A web application and service for imputing and visualizing missense variant effect maps.

Genome Genomics Mutation, Missense Software

Journal

Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944

Informations de publication

Date de publication:
01 09 2019
Historique:
received: 31 07 2018
revised: 04 12 2018
accepted: 07 01 2019
pubmed: 17 1 2019
medline: 18 6 2020
entrez: 17 1 2019
Statut: ppublish

Résumé

The promise of personalized genomic medicine depends on our ability to assess the functional impact of rare sequence variation. Multiplexed assays can experimentally measure the functional impact of missense variants on a massive scale. However, even after such assays, many missense variants remain poorly measured. Here we describe a software pipeline and application to impute missing information in experimentally determined variant effect maps. http://impute.varianteffect.org source code: https://github.com/joewuca/imputation. Supplementary data are available at Bioinformatics online.

Identifiants

DOI: 10.1093/bioinformatics/btz012 PMID: 30649215 PMC: PMC6735881
pubmed: 30649215
pii: 5288774
doi: 10.1093/bioinformatics/btz012
pmc: PMC6735881
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

3191-3193

Subventions

Organisme : NHGRI NIH HHS
ID : P50 HG004233
Pays : United States
Organisme : CIHR
Pays : Canada

Informations de copyright

© The Author(s) 2019. Published by Oxford University Press.

Références

Genome Res. 2001 May;11(5):863-74
pubmed: 11337480
Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9
pubmed: 1438297
PLoS One. 2012;7(10):e46688
pubmed: 23056405
Nat Methods. 2014 Aug;11(8):801-7
pubmed: 25075907
Genetics. 2015 Jun;200(2):413-22
pubmed: 25823446
Genome Res. 2015 Oct;25(10):1423-6
pubmed: 26430151
Genome Res. 2016 May;26(5):670-80
pubmed: 26975778
Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169
pubmed: 27899622
Am J Hum Genet. 2017 Sep 7;101(3):315-325
pubmed: 28886340
Nucleic Acids Res. 2018 Jan 4;46(D1):D1062-D1067
pubmed: 29165669
Cell Syst. 2018 Jan 24;6(1):116-124.e3
pubmed: 29226803
Mol Syst Biol. 2017 Dec 21;13(12):957
pubmed: 29269382
Hum Genet. 2018 Sep;137(9):665-678
pubmed: 30073413

Auteurs

Yingzhou Wu (Y)

Donnelly Centre, University of Toronto, Toronto, ON, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Department of Computer Science, University of Toronto, Toronto, ON, Canada.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.

Jochen Weile (J)

Donnelly Centre, University of Toronto, Toronto, ON, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Department of Computer Science, University of Toronto, Toronto, ON, Canada.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.

Atina G Cote (AG)

Donnelly Centre, University of Toronto, Toronto, ON, Canada.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.

Song Sun (S)

Donnelly Centre, University of Toronto, Toronto, ON, Canada.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.

Jennifer Knapp (J)

Donnelly Centre, University of Toronto, Toronto, ON, Canada.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.

Marta Verby (M)

Donnelly Centre, University of Toronto, Toronto, ON, Canada.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.

Frederick P Roth (FP)

Donnelly Centre, University of Toronto, Toronto, ON, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Department of Computer Science, University of Toronto, Toronto, ON, Canada.
Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
Center for Cancer Systems Biology, Dana Farber Cancer Institute, Boston, MA, USA.
Canadian Institute for Advanced Research, Toronto, ON, Canada.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › A web application and service for imputing and...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › A web application and service for imputing and...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Mutation › Mutation faux-sens › A web application and service for imputing and...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › A web application and service for imputing and...