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Title: Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer
Authors: Reis, Eduardo M.
Ojopi, Elida PB
Alberto, Fernando L.
Rahal, Paula
Tsukumo, Fernando
Mancini, Ulises M.
Guimaraes, Gustavo Stuani [UNIFESP]
Thompson, Gloria MA
Camacho, Cleber [UNIFESP]
Miracca, Elisabete
Carvalho, Andre L.
Machado, Abimael A.
Paquola, Apuã CM
Cerutti, Janete M. [UNIFESP]
Silva, Aline M. da
Pereira, Gonçalo G.
Valentini, Sandro R
Nagai, Maria A.
Kowalski, Luiz Paulo
Verjovski-Almeida, Sergio
Tajara, Eloiza H.
Dias-Neto, Emmanuel
Bengtson, Mario H.
Canevari, Renata A.
Carazzolle, Marcelo F.
Colin, Christian
Costa, Fernando F.
Costa, Maria Cristina
Estecio, Marcos R.
Esteves, Leda Isabel
Federico, Miriam H.
Guimaraes, Pedro Edson
Hackel, Christine
Kimura, Edna T.
Leoni, Suzana G.
Maciel, Ru M.
Maistro, Simone
Mangone, Flavia R.
Massirer, Katlin B.
Matsuo, Silvia E.
Nobrega, Francisco G.
Nobrega, Marina Pasetto
Nunes, Diana Noronha
Nunes, Fabio
Pandolfi, Jose Rodrigo
Pardini, Maria Inês
Pasini, Fatima Solange
Peres, Tarcisio
Rainho, Claudia Aparecida
Reis, Patricia P. dos
Rodrigus-Lisoni, Flavia Cristina
Rogatto, Silvia Regina
Santos, Andrey dos
Santos, Paulo C. dos
Sogayar, Mari Cleide
Zanelli, Cleslei F.
Head and Neck Annotation Consortiu
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
Issue Date: 1-Mar-2005
Publisher: Amer Assoc Cancer Research
Citation: Cancer Research. Philadelphia: Amer Assoc Cancer Research, v. 65, n. 5, p. 1693-1699, 2005.
Abstract: 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.
ISSN: 0008-5472
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