Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls

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Autor(es): dc.contributorEducation & Extension Organization (AREEO)-
Autor(es): dc.contributorShahid Bahonar University of Kerman-
Autor(es): dc.contributorUniversity of Tehran-
Autor(es): dc.contributorUniversity of Wisconsin-Madison-
Autor(es): dc.contributorVirginia Polytechnic Institute and State University-
Autor(es): dc.contributorUniversidade Estadual Paulista (Unesp)-
Autor(es): dc.creatorAmiri Roudbar, Mahmoud-
Autor(es): dc.creatorMohammadabadi, Mohammad Reza-
Autor(es): dc.creatorAyatollahi Mehrgardi, Ahmad-
Autor(es): dc.creatorAbdollahi-Arpanahi, Rostam-
Autor(es): dc.creatorMomen, Mehdi-
Autor(es): dc.creatorMorota, Gota-
Autor(es): dc.creatorBrito Lopes, Fernando [UNESP]-
Autor(es): dc.creatorGianola, Daniel-
Autor(es): dc.creatorRosa, Guilherme J. M.-
Data de aceite: dc.date.accessioned2022-02-22T00:25:02Z-
Data de disponibilização: dc.date.available2022-02-22T00:25:02Z-
Data de envio: dc.date.issued2020-12-11-
Data de envio: dc.date.issued2020-12-11-
Data de envio: dc.date.issued2020-05-01-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1038/s41437-020-0301-4-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/198613-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/198613-
Descrição: dc.descriptionThis study evaluated the use of multiomics data for classification accuracy of rheumatoid arthritis (RA). Three approaches were used and compared in terms of prediction accuracy: (1) whole-genome prediction (WGP) using SNP marker information only, (2) whole-methylome prediction (WMP) using methylation profiles only, and (3) whole-genome/methylome prediction (WGMP) with combining both omics layers. The number of SNP and of methylation sites varied in each scenario, with either 1, 10, or 50% of these preselected based on four approaches: randomly, evenly spaced, lowest p value (genome-wide association or epigenome-wide association study), and estimated effect size using a Bayesian ridge regression (BRR) model. To remove effects of high levels of pairwise linkage disequilibrium (LD), SNPs were also preselected with an LD-pruning method. Five Bayesian regression models were studied for classification, including BRR, Bayes-A, Bayes-B, Bayes-C, and the Bayesian LASSO. Adjusting methylation profiles for cellular heterogeneity within whole blood samples had a detrimental effect on the classification ability of the models. Overall, WGMP using Bayes-B model has the best performance. In particular, selecting SNPs based on LD-pruning with 1% of the methylation sites selected based on BRR included in the model, and fitting the most significant SNP as a fixed effect was the best method for predicting disease risk with a classification accuracy of 0.975. Our results showed that multiomics data can be used to effectively predict the risk of RA and identify cases in early stages to prevent or alter disease progression via appropriate interventions.-
Descrição: dc.descriptionDepartment of Animal Science Safiabad-Dezful Agricultural and Natural Resources Research and Education Center Agricultural Research Education & Extension Organization (AREEO)-
Descrição: dc.descriptionDepartment of Animal Science College of Agriculture Shahid Bahonar University of Kerman-
Descrição: dc.descriptionDepartment of Animal and Poultry Science College of Aburaihan University of Tehran, 465, Pakdasht-
Descrição: dc.descriptionDepartment of Surgical Sciences School of Veterinary Medicine University of Wisconsin-Madison-
Descrição: dc.descriptionDepartment of Animal and Poultry Sciences Virginia Polytechnic Institute and State University-
Descrição: dc.descriptionDepartment of Animal Sciences Sao Paulo State University Julio de Mesquita Filho (UNESP), Prof. Paulo Donato Castelane-
Descrição: dc.descriptionDepartment of Animal Sciences University of Wisconsin-Madison-
Descrição: dc.descriptionDepartment of Biostatistics and Medical Informatics University of Wisconsin-Madison-
Descrição: dc.descriptionDepartment of Animal Sciences Sao Paulo State University Julio de Mesquita Filho (UNESP), Prof. Paulo Donato Castelane-
Formato: dc.format658-674-
Idioma: dc.languageen-
Relação: dc.relationHeredity-
???dc.source???: dc.sourceScopus-
Título: dc.titleIntegration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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