Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
| Autor: | José María López-Picazo, Ruben Pio, Francesc Subirada, Teresa Ezponda, Jackeline Agorreta, Luis M. Montuenga, Angel Rubio, David Blanco, Elena Aibar, Olga Durany, Tamara Maes, Javier Gómez-Román, Miguel Ángel Antón, Maria J. Pajares, Maria D. Lozano |
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| Jazyk: | angličtina |
| Předmět: |
Lung Neoplasms
lcsh:QH426-470 lcsh:Biotechnology Exonic splicing enhancer non-small cell lung cancer [NSCLC] Color Saccharomyces cerevisiae Biology Proteomics melanophilin or Slac2-a [Mlph] Exon lcsh:TP248.13-248.65 Genetics Humans splice RNA Messenger Cloning Molecular Oligonucleotide Array Sequence Analysis Oligonucleotide Methodology Article Alternative splicing carcinoembryonic antigen-related cell adhesion molecule 1 [Ceacam1] Genetic Variation Nucleic Acid Hybridization Reproducibility of Results small cell lung cancer [SCLC] Gene Expression Regulation Neoplastic four and a half LIM domains 1 [Fhl1] lcsh:Genetics Alternative Splicing RNA splicing sushi domain-containing protein 2 [Susd2] DNA microarray heterogeneous nuclear ribonucleoproteins [hnRNP] Algorithms Biotechnology |
| Zdroj: | BMC Genomics BMC Genomics, Vol 11, Iss 1, p 352 (2010) Dadun. Depósito Académico Digital de la Universidad de Navarra instname |
| ISSN: | 1471-2164 |
| DOI: | 10.1186/1471-2164-11-352 |
| Popis: | Background Microarrays strategies, which allow for the characterization of thousands of alternative splice forms in a single test, can be applied to identify differential alternative splicing events. In this study, a novel splice array approach was developed, including the design of a high-density oligonucleotide array, a labeling procedure, and an algorithm to identify splice events. Results The array consisted of exon probes and thermodynamically balanced junction probes. Suboptimal probes were tagged and considered in the final analysis. An unbiased labeling protocol was developed using random primers. The algorithm used to distinguish changes in expression from changes in splicing was calibrated using internal non-spliced control sequences. The performance of this splice array was validated with artificial constructs for CDC6, VEGF, and PCBP4 isoforms. The platform was then applied to the analysis of differential splice forms in lung cancer samples compared to matched normal lung tissue. Overexpression of splice isoforms was identified for genes encoding CEACAM1, FHL-1, MLPH, and SUSD2. None of these splicing isoforms had been previously associated with lung cancer. Conclusions This methodology enables the detection of alternative splicing events in complex biological samples, providing a powerful tool to identify novel diagnostic and prognostic biomarkers for cancer and other pathologies. |
| Databáze: | OpenAIRE |
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