Fig. 3: The ctDNA-based RB-LOH signature predicts clinical outcome in advanced HR+/HER2- breast cancer treated with endocrine therapy and a CDK4/6 inhibitor.

a A plasma sample was obtained from 124 patients within 48 h prior to starting endocrine therapy and CDK4/6 inhibition (CDK-Validation-1 cohort). ctDNA-based signatures were applied in plasma samples with a TF ≥3% (n = 87). b Boxplots of RB-LOH ctDNA-based signature score in patients with complete or partial response (CR/PR, n = 26), stable disease (SD, n = 32) and progressive disease (PD, n = 18). For the boxplot, center line indicates median; box limits indicate upper and lower quartiles; whiskers indicate 1.5× interquartile range. P-values (p) were determined by two-tailed unpaired t-tests. c Kaplan-Meier curves of PFS (left) and OS (right) of the RB-LOH ctDNA-based signature. Each patient group is based on tertiles. P-values (p) were determined by Log Rank Test. d Forest plots of hazard ratios (HRs) for PFS (left) and OS (right) of the RB-LOH DNA-based signature when evaluated in plasma alone (i.e., plasma–univariate; n = 87), in plasma when adjusted for TF (n = 87), in plasma when adjusted for PAM50 RNA-based subtypes (n = 53), in plasma when adjusted for TF + PAM50 + clinical variables (n = 53), in tissue alone (i.e., tissue–univariate; n = 63) and in plasma when adjusted for tissue and vice-versa (n = 28). Data are presented as the hazard ratios (HR) with error bars showing 95% confidence intervals. e Average ctDNA signal of 16 features of the RB-LOH DNA-based signature (column on the left), weight and direction of each feature (column in the middle) in the original signature as reported in Xia et al.¹⁰ and mean change of the 16 features (column on the right) in 7 patients with paired plasma samples (baseline pre-treatment vs post-CDK4/6 inhibitor treatment). f ctDNA-based signature scores of the RB-LOH signature, the Luminal A signature, the 13q14.2 RB1 locus, and TF across 7 patients with paired plasma samples (baseline vs post-CDK4/6 inhibitor treatment). P-values (p) were determined by two-tailed paired t-tests. Source data are provided as a Source Data file.