Natural history of germline BRCA1 mutated and BRCA wild-type triple-negative breast cancer.

We report a deep next-generation sequencing (NGS) analysis of 13 sequentially sampled tumours, eight sequentially sampled circulating tumour DNA (ctDNA) and three germline DNA samples over the life history of three triple-negative breast cancer (TNBC) patients, two of whom had germline pathogenic BRCA1 mutation, to unravel tumour evolution. Tumour tissue from all timepoints and germline DNA was subjected to whole exome sequencing (WES), custom amplicon deep sequencing (30,000X) of a WES-derived somatic mutation panel, and SNP arrays for copy number variation (CNV), while whole transcriptome sequencing (RNA-Seq) was performed only on somatic tumour. There was enrichment of homologous-recombination deficiency (HRD) signature in all tumours and widespread CNV, which remained largely stable over time. Somatic tumour mutation numbers varied between patients and within each patient (range 70-216, one outlier). There was minimal mutational overlap between patients with TP53 being the sole commonly mutated gene, but there was substantial overlap in sequential samples in each patient. Each patient's tumour contained a founding ('stem') clone at diagnosis, which persisted over time, from which all other clones ('subclone') were derived ('branching evolution'), which contained mutations in well-characterized cancer-related genes like PDGFRB, ARID2, TP53 (Patient_02), TP53, BRAF, BRIP1, CSF3R (Patient_04), and TP53, APC, EZH2 (Patient_07). Including stem and subclones, tumours from all patients were polyclonal at diagnosis and during disease progression. Circulating tumour DNA (ctDNA) recapitulated most tissue-derived stem-clonal and subclonal mutations while detecting some additional subclonal mutations. RNA-Seq revealed a stable basal-like pattern, with most highly expressed variants belonging to stem clone.