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Phevor specifications

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Unique identifier OMICS_04802
Name Phevor
Alternative name PHEnotype driven Variant Ontological Re-ranking tool
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Mark Yandell

Publication for PHEnotype driven Variant Ontological Re-ranking tool

Phevor citations

 (8)
library_books

Evaluating phenotype driven approaches for genetic diagnoses from exomes in a clinical setting

2017
Sci Rep
PMCID: 5647373
PMID: 29044180
DOI: 10.1038/s41598-017-13841-y

[…] genes using a random-walk-with-restart algorithm searching gene interaction networks. a bayesian approach is used to evaluate deleterious variants in the exome to known disease-gene associations., phevor integrates phenotype, gene function, and disease information with genomic data targeting both known variation and disease causing alleles not previously implicated in disease. phevor combines […]

library_books

Leveraging network analytics to infer patient syndrome and identify causal genes in rare disease cases

2017
BMC Genomics
PMCID: 5558185
PMID: 28812537
DOI: 10.1186/s12864-017-3910-4

[…] the similarity between the phenotypic profile and disease, and this score is in turn used to rank variants that reside in disease-implicated genes., a number of tools, such as phenolyzer [], phevor2 [], phen-gen [], genecards [], and exomiser [] leverage databases of gene-disease-phenotype relationships and phenotype information to prioritize candidate genes. all of these tools, […]

library_books

A pipeline combining multiple strategies for prioritizing heterozygous variants for the identification of candidate genes in exome datasets

2017
Hum Genomics
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] of heterozygous variants using exome-sequencing datasets in familial meniere disease: an in-house pathogenic variant (pavar) score, the variant annotation analysis and search tool (vaast-phevor), exomiser-v2, cadd, and fathmm. we also validated the method by a benchmarking procedure including causal mutations in synthetic exome datasets., pavar and vaast were able to select […]

library_books

POLR2C Mutations Are Associated With Primary Ovarian Insufficiency in Women

2017
PMCID: 5650244
PMID: 29367954
DOI: 10.1210/js.2016-1014

[…] mutation taster (http://www.mutationtaster.org/), polyphen (http://genetics.bwh.harvard.edu/pph2), and phylop []. in both analyses, the phenotype driven variant ontological re-ranking tool (phevor) feature was used to further prioritize genes for analysis using premature ovarian failure and poi as filters []., rna was isolated from whole blood from the proband and two women with poi […]

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

[…] do so [, ]. alternatively, extasy ranks variants by combining input phenotype similarity scores with scores computed between input genotype data and “fused” human and non-human genomic data, whereas phevor combines input phenotype data with data from human and non-human ontologies to reprioritize externally pre-computed ranks [, ]. as with phen-gen, the inclusion in these analyses […]

library_books

Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency

2015
Genet Med
PMCID: 4916229
PMID: 26562225
DOI: 10.1038/gim.2015.137

[…] human phenotypes is frequently all that is necessary. extasy also incorporates multiple lines of evidence, including clinical phenotypes to predict the deleteriousness of nonsynonymous mutations. phevor compares patients and diseases by using an ontology propagation approach using the mammalian phenotype ontology, hpo, and gene ontology terms. although the phevor method increases the number […]


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Phevor institution(s)
Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA; Utah Science, Technology, and Research Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA; Department of Pathology, University of Utah, Salt Lake City, UT, USA; ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT, USA; Omicia Inc., Oakland, CA, USA; Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
Phevor funding source(s)
Supported by the National Institute of General Medical Sciences (NIGMS) grant R01GM104390, NIGMS grant R01GM104390, National Human Genome Research Institute (NHGRI) grant R44HG006579, NHGRI grant R01HG004341, NIH National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) grant R01DK084198, NIDDK grant DK091374 and by grant 1ULTR001067 from the NIH National Center for Advancing Translational Sciences.

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