| Author | Feronato, Sofia Galvão | |
| Author | Silva, Maria Luiza Matos | |
| Author | Izbicki, Rafael | |
| Author | Farias, Ticiana D. J. | |
| Author | Shigunov, Patrícia | |
| Author | Dallagiovanna, Bruno | |
| Author | Passetti, Fabio | |
| Author | Santos, Hellen Geremias dos | |
| Access date | 2022-11-07T19:27:19Z | |
| Available date | 2022-11-07T19:27:19Z | |
| Document date | 2022 | |
| Citation | 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. | en_US |
| ISSN | 2075-4426 | en_US |
| URI | https://www.arca.fiocruz.br/handle/icict/55521 | |
| Language | por | en_US |
| Publisher | MDPI | en_US |
| Rights | open access | en_US |
| Subject in Portuguese | Modelo LASSO | en_US |
| Title | Selecting genetic variants and interactions associated with amyotrophic lateral sclerosis: a Group LASSO approach | en_US |
| Type | Article | en_US |
| DOI | 10.3390/jpm12081330 | |
| Abstract | 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. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. | en_US |
| Affilliation | Universidade Federal de São Carlos. Departamento de Estatística. São Carlos, SP, Brasil. | en_US |
| Affilliation | Universidade Federal de São Carlos. Departamento de Estatística. São Carlos, SP, Brasil. | en_US |
| Affilliation | 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. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. | en_US |
| Subject | Amyotrophic Lateral Sclerosis | en_US |
| Subject | Genome-Wide Association Study | en_US |
| Subject | Polymorphism, Single Nucleotide | en_US |
| Subject | Sequence Analysis | en_US |
| Subject in Spanish | Esclerosis Amiotrófica Lateral | en_US |
| Subject in Spanish | Estudio de Asociación del Genoma Completo | en_US |
| Subject in Spanish | Polimorfismo de Nucleótido Simple | en_US |
| Subject in Spanish | Análisis de Secuencia | en_US |
| Subject in French | Sclérose latérale amyotrophique | en_US |
| Subject in French | Étude d'association pangénomique | en_US |
| Subject in French | Polymorphisme de nucléotide simple | en_US |
| Subject in French | Analyse de séquence | en_US |
| DeCS | Esclerose Amiotrófica Lateral | en_US |
| DeCS | Estudo de Associação Genômica Ampla | en_US |
| DeCS | Polimorfismo de Nucleotídeo Único | en_US |
| DeCS | Análise de Sequência | en_US |
