Gwas study database management

Catalog of Published Genome-Wide Association Studies ...

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The genome-wide association study (GWAS) publications in the Catalog include a primary GWAS analysis, defined as array-based genotyping and analysis of 100,000+ pre-QC SNPs selected to tag variation across the genome and without regard to gene content. GWAS data from published studies which are incorporated into new GWAS analyses are eligible, provided they meet the other criteria.

Catalog of Published Genome-Wide Association Studies ...

Genome-Wide Association Studies Fact Sheet - National ...

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SNPpy - Database Management for SNP Data from GWAS Studies Faheem Mitha, Herodotos Herodotou, Nedyalko Borisov, Chen Jiang, Josh Yoder, and Kouros Owzar Abstract Background: We describe SNPpy, a hybrid script database system using the Python SQLAlchemy library coupled with the PostgreSQL database to manage genotype

Genome-Wide Association Studies Fact Sheet - National ...

SNPpy - Database Management for SNP Data from GWAS Studies

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2/15/2010 · The GWAS Analyzer database stores family structure information about the individuals studied, their genotypes, their phenotypes and results from statistical analyses associating SNPs with the phenotypes under study. The database is also loaded with data from multiple public genomic resources, including genes, microRNAs, splice sites, expression ...

SNPpy - Database Management for SNP Data from GWAS Studies

GWAS Analyzer: integrating genotype, phenotype and public ...

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We describe SNPpy, a hybrid script database system using the Python SQLAlchemy library coupled with the PostgreSQL database to manage genotype data from Genome-Wide Association Studies (GWAS). This system makes it possible to merge study data with HapMap data and merge across studies for meta ...

GWAS Analyzer: integrating genotype, phenotype and public ...

SNPpy - Database Management for SNP Data from Genome Wide ...

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PostgreSQL database to manage genotype data from Genome-Wide Association Studies (GWAS). This system makes it possible to merge study data with HapMap data and merge across studies for meta ...

SNPpy - Database Management for SNP Data from Genome Wide ...

SNPpy - Database Management for SNP Data from Genome Wide ...

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5/17/2011 · To help resolve these issues, we present GWASpi, a user-friendly, multiplatform, desktop-able application for the management and analysis of GWAS data, with a novel approach on database technologies to leverage the most out of commonly available desktop hardware.

SNPpy - Database Management for SNP Data from Genome Wide ...

Genome-wide association studies pipeline (GWASpi): a ...

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6/30/2018 · A genome-wide association study (GWAS) is an approach used in genetics research to associate specific genetic variations with particular diseases. The method involves examining genetic variations (genotypes) across the complete sequences of …

Genome-wide association studies pipeline (GWASpi): a ...

Genome - Wide Association Studies (GWAS) Policy

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11/30/2014 · In the past few years, genome-wide association study (GWAS) has made great successes in identifying genetic susceptibility loci underlying many complex diseases and traits. The findings provide important genetic insights into understanding pathogenesis of diseases. In this paper, we present an ...

Genome - Wide Association Studies (GWAS) Policy

Statistical analysis for genome-wide association study

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gwas free download. rtm-gwas An innovative GWAS procedure for studies on germplasm ... IT Management Application Performance Management Application Lifecycle Management IT Asset Management Database Management Cloud Management Network Monitoring Help Desk Issue ... Although many pathway analysis tools have been developed for case-control study ...

Statistical analysis for genome-wide association study

gwas free download - SourceForge

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12/4/2013 · These diverse GWAS data are integrated in a flexible and coherent data model that was described previously in an earlier incarnation of the database, named HGVbaseG2P. 5 …

gwas free download - SourceForge

GWAS Central: a comprehensive resource for the comparison ...

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CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Background: We describe SNPpy, a hybrid script database system using the Python SQLAlchemy library coupled with the PostgreSQL database to manage genotype data from Genome-Wide Association Studies (GWAS). This system makes it possible to merge study data with HapMap data and merge across studies for meta …

GWAS Central: a comprehensive resource for the comparison ...

CiteSeerX — SNPpy- Database Management for SNP Data from ...

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SNPpy--database management for SNP data from genome wide association studies. View / Download 880.0 Kb. Date ... This system makes it possible to merge study data with HapMap data and merge across studies for meta-analyses, including data filtering based on the values of phenotype and Single-Nucleotide Polymorphism (SNP) data. ... a practical ...

CiteSeerX — SNPpy- Database Management for SNP Data from ...

SNPpy--database management for SNP data from genome wide ...

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NIH GWAS Policy applies to: Data Management The proposed policy defines how investigators may submit and request access to GWAS data for research purposes. Investigators using GWAS data from the NIH database will continue to ensure the privacy and confidentiality of the individuals that participated in the original genetic association studies.

SNPpy--database management for SNP data from genome wide ...

NIH Data Sharing Policy for Genome-wide Association ...

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The National Institutes of Health (NIH) has an established central data repositorycalled the database of Genotypes and Phenotypes (dbGaP) for securely storing and sharing human datasubmitted to NIH under the Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies (GWAS).

NIH Data Sharing Policy for Genome-wide Association ...

(GWAS) - National Institutes of Health

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SNPpy--database management for SNP data from genome wide association studies. Journal Article BACKGROUND: We describe SNPpy, a hybrid script database system using the Python SQLAlchemy library coupled with the PostgreSQL database to manage genotype data from Genome-Wide Association Studies (GWAS).

(GWAS) - National Institutes of Health

SNPpy--database management for SNP data from genome wide ...

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SNPpy--database management for SNP data from genome wide association studies. ... database to manage genotype data from Genome-Wide Association Studies (GWAS). This system makes it possible to merge study data with HapMap data and merge across studies for meta-analyses, including data filtering based on the values of phenotype and Single ...

SNPpy--database management for SNP data from genome wide ...

SNPpy--database management for SNP data from genome wide ...

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In this study, we set out to design a publicly available GWAS mapping platform that comprises genotype information on a set of accessions that will help to understand and dissect the genetic ...

SNPpy--database management for SNP data from genome wide ...

Open access resources for genome-wide association mapping ...

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Genome - Wide Association Studies (GWAS) Policy FACT SHEET - Genome - Wide Association Studies (GWAS) Policy Updated October 2010 National Institutes of Health 1 What is GWAS? A genome-wide association study (GWAS) is an approach used in genetics research to associate specific genetic variations with particular diseases. The method involves

Open access resources for genome-wide association mapping ...

Genome - Wide Association Studies (GWAS) Policy

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Statistical power in a genome-wide association study (GWAS) for four different sample sizes assuming a discrete trait with lifetime prevalence of 0.01 (similar to schizophrenia, bipolar disorder ...

Genome - Wide Association Studies (GWAS) Policy

(PDF) Genome-Wide Association Studies: A Primer

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SNPpy - Database Management for SNP Data from Genome Wide Association Studies score: 0.93577239, PLoS ONE, 2011, Mitha, Faheem et. al. ... Accounting for multiple comparisons in a genome-wide association study (GWAS) score: 0.93401817, BMC …

(PDF) Genome-Wide Association Studies: A Primer

Database: gwas - UCSC Genomics Text Indexing

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11/27/2013 · Which is the best agile software project management tool? ... What is the next big methodological approach to studying the genetics of disease given the shortcomings of GWAS (Genome-Wide Association Study... How is epistasis quantified in GWAS studies? ... Can't we pool all GWAS studies into one giant database to detect new associations (and ...

Database: gwas - UCSC Genomics Text Indexing

What are the drawbacks of GWAS (Genome-Wide Association ...

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To help resolve these issues, we present GWASpi, a user-friendly, multiplatform, desktop-able application for the management and analysis of GWAS data, with a novel approach on database technologies to leverage the most out of commonly available desktop hardware.

What are the drawbacks of GWAS (Genome-Wide Association ...

Genome-wide association studies pipeline (GWASpi ...

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Gwas Study Rui Ye Yale University, rui.ye@yale.edu ... genotype and phenotype data are downloaded from Database of Genotypes and phenotypes (dbGaP, Study Accession: phs000336.v1.p1) to a secure server at Yale University and decrypted ... All processes of data cleaning and management are performed by PLINK v 1.0726.

Genome-wide association studies pipeline (GWASpi ...

Pirnas Variants And Lung Cancer Risk: A Post-Gwas Study

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NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies (GWAS) NOT-OD …

Pirnas Variants And Lung Cancer Risk: A Post-Gwas Study

NOT-OD-07-088: Policy for Sharing of Data Obtained in NIH ...

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1/8/2013 · Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized ∼265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic ...

NOT-OD-07-088: Policy for Sharing of Data Obtained in NIH ...

Population genomic and genome-wide association studies of ...

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Genome-wide association studies (GWAS) have rapidly become a standard method for disease gene discovery. A substantial number of recent GWAS indicate that for most disorders, only a few common variants are implicated and the associated SNPs explain only a small fraction of the genetic risk. This review is written from the viewpoint that findings from the GWAS provide preliminary genetic ...

Population genomic and genome-wide association studies of ...

Prioritizing GWAS Results: A Review of Statistical Methods ...

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Key words Data management, Population stratification, Genetic association, Binomial trait, Quanti- tative trait, Multidimensional scaling, PLINK 1 Introduction PLINK is a freely available, widely used open-source toolset for genetic association that allows for the study of large datasets of genotypes and phenotypes [1].

Prioritizing GWAS Results: A Review of Statistical Methods ...

(PDF) Using PLINK for Genome-Wide Association Studies ...

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This study reana-lyzed existing data from three genome-wide association studies (GWAS) using a novel computational biostatistics approach (muGWAS), which had been validated in studies of 600–2000 subjects in epilepsy and autism.

(PDF) Using PLINK for Genome-Wide Association Studies ...

Genome Wide Association Studies (GWAS) - academia.edu

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An adequately powered genomewide association study is currently the method of choice for identifying genes that influence complex disease. 6 The GABRIEL (A Multidisciplinary Study to Identify the ...

Genome Wide Association Studies (GWAS) - academia.edu

A Large-Scale, Consortium-Based Genomewide Association ...

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7/1/2014 · Opioid dependence (OD) is associated with serious medical, legal, and social problems and co-occurring psychiatric disorders. The cost of OD to society in 2002 was approximately $181 billion .Although genome-wide association study (GWAS) is a method of choice to identify risk genes for complex traits, none has been published for OD, despite an estimated heritability of >.60 .

A Large-Scale, Consortium-Based Genomewide Association ...

Genome-Wide Association Study of Opioid Dependence ...

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8/2/2018 · We performed a genome-wide association study (GWAS) on 173 H. pylori isolates from the European population (hpEurope) with known disease aetiology, including 49 from individuals with gastric cancer. ... our current implementation should not be used …

Genome-Wide Association Study of Opioid Dependence ...

A GWAS on Helicobacter pylori strains points to genetic ...

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SNPpy--database management for SNP data from genome wide association studies. ... This system makes it possible to merge study data with HapMap data and merge across studies for meta-analyses, including data filtering based on the values of phenotype and Single-Nucleotide Polymorphism (SNP) data. ... SNPpy is a practical and extensible solution ...

A GWAS on Helicobacter pylori strains points to genetic ...

SNPpy--database management for SNP data from genome wide ...

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4/19/2016 · The aim of the present study was to compare the power of single nucleotide polymorphism (SNP)-based genome-wide association study (GWAS) and haplotype-based GWAS for quantitative trait loci (QTL) detection, and to detect novel candidate genes affecting economically important traits in a purebred Duroc population comprising seven-generation pedigree.

SNPpy--database management for SNP data from genome wide ...

SNP- and haplotype-based genome-wide ... - BMC Genetics

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5/20/2014 · Genome wide association studies (GWAS) have revealed a large number of links between genome variation and complex disease. Among other benefits, it is expected that these insights will lead to new therapeutic strategies, particularly the identification of new drug targets. In this paper, we evaluate the power of GWAS studies to find drug targets by examining how many existing drug targets have ...

SNP- and haplotype-based genome-wide ... - BMC Genetics

GWAS and drug targets | BMC Genomics | Full Text

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9/11/2015 · In this study, GWAS based on re-sequencing approach was conducted in a set of rice landraces or varieties for mesocotyl elongation as a key character enhancing rice seedling emergence, especially after dry seeding with relatively higher sowing depth.

GWAS and drug targets | BMC Genomics | Full Text

Genome-wide Association Study (GWAS) of mesocotyl ...

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Increases the usage of existing genome-wide association study (GWAS) results. DistiLD database performs three important tasks: (i) published GWAS are collected from several sources and linked to standardized, international disease codes; (ii) data from the International HapMap program are analyzed to define linkage disequilibrium (LD) blocks onto which single nucleotide polymorphisms (SNPs ...

Genome-wide Association Study (GWAS) of mesocotyl ...

DistiLD Database - omicX - omictools.com

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Database Backed Program For Management Of Snp Data? I'm writing to ask if anyone is aware of database backed programs for management of SNP data, bes... GWAS conditional analysis . ... My task is to perform the GWAS study for an enzyme a... Trying to reproduce a GWAS analysis . Hello. I've been recently trying to reproduce the datasets from ...

DistiLD Database - omicX - omictools.com

GWAS analysis tool - biostars.org

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Genome-Wide Association Study (GWAS) in Upper Gastrointestinal (UGI) Cancers (July 26, 2013 version) INTRODUCTION AND STATEMENT OF POLICY The National Institutes of Health (NIH) has an established central data repository called the database of Genotypes and Phenotypes (dbGaP) for securely storing and sharing human data submitted to NIH under the

GWAS analysis tool - biostars.org

DATA USE CERTIFICATION AGREEMENT National Cancer Institute ...

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GWASpi is a start-to-finish GWAS management application that uses a novel approach on database technologies to reduce in up to two orders of magnitude the time needed to perform the fundamental steps of a GWAS. GWAS based on Single Nucleotide Polymorphism (SNP) arrays are the most widely used approach to detect loci associated to human traits.

DATA USE CERTIFICATION AGREEMENT National Cancer Institute ...

GWASpi 2.0.2 – Genome Wide Association Study pipeline

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6/21/2013 · Many genomic elements in humans are associated with behavior, including educational attainment. In a genome-wide association study including more than 100,000 samples, Rietveld et al. (p. [1467][1], published online 30 May; see the Perspective by [ Flint and Munafò ][2]) looked for genes related to educational attainment in Caucasians. Small genetic effects at three loci appeared to impact ...

GWASpi 2.0.2 – Genome Wide Association Study pipeline

GWAS of 126,559 Individuals Identifies Genetic Variants ...

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GWAS policy applies genome-wide association research utilizing genetic materials data collected both prospectively retrospectively. prospective studies, which GWAS conceived within study designs the time research participants provide consent, NIH expects specific discussion within informed consent process documentation participants genotype ...

GWAS of 126,559 Individuals Identifies Genetic Variants ...

Policy for Sharing of Data Obtained in NIH Supported or ...

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A Genome-Wide Association Study Identifies the Skin ... and Marjolein Peters for their help in creating the GWAS database and Karol Estrada and Maksim V Struchalin for their support in creation and analysis of the imputed data. ... The generation and management of GWAS genotype data for the Rotterdam Study was supported by the Netherlands ...

Policy for Sharing of Data Obtained in NIH Supported or ...

A Genome-Wide Association Study Identifies the Skin Color ...

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9/19/2015 · Extreme‐phenotype genome‐wide association study (XP‐GWAS): a method for identifying trait‐associated variants by sequencing pools of individuals selected from a diversity panel ... To test the reproducibility of the phenotypic data downloaded from the GRIN database, replicated field trials (Experimental procedures) were performed using ...

A Genome-Wide Association Study Identifies the Skin Color ...

Extreme‐phenotype genome‐wide association study (XP‐GWAS ...

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Search for multiple associations in GWAS data. Project description. GWAS(genome wide associated study) is a powerful method in genetics especially in the light of human health science. It allows us to find genetic markers (predominantly SNP - single nucleotide …

Extreme‐phenotype genome‐wide association study (XP‐GWAS ...

GitHub - anton-shikov/GWAS_project

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Check out our new tutorial videos! Gramene Diversity Overview, MLM Analysis with TASSEL Focus of the Genetic Diversity module Characterizing the genetic basis of variation in plants and linking to observable traits will provide an important framework for understanding population structure, evolutionary patterns, and could potentially significantly increase the efficiency of selections made in ...

GitHub - anton-shikov/GWAS_project
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