Response to Comment on "DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification"

Following the Comment of Stewart et al., we repeated our analysis on sequencing runs from The Cancer Genome Atlas (TCGA) using their suggested parameters. We found signs of oxidative damage in all sequence contexts and irrespective of the sequencing date, reaffirming that DNA damage affects mutation-calling pipelines in their ability to accurately identify somatic variations. Previously, we devised a metric termed the global imbalance value (GIV) to evaluate how mutagenic damage affects sequencing accuracy (1). We showed that mutagenic damage is pervasive in public sequencing datasets and confounds the identification of somatic variants with low to moderate (1 to 5%) allelic frequency. Following our publication, the principle of global imbalance was incorporated by the International Cancer Genome Consortium (ICGC) as one of five measures used to construct a quality rating for each cancer genome (2).