• Asian Pacific Journal of Cancer Prevention
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• v.15 no.16
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• pp.6961-6967
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• 2014

Cytokine gene single nucleotide polymorphisms (SNPs) are involved in the genesis and progression of hepatocellular carcinoma (HCC). We hypothesized that combined effects of cytokine gene SNPs and SNP-SNP interactions are associated with HCC risk. Six SNPs in cytokine genes (IL-2, IFN-${\gamma}$, IL-$1{\beta}$, IL-6, and IL-10) were genotyped in a study of 720 Chinese HCC cases and 784 cancer-free controls. Although none of these SNPs individually had a significant effect on the risk of HCC, we found that the combined effects of these six SNPs may contribute to HCC risk (OR=1.821, 95% CI=1.078-3.075). This risk was pronounced among smokers, drinkers, and hepatitis B virus carriers. A SNP-SNP interaction between IL-2-330 and IFN-${\gamma}$-1615 was associated with an increased HCC risk (OR=1.078, 95% CI=1.022-1.136). In conclusion, combined effects of SNPs and SNP-SNP interactions in cytokine genes may contribute to HCC risk.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.154-154
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• 2017

In accordance with the opening of the Korean rice market, this study was focused on establishment of database for discriminating the Korean rice varieties and imported brand rices using DNA markers. In this study, the SNP markers were developed using single nucleotide polymorphisms between the reference sequences of japonica and them of 40 brand rices which collected in Australia, China, Thailand, United States and Vietnam. The developed SNP markers were screened to a total of 360 rices including 320 Korean rice varieties and 40 imported brand rices. We selected polymorphic markers among Korean bred rive varieties and imported brand rices. The selected markers were classified into 3 grades. The markers of A grade produced DNA band in 360 rices of 30~40%, B grades produced in 40~60%, and C grades produced bands over 60% rices. First, we tried to set-up the discriminating system using the minimum SNP markers of A grade. Especially, a set of sixteen SNP markers could identify among Korean bred rice varieties and imported brand rices. Additionally, some SNP markers like NSb for Pib gene, JJ80-T for Pi5 and YL155/YL87 for Pita which linked to resistance genes to blast were used to fingerprinting system. These markers were set-up as multiplex set for enhancing the identification efficiency among rice varieties. Finally, the selected SNP markers would be used to the fluidigm assay to construct the database for elaborate discrimination of rice varieties.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.12
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• pp.1543-1551
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• 2010

A major aim of cattle genome research is to identify candidate genes associated with meat quantity and quality through QTL analysis for application in the livestock industry. Therefore, this study focused on discovery of useful SNPs within the LOC534614 gene, containing 12273_165 SNP which is located on the same site as the QTL on chromosome 6, and evaluation of the association between SNP and body weight and cold carcass weight in Hanwoo (Korean cattle) As a result of a BLAST search of the NCBI web site, we discovered that the mRNA sequence of the LOC534614 gene was similar to that of the coiled-coil domain containing 158 (CCDC158) for dog and human. According to the direct DNA sequence from the CCDC158 gene, we identified 19 polymorphic SNPs within exons and their flanking regions. Among them, 17 polymorphic SNPs were selected for genotyping in Hanwoo (n = 476) and seventeen marker haplotypes containing 12273_165 SNP (frequency >0.1) were identified. As a result of the association between 17 polymorphic SNPs and Hanwoo (n = 476), g.8778G>A SNP in exon 6 was found to be a non-synonymous SNP, and was significantly associated with body weight and cold carcass weight (p<0.05). We discovered 19 polymorphic SNPs in the CCDC158 gene on the QTL region of BTA 6 in Hanwoo and identified that the g.8778G>A SNP was significantly associated with body weight and cold carcass weight (p<0.05), which causes an amino acid variation from valine to methionine. Furthermore, statistical analysis demonstrated that the CCDC158 gene is strongly associated with body weight and cold carcass weight in Hanwoo. In this regard, the g.8778G>A SNP in the CCDC158 gene can be useful as a positional candidate for body weight and cold carcass weight for marker-assisted selection in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.8
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• pp.1061-1065
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• 2005

Growth rate is one of the economically important quantitative traits that affect carcass quantity in beef cattle. Two genes, bovine insulin-like growth factor I (IGF-I) and myogenic factor 5 (MYF5), were chosen as candidate genes for growth traits due to their important role in growth and development of mammals. The objectives of this study were to determine gene-specific single nucleotide polymorphism (SNP) markers of the IGF-I and MYF5 positional candidate genes and to investigate their associations with growth traits in Korean cattle. Genotyping of the SNP markers in these candidate genes was carried out using the single strand conformation polymorphism (SSCP) analysis. The frequencies of A and B alleles were 0.72 and 0.28 for IGF-I gene and 0.39 and 0.61 for MYF5 gene, respectively, in Korean cattle population examined. The gene-specific SNP marker association analysis indicated that the SNP genotype in IGF-I gene showed a significant association (p<0.05) with weight at 3 months (W3), and cows with AB genotype had higher W3 than BB genotype cows. The SNP genotype of MYF5 gene was found to have a significant effect (p<0.05) on the weight at 12 months (W12) and average daily gain (ADG), and cows with BB and AB genotypes had higher W12 and ADG compared with cows with AA genotype, respectively. However, no significant association between the SNP genotypes and any other growth traits was detected. The gene-specific SNP markers in the IGF-I and MYF5 candidate genes may be useful for selection on growth traits in Korean cattle.

• Parasites, Hosts and Diseases
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• v.59 no.1
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• pp.15-22
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• 2021

Artemisinin resistance (ART) has been confirmed in Greater Mekong Sub-region countries. Currently, C580Y mutation on Pfkelch13 gene is known as the molecular marker for the detection of ART. Rapid and accurate detection of ART in field study is essential to guide malaria containment and elimination interventions. A simple method for collection of malaria-infected blood is to spot the blood on filter paper and is fast and easy for transportation and storage in the field study. This study aims to evaluate LAMP-SNP assay for C580Y mutation detection by introducing an extra mismatched nucleotide at the 3' end of the FIP primer. The LAMP-SNP assay was performed in a water bath held at a temperature of 56℃ for 45 min. LAMP-SNP products were interpreted by both gel-electrophoresis and HNB-visualized changes in color. The method was then tested with 120 P. falciparum DNA from dried blood spot samples. In comparing the LAMP-SNP assay results with those from DNA sequencing of the clinical samples, the 2 results fully agreed to detect C580Y. The sensitivity and specificity of the LAMP-SNP assay showed 100%. There were no cross-reactions with other Plasmodium species and other Pfkelch13 mutations. The LAMP-SNP assay performed in this study was rapid, reliable, and useful in detecting artemisinin resistance in the field study.

• Food Science of Animal Resources
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• v.29 no.1
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• pp.108-113
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• 2009

Apolipoprotein E (APOE) is a plasma lipoprotein in mammals and plays an important role in the transport and metabolism of lipids such as phospholipids and triglycerides. Therefore, the APOE gene could be a candidate gene controlling lipid metabolism in beef cattle. This study was performed to identify single nucleotide polymorphisms (SNP) in the APOE gene and to investigate the effects of SNP genotype on the carcass traits such as meat quantity and quality in Korean cattle. For PCR amplification, pooled DNA made from unrelated 60 individuals was prepared and primer pairs were designed based on the cDNA sequence of exon 4 region of the bovine APOE gene. A SNP was identified at position 2034 (T/C substitution) of the exon 4 region in the APOE gene. PCR-RFLP procedure with restriction enzyme ACC I was developed for determining the SNP genotype for each of a total of 309 animals with pedigree information and performance records through the national progeny testing program. The frequencies of the genotypes TT, TC and CC were 10.9, 46.9 and 42.2%. Gene frequencies were 0.344 for T allele and 0.656 for C allele. The g.2034T>C SNP genotype showed a significant effect (p<0.05) on dressing percentage and meat color, respectively. Animals with the TT genotype showed higher dressing percentage than those with the CC genotype, and TT genotype had desirable meat color compared with CC genotype. These results suggest that the g.2034T>C SNP genotype of the APOE gene may be useful as a DNA marker for meat quantity index and dressing percentage in Korean cattle.

• Journal of Animal Science and Technology
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• v.51 no.5
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• pp.353-360
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• 2009

When 14 microsatellite (MS) markers were applied in the identifying test for 480 Hanwoo, the discriminating power was estimated as $3.43{\times}10^{-27}$ based on the assumption of a random mating group (PI). This rate is 1,000 times higher than that of 60 single nucleotide polymorphism (SNP) markers. On the other hand, the power of the 60 SNP markers was estimated as $4.69{\times}10^{-20}$ and $8.02{\times}10^{-12}$ on the assumption of a half-sib mating group ($PI_{half-sibs}$) and a full-sib mating group ($PI_{sibs}$), respectively. These powers were 10 times and 10,000 times higher than those of the 14 MS markers. The results indicated that the total number of alleles (MS vs SNP = 146 vs 120) acted as a key factor for the discriminating power in a random mating population, and the total number of markers (MS vs SNP = 14 vs 60) was a dominant influence on the power in half-sib and full-sib populations. In the Hanwoo population, in which it was assumed that the entire population is the enormous half-sib group formed by the absolute genetic contribution of a few nuclear bulls, there will be only a 10 times difference in the discriminating power between the 14 MS markers and the 60 SNP makers. However, the probability of not excluding a candidate parent pair from the parentage of an arbitrary offspring, given that only the genotype of the offspring ($PNE_{pp}$) was 1,000 times higher as shown by the 14 MS markers than that by the 60 SNP markers. The strong points of SNP makers are the stability of the variation (low mutation rate) and automation of high-throughput genotyping. In order to apply these merits for the practical and constant Hanwoo identity test, research and development are required to set a cost-effective platform and produce a homemade apparatus for SNP genotyping.

• Communications for Statistical Applications and Methods
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• v.15 no.2
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• pp.265-271
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• 2008

It is commonly believed that diseases of human or economic traits of livestock are caused not by single genes acting alone, but multiple genes interacting with one another. This issue is difficult due to the limitations of parametric-statistic methods of gene effects. So we introduce multifactor-dimensionality reduction(MDR) as a methods for reducing the dimensionality of multilocus information. The MDR method is nonparametric (i. e., no hypothesis about the value of a statistical parameter is made), model free (i. e., it assumes no particular inheritance model) and is directly applicable to case-control studies. Application of the MDR method revealed the best model with an interaction effect between the SNPs, SNP1 and SNP3, while only one main effect of SNP1 was statistically significant for LMA (p < 0.01) under a general linear mixed model.

• Proceedings of the Korean Information Science Society Conference
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• 2004.10b
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• pp.253-255
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• 2004

인간(human)에게 나타나는 다양성(variation)은 인체의 유전체(genome) 안에서 발생된 SNP(Single Nucleotide Polymorphism)에 의해 나타난다고 알려져 있다. 유전체내의 SNP과 다양성에 대한 연관 연구(Associate study)를 할 때에 약 30여 억 개로 추정되는 염기서열(DNA sequence)물 모두 분석한다면 많은 비용과 시간을 필요로 할 것이다. 이런 비용과 시간을 줄이기 위친 적은 수의 대표 SNP(=tagSNP)을 찾는 연구가 현재 진행 중이다. 우리는 LD계수｜D;｜을 block 분할에 이용하여 생물학적인 의미를 부여한 후, 전산적인 최적해를 찾는 접근을 이용했다. 또한, 기존 연구에서는 large-scale data에 대한 처리가 불가능해서 chromosome의 일부분의 데이터에 대해서안 분석이 시도되었다. 더욱 광범위한 분석을 위해서 chromosome 단위의 처리가 필요하다. 우리는 chromosome단위의 SNP data를 한 번에 처리가 가능한 시스템인 MarSel를 구현하였다

• BMB Reports
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• v.38 no.1
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• pp.24-27
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• 2005

The role of 3' exonuclease excision in DNA polymerization was evaluated for primer extension using inert allele specific primers with exonuclease-digestible ddNMP at their 3' termini. Efficient primer extension was observed in amplicons where the inert allele specific primers and their corresponding templates were mismatched. However, no primer-extended products were yielded by matched amplicons with inert primers. As a control, polymerase without proofreading activity failed to yield primer extended products from inert primers regardless of whether the primers and templates were matched or mismatched. These data indicated that activation was undertaken for the inert allele specific primers through mismatch proofreading. Complementary to our previously developed SNP-operated on/off switch, in which DNA polymerization only occurs in matched amplicon, this new mutation detection assay mediated by $exo^+$ DNA polymerases has immediate applications in SNP analysis independently or in combination of the two assays.