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BMC Genomics

, 11:352

First Online: 03 June 2010Received: 21 December 2009Accepted: 03 June 2010


BackgroundMicroarrays 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.

ResultsThe 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.

ConclusionsThis 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.

AbbreviationsNSCLCnon-small cell lung cancer

Ceacam1carcinoembryonic antigen-related cell adhesion molecule 1

SCLCsmall cell lung cancer

Fhl1four and a half LIM domains 1

Mlphmelanophilin or Slac2-a

Susd2sushi domain-containing protein 2

hnRNPheterogeneous nuclear ribonucleoproteins.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-11-352 contains supplementary material, which is available to authorized users.

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Autor: Ruben Pio - David Blanco - Maria Jose Pajares - Elena Aibar - Olga Durany - Teresa Ezponda - Jackeline Agorreta - Javier 


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