R3HK7Z last accessed: 2022-11-04

dgva
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

Other names: Database of Genomic Variants Archive, DGVa, DGVarchive, dgva

The DGVa team accepts direct submissions from researchers and also curates data from the published literature. As part of a regular exchange, DGVa data is sent to its partner archive, dbVar (hosted by the National Center for Biotechnology Information) and reciprocally, dbVar sends data to DGVa. Data can be accessed in a number of ways: GVF files, browserd in Ensembl or dowloaded from BioMart. DGVa is the primary supplier of data to the Database of Genomic Variants (DGV), hosted by the The Centre for Applied Genomics in Toronto, Canada. DGV provides extra curation and interpretation services and maintains the most comprehensive resource for genomic structural variation in humans.

Webpage:

http://www.ebi.ac.uk/dgva/

Licence:

Name: Public Domain
URL: https://www.ebi.ac.uk/about/terms-of-use

Publications:

Publications
More detailed information about this field from each metasource.

DbVar and DGVa: public archives for genomic structural variation
PMID: 23193291
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

DbVar and DGVa: public archives for genomic structural variation PubMed citations: 118.

118 articles citing: DbVar and DGVa: public archives for genomic structural variation

Whole-exome sequencing identified mutational profiles of urothelial carcinoma post kidney transplantation. PMID:35864526
Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data. PMID:35461238
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. PMID:35347328
PTCHD1: Identification and Neurodevelopmental Contributions of an Autism Spectrum Disorder and Intellectual Disability Susceptibility Gene. PMID:35328080
Detecting structural variations with precise breakpoints using low-depth WGS data from a single oxford nanopore MinION flowcell. PMID:35296758
Integrating whole-genome sequencing with multi-omic data reveals the impact of structural variants on gene regulation in the human brain. PMID:35288716
Whole exome analysis of patients in Japan with hearing loss reveals high heterogeneity among responsible and novel candidate genes. PMID:35248088
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. PMID:35220969
Characterizing mobile element insertions in 5675 genomes. PMID:35212372
GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing. PMID:35176773
Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data. PMID:35176018
DeepSVP: Integration of genotype and phenotype for structural variant prioritization using deep learning. PMID:34951628
Diagnosis of Shashi-Pena Syndrome Caused by Chromosomal Rearrangement Using Nanopore Sequencing. PMID:34841066
Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation. PMID:34772337
FusionGDB 2.0: fusion gene annotation updates aided by deep learning. PMID:34755868
Chromosomal variants accumulate in genomes of the spontaneous aborted fetuses revealed by chromosomal microarray analysis. PMID:34727132
The European Variation Archive: a FAIR resource of genomic variation for all species. PMID:34718739
The UCSC Genome Browser database: 2022 update. PMID:34718705
Biallelic FRA10AC1 variants cause a neurodevelopmental disorder with growth retardation. PMID:34694367
FusionAI: Predicting fusion breakpoint from DNA sequence with deep learning. PMID:34646994
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. PMID:34621504
AutoCNV: a semiautomatic CNV interpretation system based on the 2019 ACMG/ClinGen Technical Standards for CNVs. PMID:34615484
Methods and Developments in Graphical Pangenomics. PMID:34456520
X-CNV: genome-wide prediction of the pathogenicity of copy number variations. PMID:34407882
InvertypeR: Bayesian inversion genotyping with Strand-seq data. PMID:34332539
A Novel Computational Framework to Predict Disease-Related Copy Number Variations by Integrating Multiple Data Sources. PMID:34267783
NPSV: A simulation-driven approach to genotyping structural variants in whole-genome sequencing data. PMID:34195837
Whole genome sequencing reveals a frameshift mutation and a large deletion in YY1AP1 in a girl with a panvascular artery disease. PMID:33971976
Knowledge bases and software support for variant interpretation in precision oncology. PMID:33971666
A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome. PMID:33833373
Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability. PMID:33741065
Detecting Causal Variants in Mendelian Disorders Using Whole-Genome Sequencing. PMID:33606250
Whole genome sequencing of 10K patients with acute ischaemic stroke or transient ischaemic attack: design, methods and baseline patient characteristics. PMID:33443231
Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches. PMID:33437151
The UCSC Genome Browser database: 2021 update. PMID:33221922
Comparative assessments of indel annotations in healthy and cancer genomes with next-generation sequencing data. PMID:33167946
Towards a better understanding of the low recall of insertion variants with short-read based variant callers. PMID:33148192
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Implications of germline copy-number variations in psychiatric disorders: review of large-scale genetic studies. PMID:32958875
The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery. PMID:32827758
Long-read-based human genomic structural variation detection with cuteSV. PMID:32746918
Mapping and characterization of structural variation in 17,795 human genomes. PMID:32460305
Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR. PMID:32424072
FGviewer: an online visualization tool for functional features of human fusion genes. PMID:32421816
Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. PMID:32383760
VALOR2: characterization of large-scale structural variants using linked-reads. PMID:32192518
Pan-genomics in the human genome era. PMID:32034321
Structural variation in the sequencing era. PMID:31729472
Evaluation of computational genotyping of structural variation for clinical diagnoses. PMID:31494671
Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome. PMID:31494266
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. PMID:31375807
VIPdb, a genetic Variant Impact Predictor Database. PMID:31283070
Impact of Genetic Variation on CRISPR-Cas Targeting. PMID:31021199
Genetic Variations and Precision Medicine. PMID:31019429
A Review of the Genomic Analysis of Children Presenting with Developmental Delay/Intellectual Disability and Associated Dysmorphic Features. PMID:30899624
mGAP: the macaque genotype and phenotype resource, a framework for accessing and interpreting macaque variant data, and identifying new models of human disease. PMID:30841849
Characterizing the Major Structural Variant Alleles of the Human Genome. PMID:30661756
Systematics for types and effects of DNA variations. PMID:30591019
Ensembl variation resources. PMID:30576484
Identification of deleterious and regulatory genomic variations in known asthma loci. PMID:30541564
Changing Trends in Computational Drug Repositioning. PMID:29874824
A genome-wide survey of mutations in the Jurkat cell line. PMID:29739316
MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases. PMID:29704307
Late diagnosis of a truncating WISP3 mutation entails a severe phenotype of progressive pseudorheumatoid dysplasia. PMID:29258992
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. PMID:29254494
Genome Variation Map: a data repository of genome variations in BIG Data Center. PMID:29069473
Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle. PMID:28985340
HUMA: A platform for the analysis of genetic variation in humans. PMID:28967693
Settling the score: variant prioritization and Mendelian disease. PMID:28804138
Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements. PMID:28735859
ASPsiRNA: A Resource of ASP-siRNAs Having Therapeutic Potential for Human Genetic Disorders and Algorithm for Prediction of Their Inhibitory Efficacy. PMID:28696921
Genetic insights into juvenile idiopathic arthritis derived from deep whole genome sequencing. PMID:28572608
A deep intronic CLRN1 (USH3A) founder mutation generates an aberrant exon and underlies severe Usher syndrome on the Arabian Peninsula. PMID:28469144
Drug repurposing from the perspective of pharmaceutical companies. PMID:28369768
Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings. PMID:28315672
Role of Structural Bioinformatics in Drug Discovery by Computational SNP Analysis: Analyzing Variation at the Protein Level. PMID:28302551
Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. PMID:28188534
Dosage sensitivity is a major determinant of human copy number variant pathogenicity. PMID:28176757
Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. PMID:27993330
The novel homozygous KCNJ10 c.986T>C (p.(Leu329Pro)) variant is pathogenic for the SeSAME/EAST homologue in Malinois dogs. PMID:27966545
A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease. PMID:27569544
The Ensembl Variant Effect Predictor. PMID:27268795
Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline. PMID:27148569
Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. PMID:27049631
Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation. PMID:27011785
Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. PMID:26746786
Integrating population variation and protein structural analysis to improve clinical interpretation of missense variation: application to the WD40 domain. PMID:26740553
Taking Bioinformatics to Systems Medicine. PMID:26677177
Wham: Identifying Structural Variants of Biological Consequence. PMID:26625158
ClinVar: public archive of interpretations of clinically relevant variants. PMID:26582918
rVarBase: an updated database for regulatory features of human variants. PMID:26503253
PhytoPath: an integrative resource for plant pathogen genomics. PMID:26476449
FROG - Fingerprinting Genomic Variation Ontology. PMID:26244889
Improving the Sequence Ontology terminology for genomic variant annotation. PMID:26229585
Detection of Genomic Structural Variants from Next-Generation Sequencing Data. PMID:26161383
Sites of instability in the human TCF3 (E2A) gene adopt G-quadruplex DNA structures in vitro. PMID:26029241
GFVO: the Genomic Feature and Variation Ontology. PMID:26019997
DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data. PMID:26013811
The impact of DNA input amount and DNA source on the performance of whole-exome sequencing in cancer epidemiology. PMID:25990554
Leveraging the power of high performance computing for next generation sequencing data analysis: tricks and twists from a high throughput exome workflow. PMID:25942438
Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PMID:25923345
DNA methylation modifies urine biomarker levels in 1,6-hexamethylene diisocyanate exposed workers: a pilot study. PMID:25445006
Gene: a gene-centered information resource at NCBI. PMID:25355515
euL1db: the European database of L1HS retrotransposon insertions in humans. PMID:25352549
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Copy number variation analysis in the context of electronic medical records and large-scale genomics consortium efforts. PMID:24672537
Clinical application of targeted and genome-wide technologies: can we predict treatment responses in chronic lymphocytic leukemia? PMID:24611071
Multigene families of immunoglobulin domain-containing innate immune receptors in zebrafish: deciphering the differences. PMID:24548770
Variation ontology: annotator guide. PMID:24533660
Ensembl 2014. PMID:24316576
Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants. PMID:24285302
InvFEST, a database integrating information of polymorphic inversions in the human genome. PMID:24253300
CNVannotator: a comprehensive annotation server for copy number variation in the human genome. PMID:24244640
ClinVar: public archive of relationships among sequence variation and human phenotype. PMID:24234437
The Database of Genomic Variants: a curated collection of structural variation in the human genome. PMID:24174537
Ensembl Genomes 2013: scaling up access to genome-wide data. PMID:24163254
Pipit: visualizing functional impacts of structural variations. PMID:23803468
The 2013 Nucleic Acids Research Database Issue and the online molecular biology database collection. PMID:23203983

Tags:

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human genes and diseases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

general polymorphism databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

biology
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

dna
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

genomes
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

molecular biology
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

biochemistry
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

bioinformatics
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

biotechnology
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

gene expression
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

gene mapping
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

genetics
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: Database of Genomic Variants Archive; editing status 2019-02-13; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3HK7Z last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

dna structural variation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

data integration and warehousing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

rare diseases
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

human genes and diseases polymorphism dna genomes molecular biology biochemistry bioinformatics biotechnology gene expression gene mapping genetics genomics dna structural variation data integration and warehousing rare diseases

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Publications
More detailed information about this field from each metasource.

DbVar and DGVa: public archives for genomic structural variation
PMID: 23193291
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780

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Database of Genomic Variants

Database of genomic structural VARiation

The Centre for Applied Genomics Databases

European Variation Archive

Database resources of the National Center for Biotechnology Information

DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources

ChEMBL

European Nucleotide Archive

BioStudies

GWAS Diagram Browser

Ensembl

BioModels

The European Bioinformatics Institute Tools

MGnify

TIARA - Total Integrated Archive of short-Read and Array

BioImage Archive

FlyMine

Manually Curated Database of Rice Proteins

Portal de Datos Genómicos del SNDG

Alamut

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Licence:

Publications: Publications More detailed information about this field from each metasource. × DbVar and DGVa: public archives for genomic structural variation PMID: 23193291 metasource: bio.tools version: extracted_at: 2022-11-04T11:30:57.636780 Close

More to explore:

1/20

Database of Genomic Variants

Database of genomic structural VARiation

The Centre for Applied Genomics Databases

European Variation Archive

Database resources of the National Center for Biotechnology Information

DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources

ChEMBL

European Nucleotide Archive

BioStudies

GWAS Diagram Browser

Ensembl

BioModels

The European Bioinformatics Institute Tools

MGnify

TIARA - Total Integrated Archive of short-Read and Array

BioImage Archive

FlyMine

Manually Curated Database of Rice Proteins

Portal de Datos Genómicos del SNDG

Alamut

Publications:

Publications
More detailed information about this field from each metasource.

DbVar and DGVa: public archives for genomic structural variation
PMID: 23193291
metasource: bio.tools
version: extracted_at: 2022-11-04T11:30:57.636780