Fig. 2

Detection of microsatellite instability from cell-free DNA. Microsatellite unstable tumors were identified from 121 samples (105 unique patients) with ≥ 0.1 circulating tumor DNA fraction by plotting the number of mutations (Y-axis, including intronic and synonymous variants) versus the fraction of unstable microsatellite loci (X-axis). Indels and single nucleotide variants are kept separate for each sample, colored according to the right legend. The dashed vertical line at 0.10 fraction unstable microsatellites denotes the cutoff to reliably detect microsatellite instability. Two separate cell-free DNA samples were profiled for P-GZA003, and both demonstrated microsatellite instability. Note that although individual P-KLIN014, sample 20170058, demonstrated > 0.1 fraction unstable microsatellite loci, it was classified as microsatellite stable. The sample had a high circulating tumor DNA fraction (0.80), lacked an increase in number of mutations and displayed high copy-number burden, indicative of a chromosomal instability phenotype