Figure 3.

Mutational processes associated with HDM. (A) Two mutational patterns that are significantly higher in patients after HDM treatment were identified by de novo mutational signature analysis. Both mutational patterns are highly similar to that in COSMIC SBS3. Six possible substitutions (C→A, C→G, C→T, T→A, T→C, and T→G) of pyrimidines have been illustrated for the bases from 5′ to 3′, which creates 96 (4 × 6 × 4) possible contexts. Color coding was used to separate 6 possible options and the relative contribution of each context (x-axis) is given on the y-axis. Etiology of each signature is estimated by using their cosine distance to published SBS signatures in COSMIC mutational signatures data files. (B) Absolute (right) and relative (left) contributions (y-axis) of single nucleotide mutational signatures (SBS) and ID signature in the RVD-alone and RVD + HDM groups (x-axis in each panel). (C) De novo extracted ID signature that is significantly higher in the HDM group. Small indels were separated into 84 possible options and color coded by major event classification. Single–base pair deletions (orange) and insertions (green) are further broken down into groups based on the homopolymer (repeating the same base after the indel) length. Insertions (blue color shades) and deletions (red color shades) that are 2, 3, 4, or 5 bp or longer were separated into subgroups based on repeated sequence of event on the 3′ end of each sequence. Deletions that have microhomology (presence of the same short sequence) on either the 5′ or 3′ site of the event (purple shades) were also separated into subgroups based on the lengths of the deleted sequence and microhomology site. Similar to SBS signatures, cosine distance to published ID signatures on the COSMIC website was calculated by downloading the ID signature database using the GRCh38 genome.