Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm.

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Exon arrays have limitations in validating splicing events.
• Commercial exon-junction arrays offer improved splicing analysis.
• RNA sequencing (RNA-seq) is a reference technology for genome-wide splicing analysis.

Purpose of the Study:

• Compare the performance of RNA-seq and junction arrays for alternative splicing analysis.
• Evaluate the utility of junction arrays as an alternative to RNA-seq.
• Validate findings using Polymerase Chain Reaction (PCR) experiments.

Main Methods:

• Utilized RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array).
• Adapted the EventPointer algorithm for both RNA-seq and junction array data.
• Treated three breast cancer cell lines with CX-4945 to induce splicing changes.
• Performed over 200 PCR experiments for validation.

Main Results:

• High coherence observed between RNA-seq and junction arrays, with EventPointer correlation over 0.90.
• RNA-seq identified novel splicing events beyond probe limitations.
• Junction array detection power is equivalent to RNA-seq with up to 60 million reads.

Conclusions:

• Exon-junction arrays are a viable alternative to RNA-seq for detecting alternative splicing.
• This is particularly true when focusing on well-described transcriptional regions.
• The study provides a comprehensive comparison and validation of these two transcriptomic technologies.