Consistent asymmetry in DNA damage artefacts across target regions in exome sequencing data

Oxidative damage can introduce G>T mutations upon DNA replication. When this damage occurs ex vivo, sequenced DNA exhibits strand asymmetry, whereby sequence alignment yields G>T mismatches without corresponding C>A mismatches on the complementary strand at a given locus. Strand asymmetry is used to identify potential sequencing artefacts in somatic variant calls in cancer sequencing projects. Consistent with previous studies, we found that the strandedness of this asymmetry is frequently shared across targeted capture regions. However, while some exome sequencing datasets displayed consistent asymmetry relative to the forward reference strand, some surprisingly showed asymmetry relative to the transcription strand. Though oxidation is the principle cause of artefactual G>T mutations, we propose that the asymmetry stems from the use of single-stranded exome capture probes, as we did not find consistent asymmetry in matched whole genome sequencing. We further propose that high levels of asymmetry can be indicative of oxidation artefacts in the reported somatic variant calls of some samples. While most analysed cohorts showed low to moderate asymmetry, in one cohort (testicular germ cell tumour), approximately half of the reported G>T somatic mutations were likely to be oxidative damage artefacts, as indicated by the extent of asymmetry in mismatches and variants.