Fig. 3

Counts and distribution of false-positive calls by variant types within the consensus targeted region (CTR) indicated more FFPE damage in surface FFPE samples. A The average number of false-positive calls is plotted with standard error of the mean (SEM) for four variant types within the CTR for the fresh DNA and various FFPE sample groups. The variant types were (1) indels, (2) hydrolytic deamination introduced artifacts (G:C>A:T transitions), (3) oxidative damage artifacts (G:C>T:A transversions), and (4) other FP calls. The number of samples for each sample group is inserted at the top right corner of each subplot. B Normalized G:C>A:T variants number (number of G:C>A:T variants divided by mean G:C>A:T variants in QC passed inner FFPE sample for AZ650, BRP, and TFS; number of G:C>A:T variants divided by mean G:C>A:T variants in QC failed inner FFPE sample for ILM) for each panel over three FFPE sample groups (QC-passed inner FFPE samples vs QC-failed inner FFPE samples vs surface FFPE samples)