Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer

Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer

Autor Reis, Eduardo M. Google Scholar
Ojopi, Elida PB Google Scholar
Alberto, Fernando L. Google Scholar
Rahal, Paula Google Scholar
Tsukumo, Fernando Google Scholar
Mancini, Ulises M. Google Scholar
Guimaraes, Gustavo Stuani Autor UNIFESP Google Scholar
Thompson, Gloria MA Google Scholar
Camacho, Cleber Autor UNIFESP Google Scholar
Miracca, Elisabete Google Scholar
Carvalho, Andre L. Google Scholar
Machado, Abimael A. Google Scholar
Paquola, Apuã CM Google Scholar
Cerutti, Janete M. Autor UNIFESP Google Scholar
Silva, Aline M. da Google Scholar
Pereira, Gonçalo G. Google Scholar
Valentini, Sandro R Google Scholar
Nagai, Maria A. Google Scholar
Kowalski, Luiz Paulo Google Scholar
Verjovski-Almeida, Sergio Google Scholar
Tajara, Eloiza H. Google Scholar
Dias-Neto, Emmanuel Google Scholar
Bengtson, Mario H. Google Scholar
Canevari, Renata A. Google Scholar
Carazzolle, Marcelo F. Google Scholar
Colin, Christian Google Scholar
Costa, Fernando F. Google Scholar
Costa, Maria Cristina Google Scholar
Estecio, Marcos R. Google Scholar
Esteves, Leda Isabel Google Scholar
Federico, Miriam H. Google Scholar
Guimaraes, Pedro Edson Google Scholar
Hackel, Christine Google Scholar
Kimura, Edna T. Google Scholar
Leoni, Suzana G. Google Scholar
Maciel, Ru M. Google Scholar
Maistro, Simone Google Scholar
Mangone, Flavia R. Google Scholar
Massirer, Katlin B. Google Scholar
Matsuo, Silvia E. Google Scholar
Nobrega, Francisco G. Google Scholar
Nobrega, Marina Pasetto Google Scholar
Nunes, Diana Noronha Google Scholar
Nunes, Fabio Google Scholar
Pandolfi, Jose Rodrigo Google Scholar
Pardini, Maria Inês Google Scholar
Pasini, Fatima Solange Google Scholar
Peres, Tarcisio Google Scholar
Rainho, Claudia Aparecida Google Scholar
Reis, Patricia P. dos Google Scholar
Rodrigus-Lisoni, Flavia Cristina Google Scholar
Rogatto, Silvia Regina Google Scholar
Santos, Andrey dos Google Scholar
Santos, Paulo C. dos Google Scholar
Sogayar, Mari Cleide Google Scholar
Zanelli, Cleslei F. Google Scholar
Head and Neck Annotation Consortiu Google Scholar
Instituição Universidade de São Paulo (USP)
Universidade Federal de São Paulo (UNIFESP)
Hosp Canc AC Camargo
Universidade Estadual de Campinas (UNICAMP)
Univ Estadual Paulista
Fac Med Sao Jose Rio Preto
Resumo A detailed genome mapping analysis of 213,636 expressed sequence tags (EST) derived from nontumor and tumor tissues of the oral cavity, larynx, pharynx, and thyroid was done. Transcripts matching known human genes were identified; potential new splice variants were flagged and subjected to manual curation, pointing to 788 putatively new alternative splicing isoforms, the majority (75%) being insertion events. A subset of 34 new splicing isoforms (5% of 788 events) was selected and 23 (68%) were confirmed by reverse transcription-PCR and DNA sequencing. Putative new genes were revealed, including six transcripts mapped to well-studied chromosomes such as 22, as well as transcripts that mapped to 253 intergenic regions. in addition, 2,251 noncoding intronic RNAs, eventually involved in transcriptional regulation, were found. A set of 250 candidate markers for loss of heterozygosis or gene amplification was selected by identifying transcripts that mapped to genomic regions previously known to be frequently amplified or deleted in head, neck, and thyroid tumors. Three of these markers were evaluated by quantitative reverse transcription-PCR in an independent set of individual samples. Along with detailed clinical data about tumor origin, the information reported here is now publicly available on a dedicated Web site as a resource for further biological investigation. This first in silico reconstruction of the head, neck, and thyroid transcriptomes points to a wealth of new candidate markers that can be used for future studies on the molecular basis of these tumors. Similar analysis is warranted for a number of other tumors for which large EST data sets are available.
Idioma Inglês
Data de publicação 2005-03-01
Publicado em Cancer Research. Philadelphia: Amer Assoc Cancer Research, v. 65, n. 5, p. 1693-1699, 2005.
ISSN 0008-5472 (Sherpa/Romeo, fator de impacto)
Publicador Amer Assoc Cancer Research
Extensão 1693-1699
Fonte http://dx.doi.org/10.1158/0008-5472.CAN-04-3506
Direito de acesso Acesso aberto Open Access
Tipo Artigo
Web of Science WOS:000227294600012
Endereço permanente http://repositorio.unifesp.br/handle/11600/28166

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