Extended Data Fig. 10: Comparison of copy number alterations in tumor biopsies and matched cfDNA samples.
From: High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
(a) Heatmap of all genes where an amplification or a homozygous deletion was found in either the tumor biopsy or cfDNA. The samples are interleaved (i.e. tumor biopsy and cfDNA) and represented along the rows, whilst genes are ordered in columns relative to their genomic coordinates. (b, c) Receiver operating characteristic curves comparing (b) copy number amplifications and (c) homozygous deletions detected in the tumor biopsies with the absolute copy numbers inferred in cfDNA. Each tumor-cfDNA sample pair was used to construct individual curves. These were averaged after fitting a local polynomial regression and estimating the sensitivities over fixed intervals of specificities. In (a–c), only tumor-cfDNA sample pairs from n = 49 patients with ctDNA fraction >10% were used. (d) Four MBC patients: MSK-VB-0006, MSK-VB-0044, MSK-VB-0059 and MSK-VB-0069 with a reported amplification of ERBB2 on chromosome 17q are shown together with one NSCLC patient, MSK-VL-0044 with a reported MET amplification on chromosome 7q. The tumor biopsies are displayed on the left and the matched cfDNA are shown on the right together with the corresponding chromosome ideogram. The genomic coordinates of ERBB2 and MET are displayed by orange arrows and labelled accordingly.
