Fig. 3

Somatic copy number alterations (SCNAs) and mutational signature profiles are highly concordant between circulating cell-free DNA (cfDNA) and tumor. A Heatmap of SCNAs in cfDNA and tumor. In each row, samples from each patient are aligned tumor followed by cfDNA from top to bottom as indicated on the left. B Spearman’s coefficients of correlations between cfDNA and tumor SCNA at matched or different time points. C Representative correlation of SCNAs between pre-treatment tumor (x-axis) and pre-treatment cfDNA (y-axis) in patient CL0106. Spearman’s correlation coefficient (R) and P value are indicated. D Representative correlation of SCNAs between pre-treatment cfDNA (x-axis) and post-treatment cfDNA (y-axis) in patient CL0106. Spearman’s correlation coefficient (R) and P value are indicated. E Clinical characteristics, TMB, HRD score, and mutational signature profiles in cfDNA and tumor COSMIC mutational signature version 3.2 [40] is computed and shown in the heatmap. Platinum-sensitive defined as disease progression ≥ 90 days after first-line platinum-based chemotherapy, and platinum-resistant disease progression < 90 days or during first-line chemotherapy. F Correlation of mutational signature proportions between tumor (x-axis) and cfDNA (y-axis). G Distribution of Jaccard index of mutational signatures between cfDNA and tumor at matched or different time points. H Correlation of HRD scores in pre-treatment cfDNA (x-axis) and tumor (y-axis). Abbreviations: SCNA: somatic copy number alteration; cfDNA: circulating cell-free DNA; cfDNA: circulating free DNA; SCNA: somatic copy number alteration; TMB: tumor mutational burden; HRD: homologous recombination repair deficiency; TIL: tumor infiltrating lymphocytes; CR: complete response; PR: partial response; SD: stable disease; PD: progressive disease; NE: not evaluable; NA: not assessed; COSIMIC: Catalogue of Somatic Mutations in Cancer: Psensitive: platinum sensitivity; prior IO: prior immunotherapy