Fig. 3: CNA profiles in liquid biopsies reflect tumor aberrations and allow monitoring of tumor evolution.

a Comparison of CNAs detected in cfDNA versus matched tumor biopsies. Only sample pairs with tumor-derived DNA detected in cfDNA based on ichorCNA are shown (n = 29 sample pairs); four copy-number neutral sample pairs were omitted from the plot. Patients are grouped according to CNA state in cfDNA relative to the matched tumor biopsy. Gray represents CNAs detected in both cfDNA and matched tumor biopsy, orange indicates CNAs detected only in cfDNA, and turquoise represents CNAs detected only in the tumor biopsy. The CNAs detected in cfDNAs versus matched tumor biopsies are summarized in a bar plot (bottom). b CNA plot (ichorCNA) of an EwS cfDNA sample (EwS_90_1) before (middle) and after (bottom) in silico size selection to the range of 90–150 bp. A subclonal CNA on chromosome 16 (indicated by black arrows) that was clearly visible in the tumor biopsy (top) became detectable in the matched cfDNA sample only after in silico size selection. c CNA profiles (ichorCNA) of longitudinal cfDNA samples derived from the same patient (EwS_5) support the monitoring of somatic clonal evolution for individual patients. The filtered CNA profiles of samples collected at diagnosis and two subsequent relapses are shown. The day of sample collection relative to the day of diagnosis is indicated (left). Inferred chromosomal gains are shown in red, inferred deletions are shown in green, and CNA-neutral regions are shown in blue.