Extended Data Fig. 8: Detection of ctDNA after one cycle of systemic therapy.

a, Scatterplot showing the log-fold change in ctDNA after 1 cycle of therapy measured by CAPP-Seq or PhasED-Seq for patients receiving RCHOP therapy. Dotted lines show the previously established threshold of a 2-log reduction in ctDNA for molecular response. Undetectable samples fall on the axes; the correlation coefficient represents a Spearman rho for the samples detected by both CAPP-Seq and PhasED-Seq. b, Detection rate of ctDNA samples after 1 cycle of therapy by PhasED-Seq vs CAPP-Seq. Patients with eventual disease progression are shown in red, while patients without eventual disease progression are shown in blue. c, ROC curve for detection of ctDNA after 2 cycles of treatment. Positive samples include 22 samples from patients with eventual disease progression, and therefore are known to have residual disease. Negative samples are from 4,280 tests on healthy controls as described in Extended Data Fig. 6a. d, Waterfall plot showing the change in ctDNA levels measured by CAPP-Seq after 1 cycle of first-line therapy in patients with DLBCL. Patients with undetectable ctDNA by CAPP-Seq are shown as ‘ND’ (‘not detected’), in darker colors. The colors of the bars also indicate the eventual clinical outcomes for these patients. e, A Kaplan-Meier plot showing the event-free survival for 33 DLBCL patients with undetectable ctDNA measured by CAPP-Seq after 1 cycle of therapy. f, A Kaplan-Meier plot and two-sided log-rank test showing the event-free survival of 33 patients shown in f) (undetectable ctDNA by CAPP-Seq) stratified by ctDNA detection via PhasED-Seq at this same time-point (cycle 2, day 1). g, A Kaplan-Meier plot and two-sided log-rank test showing the event-free survival for 82 patients with DLBCL stratified by ctDNA at cycle 2, day 1 separated into 3 strata – patients failing to achieve an early molecular response (red), patients with an early molecular response who still have detectable ctDNA by PhasED-Seq and/or CAPP-Seq (grey), and patients who have a stringent molecular remission (undetectable ctDNA by PhasED-Seq and CAPP-Seq; blue).