Extended Data Fig. 6: DNA methylation clustering of primary tumor genomes.
From: The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer
a, Heatmap of methylation data following consensus clustering of primary tumors (columns) based on the standardized CpG probe intensities (M-values) of the 1% most variable CpG probes (rows; number of probes = 3,645) across all primary tumor samples (n = 126). The heatmap scale shows the beta values. Five methylation clusters were identified (MET.1—MET.5), and each patient (column) is annotated with survival group (LTS, long-term survivor; MTS, moderate-term survivor; STS, short-term survivor), age at diagnosis (quartiles), and self-reported smoking history. Tumor samples are also classified according to CCNE1 amplification (amp) status, BRCA1 alteration status, CIBERSORTx absolute (abs) immune scores (quartiles), and molecular subtype11 (C1, mesenchymal; C2, immunoreactive; C4, differentiated; C5, proliferative). Bars in the bottom panel represent the BRCA1 (orange) and BRCA2 (blue) type homologous recombination deficiency (CHORD28) scores of each tumor sample. b, Kaplan–Meier analysis of progression-free (PFS) and overall survival (OS) in patients stratified by methylation clusters. P values calculated by Mantel–Cox log-rank test and dotted lines indicate median survival in years since diagnosis.
