Background Triple-negative breast cancer (TNBC) is associated with poor survival rate and high genomic instability, generating complex tumour genomes. However, the processes generating this complexity are poorly studied over time. Here, we study the temporal dynamics of TNBC somatic mutations, revealing major transitions in tumour genome evolution, from diagnostic biopsies, through treatment, to cancer remission or recurrence. Methods Deep whole exome sequencing and CUTseq, a reduced representation whole genome sequencing approach, were performed in parallel, to comprehensively identify short nucleotide variants (SNVs), copy number alterations (CNAs) and aneuploidies genome-wide. We profiled (N=74) tumour samples from 22 patients across the course of disease, including spatially diverse samples from many tumours, allowing us to observe the gain and loss of candidate driver variants over time. Results As expected, tumour infiltrating lymphocyte (TIL) levels and residual cancer burden (RCB) score were negatively correlated, with good responses to neoadjuvant chemotherapy (NACT) seen in pre-treatment samples with high infiltration. In general, SNV mutational burden remained stable across disease progression and RCB classes. Recurrent SNVs across the cohort implicated several known TNBC driver genes in disease progression and response to treatment, with TP53, MICA, CYP2D6, BRCA1 and BRCA2 frequently altered. However, the presence of candidate driver SNVs in these genes often varied throughout a patient’s treatment, including the loss of those seen in a given driver gene in pre-treatment samples, but gain of novel variants in the same gene at later time points. Dramatic structural dynamics were seen in all tumours, including abundant CNA including chromosome arm aneuploidies seen in pre-treatment samples, followed by frequent loss of these alterations post-treatment, and their re-emergence at recurrence. Whole genome duplication (WGD) events appear to drive these dynamics, with a higher frequency of pre-treatment WGD seen in patients with the best response to NACT. Conclusions Comprehensive longitudinal profiling demonstrates the complex interplay of SNVs and copy number alterations during TNBC progression, leading to diverse evolutionary trajectories and patient outcomes. Complex mutational patterns emerge as important features during progression, with WGD events emerging as potential candidate biomarkers of response at both tumour establishment and recurrence.
Long-read methylation analysis by a nanopore sequnecer PromethION was performed using breast samples collected from breast cacner patients.
Identification of human deubiquitylating enzymes whose knock out result in hypersensitivity to DNA damaging agents, by comparing the sequence reads of ‘barcode region’ from mixed cell culture.
We propose to definitively characterise the somatic genetics of 29 matched pair cell lines through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.
We performed whole-genome sequencing of 137 tumours and their matched-normal (adjacent tissue) samples to identify tumours with high rates of somatic retrotransposition
Targetted capture and resequencing of 94 known myeloid genes across MPN trials (PT1 and Voriconazole study) as well as remaining MPN samples. New bait design Jan 2014.
Sequencing data related the PFA ependymoma study (Michealraj et al., Cell 2020), a lethal glial malignancy of the hindbrain found in babies and toddlers.
1 sample is pure plasmid DNA and 10 samples are cell pellets for genomic DNA extraction. CRISPR PCR1 and PCR2 indexing - Please use standard Kozuke primers.
Somatic mutations (burdens and signatures) and clonal dynamics in normal human tissues from the gastrointestinal tract of individuals with tumour predisposition syndromes and DNA damage repair defects.
1 sample is pure plasmid DNA and 8 samples are cell pellets for genomic DNA extraction. CRISPR PCR1 and PCR2 indexing - Please use standard Kozuke primers.
