPs.

• Journal of the Korean Geographical Society
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• v.39 no.6 s.105
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• pp.971-983
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• 2004

It is increasingly clear that student mastery of concepts and skills in geographic education is based on a complex set of variables. Sex and gender are the key variables. Much has been written about biological sex differences in learning, but less attention has been paid to the impacts of socio-cultural gender on learning geography. As such, the aims of this paper are two-fold. First, to examine theories which seek to explain why males and females might differ in their geographic and spatial knowledge or skill. Second, to examine the extent of sex differences and gender traits in the geographic learning. The results of study illustrate clearly that there are more similarities than differences between the sexes. Therefore, there are significant gender differences between the preferences of regions, contents, activities in the secondary geographic learning. The results also provide insights into improving contents and method of geographic education.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2021.04a
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• pp.9-9
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• 2021

Mutation breeding is useful for improving agronomic characteristics of various crops. In this study, we constructed soybean Mutant Diversity Pool (MDP) from 1,695 gamma-irradiated mutants through two selection phases over M1 to M12 generations; we selected 523 mutant lines exhibiting at least 30% superior agricultural characteristics, and, second, we eliminated redundant morphological phenotypes in the M12 generation. Finally, we constructed 208 MDP lines and investigated 11 agronomic traits. We then assessed the genetic diversity and inter-relationships of these MDP lines using target region amplification polymorphism (TRAP) markers. Among the different TRAP primer combinations, polymorphism levels and PIC values averaged 59.71% and 0.15, respectively. Dendrogram and population structure analyses divided the MDP lines into four major groups. According to an analysis of AMOVA, the percentage of inter-population variation among mutants was 11.320 (20.6%), whereas mutant inter-population variation ranged from 0.231 (0.4%) to 14.324 (26.1%). Overall, the genetic similarity of each cultivar and its mutants were higher than within other mutant populations. In an analysis of the genome-wide association study (GWAS) using based on the genotyping-by-sequencing (GBS), we detected 66 SNPs located on 13 different chromosomes were found to be highly associated with four agronomic traits: days of flowering (33 SNPs), flower color (16 SNPs), node number (6 SNPs), and seed coat color (11 SNPs). These results are consistent with those previously reported for other genetic resource populations, including natural accessions and recombinant inbred line. Our observations suggest that genomic changes in mutant individuals induced by gamma rays occurred at the same loci as those of natural soybean population. This study has demonstrated that the integration of GBS and GWAS can serve as a powerful complementary approach to gamma-ray mutation for the dissection of complex traits in soybean.

• Journal of Ginseng Research
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• v.48 no.3
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• pp.310-322
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• 2024

Background: Osteosarcopenia is a common condition characterized by the loss of both bone and muscle mass, which can lead to an increased risk of fractures and disability in older adults. The study aimed to elucidate the response of various mouse strains to treatment with Rg3, one of the leading ginsenosides, on musculoskeletal traits and immune function, and their correlation. Methods: Six Collaborative Cross (CC) founder strains induced muscle atrophy and bone loss with dexamethasone (15 mg/kg) treatment for 1 month, and half of the mice for each strain were orally administered Rg3 (20 mg/kg). Different responses were observed depending on genetic background and Rg3 treatment. Results: Rg3 significantly increased grip strength, running performance, and expression of muscle and bone health-related genes in a two-way analysis of variance considering the genetic backgrounds and Rg3 treatment. Significant improvements in grip strength, running performance, bone area, and muscle mass, and the increased gene expression were observed in specific strains of PWK/PhJ. For traits related to muscle, bone, and immune functions, significant correlations between traits were confirmed following Rg3 administration compared with control mice. The phenotyping analysis was compiled into a public web resource called Rg3-OsteoSarco. Conclusion: This highlights the complex interplay between genetic determinants, pathogenesis of muscle atrophy and bone loss, and phytochemical bioactivity and the need to move away from single inbred mouse models to improve their translatability to genetically diverse humans. Rg3-OsteoSarco highlights the use of CC founder strains as a valuable tool in the field of personalized nutrition.

• Animal Bioscience
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• v.37 no.3
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• pp.461-470
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• 2024

Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. Methods: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, F_st, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. Results: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, F_st, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. Conclusion: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.