Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

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Abstract
Benjamin Blencowe and colleagues report the application of next-generation sequencing technology to alternative splicing in the human genome. They detect alternative splicing events in 85% of multiexon genes, and conclude that there are approximately 100,000 such events in major human tissues. We carried out the first analysis of alternative splicing complexity in human tissues using mRNA-Seq data. New splice junctions were detected in ∼20% of multiexon genes, many of which are tissue specific. By combining mRNA-Seq and EST-cDNA sequence data, we estimate that transcripts from ∼95% of multiexon genes undergo alternative splicing and that there are ∼100,000 intermediate- to high-abundance alternative splicing events in major human tissues. From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels.