scholarly journals SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data

2008 ◽  
Vol 24 (14) ◽  
pp. 1643-1644 ◽  
Author(s):  
C. Morcillo-Suarez ◽  
J. Alegre ◽  
R. Sangros ◽  
E. Gazave ◽  
R. de Cid ◽  
...  
Keyword(s):  
Snp Analysis ◽  
Web Based ◽  
Snp Data ◽  
Statistical Genomics

scholarly journals Web-Based Software for Storage, Statistical Processing and Analysis of SNP Data in Studies on Complex Disorders

2009 ◽  
Vol 12 (1) ◽  
pp. 9-14 ◽  
Author(s):  
E Betcheva ◽  
C Betchev ◽  
D Toncheva
Keyword(s):  
High Speed ◽  
Association Studies ◽  
Statistical Processing ◽  
Candidate Gene Approach ◽  
Snp Analysis ◽  
Nucleotide Polymorphisms ◽  
Web Based ◽  
Complex Disorders ◽  
Snp Data ◽  
Custom Design

Web-Based Software for Storage, Statistical Processing and Analysis of SNP Data in Studies on Complex DisordersSingle nucleotide polymorphisms (SNPs) have become a very powerful tool for molecular genetics studies. Public databases provide information on over 10 million polymorphisms in the human genome. The candidate gene approach and genomewide association studies through SNP analysis have opened a new avenue for defining the genetics of complex disorders. However, analysis of large numbers of SNPs is time-consuming, cost-intensive, and requires huge experimental and statistical resources in association studies. We have developed a web-based product that facilitates the processing and statistical analysis of SNP-genotyping data for casecontrol association studies and provides for custom design, a structured database and practical export layout. Here we describe the software product database and how it helps in high-speed comprehensive SNP analysis.

scholarly journals Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 201
Author(s):  
Sang Mee Hwang ◽  
Hee Won Cho ◽  
Tae Yeul Kim ◽  
Jeong Su Park ◽  
Jongtak Jung ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acinetobacter Baumannii ◽  
Genome Sequencing ◽  
Snp Analysis ◽  
Whole Genome ◽  
Phylogenetic Tree Analysis ◽  
Web Based ◽  
Hospital Outbreak ◽  
Carbapenem Resistant ◽  
Bioinformatics Tools

Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.

scholarly journals Empirical Bayesian approach to testing multiple hypotheses with separate priors for left and right alternatives

2018 ◽  
Vol 17 (4) ◽  
Author(s):  
Naveen K. Bansal ◽  
Mehdi Maadooliat ◽  
Steven J. Schrodi
Keyword(s):  
Empirical Bayes ◽  
Bayes Rule ◽  
Test Statistic ◽  
Data Set ◽  
Web Based ◽  
Multiple Hypotheses ◽  
Snp Data ◽  
Genome Wide ◽  
Shiny App ◽  
User Friendly

Abstract We consider a multiple hypotheses problem with directional alternatives in a decision theoretic framework. We obtain an empirical Bayes rule subject to a constraint on mixed directional false discovery rate (mdFDR≤α) under the semiparametric setting where the distribution of the test statistic is parametric, but the prior distribution is nonparametric. We proposed separate priors for the left tail and right tail alternatives as it may be required for many applications. The proposed Bayes rule is compared through simulation against rules proposed by Benjamini and Yekutieli and Efron. We illustrate the proposed methodology for two sets of data from biological experiments: HIV-transfected cell-line mRNA expression data, and a quantitative trait genome-wide SNP data set. We have developed a user-friendly web-based shiny App for the proposed method which is available through URL https://npseb.shinyapps.io/npseb/. The HIV and SNP data can be directly accessed, and the results presented in this paper can be executed.

Pharmacogenomic analysis from a phase III study of pemetrexed plus carboplatin (PC) versus etoposide plus carboplatin (EC) in chemonaive patients (pts) with extensive-stage disease small cell lung cancer (ED-SCLC)

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 8030-8030
Author(s):  
E. F. Smit ◽  
M. A. Socinski ◽  
B. P. Mullaney ◽  
S. P. Myrand ◽  
E. Powell ◽  
...  
Keyword(s):  
Excision Repair ◽  
Folate Receptor ◽  
Phase Iii ◽  
P Value ◽  
Snp Analysis ◽  
Tissue Samples ◽  
Snp Data ◽  
Stage Disease ◽  
Phase Iii Study ◽  
Hardy Weinberg Equilibrium

8030 Background: We have reported results of a randomized phase III trial in chemonaive patients with ED-SCLC comparing PC to EC. Study enrollment was closed for futility but pharmacogenomic endpoints were not reported. Here we report the results of immunohistochemistry (IHC) analysis from tumor tissues and single nucleotide polymorphism (SNP) analysis of selected genes implicated in pemetrexed, carboplatin, or etoposide activity. Methods: Proteins studied by validated IHC on Benchmark XT were thymidylate synthase (TS), excision repair cross complementing-1 (ERCC1), glycinamide ribonucleotide formyl transferase (GARFT), and folylpolyglutamate synthetase (FPGS). SNP data from whole blood were genotyped by massArray mass spectrometry from 611 samples. One hundred fifty-eight SNPs were genotyped for TS, FPGS, γ-glutamyl hydrolase (GGH), methylene tetrahydrofolate reductase (MTHFR), folate receptor- α (FR-α), solute carrier 19A1 (SLC19A1) and adjacent regions. Allele frequency and Hardy-Weinberg equilibrium were calculated for each SNP. Results: Of 408 tissue samples (from 908 enrolled pts) available for IHC, 336 samples were assayed for > 1 assay target. The IHC analyses showed improved OS in the EC arm relative to the PC arm for patients with low TSnuclear (12.9 vs 7.5 month, p < 0.001, interaction p value = 0.017). There was no differential treatment effect within the PC arm for low vs. high TS. High vs low ERCC1 levels did not predict outcome following C exposure. GARFT was not associated with outcome by treatment. SNP rs2838952 (adjacent to SLC19A1) was significant for improved OS (HR = 0.590, p = 0.01) in both study arms. SNP rs12379987 (FPGS) was significantly associated with treatment for OS (interaction p value = 0.036). Exploratory analyses found associations between additional SNPs and PFS within and across treatments. Conclusions: Pharmacogenomic analyses of tumor samples show that low TSnuclear expression correlates with OS in the EC arm. Two germline SNPs in regions including FPGS and SLC19A1 were associated with better OS. Further analysis of these pharmacogenomic results is ongoing. [Table: see text]

EVALUATION OF BIODIVERSITY IN RUSSIAN LOCAL GOAT BREEDS BASED ON WHOLE-GENOME SNP ANALYSIS

2020 ◽  
pp. 434-436
Author(s):  
A. Dotsev ◽  
V. Volkova ◽  
M. Selionava ◽  
M. Fornara ◽  
H. Reyer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Pool ◽  
Snp Analysis ◽  
Whole Genome ◽  
Effective Population ◽  
Biodiversity Indicators ◽  
Snp Data ◽  
The World ◽  
Population Sizes ◽  
First Time

The genetic diversity of Russian local goats was estimated for the first time based on whole-genome SNP data. The tendencies of decrease in the effective population sizes were revealed, but the calculated biodiversity indicators are not inferior to the values obtained for the world goat breeds. The results indicate that there are still possibilities to preserve the valuable gene pool of local breeds.

scholarly journals Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1972
Author(s):  
Emil Krupa ◽  
Nina Moravčíková ◽  
Zuzana Krupová ◽  
Eliška Žáková
Keyword(s):  
Genetic Diversity ◽  
Correlation Coefficients ◽  
Pedigree Analysis ◽  
Minimum Size ◽  
Snp Analysis ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Snp Data ◽  
Inbreeding Rate

Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in the pedigree analysis. The SNP analysis (n = 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (Ne) were evaluated. The correlations between inbreeding based on the runs of homozygosity (FROH) and pedigree (FPED) were also calculated. The average FPED for all animals was 3.44%, while the FROH varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The Ne, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49–0.54) were observed between FPED and FROH. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data.

DataBiNS-Viz: A Web-Based Tool for Visualization of Non-Synonymous SNP Data

2008 ◽  
Vol 01 (04) ◽  
pp. 233-236
Author(s):  
Fong Chun Chan ◽  
Edward A. Kawas ◽  
Mark D. Wilkinson ◽  
Scott J. Tebbutt
Keyword(s):  
Web Based ◽  
Snp Data

The PBL-Evaluator: a web-based tool for assessment in tutorials

1998 ◽  
Vol 62 (9) ◽  
pp. 671-674
Author(s):  
JF Chaves ◽  
JA Chaves ◽  
MS Lantz
Keyword(s):  
Web Based

Using Popular Mobile Devices in Voice Therapy

2013 ◽  
Vol 23 (3) ◽  
pp. 82-87 ◽  
Author(s):  
Eva van Leer
Keyword(s):  
Exercise Behavior ◽  
Voice Therapy ◽  
Pure Oxygen ◽  
Mobile Platforms ◽  
Self Monitoring ◽  
Web Based ◽  
Motivational Messages ◽  
Related Information ◽  
Health Related ◽  
Tailored Approach

Mobile tools are increasingly available to help individuals monitor their progress toward health behavior goals. Commonly known commercial products for health and fitness self-monitoring include wearable devices such as the Fitbit© and Nike + Pedometer© that work independently or in conjunction with mobile platforms (e.g., smartphones, media players) as well as web-based interfaces. These tools track and graph exercise behavior, provide motivational messages, offer health-related information, and allow users to share their accomplishments via social media. Approximately 2 million software programs or “apps” have been designed for mobile platforms (Pure Oxygen Mobile, 2013), many of which are health-related. The development of mobile health devices and applications is advancing so quickly that the Food and Drug Administration issued a Guidance statement with the purpose of defining mobile medical applications and describing a tailored approach to their regulation.

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