• Title, Summary, Keyword: single nucleotide polymorphism

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Genome-wide Single Nucleotide Polymorphism-based Assay for Phylogenetic Relationship of the Flammulina velutipes (팽이버섯(Flammulina velutipes)의 Genome-wide SNP (Single Nucleotide Polymorphism)에 의한 계통 분석)

  • Woo, Sung-I;Kim, Eun-Seon;Han, Jae-Gu;Jang, Kab Yeul;Shin, Pyung-Gyun;Oh, Youn-Lee;Oh, Min Ji;Jo, Sung-Hwan;Lee, Jeong-Hee;Kim, Kyung-Soo;Kong, Won-Sik
    • The Korean Journal of Mycology
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    • v.43 no.4
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    • pp.231-238
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    • 2015
  • Genome-wide reanalyzed data of 25 Flammulina strains were compared against the reference genome (KACC42780) to establish a genome-wide single nucleotide polymorphism (SNP). The rate of mapping differences between the strains reflected in the strain variation in its result. Genome-wide SNPs distribution divided into types of homozygous SNP and heterozygous SNP moreover all of the strains demonstrated a wide variation in all of the regions. In the further study of topological relationship between the collected strains, phylogenetic tree was separated into 3 major groups. Group I contained F. velutipes var. related strains of ASI 4062, 4148, 4195. Group 2 contained strains that are different species of ASI 4188 F. elastica, ASI 4190 F. fennae, and ASI 4194 F. rossica. The other 19 strains F. velutipes were classified as a single group. However, further experiment to discriminate its genetic relationship between the white group and brown group did not verify its validity. The inferred tree exhibited a phylogenetic relationship between Korea white fruitbody forming strains of ASI 4210, 4166, 4178 and Japan white fruitbody forming strains of ASI 4209, 4167 confirmed to be genetically closely related.

Design and Implementation of a Web-Based Search Engine for Single Nucleotide Polymorphism Data (웹기반의 Single Nucleotide Polymorphism 데이터 검색 시스템의 설계 및 구현)

  • 양진옥;김상수
    • Proceedings of the Korean Information Science Society Conference
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    • pp.160-162
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    • 2002
  • SNP는 개인과 개인간의 DNA에 존재하는 한 염기 쌍의 차이(single base-pair variation)이다. SNP를 이용하면 사람마다 다른 유전병의 형태 등을 규명할 수 있다. 본 논문에서는 한국생명공학연구원의 유전체 사업단에서 개발해 오고 있는 웹기반 SNP데이터 검색 시스템의 설계와 구현에 대해서 설명한다. 본 시스템은 일반 속성(attribute)을 저장하고 검색하기 위해 PostgreSQL DBMS를 사용하고, DNA 시퀸스 검색을 위해 BLAST검색엔진을 사용한 약결합 아키텍쳐(loosely-coupled architecture)를 채택하고 있다. 즉, 일반 속성으로 저장될 수 있는 데이터들은 데이터베이스의 테이블들의 컬럼 값으로 저장하고 SQL 언어를 통해 검색할 수 있도록 하였으며, DNA 시퀸스 검색을 위해서는 BLAST에서 제공하는 인덱스를 구축하고 BLAST 명령어를 사용하여 검색할 수 있도록 하였다. 또한, 결과 분석 모듈을 구현하여 검색 결과들이 다른 웹 사이트의 데이터를 가리키도록 하였다.

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Comparison of the Affymetrix SNP Array 5.0 and Oligoarray Platforms for Defining CNV

  • Kim, Ji-Hong;Jung, Seung-Hyun;Hu, Hae-Jin;Yim, Seon-Hee;Chung, Yeun-Jun
    • Genomics & Informatics
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    • v.8 no.3
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    • pp.138-141
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    • 2010
  • Together with single nucleotide polymorphism (SNP), copy number variations (CNV) are recognized to be the major component of human genetic diversity and used as a genetic marker in many disease association studies. Affymetrix Genome-wide SNP 5.0 is one of the commonly used SNP array platforms for SNP-GWAS as well as CNV analysis. However, there has been no report that validated the accuracy and reproducibility of CNVs identified by Affymetrix SNP array 5.0. In this study, we compared the characteristics of CNVs from the same set of genomic DNAs detected by three different array platforms; Affymetrix SNP array 5.0, Agilent 2X244K CNV array and NimbleGen 2.1M CNV array. In our analysis, Affymetrix SNP array 5.0 seems to detect CNVs in a reliable manner, which can be applied for association studies. However, for the purpose of defining CNVs in detail, Affymetrix Genome-wide SNP 5.0 might be relatively less ideal than NimbleGen 2.1M CNV array and Agilent 2X244K CNV array, which outperform Affymetrix array for defining the small-sized single copy variants. This result will help researchers to select a suitable array platform for CNV analysis.

Investigation of Single Nucleotide Polymorphisms in Porcine Chromosome 2 Quantitative Trait Loci for Meat Quality Traits

  • Do, K.T.;Ha, Y.;Mote, B.E.;Rothschild, M.F.;Choi, B.H.;Lee, S.S.;Kim, T.H.;Cho, B.W.;Kim, K.S.
    • Asian-Australasian Journal of Animal Sciences
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    • v.21 no.2
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    • pp.155-160
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    • 2008
  • Several studies have reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2 (http://www.animalgenome.org/QTLdb/pig.html). For application of the molecular genetic information to the pig industry through marker-assisted selection, single nucleotide polymorphism (SNP) markers were analyzed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes with DNA from commercial pig breeds such as Berkshire, Yorkshire, Landrace, Duroc and Korean Native pig. A total of 34 SNPs were identified in 15 PCR products producing an average of one SNP in every 253 bp. PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to investigate allele frequencies in five commercial pig breeds in Korea. Eight of the SNPs appear to be fixed in at least one of the five pig breeds, which indicates that different selection among pig breeds might be applied to these SNPs. Polymorphisms detected in the PTH, CSF2 and FOLR genes were chosen to genotype a Berkshire-Yorkshire pig breed reference family for linkage and association analyses. Using linkage analysis, PTH and CSF2 loci were mapped to pig chromosome 2, while FOLR was mapped to pig chromosome 9. Association analyses between SNPs in the PTH, CSF2 and FOLR suggested that the CSF2 MboII polymorphism was significantly associated with several pork quality traits in the Berkshire and Yorkshire crossed F2 pigs. Our current findings provide useful SNP marker information to fine map QTL regions on pig chromosome 2 and to clarify the relevance of SNP and quantitative traits in commercial pig populations.

An Overview of Matrix Metalloproteinase 9 Polymorphism and Gastric Cancer Risk

  • Verma, Sugreev;Kesh, Kousik;Gupta, Arnab;Swarnakar, Snehasikta
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.17
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    • pp.7393-7400
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    • 2015
  • Matrix metalloproteinase (MMP) 9, a key member of multifunctional family of zinc dependent endopeptidases has been found to be upregulated during inflammation and in some cancers. MMPs cleave extracellular matrix (ECM) proteins and play critical roles in cellular apoptosis, angiogenesis, tumor growth and metastasis. Several genetic polymorphisms have been identified that show allele specific effects on MMP9 regulation and are associated with gastric cancer, the fourth most common malignancy in the world. Besides Helicobacter pylori infection, genetic predisposition is another documented risk factor for gastric carcinoma. The single nucleotide polymorphism (SNP) at position -1562C/T of MMP9 results in the modulation for binding of transcription factors to the MMP9 gene promoter and thereby causes differences in protein expression and enzymatic activity. MMP9 transcriptional regulation during gastric cancer development remains poorly known although several studies have demonstrated associations between MMP9 -1562 C/T polymorphism with different diseases. Knowledge on mechanisms of MMP9 upregulation during gastric cancer may provide new paradigm in diagnostics and therapeutics.

Effect of a c-MYC Gene Polymorphism (g.3350G>C) on Meat Quality Traits in Berkshire

  • Oh, J.D.;Kim, E.S.;Lee, H.K.;Song, K.D.
    • Asian-Australasian Journal of Animal Sciences
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    • v.28 no.11
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    • pp.1545-1550
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    • 2015
  • c-MYC (v-myelocytomatosis viral oncogene homologue) is a transcription factor that plays important role in many biological process including cell growth and differentiation, such as myogenesis and adipogenesis. In this study, we aimed to detect MYC gene polymorphisms, their genotype frequencies and to determine associations between these polymorphisms and meat quality traits in Berkshire pigs. We identified a single nucleotide polymorphism (SNP) in intron 2 of MYC gene by Sanger sequencing, i.e., g.3350G>C (rs321898326), that is only found in Berkshire pigs, but not in other breeds including Duroc, Landrace, and Yorkshire pigs that were used in this study. Genotypes of total 378 Berkshire pigs (138 sows and 240 boars) were determined using Hha I restriction enzyme digestion after polymerase chain reaction. Observed allele frequencies of GG, GC, and CC genotypes were 0.399, 0.508, and 0.093 respectively. Statistical analysis indicated that the g.3350G>C polymorphism was significantly associated with $pH_{45min}$ and cooking loss (p<0.05), suggesting that g.3350G>C SNP can be used for pre-selection of $pH_{45min}$ and cooking loss traits in Berkshire pigs.

Rapid Identification of Ginseng Cultivars (Panax ginseng Meyer) Using Novel SNP-Based Probes

  • Jo, Ick-Hyun;Bang, Kyong-Hwan;Kim, Young-Chang;Lee, Jei-Wan;Seo, A-Yeon;Seong, Bong-Jae;Kim, Hyun-Ho;Kim, Dong-Hwi;Cha, Seon-Woo;Cho, Yong-Gu;Kim, Hong-Sig
    • Journal of Ginseng Research
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    • v.35 no.4
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    • pp.504-513
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    • 2011
  • In order to develop a novel system for the discrimination of five ginseng cultivars (Panax ginseng Meyer), single nucleotide polymorphism (SNP) genotyping assays with real-time polymerase chain reaction were conducted. Nucleotide substitution in gDNA library clones of P. ginseng cv. Yunpoong was targeted for the SNP genotyping assay. From these SNP sites, a set of modified SNP specific fluorescence probes (PGP74, PGP110, and PGP130) and novel primer sets have been developed to distinguish among five ginseng cultivars. The combination of the SNP type of the five cultivars, Chungpoong, Yunpoong, Gopoong, Kumpoong, and Sunpoong, was identified as 'ATA', 'GCC', 'GTA', 'GCA', and 'ACC', respectively. This study represents the first report of the identification of ginseng cultivars by fluorescence probes. An SNP genotyping assay using fluorescence probes could prove useful for the identification of ginseng cultivars and ginseng seed management systems and guarantee the purity of ginseng seed.

Estimation of Haplotype Proportions in Single Necleotide Polymorphism Group Using EM Algorithm (EM 알고리듬을 이용한 단일염기변이 (SNP;SINGLE NUCLEOTIDE POLYMORPHISM)군의 일배체형 (HAPLOTYPE) 비율 추정)

  • 김선우;김종원;이경아
    • The Korean Journal of Applied Statistics
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    • v.16 no.2
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    • pp.195-202
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    • 2003
  • Haplotype analysis in SNP is very useful for the study of complex genetic disease due to low cost and high efficiency comparing to individual analysis of each SNP, and is functionally important in biological view. But, the gametic phase of haplotypes is usually unknown in SNP group, and it is difficult to predict haplotype proportions. In this study, haplotype proportions were estimated using EM algorithm from diploid data of SNP group in solid tumor group and normal group. From these results, linkage disequilibrium among SNPs was analyzed.

VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism

  • Kim, HyoYoung;Sung, Samsun;Cho, Seoae;Kim, Tae-Hun;Seo, Kangseok;Kim, Heebal
    • Asian-Australasian Journal of Animal Sciences
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    • v.27 no.12
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    • pp.1691-1694
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    • 2014
  • Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.