Extended Data Fig. 9: H3K27ac cfChIP-seq distinguishes prostate cancer subtype-specific FOXA1 binding sites.

(a) H3K4me3 cfChIP-seq signal at the FOXA1 promoter in prostate adenocarcinoma (PRAD) vs. neuroendocrine prostate cancer (NEPC) for N = 25 biologically independent samples. (b) Aggregate H3K27ac cfChIP signal at Boxplots indicate aggregate signal at the indicated sites for the indicated epigenetic features for N = 29 biologically independent samples. NEPC-FOXA1 and PRAD-FOXA1 indicate FOXA1 binding sites that are preferentially bound in neuroendocrine prostate cancer (NEPC) compared to prostate adenocarcinoma (PRAD), as described previously¹⁷. Aggregate signal at differential FOXA1 binding sites for each sample is normalized to signal at shared FOXA1 binding sites that are common to NEPC and PRAD. Wilcoxon test two-sided p-values are indicated. Boxplots indicate area under the curve for the aggregate cfChIP-seq profile for each sample. Lower, middle, and upper hinges indicate 25^th, 50^th, and 75^th percentiles; whiskers extend to 1.5 x the inter-quartile ranges (IQR).