Fig. 3.

Copy number profiles are stable. Ultra-low pass whole genome sequencing (ULP-WGS) was performed on all 42 ctDNA samples and tumor fraction and copy number data derived using ichorCNA. a Genome-wide copy profile of patient RP-466, derived from ULP-WGS on liquid biopsy ctDNA, showing changes in focal event resolution resulting from shifts in tumor fraction. Dark green segments represent a copy number of 1; blue represent neutral or 2 copies, brown and red represent 3 and 4+, respectively. b Scatter plot of computed log-ratios in ULP-WGS, compared to those derived from WES or TPS data using binned read-count of on and off target bins. c Discrete copy number confusion matrix for ULP-WGS based calls at first and last time points. All samples had tumor fraction ≥10%. Genomic positions assayed between first and last time points were uniformly and randomly sampled, and discrete copy number states were capped between one and seven during initial ichorCNA analyses