ArticleBMC genomics2010
Development of a novel splice array platform and its application in the identification of alternative splice variants in lung cancer.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Article
- A large-scale analysis of alternative splicing reveals a key role of QKI in lung cancer.Molecular oncology · 2016Article
- EventPointer: an effective identification of alternative splicing events using junction arrays.BMC genomics · 2016Article
- A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1.Genome research · 2016Article
- Putative Prostate Cancer Risk SNP in an Androgen Receptor-Binding Site of the Melanophilin Gene Illustrates Enrichment of Risk SNPs in Androgen Receptor Target Sites.Human mutation · 2016Article
- RNA-seq analysis of lung adenocarcinomas reveals different gene expression profiles between smoking and nonsmoking patients.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2015Article
- SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples.Nucleic acids research · 2014Article
- The RNA-binding protein QKI suppresses cancer-associated aberrant splicing.PLoS genetics · 2014Article
- Article
- Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays.Plant methods · 2012Article
- Splicing programs and cancer.Journal of nucleic acids · 2012Article
- Identification of novel deregulated RNA metabolism-related genes in non-small cell lung cancer.PloS one · 2012Article
Corrections and comments
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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