Fig. 3

A Quantitative levels of BRCA1 methylation (VEF value for region CpG14–34) in blood and tumor samples of breast cancer patients from whom blood samples had BRCA1 methylation levels above the blood-specific cutoff. Solid lines connect matched samples; lines and dots are colored according to tumor receptor status. Gray boxes outline patients with BRCA1 methylation not enriched (left) or enriched (right) in tumors; dotted line represents cutoff value for BRCA1 methylation positivity in tumor tissue. Both quantitative (ANOVA) and qualitative (Wilcoxon rank sum) tests confirm significant difference between subsets of blood VEF values (shown by square bracket).) Allele specificity of BRCA1 methylation in blood and tumor samples from breast cancer patients heterozygous for SNP rs799905 (N = 11). Preferential methylation of one of the alleles is evaluated and plotted as fold enrichment, with allele-specific preference in methylation in blood on the x-axis and in tumor on the y-axis. Gray shading indicates quadrants supporting concordant allelic methylation in matched blood and tumor. Data points falling in the upper-right quadrant indicate the reference allele of rs799905 to be the predominantly methylated allele in blood and tumor, while data points falling in the lower-left quadrant indicate the alternative allele of rs799905 to be the predominantly methylated allele in blood and tumor. Dots (representing matched sample pairs) are colored according to BRCA1 methylation status in tumor and blood with their size representing fold amplification of the methylated allele in tumor tissue compared to the corresponding blood sample. The crossed-out dot represents an individual with comparable methylation of both alleles in blood but predominantly the reference-allele methylated in tumor, likely reflecting the tumor to have originated from one out of two methylated lineages of normal cells (see main text). Inf, infinity value, i.e., exclusive methylation of a single allele. C Fractions of TNBC and HER2–/ER < 10% tumors (N = 72) characterized by different molecular mechanisms of BRCA1 inactivation (methylation [blue] or mutation [green]) and its potential time of emergence (constitutional/germline [solid fill] or somatic [stripe pattern])