Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma

Detalhes bibliográficos
Autor(a) principal: Wajnberg, Gabriel
Data de Publicação: 2015
Outros Autores: Carvalho, Benilton S., Ferreira, Carlos G., Passeti, Fabio
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/13102
Resumo: Instituto Nacional de Câncer (INCA). Coordenação de Pesquisa Clínica. Unidade de Bioinformática. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Programa de Pós-Graduação em Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.
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spelling Wajnberg, GabrielCarvalho, Benilton S.Ferreira, Carlos G.Passeti, Fabio2016-03-10T14:37:15Z2016-03-10T14:37:15Z2015WAJNBERG, Gabriel; et al. Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma. BioMed Research International, v.2015, Article ID 902419, 10p, 2015.2314-6133https://www.arca.fiocruz.br/handle/icict/1310210.1155/2015/9024192314-6141engHindawi Publishing CorporationCombined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesotheliomainfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleInstituto Nacional de Câncer (INCA). Coordenação de Pesquisa Clínica. Unidade de Bioinformática. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Programa de Pós-Graduação em Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.Universidade Estadual de Campinas. Escola de Ciências Médicas. Departamento de Genética Médica. Campinas, SP, Brasil.Instituto Nacional de Câncer (INCA). Coordenação de Pesquisa Clínica. Rio de Janeiro, RJ, Brasil.Instituto Nacional de Câncer (INCA). Coordenação de Pesquisa Clínica. Unidade de Bioinformática. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Programa de Pós-Graduação em Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.Copy number variation is a class of structural genomic modifications that includes the gain and loss of a specific genomic region, which may include an entire gene. Many studies have used low-resolution techniques to identify regions that are frequently lost or amplified in cancer. Usually, researchers choose to use proprietary or non-open-source software to detect these regions because the graphical interface tends to be easier to use. In this study, we combined two different open-source packages into an innovative strategy to identify novel copy number variations and pathways associated with cancer. We used a mesothelioma and ependymoma published datasets to assess our tool. We detected previously described and novel copy number variations that are associated with cancer chemotherapy resistance. We also identified altered pathways associated with these diseases, like cell adhesion in patients with mesothelioma and negative regulation of glutamatergic synaptic transmission in ependymoma patients. In conclusion, we present a novel strategy using open-source software to identify copy number variations and altered pathways associated with cancer.EpendimomaMesotheliomaCancerEpendimomaMesoteliomaCâncerinfo: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/13102/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALfabio_passeti_etal_IOC_2015.pdffabio_passeti_etal_IOC_2015.pdfapplication/pdf1994023https://www.arca.fiocruz.br/bitstream/icict/13102/2/fabio_passeti_etal_IOC_2015.pdf7396612e0c00615eca9882df1da18d3aMD52TEXTfabio_passeti_etal_IOC_2015.pdf.txtfabio_passeti_etal_IOC_2015.pdf.txtExtracted texttext/plain39627https://www.arca.fiocruz.br/bitstream/icict/13102/3/fabio_passeti_etal_IOC_2015.pdf.txt08a87bf379b1417e7046ec2ca08d5ffeMD53icict/131022023-09-05 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dc.title.pt_BR.fl_str_mv Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma
title Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma
spellingShingle Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma
Wajnberg, Gabriel
Ependimoma
Mesothelioma
Cancer
Ependimoma
Mesotelioma
Câncer
title_short Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma
title_full Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma
title_fullStr Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma
title_full_unstemmed Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma
title_sort Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma
author Wajnberg, Gabriel
author_facet Wajnberg, Gabriel
Carvalho, Benilton S.
Ferreira, Carlos G.
Passeti, Fabio
author_role author
author2 Carvalho, Benilton S.
Ferreira, Carlos G.
Passeti, Fabio
author2_role author
author
author
dc.contributor.author.fl_str_mv Wajnberg, Gabriel
Carvalho, Benilton S.
Ferreira, Carlos G.
Passeti, Fabio
dc.subject.en.pt_BR.fl_str_mv Ependimoma
Mesothelioma
Cancer
topic Ependimoma
Mesothelioma
Cancer
Ependimoma
Mesotelioma
Câncer
dc.subject.decs.pt_BR.fl_str_mv Ependimoma
Mesotelioma
Câncer
description Instituto Nacional de Câncer (INCA). Coordenação de Pesquisa Clínica. Unidade de Bioinformática. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Programa de Pós-Graduação em Biologia Computacional e de Sistemas. Rio de Janeiro, RJ, Brasil / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.
publishDate 2015
dc.date.issued.fl_str_mv 2015
dc.date.accessioned.fl_str_mv 2016-03-10T14:37:15Z
dc.date.available.fl_str_mv 2016-03-10T14:37:15Z
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 WAJNBERG, Gabriel; et al. Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma. BioMed Research International, v.2015, Article ID 902419, 10p, 2015.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/13102
dc.identifier.issn.none.fl_str_mv 2314-6133
dc.identifier.doi.none.fl_str_mv 10.1155/2015/902419
dc.identifier.eissn.none.fl_str_mv 2314-6141
identifier_str_mv WAJNBERG, Gabriel; et al. Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma. BioMed Research International, v.2015, Article ID 902419, 10p, 2015.
2314-6133
10.1155/2015/902419
2314-6141
url https://www.arca.fiocruz.br/handle/icict/13102
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Hindawi Publishing Corporation
publisher.none.fl_str_mv Hindawi Publishing Corporation
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/13102/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/13102/2/fabio_passeti_etal_IOC_2015.pdf
https://www.arca.fiocruz.br/bitstream/icict/13102/3/fabio_passeti_etal_IOC_2015.pdf.txt
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