Year-end Sale % OFF 
Abstract
BackgroundRNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to splicing events. Commercial arrays that include probes within exon junctions have been developed in order to overcome this problem.We compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of transcript splicing events. Three different breast cancer cell lines were treated with CX-4945, a drug that severely affects splicing. To enable a direct comparison of the two platforms, we adapted EventPointer, an algorithm that detects and labels alternative splicing events using junction arrays, to work also on RNA-seq data. Common results and discrepancies between the technologies were validated and/or resolved by over 200 PCR experiments.ResultsAs might be expected, RNA-seq appears superior in cases where the technologies disagree and is able to discover novel splicing events beyond the limitations of physical probe-sets. We observe a high degree of coherence between the two technologies, however, with correlation of EventPointer results over 0.90. Through decimation, the detection power of the junction arrays is equivalent to RNA-seq with up to 60 million reads.ConclusionsOur results suggest, therefore, that exon-junction arrays are a viable alternative to RNA-seq for detection of alternative splicing events when focusing on well-described transcriptional regions.
Highlights
RNA-seq is a reference technology for determining alternative splicing at genome-wide level
The development of exon microarrays enabled the transcriptomic study of differential splicing events, but Polymerase Chain Reaction (PCR) validation rates for identification of splice differences via microarray analysis tend to be lower than those observed for identification of
Various published works compare the performance of RNA-seq and expression microarrays for the analysis of gene expression [12, 13], but a thorough evaluation of both technologies in terms of their ability to detect differential Alternative Splicing (AS) events has yet to be presented
Summary
RNA-seq is a reference technology for determining alternative splicing at genome-wide level. We compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of transcript splicing events. The development of exon microarrays enabled the transcriptomic study of differential splicing events, but PCR validation rates for identification of splice differences via microarray analysis tend to be lower than those observed for identification of. Various published works compare the performance of RNA-seq and expression microarrays for the analysis of gene expression [12, 13], but a thorough evaluation of both technologies in terms of their ability to detect differential AS events has yet to be presented. RNA-seq technology (using the Illumina HiSeq platform) and junction arrays commercialized by Affymetrix (Human Transcriptome array, or HTA). In the former, the subject of analysis is the transcript (or isoform), whereas in the latter, the subject(s) are the splicing events themselves
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
