Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approach

Detalhes bibliográficos
Autor(a) principal: Feronato, Sofia Galvão
Data de Publicação: 2022
Outros Autores: Silva, Maria Luiza Matos, Izbicki, Rafael, Farias, Ticiana D. J., Shigunov, Patrícia, Dallagiovanna, Bruno, Passetti, Fabio, Santos, Hellen Geremias dos
Tipo de documento: Artigo
Idioma: por
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/55521
Resumo: Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil.
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spelling Feronato, Sofia GalvãoSilva, Maria Luiza MatosIzbicki, RafaelFarias, Ticiana D. J.Shigunov, PatríciaDallagiovanna, BrunoPassetti, FabioSantos, Hellen Geremias dos2022-11-07T19:27:19Z2022-11-07T19:27:19Z2022FERONATO, Sofia Galvão et al. Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a group LASSO approach. J. Pers. Med., v. 12, n. 1330, p. 1–18, 2022.2075-4426https://www.arca.fiocruz.br/handle/icict/5552110.3390/jpm12081330porMDPIModelo LASSOAmyotrophic Lateral SclerosisGenome-Wide Association StudyPolymorphism, Single NucleotideSequence AnalysisEsclerosis Amiotrófica LateralEstudio de Asociación del Genoma CompletoPolimorfismo de Nucleótido SimpleAnálisis de SecuenciaSclérose latérale amyotrophiqueÉtude d'association pangénomiquePolymorphisme de nucléotide simpleAnalyse de séquenceEsclerose Amiotrófica LateralEstudo de Associação Genômica AmplaPolimorfismo de Nucleotídeo ÚnicoAnálise de SequênciaSelecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approachinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil.Universidade Federal de São Carlos. Departamento de Estatística. São Carlos, SP, Brasil.Universidade Federal de São Carlos. Departamento de Estatística. São Carlos, SP, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. / Division of Biomedical Informatics. Department of Immunology and Microbiology. University of Colorado School of Medicine. Aurora, USA.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil.Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil.Amyotrophic lateral sclerosis (ALS) is a multi-system neurodegenerative disease that affects both upper and lower motor neurons, resulting from a combination of genetic, environmental, and lifestyle factors. Usually, the association between single-nucleotide polymorphisms (SNPs) and this disease is tested individually, which leads to the testing of multiple hypotheses. In addition, this classical approach does not support the detection of interaction-dependent SNPs. We applied a two-step procedure to select SNPs and pairwise interactions associated with ALS. SNP data from 276 ALS patients and 268 controls were analyzed by a two-step group LASSO in 2000 iterations. In the first step, we fitted a group LASSO model to a bootstrap sample and a random subset of predictors (25%) from the original data set aiming to screen for important SNPs and, in the second step, we fitted a hierarchical group LASSO model to evaluate pairwise interactions. An in silico analysis was performed on a set of variables, which were prioritized according to their bootstrap selection frequency. We identified seven SNPs (rs16984239, rs10459680, rs1436918, rs1037666, rs4552942, rs10773543, and rs2241493) and two pairwise interactions (rs16984239:rs2118657 and s16984239:rs3172469) potentially involved in nervous system conservation and function. These results may contribute to the understanding of ALS pathogenesis, its diagnosis, and therapeutic strategy improvement.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/55521/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALjpm-12-01330ok.pdfjpm-12-01330ok.pdfapplication/pdf969549https://www.arca.fiocruz.br/bitstream/icict/55521/2/jpm-12-01330ok.pdf5161f441862337531af9689d8bdf5729MD52icict/555212022-11-07 16:39:07.16oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352022-11-07T19:39:07Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.en_US.fl_str_mv Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approach
title Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approach
spellingShingle Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approach
Feronato, Sofia Galvão
Modelo LASSO
Amyotrophic Lateral Sclerosis
Genome-Wide Association Study
Polymorphism, Single Nucleotide
Sequence Analysis
Esclerosis Amiotrófica Lateral
Estudio de Asociación del Genoma Completo
Polimorfismo de Nucleótido Simple
Análisis de Secuencia
Sclérose latérale amyotrophique
Étude d'association pangénomique
Polymorphisme de nucléotide simple
Analyse de séquence
Esclerose Amiotrófica Lateral
Estudo de Associação Genômica Ampla
Polimorfismo de Nucleotídeo Único
Análise de Sequência
title_short Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approach
title_full Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approach
title_fullStr Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approach
title_full_unstemmed Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approach
title_sort Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approach
author Feronato, Sofia Galvão
author_facet Feronato, Sofia Galvão
Silva, Maria Luiza Matos
Izbicki, Rafael
Farias, Ticiana D. J.
Shigunov, Patrícia
Dallagiovanna, Bruno
Passetti, Fabio
Santos, Hellen Geremias dos
author_role author
author2 Silva, Maria Luiza Matos
Izbicki, Rafael
Farias, Ticiana D. J.
Shigunov, Patrícia
Dallagiovanna, Bruno
Passetti, Fabio
Santos, Hellen Geremias dos
author2_role author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Feronato, Sofia Galvão
Silva, Maria Luiza Matos
Izbicki, Rafael
Farias, Ticiana D. J.
Shigunov, Patrícia
Dallagiovanna, Bruno
Passetti, Fabio
Santos, Hellen Geremias dos
dc.subject.other.en_US.fl_str_mv Modelo LASSO
topic Modelo LASSO
Amyotrophic Lateral Sclerosis
Genome-Wide Association Study
Polymorphism, Single Nucleotide
Sequence Analysis
Esclerosis Amiotrófica Lateral
Estudio de Asociación del Genoma Completo
Polimorfismo de Nucleótido Simple
Análisis de Secuencia
Sclérose latérale amyotrophique
Étude d'association pangénomique
Polymorphisme de nucléotide simple
Analyse de séquence
Esclerose Amiotrófica Lateral
Estudo de Associação Genômica Ampla
Polimorfismo de Nucleotídeo Único
Análise de Sequência
dc.subject.en.en_US.fl_str_mv Amyotrophic Lateral Sclerosis
Genome-Wide Association Study
Polymorphism, Single Nucleotide
Sequence Analysis
dc.subject.es.en_US.fl_str_mv Esclerosis Amiotrófica Lateral
Estudio de Asociación del Genoma Completo
Polimorfismo de Nucleótido Simple
Análisis de Secuencia
dc.subject.fr.en_US.fl_str_mv Sclérose latérale amyotrophique
Étude d'association pangénomique
Polymorphisme de nucléotide simple
Analyse de séquence
dc.subject.decs.en_US.fl_str_mv Esclerose Amiotrófica Lateral
Estudo de Associação Genômica Ampla
Polimorfismo de Nucleotídeo Único
Análise de Sequência
description Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil.
publishDate 2022
dc.date.accessioned.fl_str_mv 2022-11-07T19:27:19Z
dc.date.available.fl_str_mv 2022-11-07T19:27:19Z
dc.date.issued.fl_str_mv 2022
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv FERONATO, Sofia Galvão et al. Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a group LASSO approach. J. Pers. Med., v. 12, n. 1330, p. 1–18, 2022.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/55521
dc.identifier.issn.en_US.fl_str_mv 2075-4426
dc.identifier.doi.none.fl_str_mv 10.3390/jpm12081330
identifier_str_mv FERONATO, Sofia Galvão et al. Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a group LASSO approach. J. Pers. Med., v. 12, n. 1330, p. 1–18, 2022.
2075-4426
10.3390/jpm12081330
url https://www.arca.fiocruz.br/handle/icict/55521
dc.language.iso.fl_str_mv por
language por
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/55521/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/55521/2/jpm-12-01330ok.pdf
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repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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