No-match ORESTES explored as tumor markers

Abstract

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.

Identification of upregulated genes in oral squamous cell carcinomas

“…Potential new splice variants were flagged, putative new genes were revealed, noncoding intronic RNAs were found, and markers for loss of heterozygosis or gene amplification were selected. Mello et al, using ORESTES data as sequence tags, found, by cDNA microarrary analyses, differentially expressed genes in prostate tissues and confirmed these data by real‐time PCR.…”

Temporal blastemal cell gene expression analysis in the kidney reveals new Wnt and related signaling pathway genes to be essential for Wilms' tumor onset

“…32 The amplicons were extracted from 1% agarose gel and cloned using the InsTAclone kit (Fermentas Life Science , Hanover, MD, USA). For 225 genes, a cDNA clone that covered at least 80% of the respective hcrHMs was retrieved from our cDNA bank from the Human Cancer Genome Project.…”

Gene expression of peripheral blood lymphocytes may discriminate patients with schizophrenia from controls

“…Total RNA extraction and amplification besides microarray experiments are detailed in the supplemental material (Supplemental data 2), performed as described (Mello et al, 2009;Maschietto et al, 2011). Microarray data were deposited with the Gene Expression Omnibus (GEO) under accession number GSE19112.…”