• Title, Summary, Keyword: single nucleotide polymorphism

Search Result 787, Processing Time 0.036 seconds

MitGEN: Single Nucleotide Polymorphism DB Browser for Human Mitochondrial Genome

  • Park, Hyun Seok;Lee, Seung Uk
    • Genomics & Informatics
    • /
    • v.2 no.3
    • /
    • pp.147-148
    • /
    • 2004
  • Recently completed mitochondrial genome databses from public resources provide us with a better understanding of individual mitochondrial genomes for population genomics. By determining the substitution rate of the genomic sequences, it is plausible to derive dates on the phylogenetic tree and build a chronology of events in the evolution of human species. MitGEN is specially designed as a mitochondrial genome browser for analyzing, comparing and visualizing single nucleotide polymorphism for human mitochondrial genomes between human races for comparative genomics. It is a standalone application and is available free for non-commercial work.

SNP (Single Nucleotide Polymorphism) Detection Using Indicator-free DNA (비수식화 DNA를 이용한 SNP의 검출)

  • Choi, Yong-Sung;Park, Dae-Hee;Kwon, Young-Soo
    • Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
    • /
    • /
    • pp.224-226
    • /
    • 2003
  • In this paper, we succeeded SNP discrimination of DNA hybridization on microarray using new electrochemical system. Using the electrochemical method with a label-free DNA has Performed DNA chip microarray. This method is based on redox of an electrochemical ligand. We developed scanning system with high performance.

  • PDF

Nucleotide Polymorphism of Green-like Visual Pigment Gene from Eyed and Blind Forms of the Mexican Tetra, Astyanax fasciatus (Mexican tetra (Astyanax fasciatus)의 녹색 시간 색소포 유전자의 염기서열 다형화 현상)

  • 송춘복;쑈죠요코야마
    • Journal of Aquaculture
    • /
    • v.11 no.3
    • /
    • pp.295-301
    • /
    • 1998
  • Since the end of the Pliocene, ancestral strains of Astyanax fasciatus have been accidently washed into different caves at the time of flooding and have lost their eyes and body pigments. Availability of this independently derived cave fish and their ancestral form within a single species provided a unique opportunity for studying the process of molecular evolution of the visual pigment gene. The nucleotide sequence comparisons of an ancestral river fish and two cave fish showed that nucleotide polymorphism of a green-like visual pigment gene between the eyed and blind form of A. fasciatus was much higher than that between the same blind form. Considering the number of nucleotide substitutions per nucleotide site and the direction of the nucleotide substitutions, more nucleotide substituions between the different forms of fish rater than the same one were probably due to more frequent mutations in the eyed river form. Nucleotide substitutions per site at the intron have been ocurred more than three times faster than those at the exon. This result indicates that the functional constraint has affected the green-like visual pigment gene of the blind cave fish although its eye sight is no longer required.

  • PDF

Prediction of Chronic Hepatitis Susceptibility using Single Nucleotide Polymorphism Data and Support Vector Machine (Single Nucleotide Polymorphism(SNP) 데이타와 Support Vector Machine(SVM)을 이용한 만성 간염 감수성 예측)

  • Kim, Dong-Hoi;Uhmn, Saang-Yong;Hahm, Ki-Baik;Kim, Jin
    • Journal of KIISE:Computer Systems and Theory
    • /
    • v.34 no.7
    • /
    • pp.276-281
    • /
    • 2007
  • In this paper, we use Support Vector Machine to predict the susceptibility of chronic hepatitis from single nucleotide polymorphism data. Our data set consists of SNP data for 328 patients based on 28 SNPs and patients classes(chronic hepatitis, healthy). We use leave-one-out cross validation method for estimation of the accuracy. The experimental results show that SVM with SNP is capable of classifying the SNP data successfully for chronic hepatitis susceptibility with accuracy value of 67.1%. The accuracy of all SNPs with health related feature(sex, age) is improved more than 7%(accuracy 74.9%). This result shows that the accuracy of predicting susceptibility can be improved with health related features. With more SNPs and other health related features, SVM prediction of SNP data is a potential tool for chronic hepatitis susceptibility.

MMP1 rs1799750 Single Nucleotide Polymorphism and Lung Cancer Risk: A Meta-analysis

  • Hu, Jiang;Pan, Jun;Luo, Zhi-Guo
    • Asian Pacific Journal of Cancer Prevention
    • /
    • v.13 no.12
    • /
    • pp.5981-5984
    • /
    • 2012
  • Background: Numerous studies have investigated the association of matrix metalloproteinase 1 (MMP1) rs1799750 single nucleotide polymorphism with lung cancer susceptibility, but the findings are inconsistent. Therefore, we performed a meta-analysis to comprehensively evaluate any possible association. Methods: We searched publications from MEDLINE, EMBASE and CNKI databases which assessed links between the MMP1 rs1799750 polymorphism and lung cancer risk. We calculated the pooled odds ratio (OR) and its 95% confidence interval (95%CI) using either fixed-effects or random-effects models. Results: The meta-analysis was based on 9 publications encompassing 4,823 cases and 4,298 controls. The overall results suggested there was a significant association between the MMP1 rs1799750 polymorphism and lung cancer risk (1G vs. 2G: OR = 0.83, 95%CI = 0.73-0.94; 1G1G vs. 2G2G: OR = 0.73, 95%CI = 0.59-0.92; 1G1G vs. 1G2G/2G2G: OR = 0.87, 95%CI = 0.79-0.97; 1G1G/1G2G vs. 2G2G: OR = 0.78, 95%CI = 0.64-0.95). In the subgroup analysis by ethnicity, the association was still obvious in Asians (all P values < 0.05), but there was no association in Caucasians (all P values > 0.05). Conclusions: The MMP1 rs1799750 polymorphism is associated with decreased lung cancer risk, and a race-specific effect may exist in this association.

A Genome Wide Association Study on Age at First Calving Using High Density Single Nucleotide Polymorphism Chips in Hanwoo (Bos taurus coreanae)

  • Hyeong, K.E.;Iqbal, A.;Kim, Jong-Joo
    • Asian-Australasian Journal of Animal Sciences
    • /
    • v.27 no.10
    • /
    • pp.1406-1410
    • /
    • 2014
  • Age at first calving is an important trait for achieving earlier reproductive performance. To detect quantitative trait loci (QTL) for reproductive traits, a genome wide association study was conducted on the 96 Hanwoo cows that were born between 2008 and 2010 from 13 sires in a local farm (Juk-Am Hanwoo farm, Suncheon, Korea) and genotyped with the Illumina 50K bovine single nucleotide polymorphism (SNP) chips. Phenotypes were regressed on additive and dominance effects for each SNP using a simple linear regression model after the effects of birth-year-month and polygenes were considered. A forward regression procedure was applied to determine the best set of SNPs for age at first calving. A total of 15 QTL were detected at the comparison-wise 0.001 level. Two QTL with strong statistical evidence were found at 128.9 Mb and 111.1 Mb on bovine chromosomes (BTA) 2 and 7, respectively, each of which accounted for 22% of the phenotypic variance. Also, five significant SNPs were detected on BTAs 10, 16, 20, 26, and 29. Multiple QTL were found on BTAs 1, 2, 7, and 14. The significant QTLs may be applied via marker assisted selection to increase rate of genetic gain for the trait, after validation tests in other Hanwoo cow populations.

Fast Microchip Electrophoresis Using Field Strength Gradients for Single Nucleotide Polymorphism Identification of Cattle Breeds

  • Oh, Doo-Ri;Cheong, Il-Cheong;Lee, Hee-Gu;Eo, Seong-Kug;Kang, Seong-Ho
    • Bulletin of the Korean Chemical Society
    • /
    • v.31 no.7
    • /
    • pp.1902-1906
    • /
    • 2010
  • A microchip electrophoresis (ME) method was developed using a programmed field strength gradients (PFSG) for the single nucleotide polymorphism (SNP) based fast identification of cattle breeds. Four different Korean cattle (Hanwoo) and Holstein SNP markers amplified by allele-specific polymerase chain reaction were separated in a glass microchip filled with 0.5% poly(ethyleneoxide) ($M_r$ = 8 000 000) by PFSG as follows: 750 V/cm for 0 - 14 s, 166.7 V/cm for 14 - 31 s, 83.3 V/cm for 31 - 46 s, and 750 V/cm for 46 - 100 s. The cattle breeds were clearly distinguished within 45 s. The ME-PFSG method was 7 times and 5 times faster than the constant electric field ME method and the capillary electrophoresis- PFSG method, respectively, with a high resolving power ($R_s$ = 5.05 - 9.98). The proposed methodology could be a powerful tool for the fast and simultaneous determination of SNP markers for various cattle breeds with high accuracy.

MAP: Mutation Arranger for Defining Phenotype-Related Single-Nucleotide Variant

  • Baek, In-Pyo;Jeong, Yong-Bok;Jung, Seung-Hyun;Chung, Yeun-Jun
    • Genomics & Informatics
    • /
    • v.12 no.4
    • /
    • pp.289-292
    • /
    • 2014
  • Next-generation sequencing (NGS) is widely used to identify the causative mutations underlying diverse human diseases, including cancers, which can be useful for discovering the diagnostic and therapeutic targets. Currently, a number of single-nucleotide variant (SNV)-calling algorithms are available; however, there is no tool for visualizing the recurrent and phenotype-specific mutations for general researchers. In this study, in order to support defining the recurrent mutations or phenotype-specific mutations from NGS data of a group of cancers with diverse phenotypes, we aimed to develop a user-friendly tool, named mutation arranger for defining phenotype-related SNV (MAP). MAP is a user-friendly program with multiple functions that supports the determination of recurrent or phenotype-specific mutations and provides graphic illustration images to the users. Its operation environment, the Microsoft Windows environment, enables more researchers who cannot operate Linux to define clinically meaningful mutations with NGS data from cancer cohorts.

Single Nucleotide Polymorphism in the Promoter Region of H1 Histone Family Member N, Testis-specific (H1FNT) and Its Association Study with Male Infertility

  • Yang, Seung-Hee;Lee, Jin-U;Lee, Su-Man
    • Genomics & Informatics
    • /
    • v.8 no.4
    • /
    • pp.201-205
    • /
    • 2010
  • The H1 histone family, member N, testis-specific (H1FNT) is exclusively expressed in the testis, and had its possible role for sperm chromatin formation. The purpose of this study is to investigate any genetic association of H1FNT gene with male infertility, especially at the promoter region. We examined the promoter single nucleotide polymorphisms (SNP) of H1FNT gene which is located within transcription factor binding site for its association with male infertility. The statistical analysis showed that the -1129A>T polymorphism was present at a statistically significance in male infertility (p=0.0059 and 0.0349 for hetero and risk type, respectively). The dual-luciferase promoter assay was performed to examine the polymorphic effect of this promoter SNP by the cloning of promoter region (1700bp fragment) into pGL3-basic vector. In our plasmid based reporter system, there is no big difference between wild and risk type. In conclusion, H1FNT -1129A>T promoter SNP is statistically significant with male infertility, especially with subfertile (non-azoospermia) group. Further analysis of its functional polymorphic effect in vivo may provide the biological significance of testis-specific histone with spermatogenesis.