De novo assembly and analysis of partial tandem duplications and gene fusions in RNA-seq data

We demonstrate a method that analyzes de novo transcriptome contigs to detect partial tandem duplications (PTDs) and fusions in RNA-seq data, reporting such chimeric transcripts in seven transcriptome sequencing datasets from a range of normal tissues and developmental stages in mouse. We estimate relative expression levels of chimeric vs. wild-type transcripts, and extend contig-based detection by scanning mouse and human transcriptome assemblies, and public sequence resources, with short ‘probe’ sequences that are specific to predicted chimeras.