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Nucleic Acids Research Advance Access originally published online on March 6, 2009
Nucleic Acids Research 2009 37(8):2607-2617; doi:10.1093/nar/gkp074
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Nucleic Acids Research, 2009, Vol. 37, No. 8 2607-2617
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

No-match ORESTES explored as tumor markers

Barbara P. Mello1, Eduardo F. Abrantes1, César H. Torres1, Ariane Machado-Lima2, Rogério da Silva Fonseca1, Dirce M. Carraro1, Ricardo R. Brentani1, Luiz F. L. Reis1 and Helena Brentani1,*

1Hospital A. C. Camargo, Rua Prof. Antônio Prudente 211, São Paulo, SP, 01509-900 and 2IME/IPq-USP - Rua do Matão, 1010, São Paulo, SP, 05508-090, Brazil

*To whom correspondence should be addressed. Tel: +55-11-2189-5000-1134; Fax: +55-11-2189-5163; Email: helena{at}lbhc.hcancer.org.br.

Received October 2, 2008. Revised December 23, 2008. Accepted January 27, 2009.

Sequencing technologies and new bioinformatics tools have led to the complete sequencing of various genomes. However, information regarding the human transcriptome and its annotation is yet to be completed. The Human Cancer Genome Project, using ORESTES (open reading frame EST sequences) methodology, contributed to this objective by generating data from about 1.2 million expressed sequence tags. Approximately 30% of these sequences did not align to ESTs in the public databases and were considered no-match ORESTES. On the basis that a set of these ESTs could represent new transcripts, we constructed a cDNA microarray. This platform was used to hybridize against 12 different normal or tumor tissues. We identified 3421 transcribed regions not associated with annotated transcripts, representing 83.3% of the platform. The total number of differentially expressed sequences was 1007. Also, 28% of analyzed sequences could represent noncoding RNAs. Our data reinforces the knowledge of the human genome being pervasively transcribed, and point out molecular marker candidates for different cancers. To reinforce our data, we confirmed, by real-time PCR, the differential expression of three out of eight potentially tumor markers in prostate tissues. Lists of 1007 differentially expressed sequences, and the 291 potentially noncoding tumor markers were provided.


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