Fig. 8: Comparison of WGS data from matched fresh frozen tumor tissue and cfDNA.

a Coverage values ordered by estimated tumor context in cfDNA. b Estimates of tumor content. c Barplots showing the proportion of de novo mutation calls in cfDNA that are present in the matched fresh frozen tumor broken down by variant type. cfDNA samples with no high-confidence SVs denoted with an asterisk. d Genome-wide distribution and mutation patterns of matched fresh frozen (left) and cfDNA (right) samples for H158182. Circos plots are shown as described in Fig. 6. e Individual-level clonality analysis for H158182. (left) Scatterplot of cancer cell fraction (CCF) values for all substitutions color-coded by the estimated cluster. (middle) Phylogenetic tree representation of clusters annotated with clinically relevant variants. (right) Clone-level mutational signature analysis showing the proportion of mutations attributed to each mutational signature with total numbers of mutations in each cluster shown on the right. Whereas drivers associated with these clones could not be determined, cfDNA-specific SNV calls recapitulated mutation signatures in the FF sample, and were enriched for platinum-associated mutational signatures pointing to the existence of therapy-exposed tumor subclones in circulation. (repeat deletion: repeat-mediated deletion, m-homology: microhomology-mediated deletion, deletion other: all other deletions, TRA: translocation, DUP: duplication, DEL: deletion, INV: inversion). Source data for panels a, b are provided in Supplementary Data 11. Source data for panel c are provided at the data repository. Raw data for panels d, e can be accessed at the dbGAP study.