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Phevor specifications

Information


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

 (9)
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

[…] his form of matching. However, as we have shown here for cases in a clinical setting, tools which have a gene discovery rather than diagnostic emphasis may give misleading results.Most tools (eXtasy, Phevor, Phen-Gen, OVA and Exomiser hiPHIVE) integrate human and non-human genomic data which underlies their gene discovery focus. Our analyses, which utilise clinical exome data with known molecular […]

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

[…] + VAAST [], Phenolyzer + ANNOVAR [], PDR + Ingenuity Variant Analysis), while others offer it as part of the tool (Phen-Gen, Exomiser). Similarly, by partnering or independently, many of these tools (Phevor2 + VAAST, PDR + Ingenuity Variant Analysis, Phen-Gen, Exomiser) can provide family-based analysis involving several samples, useful for identifying variants compatible with the disease inherita […]

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

[…] g to top 10, 20, or 50. ROC curves were generated to determine the ability to predict real causal variants based on models consisting of the combination of the five systems (PAVAR, Exomiser v2, VAAST-Phevor, CADD, and FATHMM) and each individual system. In all the cases, the analyses were performed for the top 10, 20, and 50 ranked variants and using different control datasets to filter for privat […]

call_split

POLR2C Mutations Are Associated With Primary Ovarian Insufficiency in Women

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

[…] to expected protein effects using SIFT (http://sift.jcvi.org/), 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 []. […]

library_books

The Current Landscape of Genetic Testing in Cardiovascular Malformations: Opportunities and Challenges

2016
PMCID: 4959014
PMID: 27504451
DOI: 10.3389/fcvm.2016.00022

[…] algorithms using multiple features, such as the predicted effect of a variant on protein function (). Variant prioritization applications that incorporate human phenotype data in this manner include Phevor, Phen-Gen, and Exomiser (–). There is evidence that incorporation of structured human phenotype data does improve performance (). Importantly, computational algorithms based on semantic similar […]

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 of gene-to-phen […]

Citations

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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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