Fig. 3: Cancer driver gene aberration in BCLM CSF cfDNA samples.

Uppermost bar plot show tumour mutational burden (TMB) by sample. Stacked bar plot below shows mutational subtype for each sample as fraction of all variants (excluding synonymous). Banners indicate primary tumour histological subtype and ER and HER2 status. Main plot shows the 35 most frequently altered cancer driver genes (alterations include non-silent somatic mutation or high-level copy number change) in CSF cfDNA as follows; Cancer Gene Census (CGC) gene altered in at least 4 cases; breast cancer driver gene (defined in Methods) altered in at least 3 cases. Right side bar plot shows percentage of CSF cfDNA samples (n = 21) with gene alterations that are unique to the CSF sample (green) or shared with any other site per individual (grey). Left side bar plot shows genomic alteration rate in the MBC cohort. See Supplementary Fig. 14 for extended data on matched plasma cfDNA, primary tumour and metastasis samples, and Supplementary Table 4 for frequently altered cancer driver genes in plasma cfDNA. Gene names are highlighted in red if genomic alteration rate was significantly different (p ≤ 0.05 by Chi-square test two-sided) in BCLM cohort compared to a publicly available dataset of 216 metastatic breast cancer (MBC cohort) samples (see Methods). Extended data in Supplementary Data 4 displays the significance values for this comparison.