The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.
Brentani H., Caballero OL., Camargo AA., da Silva AM., da Silva WA., Dias Neto E., Grivet M., Gruber A., Guimaraes PEM., Hide W., Iseli C., Jongeneel CV., Kelso J., Nagai MA., Ojopi EPB., Osorio EC., Reis EMR., Riggins GJ., Simpson AJG., de Souza S., Stevenson BJ., Strausberg RL., Tajara EH., Verjovski-Almeida S., Acencio ML., Bengtson MH., Bettoni F., Bodmer WF., Briones MRS., Camargo LP., Cavenee W., Cerutti JM., Coelho Andrade LE., Costa dos Santos PC., Ramos Costa MC., da Silva IT., Estécio MRH., Sa Ferreira K., Furnari FB., Faria M., Galante PAF., Guimaraes GS., Holanda AJ., Kimura ET., Leerkes MR., Lu X., Maciel RMB., Martins EAL., Massirer KB., Melo ASA., Mestriner CA., Miracca EC., Miranda LL., Nobrega FG., Oliveira PS., Paquola ACM., Pandolfi JRC., Campos Pardini MIDM., Passetti F., Quackenbush J., Schnabel B., Sogayar MC., Souza JE., Valentini SR., Zaiats AC., Amaral EJ., Arnaldi LAT., de Araújo AG., de Bessa SA., Bicknell DC., Ribeiro de Camaro ME., Carraro DM., Carrer H., Carvalho AF., Colin C., Costa F., Curcio C., Guerreiro da Silva IDC., Pereira da Silva N., Dellamano M., El-Dorry H., Espreafico EM., Scattone Ferreira AJ., Ayres Ferreira C., Fortes MAHZ., Gama AH., Giannella-Neto D., Giannella MLCC., Giorgi RR., Goldman GH., Goldman MHS., Hackel C., Ho PL., Kimura EM., Kowalski LP., Krieger JE., Leite LCC., Lopes A., Luna AMSC., Mackay A., Mari SKN., Marques AA., Martins WK., Montagnini A., Mourão Neto M., Nascimento ALTO., Neville AM., Nobrega MP., O'Hare MJ., Otsuka AY., Ruas de Melo AI., Paco-Larson ML., Guimarães Pereira G., Pereira da Silva N., Pesquero JB., Pessoa JG., Rahal P., Rainho CA., Rodrigues V., Rogatto SR., Romano CM., Romeiro JG., Rossi BM., Rusticci M., Guerra de Sá R., Sant' Anna SC., Sarmazo ML., Silva TCDLE., Soares FA., Sonati MDF., de Freitas Sousa J., Queiroz D., Valente V., Vettore AL., Villanova FE., Zago MA., Zalcberg H., Human Cancer Genome Project/Cancer Genome Anatomy Project Annotation Consortium None., Human Cancer Genome Project Sequencing Consortium None.
Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the information within the human genome in the fight against cancer, we have deposited some two million expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define approximately 23,500 genes, of which only approximately 1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes reveals that <1% do not have corresponding ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body. More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants (although the one-pass nature of the data necessitates careful validation) and many alternatively spliced transcripts. Although widely exploited by the scientific community, vindicating our totally open source policy, the EST data generated still provide extensive information that remains to be systematically explored, and that may further facilitate progress toward both the understanding and treatment of human cancers.