Supplementary Figures S1-S7 from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation

Supp. Fig. 1 Differential methylation across prostate cancer disease states Supp. Fig. 2 NEMO panel design Supp. Fig. 3 Tumor content estimation with a minimal set of informative regions Supp. Fig. 4 Scoring CRPC-NE in circulation with the phenotype evidence (PE) score Supp. Fig. 5 Probing the CRPC spectrum with NEMO Supp. Fig. 6 Clinical utility of the NEMO assay Supp. Fig. 7 Copy number estimation using the NEMO assay</p

Supplementary Tables S1-S10 from Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation

S1: Motif enrichment results around differentially methylated sites in CRPC-NE vs CRPC-Adeno solid tissue biopsy eRRBS data (Beltran2016) S2A: PSA and treatment timepoints for the PRIME cohort S2BPSA and treatment timepoints for the Wu2020 cohort S3Sequencings statistics for samples profiled with the NEMO panel (Notice that sequencing run and Dataset might differ) S4: NEMO tumor content (TC) and PE score estimation of all study samples (NEMO generated and reprocessed data) S5: Association between gene expression and proximal DNA methylation for the PDX EPIC cohort (pdx) and WCDT cohort (biopsies) S6A: Alisertib cohort survival data S6B: Chemo trial cohort survival data S7: Inclusion criteria for the two phase 2 trial cohorts S8:References of masked samples and samples sequenced in this work S9: Description of informative regions included in the NEMO panel S10: Mean CpG coverage in NEMO regions for reprocessed data (only CpG sites with at least 10x coverage are retained)</p