Protein altering and splice site mutations detected in TRAF3 using RNA-seq. (A) RNA-seq analysis of 14 cBCL tumor samples allowed detection of multiple SNVs in the TRAF3 gene. Examples of SNVs predicted (left) to cause premature truncation were detected, as well as (right) a single variant affecting a canonical splice site. (B) The splicing patterns in the terminal 4 exons of TRAF3 as detected in 7 of the RNA-seq libraries are shown. Splicing events are represented as arcs, and the number of unique reads supporting each event is shown. We observed minimal evidence for alternative splicing within TRAF3 with 2 exceptions. In the single sample with a splice acceptor site mutated (red), the affected exon appeared to be skipped in approximately half of the TRAF3 transcripts, with 32 reads supporting the skipping event and 23 reads supporting the inclusion of this exon. A second sample (brown), alternative splicing involving the same exon was observed. Neither RNA-seq nor amplicon sequencing revealed mutations affecting the canonical splice sites in this case.