• 한국동물위생학회지
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• 제42권4호
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• pp.217-225
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• 2019

To detect Single nucleotide polymorphisms (SNP) markers associated with Bovine viral diarrhea virus (BVDV) and Bovine respiratory syncytial virus (BRSV) S/P ratio in Korean Holstein dairy cattle, Genome-wide association study (GWAS) was performed using Illumina BovineSNP50 Beadchip. The number of phenotype data and genotype data were 107, and 294. respectively. Phenotype data were collected for four periods (0 week, 1 week, 4 week, 24 week) after having vaccinated (0 week no vaccinated period). A total of 36,257 SNPs was remained after quality control had been done by PLINK. The result of GWAS showed 6 SNP markers (BTB-01704243, BTB-01594395, ARS-BFGL-NGS-118070, ARS-BFGL-NGS-111365, BTA-65410-no-rs, Hapmap38331-BTA-61256) under BVDV and 4 SNP markers (ARS-BFGL-NGS-109861, Hapmap53701-rs29017064, ARS-BFGL-NGS-71055, BTA-11232-no-rs) under BRSV. And also, 10 candidate genes found through 10 SNP markers (TBX18, CEP162, PAFAH1B1, METTL16, BRCA1, RND2, POLK, ENSBTAG00000051724, ADAM18, NRG3).

• Asian-Australasian Journal of Animal Sciences
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• 제26권10호
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• pp.1374-1378
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• 2013

Based on a quantitative traits locus (QTL) study using a $F_2$ intercross between Landrace and Korean native pigs, a significant QTL affecting teat numbers in SSC7 was identified. The strong positional candidate gene, TBC1D21, was selected due to its biological function for epithelial mesenchymal cell development. Sequence analysis revealed six single nucleotide polymorphisms (SNPs) in the TBC1D21 gene. Among these, two SNP markers, one silent mutation (SNP01) for g.13,050A>G and one missense mutation (SNP04) for c.829A>T (S277C), were genotyped and they showed significant associations with teat number traits (p value = 6.38E-05 for SNP01 and p value = 1.06E-07 for SNP04 with total teat numbers). Further functional validation of these SNPs could give valuable information for understanding the teat number variation in pigs.

• BMB Reports
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• 제46권8호
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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/].

• 한국정보통신학회:학술대회논문집
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• 한국정보통신학회 2012년도 추계학술대회
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• pp.780-783
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• 2012

최근 SoC 업계에서는 다양한 다중 버스 구조가 사용되고 있다. 그러나, 무분별한 버스 층의 남용은 통신 자원과 실리콘 면적의 낭비를 초래한다. 본 논문은 이러한 낭비를 막기 위한 최적의 다중 버스 구조를 탐색하는 정량적 분석법을 소개한다. 본 방법은 다양한 온칩 버스 프로토콜의 특성을 수학적 모델 형태로 반영하여 서로 다른 프로토콜을 기반으로 합성된 버스 구조간 비교가 가능하다. 예제를 대상을 실험한 결과 AHB, AXI, SNP 프로토콜 기반으로 합성된 다중 버스 구조 중 SNP 기반으로 합성된 버스 구조가 AXI 기반의 다중 버스 구조 대비 20% 더 성능이 좋으며 제안된 방법들을 통한 시간 복잡도도 상당히 저감된 것으로 확인되었다.

• Plant Biotechnology Reports
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• 제4권4호
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• pp.243-251
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• 2010

Nitric oxide (NO) has been shown to be involved in diverse physiological processes in microbes, animals and plants. In this study, the involvement of NO in the development and possible roles in oxidative stress protection of Chinese cabbage (Brassica rapa subsp. pekinensis cv. Samrack-ulgari) seedlings were investigated. Exogenous application of sodium nitroprusside (SNP) retarded root elongation, while increasing lateral root formation of Chinese cabbage. Plants showed no signs of external stress due to SNP application in true leaves. Cotyledons of 3-week-old Chinese cabbage plants were found to be highly sensitive to SNP application. Treated cotyledons displayed rapid tissue collapse and associated cell death. Although SNP application reduced root growth under normal growth conditions, it also enhanced methyl viologen (MV)-mediated oxidative stress tolerance. Analysis of SNP application to Chinese cabbage leaf disks, revealed SNP-induced tolerance against oxidative stresses by MV and $H_2O_2$, and evidence includes prevention of chlorophyll loss, superoxide anion (${O_2}^-$) accumulation and lipid peroxidation. This report supports a role for nitric oxide in modulating early seedling development, programmed cell death and stress tolerance in Chinese cabbage.

• Journal of Plant Biotechnology
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• 제43권1호
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• pp.1-11
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• 2016

Single nucleotide polymorphism (SNP) is an abundant form of genetic variation within individuals of species. DNA polymorphism can arise throughout the whole genome at different frequencies in different species. SNP may cause phenotypic diversity among individuals, such as individuals with different color of plants or fruits, fruit size, ripening, flowering time adaptation, quality of crops, grain yields, or tolerance to various abiotic and biotic factors. SNP may result in changes in amino acids in the exon of a gene (asynonymous). SNP can also be silent (present in coding region but synonymous). It may simply occur in the noncoding regions without having any effect. SNP may influence the promoter activity for gene expression and finally produce functional protein through transcription. Therefore, the identification of functional SNP in genes and analysis of their effects on phenotype may lead to better understanding of their impact on gene function for varietal improvement. In this mini-review, we focused on evidences revealing the role of functional SNPs in genes and their phenotypic effects for the purpose of crop improvements.

• 한국축산식품학회:학술대회논문집
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• 한국축산식품학회 2006년도 정기총회 및 제37차 춘계 국제학술발표대회
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• pp.112-116
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• 2006

본 연구는 인간과 동물의 식욕조절, 에너지 대사, 체지방 축적 및 지방 대사에 핵심적인 역할을 담당하는 비만 유전자 leptin의 SNP를 검색하고, 이들 SNP 마커와 한우의 도체 및 육질형질들과의 연관성을 구명하여 고급육 생산 한우 조기 선발 및 육질 진단을 위한 분자 표지 마커로 활용하기 위하여 수행하였다. 한우 leptin 유전자의 exon 2 및 3번 영역을 포함한 염기서열 분석결과 총 3개의 SNP를 검출하였고, PCR-RFLP및 SSCP기법을 이용하여 SNP유전자형을 분석한 결과 exon 2 영역 내 C1180T SNP부위가 한우의 근내 지방도 및 등지방 두께와 유의적인 연관성(p<0.05)이 있는 것으로 나타났다. 따라서, 본 연구를 통해 개발된 한우 leptin 유전자의 특정한 SNP marker는 근내 지방도가 우수한 고급육을 생산하는 한우의 조기식별 및 마블링 등 육질진단에 매우 유용한 DNA 표지인자로 활용할 수 있을 기대된다.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• 제34권4호
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• pp.450-455
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• 2008

A Single Nucleotide Polymorphism (SNP) is a small genetic change or variation that can occur within a DNA sequence. It's the difference of one base at specific base pair position. SNP variation occurs when a single nucleotide, such as an A, replaces one of the other three nucleotide letters-C, G, or T. On average, SNP occur in the human population more than 1 percent of the time. They occur once in every 300 nucleotides on average, which means there are roughly 10 million SNPs in the human genome. Because SNPs occur frequently throughout the genome and tend to be relatively stable genetically, they serve as excellent biological markers. They can help scientists locate genes that are associated with disease such as heart disease, cancer, diabetes. They can also be used to track the inheritance of disease genes within families. SNPs may also be associated with absorbance and clearance of therapeutic agents. In the future, the most appropriate drug for an individual could be determined in advance of treatment by analyzing a patient's SNP profile. This pharmacogenetic strategy heralds an era in which the choice of drugs for a particular patient will be based on evidence rather than trial and error (so called "personalized medicine").

• Journal of Animal Science and Technology
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• 제64권5호
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• pp.830-841
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• 2022

Genetic analysis has great potential as a tool to differentiate between different species and breeds of livestock. In this study, the optimal combinations of single nucleotide polymorphism (SNP) markers for discriminating the Yeonsan Ogye chicken (Gallus gallus domesticus) breed were identified using high-density 600K SNP array data. In 3,904 individuals from 198 chicken breeds, SNP markers specific to the target population were discovered through a case-control genome-wide association study (GWAS) and filtered out based on the linkage disequilibrium blocks. Significant SNP markers were selected by feature selection applying two machine learning algorithms: Random Forest (RF) and AdaBoost (AB). Using a machine learning approach, the 38 (RF) and 43 (AB) optimal SNP marker combinations for the Yeonsan Ogye chicken population demonstrated 100% accuracy. Hence, the GWAS and machine learning models used in this study can be efficiently utilized to identify the optimal combination of markers for discriminating target populations using multiple SNP markers.

• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2010년도 추계학술발표대회
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• pp.95-98
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• 2010

최근 차세대 시퀀싱 기술의 급속한 발전에 따라 서열 정보의 해독이 비교적 쉬워지면서 개인별 맞춤의학의 실현에 대한 기대와 관심이 높아지고 있다. 각 개인의 서열 정보 사이에는 SNP (single nucleotide polymorphism), Indel, CNV (copy number variation) 등의 다양한 유전적 구조 변이가 존재하며, 이러한 서열 정보의 부분적 차이는 각 개인의 유전적 특성 및 질병 감수성 등과 밀접한 관련을 갖는다. 본 연구에서는 차세대 시퀀싱 결과로 산출되는 수많은 짧은 DNA 서열 조각인 리드 데이터를 이용한 SNP 추출 알고리즘을 제안한다. 제안된 알고리즘에서는 레퍼런스 시퀀스의 각 위치에 대한 리드 시퀀스의 매핑 정보를 기반으로 SNP 후보 영역을 추출하며, 품질 정보 등을 활용하여 에러 발생률을 최소화한다. 또한 대규모 시퀀싱 데이터와 SNP 구조 변이 데이터의 효율적인 저장/검색을 지원하는 시각적 분석 도구를 구현하여 제안된 방식의 유용성을 검증한다.