Nat Commun. 2016 May 2;7:11383.
The topography of mutational processes in breast cancer genomes.
Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg A, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JW, Borresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, Nik-Zainal S.
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridgeshire CB10 1SD, UK; Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK; Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos NM 87545, New Mexico, USA; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos NM 87545, New Mexico, USA; Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund SE-223 81, Sweden; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam 3015CN, The Netherlands; Radboud University, Faculty of Science, Department of Molecular Biology, 6525GA Nijmegen, The Netherlands; Department of Pathology, College of Medicine, Hanyang University, Seoul 133-791, South Korea; Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium; Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, Texas 77230, USA; Department of Radiation Oncology, and department of Laboratory Medicine, Radboud university medical center, Nijmegen 6525GA, The Netherlands; Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus, Wilrijk, Belgium and Center for Oncological Research, University of Antwerp, Antwerp B-2610, Belgium; Centre for Clinical Research and School of Medicine, University of Queensland, Brisbane, Queensland 4059, Australia; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland; Department of Breast Surgical Oncology, University of Texas MD Anderson Cancer Center, 1400 Pressler Street,Houston, Texas 77030, USA; Department of Surgical Oncology, University of Dundee, Dundee DD1 9SY, UK; Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo 0310, Norway; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, Oslo 0310, Norway; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Synergie Lyon Cancer, Centre Léon Bérard, 28 rue Laennec, Lyon Cedex 08, France; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK.
Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription, DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Furthermore, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.
PMID: 27136393
DOI: 10.1038/ncomms11383
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