Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme.

"the code is also available on gitlab ( https://gitlab com/genomicsengland/genomics_england_publications/100k_cancer_programme/ ) and has been uploaded to 10 5281/zenodo 8311292."

"Competing interests Genomics England is a company wholly owned by the UK DHSC and was created in 2013 to introduce WGS into healthcare in conjunction with NHS England. All authors affiliated with Genomics England (A. Sosinsky, J.A., C.T., S. Henderson, L.J., A.H., P.A., G.C., J.M., S.W., K.B., D.P., M.B.P., N.V., A.R.-M., D.P.-G., J.L., J.P., A. Siddiq, T.Z., T.C., O.Y., T.F., A.R., M.C. and N.M.) are, or were, salaried by or seconded to Genomics England. D.B. and C.K. are full-time employees and shareholders of Illumina. A.H. has received speaker fees from Gilead, Roche, Pfizer, Jazz, AbbVie, Incyte and Astellas. N.M. has provided consulting and advisory support for Pfizer, Guardant, Seagen and Janssen, and received speaker fees from Novartis, Pfizer and Servier outside of the submitted work. The remaining authors declare no competing interests."

"We thank the participants, who made this work possible. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited, a wholly owned company of the Department of Health and Social Care (DHSC). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council also funded the research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the NHS as part of their care and support. We are grateful for the support from Dame S. Hill and the team at NHS England for establishing and funding the 13 Genomic Medicine Centres. We thank all of the NHS Genomic Medicine Centres across England: East of England; Imperial College and West London; Greater Manchester; North Thames; Northwest Coast; North East and Cumbria; Oxford; South Thames; South West; West of England; Wessex; West Midlands; and Yorks and Humber. They enabled the NHS contribution, including the clinical return of results within the NHS in a standardized and validated format. M.C. is a National Institute for Health and Care Research (NIHR) Senior Investigator Alumnus. This work is part of the portfolio of translational research at the NIHR Biomedical Research Centres at Barts, Cambridge University Hospitals NHS Foundation Trust, Great Ormond Street Foundation NHS Trust, Manchester University NHS Foundation Trust, Newcastle Hospitals NHS Foundation Trust, Oxford University Hospitals NHS Foundation Trust, Guys and St Thomas’ NHS Foundation Trust and University College London NHS Foundation Trust. We thank the NHS Genomic Laboratory Hubs and those who worked to create the National Genomic Test Directory and undertake its annual review, and the NHS GMS. This work was made possible through the generosity of NHS patients and uses clinical data from the NHS and NHS Digital. We thank all the staff at Genomics England Ltd and the Genomics England Research Consortium members. We thank the Illumina Laboratory Services team at Hinxton for their advice and for undertaking the WGS. We thank University College London, Cancer Research Technology and the TRACERx Team for providing the lung tumor samples that were used in the WGS pipeline validation. We thank J. Chalker, Great Ormond Street Hospital for Children NHS Foundation Trust, and A. Wallace, Manchester Centre for Genomic Medicine for sharing data from the orthogonal genomic tests that were used in the WGS pipeline validation. D.C. was solely funded by a Cancer Research UK grant (no. C1298/A8362) awarded to R. Houlston at The Institute of Cancer Research UK. B.N. was funded through the Cancer Research UK Birmingham Centre award no. C17422/A25154."