• Asian-Australasian Journal of Animal Sciences
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• v.25 no.1
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• pp.28-32
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• 2012

In the present study, we evaluated the informativeness of SNPs genotyped by the Illumina Bovine SNP50K assay in different cattle breeds. To investigate these on a genome-wide scale, we considered 52,678 SNPs spanning the whole autosomal and X chromosomes in cattle. Our study samples consists of six different cattle breeds. Across the breeds approximately 72 and 6% SNPs were found polymorphic and fixed or close to fix in all the breeds, respectively. The variations in the average minor allele frequency (MAF) were significantly different between the breeds studied. The level of average MAF observed in Hanwoo was significantly lower than the other breeds. Hanwoo breed also displayed the lowest number of polymorphic SNPs across all the chromosomes. More importantly, this study indicated that the Bovine SNP50K assay will have reduced power for genome-wide association studies in Hanwoo as compared to other cattle breeds. Overall, the Bovine SNP50K assay described in this study offer a useful genotyping platform for mapping quantitative trait loci (QTLs) in the cattle breeds. The assay data represent a vast and generally untapped resource to assist the investigation of the complex production traits and the development of marker-assisted selection programs.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2663-2667
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• 2014

Background: Single nucleotide polymorphisms of C-reactive protein (CRP) have been shown to be related to circulating CRP level, risk and prognosis in cancer patients. However, accumulating evidence of rs1800947 involvement in risk of cancer is inconsistent. Thus, a meta-analysis was performed to obtain a more precise relationship. Materials and Methods: The pooled odds ratio (OR) and its 95% confidence interval were assessed in 10 eligible articles with 12 studies containing 5,601 cancer cases and 8,669 cancer-free controls. Results: No significant association was observed overall and in subgroups in comparison of genotype GC vs GG ($P_H$=0.847, OR=0.939, 95%CI=0.810-1.087), GC/CC vs GG ($P_H$=0.941, OR=1.021, 95%CI=0.901-1.157) and allele C vs G ($P_H$=0.933, OR=1.026, 95%CI=0.909-1.159). However, statistically significance was evident in comparison of genotype CC vs GG in cancer risk ($P_H$=0.586, OR=2.854, 95%CI= 1.413-5.763), especially in colorectal cancer ($P_H$=0.481, OR=4.527, 95%CI= 1.664- 12.315). Conclusions: Genotype CC of rs1800947 in the CRP gene is strongly associated with increased cancer risk, particularly in colorectal cancer.

• Journal of the Korean Wood Science and Technology
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• v.46 no.4
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• pp.402-414
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• 2018

Species identification of wood provides important information for archaeology, restoration of cultural assets, preventing illegal logging, and more. Wood species are usually identified based on their anatomical features with the use of a microscope. However, this method may not be able to distinguish between anatomically similar species or subspecies. To overcome this problem, wood species need to be identified at the molecular level using DNA sequencing. However, unlike living plant cells, wood is difficult to pulverize using a mortar, and DNA extraction from dried wood is challenging. To solve these problems, we propose a pretreatment method in which wood is pulverized using 60-grit sandpaper and hydrated with water for 2 days. Using this method, we were able to stably amplify the rpoB gene from the extracted DNA of Pinus rigida. In addition, sequence analysis of the rpoB gene revealed six single nucleotide polymorphisms (SNPs), which classified the rpoB sequences in the genus Pinus into five groups. Our data indicate that although these SNPs were not suitable for species identification, they can potentially be used to determine the origin of different wood subspecies or individual samples of wood.

• Journal of the Korean Data and Information Science Society
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• v.24 no.2
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• pp.277-287
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• 2013

It is important to detect the gene-gene interaction in GWAS (genome-wide association study). There have been many studies on detecting gene-gene interaction. The one is D-MDR (dummy multifoactor dimensionality reduction) method. The goal of this study is to evaluate the power of D-MDR for identifying gene-gene interaction by simulation. Also we applied the method on the identify interaction effects of single nucleotide polymorphisms (SNPs) responsible for economic traits in a Korean cattle population (real data).

• Genomics & Informatics
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• v.10 no.4
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• pp.244-248
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• 2012

Oxidative stress, which results in an excessive product of reactive oxygen species (ROS), is one of the fundamental mechanisms of the development of hypertension. In the vascular system, ROS have physical and pathophysiological roles in vascular remodeling and endothelial dysfunction. In this study, ROS-hypertension-related genes were collected by the biological literature-mining tools, such as SciMiner and gene2pubmed, in order to identify the genes that would cause hypertension through ROS. Further, single nucleotide polymorphisms (SNPs) located within these gene regions were examined statistically for their association with hypertension in 6,419 Korean individuals, and pathway enrichment analysis using the associated genes was performed. The 2,945 SNPs of 237 ROS-hypertension genes were analyzed, and 68 genes were significantly associated with hypertension (p < 0.05). The most significant SNP was rs2889611 within MAPK8 (p = $2.70{\times}10^{-5}$; odds ratio, 0.82; confidence interval, 0.75 to 0.90). This study demonstrates that a text mining approach combined with association analysis may be useful to identify the candidate genes that cause hypertension through ROS or oxidative stress.

• Journal of the Korean Data and Information Science Society
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• v.20 no.1
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• pp.171-178
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• 2009

In order to make the high quality Korean cattle, it has been identified the gene which influence to various economic characters. In this paper, we introduce Restricted Partition Method for gene-gene interaction analysis. Further, economic traits, longissimus muscle dorsi area (LMA), carcass cold weight (CWT) and average daily gain (ADG) are applied with Restricted Partition Method (RPM). The SNP (19_1)$^*$SNP (28_2) was selected and was best marker on Single nucleotide polymorphisms (SNPs). It also influenced SNP (19_1)$^*$SNP (28_2) was an very important marker for economic character and to make the thing know it became.

• Biomedical Science Letters
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• v.20 no.4
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• pp.221-226
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• 2014

High-density lipoprotein (HDL) cholesterol levels are associated with decreased risk of coronary artery disease. Several genome-wide association studies (GWAS) for HDL cholesterol levels have implicated Lipoprotein lipase (LPL) as possibly being causal. Herein, the association between single nucleotide polymorphism (SNP) rs10503669 in the LPL gene and HDL cholesterol levels and triglyceride levels was tested in the Korean population. A total of 994 subjects from Seoul City were included in a replication study with LPL SNP rs10503669. SNP rs10503669 in the LPL gene was associated with mean HDL cholesterol levels (effect per allele 3.13 mg/dL, P<0.0001) and triglyceride levels (effect per allele -18.0 mg/dL, P=0.0026). Subjects with the CA/AA genotype had a 0.42-fold (range 0.23~0.77-fold) lower risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. When analyzed by gender, the association of LPL was stronger in men than in women. This study clearly demonstrates that genetic variants in LPL influence HDL cholesterol levels and triglyceride levels in Korean adults.

• BMB Reports
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• v.45 no.1
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• pp.47-50
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• 2012

The International HapMap Project and the Human Genome Diversity Project (HGDP) provide plentiful resources on human genome information to the public. However, this kind of information is limited because of the small sample size in both databases. A Genome-Wide Association Study has been conducted with 8,842 Korean subjects as a part of the Korea Association Resource (KARE) project. In an effort to build a publicly available browsing system for genome data resulted from large scale KARE GWAS, we developed the KARE browser. This browser provides users with a large amount of single nucleotide polymorphisms (SNPs) information comprising 1.5 million SNPs from population-based cohorts of 8,842 samples. KAREBrowser was based on the generic genome browser (GBrowse), a web-based application tool developed for users to navigate and visualize the genomic features and annotations in an interactive manner. All SNP information and related functions are available at the web site http://ksnp.cdc. go.kr/karebrowser/.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.9
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• pp.4057-4060
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• 2015

Cigarette smoke contains oxidants and free radicals which are carcinogens that can induce mutations in humans. Single nucleotide polymorphisms (SNPs) are the most frequent genetic alterations found in the human genome. In the present study, we have examined the ability of the murine double minute 2 (Mdm2) (rs769412) A>G polymorphism in cigarette smokers to predict risk of cancers. Our results showed that of smokers, 87% were found with AA genotype, 10% with heterozygous AG genotype, and 3% with GG genotype. The heterozygous AG genotype was observed in a lower percentage of smokers (10%) as compared to non-smokers (18%), whereas, homozygous AA genotype was observed in lower percentage of non-smokers (81%) as compared to the smokers (87%). The results from present study support the association with an allele and AG genotype in non-smokers. However, further studies are required to establish the role of Mdm2 (rs769412) C>T in cigarettes smokers and diseases.

• Horticultural Science & Technology
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• v.35 no.2
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• pp.149-164
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• 2017

Next generation sequencing (NGS) technologies have led to the rapid accumulation of genome sequences through whole-genome sequencing and re-sequencing of crop species. Genomic resources provide the opportunity for a new revolution in plant breeding by facilitating the dissection of complex traits. Among vegetable crops, reference genomes have been sequenced and assembled for several species in the Solanaceae and Cucurbitaceae families, including tomato, pepper, cucumber, watermelon, and melon. These reference genomes have been leveraged for re-sequencing of diverse germplasm collections to explore genome-wide sequence variations, especially single nucleotide polymorphisms (SNPs). The use of genome-wide SNPs and high-throughput genotyping methods has led to the development of new strategies for dissecting complex quantitative traits, such as genome-wide association study (GWAS). In addition, the use of multi-parent populations, including nested association mapping (NAM) and multiparent advanced generation intercross (MAGIC) populations, has helped increase the accuracy of quantitative trait loci (QTL) detection. Consequently, a number of QTL have been discovered for agronomically important traits, such as disease resistance and fruit traits, with high mapping resolution. The molecular markers for these QTL represent a useful resource for enhancing selection efficiency via marker-assisted selection (MAS) in vegetable breeding programs. In this review, we discuss current genomic resources and marker-trait association analysis to facilitate genome-assisted breeding in vegetable species in the Solanaceae and Cucurbitaceae families.