Insights for precision healthcare from the 100,000 Genomes Cancer Programme

Abstract The Cancer Programme of the 100,000 Genomes Project was a transformational UK government initiative that aimed to bring whole genome sequencing (WGS) to cancer patients and evaluate the opportunities for precision cancer care. Genomics England, in partnership with NHS England, generated whole genome analyses for 13,880 solid tumours across 33 different cancer types, and genomic data were linked with real-world health data within a secure national research environment. Here, we report the overall findings of the programme, focusing on clinical actionability and potential wider clinical significance. We found variation between cancer types in the incidence of somatic mutations of different types in genes currently recommended for standard-of-care testing. For example, 94% of glioblastoma multiforme cases had small variants and 54% had copy number aberrations (CNAs) in at least one gene recommended for clinical testing, whereas sarcoma was found to have the highest proportion of actionable structural variants (13%). We confirmed the importance of utilising pan- genomic markers, such as mutational signatures, with 51% of high grade serous ovarian cancer cases showing homologous recombination deficiency, 13% of which were associated with pathogenic germline variants, indicating the value of combined somatic and germline analyses. We also observed a significant co-occurrence of somatic small variants and CNAs in several known oncogenes including EGFR, GNAS, BRAF, and KRAS. Our findings demonstrate the value of combining genomic testing with real world clinical and treatment data to inform clinical recommendations for genomic testing in cancer, to enable survival analysis and improve understanding of the long-term effects of clinical cancer genomics on patient outcomes.