Sequencing genomic DNA reliably detects clearly pathogenic mutations like small indels, nonsense or missense mutations etc. But the effect of potential regulatory mutations can be analyzed best on mRNA/cDNA level (especially splice site mutations). I was wondering whether a capture-based gene panel like TruSightOne (which was designed for genomic DNA) would also work on cDNA (of course all the intronic probes would be wasted) or whether this would create a mess in the alignment/variant calling. Has anybody tried this? Thanks for any shared experience or educated guess :-)