Cartoon showing workflow for phylogenetic reconstruction. Multiregion whole-exome sequencing data from MSH6-proficient and MSH6-deficient microdissected patches (n = 22 tumors, between two and six patches per patient) are used to generate a binary SNV matrix to infer phylogenies using the maximum parsimony method (PAUP package). Scale bars indicate branch length and evolutionary distance expressed as substitution burden. The read length distribution of the MSH6 and MSH3 homopolymers is plotted separately (MSIsensor package) and compared against the reference MSH6 and MSH3 IHC of the input sample for verification. Finally, MSH6 labeling is overlaid on the phylogeny to reconstruct homopolymer evolution.
