Fig. 4: BCLM CNA landscape and gene set enrichment.

a Genome wide purity-adjusted CNA plots of all samples (CSF cfDNA (n = 21), plasma cfDNA (n = 11), primary tumour (n = 18) and metastasis (n = 8) showing frequency of copy number gain (red bars, positive y-axis) and copy number loss (blue bars, negative y-axis) at a gene level. b Volcano plots displaying comparison of CNA frequency per gene, between CSF cfDNA and primary tumours (upper panels) and between CSF cfDNA and plasma cfDNA (lower panels). Delta proportion (y-axis) is the proportional difference in CNA frequency between sample types. Significance (x-axis, -log₁₀ p-value) obtained by Chi-squared proportion test (two-sided) compares CNA event proportion per gene between sample types (source data are provided as a Source Data file). Gene names are annotated if delta proportion is ≥ ± 0.20 and -log₁₀ p-value ≥ 1.5 (as shown in Supplementary Fig. 15). c Gene set enrichment analysis. Genes enriched for alterations (including non-silent somatic mutation or high-level copy number change) in CSF cfDNA (n = 257) and/or plasma cfDNA (n = 160) vs. matched primary tumour, underwent statistical overrepresentation test using GO biological process (PANTHER). Displayed terms were retained if -log₁₀ p-value was ≥ 3.0 in either sample type (Fisher’s exact test, adjusted for multiple testing using the Benjamini-Hochberg procedure with an overall false discovery rate of < 0.05). d Focused alteration plot of genes from the indicated GO biological processes overrepresented in CSF cfDNA vs. matched primary tumour, but not in plasma cfDNA vs. primary tumour. Banners above indicate; histological subtype (primary tumour) and CDH1 mutation status of CSF cfDNA. Left panel shows gene names and chromosomal location, grouped by GO biological processes. Bars to right show the frequency of gene alteration across CSF cfDNA samples (n = 21) with ‘cfDNA only’ indicating alterations unique to CSF cfDNA or CSF and plasma cfDNA at the time of BCLM diagnosis, and ‘shared’ occurring both in CSF cfDNA and primary tumour or metastasis sample. See Supplementary Fig. 16 for extended data on matched plasma cfDNA, primary tumour and metastasis samples.