• Genomics & Informatics
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• 제17권4호
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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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• 제29권2호
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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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• 제20권2호
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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.

• 유통과학연구
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• 제21권11호
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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.

• 대한의생명과학회지
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• 제18권2호
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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.

• 한국컴퓨터정보학회논문지
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• 제17권11호
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• pp.141-148
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• 2012

인간 유전체 정보와 관련된 기술이 발전함으로 인하여 이를 이용한 질환 또는 질병에 대한 연관성을 분석하여 그 위험도나 치료 예후 등에 대한 예측하기 위한 연구가 활발히 진행되고 있다. 이러한 연구의 대부분은 대표적인 질적 표현형을 대상으로 하는 환자-대조군 연구(case-control study) 방법을 이용하고 있으며 양적 표현형에 대해서는 개별 단일 염기 변이의 연관성을 회기 분석 방법을 이용하여 규명하는 연구가 주로 수행되고 있다. 특히 복합 질병(complex disease)에 대한 위험도를 예측하기 위한 연구의 경우 흔한 변이 흔한 질환(common variants common disease)의 가정아래 주로 각각의 단일 염기 변이가 보이는 연관성 정보를 기반으로 진행되고 있으며 여러 변이의 상호 작용에 의한 영향을 분석한 결과는 상대적으로 미비하다. 이 논문에서는 양적 표현형에 대한 SNP의 연관성을 분석하고 그 결과로 발견된 SNP을 이용하여 대상 표현형의 값을 예측하기 위한 분류기를 구성하고 그 성능을 평가하였으며 분류기의 단일 염기 변이의 선택에 있어서 각각의 단일 염기 변이의 연관성을 고려할 때와 단일 염기 변이의 쌍이 보이는 연관성을 고려할 때의 분류 성능을 비교하였다.

• 대한지리학회지
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• 제39권6호
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• pp.971-983
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• 2004

학생들의 지리적 이해와 개념 발달 그리고 기능 습득 등이 복합적인 배경 변인의 영향을 받고 있음이 점점 더 분명해지고 있다. 복합적인 배경 변인 중에서 성별 차이는 오랫동안 지리학자와 심리학자들의 관심 대상이었다. 최근 지리적 지식과 공간적 능력에서 나타나는 성별 차이는 성적 고정관념을 강화하는 사회문화적 요인들에서 기인한 것이라는 주장이 제기되고 있다. 지리 학습에 영향을 미치는 주요 변인으로 고려되는 성별 차이는 단순한 차이 그 자체보다는. 다면적인 젠더에 대한 과정 변인으로 진술되고 탐구되는 것이 바람직하다. 이에 본 연구는 성별 차이와 젠더 특성이 지리 수업에 미치는 영향을 이론적으로 고찰하고. 실제 중학교 지리 수업에서 이루어지는 학습 지역과 학습 내용 그리고 학습 활동에 대한 성별 차이와 젠더 특성을 조사하였다. 연구 결과, 지리 학습에서는 성별 차이보다는 유사성이 더 많이 나타났으며. 젠더별 특성이 다양하게 나타났다. 이는 학습의 개인차를 고려하는데 적절한 것은 단순한 성별 차이보다는 좀더 구체적이고 다면적인 젠더 특성임을 시사한다. 더불어 이러한 특성들이 학습 효율성을 장려하는데 어떠한 영향을 미치는지에 대한 설명이 이루어지면, 지리 교육을 증진하는데 직접적인 도움이 될 것이다.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2021년도 춘계학술대회
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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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• 제48권3호
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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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• 제37권3호
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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.