PhenoDB statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

PhenoDB specifications

Information


Unique identifier OMICS_11205
Name PhenoDB
Restrictions to use None
Data access File download, Browse
Content license CC Attribution-NonCommercial-ShareAlike
Maintained Yes

Maintainer


  • person_outline Nara Sobreira

Publications for PhenoDB

PhenoDB citations

 (7)
call_split

A novel PRRT2 pathogenic variant in a family with paroxysmal kinesigenic dyskinesia and benign familial infantile seizures

2018
PMCID: 5793775
PMID: 29167286
DOI: 10.1101/mcs.a002287
call_split See protocol

[…] nd_1000G_gold_ standard.indels.b37.vcf) were used as training and truth sites. Indels were filtered to obtain all variants up to the 95th percentile of truth sites (5% false negative rate). Using the PhenoDB Variant Analysis Tool of PhenoDB, we prioritized heterozygous, homozygous, and compound heterozygous rare functional variants (missense, nonsense, splice site variants, and indels) shared by t […]

call_split

Familial monophasic acute transverse myelitis due to the pathogenic variant in VPS37A

2018
PMCID: 5820602
PMID: 29473047
DOI: 10.1212/NXG.0000000000000213
call_split See protocol

[…] and_1000 G_gold_standard.indels.b37.vcf) were used as training and truth sites. Indels were filtered to obtain all variants up to the 95th percentile of truth sites (5% false-negative rate).Using the PhenoDB Variant Analysis Tool of PhenoDB, we prioritized heterozygous, homozygous, and compound heterozygous rare functional variants (missense, nonsense, splice-site variants, and indels) shared by t […]

library_books

Human genome meeting 2016

2016
Hum Genomics
PMCID: 4896275
PMID: 27294413
DOI: 10.1186/s40246-016-0063-5

[…] s by the re-analysis of unsolved whole exome sequecing (WES) data. Methods To address some of these cases, we have incorporated maternal and paternal imprinting analysis and polygenic analysis to the PhenoDB Variant Analysis tool. We also analyzed WES data from 1063 samples for rare, functional variants in known imprinted genes, in the genes on pseudoautosomal regions, genes that escape X-inactiva […]

library_books

Novel bioinformatic developments for exome sequencing

2016
Hum Genet
PMCID: 4883269
PMID: 27075447
DOI: 10.1007/s00439-016-1658-6

[…] of their samples (Firth and Wright ). Such criteria are not easily imposed for most other projects and several tools have been developed to encourage and facilitate the use of phenotype information. PhenoDB (Hamosh et al. ) and PhenoTips (Girdea et al. ) are platforms that allow clinicians to enter, store and analyze structured phenotypic data. Phenominer is a tool able to extract phenotype conte […]

library_books

A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome wide diagnostics

2016
Genome Med
PMCID: 4736244
PMID: 26838676
DOI: 10.1186/s13073-016-0261-8

[…] , ]. As with Phen-Gen, the inclusion in these analyses of gene-to-phenotype data from non-human sources may blur the line between disease gene discovery and clinical application. Other tools, such as PhenoDB [, , ] and PhenoTips [, ], facilitate the collection, classification, analysis, and sharing of clinical indication data, but they do not provide a phenotypically supported connection to partic […]

library_books

Capturing phenotypes for precision medicine

2015
PMCID: 4850887
PMID: 27148566
DOI: 10.1101/mcs.a000372

[…] cian workflows to facilitate the recording of phenotypic abnormalities for patients with genetic disorders, as well as a variety of other relevant information including family and medical history (). PhenoDB is another useful web-based tool initially developed for the Centers of Mendelian Genomics project for storing and analyzing phenotypic information from families or cohorts (). Phenotypic feat […]

Citations

Looking to check out a full list of citations?

PhenoDB institution(s)
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA; FS Consulting, Salem, Massachusetts
PhenoDB funding source(s)
Supported by NHGRI (1U54HG006542).

PhenoDB reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review PhenoDB