In vitro dilution experiments of sheared genomic DNA for VCaP (prostate cancer) and UMUC-5 (bladder cancer) cell lines confirmed our ability to leverage Ion Torrent cfDNA WGS for recapitulation of whole-genome copy number profiles and detection of therapeutically relevant focal amplifications (including AR and EGFR amplifications), with high observed concordance with orthogonal targeted and genome-wide copy-number profiles at tumor contents as low as 5% (see Supplementary Figures 2 and 3, Methods, Supplementary Results) [46, 47]. Here, EGFR is linked to urinary bladder cancer.