Jorge S. Reis-Filho, Iain R. Macpherson, Hannah Bye, Judith M Bliss, Lucy Kilburn, Andrew M Wardley, Nicholas C. Turner, Katie Wilkinson, Mike Hubank, A Ring, Sarah Kernaghan, Sarah Hrebien, Belinda Kingston, Iris Faull, Richard D. Baird, Claire Swift, Isaac Garcia-Murillas, Richard B. Lanman, Kimberly C. Banks, Laura Moretti, Matthew Beaney, Rosalind J. Cutts, Rebecca Roylance, Giselle Walsh-Crestani, Kingston, Belinda [0000-0002-4921-4638], Kilburn, Lucy S [0000-0002-1987-7545], Moretti, Laura [0000-0003-0488-0140], Macpherson, Iain R [0000-0003-4295-8885], Baird, Richard D [0000-0001-7071-6483], Reis-Filho, Jorge S [0000-0003-2969-3173], Faull, Iris [0000-0001-6005-077X], Banks, Kimberly C [0000-0002-1290-3114], Lanman, Richard B [0000-0001-8122-4329], Garcia-Murillas, Isaac [0000-0001-8183-7969], Ring, Alistair [0000-0003-1230-2973], and Apollo - University of Cambridge Repository
The genomics of advanced breast cancer (ABC) has been described through tumour tissue biopsy sequencing, although these approaches are limited by geographical and temporal heterogeneity. Here we use plasma circulating tumour DNA sequencing to interrogate the genomic profile of ABC in 800 patients in the plasmaMATCH trial. We demonstrate diverse subclonal resistance mutations, including enrichment of HER2 mutations in HER2 positive disease, co-occurring ESR1 and MAP kinase pathway mutations in HR + HER2− disease that associate with poor overall survival (p = 0.0092), and multiple PIK3CA mutations in HR + disease that associate with short progression free survival on fulvestrant (p = 0.0036). The fraction of cancer with a mutation, the clonal dominance of a mutation, varied between genes, and within hotspot mutations of ESR1 and PIK3CA. In ER-positive breast cancer subclonal mutations were enriched in an APOBEC mutational signature, with second hit PIK3CA mutations acquired subclonally and at sites characteristic of APOBEC mutagenesis. This study utilises circulating tumour DNA analysis in a large clinical trial to demonstrate the subclonal diversification of pre-treated advanced breast cancer, identifying distinct mutational processes in advanced ER-positive breast cancer, and novel therapeutic opportunities., Circulating tumour DNA can provide useful information on disease burden. Here, the authors analysed circulating tumour DNA from 800 patients from a breast cancer clinical trial and investigate the subclonal nature of the disease, and identify DNA mutations associated with resistance and poor survival.