SysBiolPGWAS: simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets.

Humans Genome-Wide Association Study Computational Biology Software Multiomics Polymorphism, Single Nucleotide

Journal

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

Informations de publication

Date de publication:
01 01 2023
Historique:
received: 23 06 2022
revised: 28 10 2022
accepted: 07 12 2022
pubmed: 9 12 2022
medline: 11 1 2023
entrez: 8 12 2022
Statut: ppublish

Résumé

Post-genome-wide association studies (pGWAS) analysis is designed to decipher the functional consequences of significant single-nucleotide polymorphisms (SNPs) in the era of GWAS. This can be translated into research insights and clinical benefits such as the effectiveness of strategies for disease screening, treatment and prevention. However, the setup of pGWAS (pGWAS) tools can be quite complicated, and it mostly requires big data. The challenge however is, scientists are required to have sufficient experience with several of these technically complex and complicated tools in order to complete the pGWAS analysis. We present SysBiolPGWAS, a pGWAS web application that provides a comprehensive functionality for biologists and non-bioinformaticians to conduct several pGWAS analyses to overcome the above challenges. It provides unique functionalities for analysis involving multi-omics datasets and visualization using various bioinformatics tools. SysBiolPGWAS provides access to individual pGWAS tools and a novel custom pGWAS pipeline that integrates several individual pGWAS tools and data. The SysBiolPGWAS app was developed to be a one-stop shop for pGWAS analysis. It targets researchers in the area of the human genome and performs its analysis mainly in the autosomal chromosomes. SysBiolPGWAS web app was developed using JavaScript/TypeScript web frameworks and is available at: https://spgwas.waslitbre.org/. All codes are available in this GitHub repository https://github.com/covenant-university-bioinformatics.

Identifiants

DOI: 10.1093/bioinformatics/btac791 PMID: 36477976 PMC: PMC9825739
pubmed: 36477976
pii: 6883906
doi: 10.1093/bioinformatics/btac791
pmc: PMC9825739
pii:
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

Subventions

Organisme : NHGRI NIH HHS
ID : U24 HG006941
Pays : United States
Organisme : FIC NIH HHS
ID : U2R TW010679
Pays : United States

Informations de copyright

© The Author(s) 2022. Published by Oxford University Press.

Références

PLoS Genet. 2021 Sep 29;17(9):e1009440
pubmed: 34587156
Nat Rev Genet. 2018 Aug;19(8):491-504
pubmed: 29844615
Am J Hum Genet. 2019 Dec 5;105(6):1213-1221
pubmed: 31761295
Genome Med. 2020 Dec 2;12(1):103
pubmed: 33261662
Am J Hum Genet. 2018 May 3;102(5):717-730
pubmed: 29727686
PLoS Comput Biol. 2016 Jan 25;12(1):e1004714
pubmed: 26808494
Nat Rev Genet. 2019 Aug;20(8):467-484
pubmed: 31068683
Nat Genet. 2019 Apr;51(4):675-682
pubmed: 30926970
NAR Genom Bioinform. 2020 Aug 06;2(3):lqaa054
pubmed: 33575605
Nat Genet. 2016 Feb;48(2):214-20
pubmed: 26727659
PLoS Comput Biol. 2015 Apr 17;11(4):e1004219
pubmed: 25885710
Nucleic Acids Res. 2016 Jan 4;44(D1):D877-81
pubmed: 26657631
PLoS Comput Biol. 2010 Dec 02;6(12):e1001025
pubmed: 21152010
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Nat Methods. 2014 Mar;11(3):294-6
pubmed: 24487584
Nucleic Acids Res. 2010 Sep;38(16):e164
pubmed: 20601685
Semin Immunopathol. 2022 Jan;44(1):101-113
pubmed: 35041074
Cell Genom. 2021 Oct 13;1(1):
pubmed: 36082306
Nat Commun. 2018 Mar 2;9(1):918
pubmed: 29500431
F1000Res. 2017 Feb 1;6:97
pubmed: 28620455
Genet Epidemiol. 2009 Jan;33(1):79-86
pubmed: 18642345
Genome Biol. 2016 Dec 6;17(1):252
pubmed: 27923386
Genome Res. 2012 Sep;22(9):1790-7
pubmed: 22955989
Nat Genet. 2012 Dec;44(12):1294-301
pubmed: 23104008
Nucleic Acids Res. 2019 Jan 8;47(D1):D1005-D1012
pubmed: 30445434
Genome Res. 2005 Jul;15(7):901-13
pubmed: 15965027
Bioinformatics. 2019 Oct 1;35(19):3842-3845
pubmed: 30824912
Nucleic Acids Res. 2019 Jan 8;47(D1):D886-D894
pubmed: 30371827
Bioinformatics. 2015 Mar 1;31(5):761-3
pubmed: 25338716
Nucleic Acids Res. 2019 Jan 8;47(D1):D853-D858
pubmed: 30407534
Nat Genet. 2014 Mar;46(3):310-5
pubmed: 24487276
Am J Hum Genet. 2007 Aug;81(2):208-27
pubmed: 17668372
Bioinformatics. 2020 Feb 1;36(3):690-697
pubmed: 31504167
Nat Protoc. 2020 Sep;15(9):2759-2772
pubmed: 32709988

Auteurs

Oluwadamilare Falola (O)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.
ORCID: 0000-0003-4448-7829

Yagoub Adam (Y)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.
ORCID: 0000-0001-6874-2543

Olabode Ajayi (O)

South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town 7535, Republic of South Africa.

Judit Kumuthini (J)

South African National Bioinformatics Institute, Life Sciences Building, University of Western Cape, Cape Town 7535, Republic of South Africa.

Suraju Adewale (S)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.

Abayomi Mosaku (A)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.

Chaimae Samtal (C)

Laboratory of Biotechnology, Environment, Agri-food and Health, Faculty of Sciences Dhar El Mahraz, Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco.

Glory Adebayo (G)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.
Department of Biological Sciences, Covenant University, Ota, Ogun State 112104, Nigeria.

Jerry Emmanuel (J)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.
Department of Computer & Information Sciences, Covenant University, Ota, Ogun State 112104, Nigeria.

Milaine S S Tchamga (MSS)

African Institute for Mathematical Sciences (AIMS), Muizenberg, Cape Town 7945, South Africa.

Udochukwu Erondu (U)

Department of Computer Science, Landmark University, Omu-Aran, Kwara State 251103, Nigeria.

Adebayo Nehemiah (A)

Department of Computer Science, Landmark University, Omu-Aran, Kwara State 251103, Nigeria.
ORCID: 0000-0001-5838-8843

Suraj Rasaq (S)

Department of Computer Science, Landmark University, Omu-Aran, Kwara State 251103, Nigeria.

Mary Ajayi (M)

Department of Computer Science, Landmark University, Omu-Aran, Kwara State 251103, Nigeria.

Bola Akanle (B)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.
Center for System and Information Services, Covenant University, Ota, Ogun State 112104, Nigeria.
Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State 112104, Nigeria.

Olaleye Oladipo (O)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.
Center for System and Information Services, Covenant University, Ota, Ogun State 112104, Nigeria.
Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State 112104, Nigeria.

Itunuoluwa Isewon (I)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.
Department of Computer & Information Sciences, Covenant University, Ota, Ogun State 112104, Nigeria.
Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State 112104, Nigeria.

Marion Adebiyi (M)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.
Department of Computer Science, Landmark University, Omu-Aran, Kwara State 251103, Nigeria.
Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State 112104, Nigeria.

Jelili Oyelade (J)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.
Department of Computer & Information Sciences, Covenant University, Ota, Ogun State 112104, Nigeria.
Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State 112104, Nigeria.
ORCID: 0000-0002-5476-4992

Ezekiel Adebiyi (E)

Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State 112104, Nigeria.
Department of Computer & Information Sciences, Covenant University, Ota, Ogun State 112104, Nigeria.
Covenant Applied Informatics and Communication Africa Center of Excellence (CApIC-ACE), Covenant University, Ota, Ogun State 112104, Nigeria.
Applied Bioinformatics Division, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
ORCID: 0000-0002-1390-2359

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › SysBiolPGWAS: simplifying post-GWAS analysis...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Épidémiologie moléculaire › Étude d'association pangénomique › SysBiolPGWAS: simplifying post-GWAS analysis...
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › SysBiolPGWAS: simplifying post-GWAS analysis...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › SysBiolPGWAS: simplifying post-GWAS analysis...
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › Multi-omique › SysBiolPGWAS: simplifying post-GWAS analysis...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Polymorphisme de nucléotide simple › SysBiolPGWAS: simplifying post-GWAS analysis...