Extended Data Fig. 4: Time series genomic analysis of ctDNA samples at recurrence.
From: Tumor evolution metrics predict recurrence beyond 10 years in locally advanced prostate cancer
(A) Distribution of the proportion of ctDNA in plasma across 9 cfDNA samples in 5 participants within fragments between 90 and 150 bp in size. (B) Trajectories of changes in variant allele frequency (VAF) across cfDNA timepoints for 5 participants. Lines and dots represent synonymous and non-synonymous mutations derived from whole exome sequencing and their impact as determined by VEP. Buffy coats represent control samples. Mutations are labelled if they belong to the targeted panel used for the primary samples (purple) or if they overlap with the IntOGen (www.intogen.org) pan-cancer driver list (grey) (n = 35 mutations, n = 100 mutations, n = 111 mutations, n = 94 mutations, n = 84 mutations, top to bottom). (C) MEDICC2 copy number alteration phylogenetic tree for FI-015 with cfDNA and primary diagnostic biopsy samples. Tips of nodes represent either the ISUP Grade group (primary diagnostic biopsies) or if the sample is a cfDNA sample (red). Time since the diagnostic biopsy is labelled next to the cfDNA nodes in years (yrs). Representative copy number profiles are shown for a single cfDNA sample and the primary diagnostic biopsy that is most related to the cfDNA. Edges are labelled with copy number alteration events (for example, WGD, whole genome duplication). Below the tree the timeline shows treatment history. Each event is rounded to the nearest 6 months. Each square represents a year. Treatment descriptions are written in shorthand (ADT = Androgen Deprivation Therapy, RT = Radiotherapy, Salv. HiFU = Salvage High-intensity Focused Ultrasound).
