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Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer
Authors: Pio, R. (Rubén)
Blanco, D. (D.)
Pajares, M.J. (María José)
Aibar, E. (Elena)
Durany, O. (O.)
Ezponda, T. (T.)
Agorreta, J. (Jackeline)
Gomez-Roman, J. (J.)
Anton, M.A. (M.A.)
Rubio, A. (Ángel)
Lozano, M.D. (María Dolores)
Lopez-Picazo, J.M. (José M.)
Subirada, F. (Francesc)
Maes, T. (Tamara)
Montuenga, L.M. (Luis M.)
Keywords: NSCLC: non-small cell lung cancer
Ceacam1: carcinoembryonic antigen-related cell adhesion molecule 1
SCLC: small cell lung cancer
Ceacam1: carcinoembryonic antigen-related cell adhesion molecule 1
Fhl1: four and a half LIM domains 1
Mlph: melanophilin or Slac2-a
Susd2: sushi domain-containing protein 2
hnRNP: heterogeneous nuclear ribonucleoproteins
Issue Date: 3-Jun-2010
Publisher: BioMed Central
Publisher version: http://dx.doi.org/10.1186/1471-2164-11-352
ISBN: 0888-7543
Citation: Pio R, Blanco D, Pajares MJ, Aibar E, Durany O, Ezponda T, et al. Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer. BMC Genomics 2010 Jun 3;11:352.
Abstract
Abstract 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.
Permanent link: http://hdl.handle.net/10171/12913
Appears in Collections:DA - CIMA - Oncología - Biomarcadores - Artículos de Revista
DA - Ciencias - HAP - Artículos de revista

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