1
|
Nones K, Johnson J, Newell F, Patch AM, Thorne H, Kazakoff SH, de Luca XM, Parsons MT, Ferguson K, Reid LE, McCart Reed AE, Srihari S, Lakis V, Davidson AL, Mukhopadhyay P, Holmes O, Xu Q, Wood S, Leonard C, Beesley J, Harris JM, Barnes D, Degasperi A, Ragan MA, Spurdle AB, Khanna KK, Lakhani SR, Pearson JV, Nik-Zainal S, Chenevix-Trench G, Waddell N, Simpson PT. Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers. Ann Oncol 2019; 30:1071-1079. [PMID: 31090900 PMCID: PMC6637375 DOI: 10.1093/annonc/mdz132] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) is a powerful method for revealing the diversity and complexity of the somatic mutation burden of tumours. Here, we investigated the utility of tumour and matched germline WGS for understanding aetiology and treatment opportunities for high-risk individuals with familial breast cancer. PATIENTS AND METHODS We carried out WGS on 78 paired germline and tumour DNA samples from individuals carrying pathogenic variants in BRCA1 (n = 26) or BRCA2 (n = 22) or from non-carriers (non-BRCA1/2; n = 30). RESULTS Matched germline/tumour WGS and somatic mutational signature analysis revealed patients with unreported, dual pathogenic germline variants in cancer risk genes (BRCA1/BRCA2; BRCA1/MUTYH). The strategy identified that 100% of tumours from BRCA1 carriers and 91% of tumours from BRCA2 carriers exhibited biallelic inactivation of the respective gene, together with somatic mutational signatures suggestive of a functional deficiency in homologous recombination. A set of non-BRCA1/2 tumours also had somatic signatures indicative of BRCA-deficiency, including tumours with BRCA1 promoter methylation, and tumours from carriers of a PALB2 pathogenic germline variant and a BRCA2 variant of uncertain significance. A subset of 13 non-BRCA1/2 tumours from early onset cases were BRCA-proficient, yet displayed complex clustered structural rearrangements associated with the amplification of oncogenes and pathogenic germline variants in TP53, ATM and CHEK2. CONCLUSIONS Our study highlights the role that WGS of matched germline/tumour DNA and the somatic mutational signatures can play in the discovery of pathogenic germline variants and for providing supporting evidence for variant pathogenicity. WGS-derived signatures were more robust than germline status and other genomic predictors of homologous recombination deficiency, thus impacting the selection of platinum-based or PARP inhibitor therapy. In this first examination of non-BRCA1/2 tumours by WGS, we illustrate the considerable heterogeneity of these tumour genomes and highlight that complex genomic rearrangements may drive tumourigenesis in a subset of cases.
Collapse
Affiliation(s)
- K Nones
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J Johnson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - F Newell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - A M Patch
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - H Thorne
- kConFab Investigators, The Peter MacCallum Cancer Centre, Melbourne, VIC; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC
| | - S H Kazakoff
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - X M de Luca
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - M T Parsons
- Molecular Cancer Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - K Ferguson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - L E Reid
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - A E McCart Reed
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - S Srihari
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD
| | - V Lakis
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - A L Davidson
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD; Faculty of Medicine, The University of Queensland, Brisbane, QLD
| | - P Mukhopadhyay
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - O Holmes
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - Q Xu
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S Wood
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - C Leonard
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J Beesley
- Cancer Genetics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J M Harris
- Faculty of Health, School Biomedical Science - Queensland University of Technology, Brisbane, QLD, Australia
| | - D Barnes
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge
| | - A Degasperi
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge; Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, UK
| | - M A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD
| | - A B Spurdle
- Molecular Cancer Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - K K Khanna
- Signal Transduction Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S R Lakhani
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD; Royal Brisbane & Women's Hospital, Pathology Queensland, Brisbane, QLD, Australia
| | - J V Pearson
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S Nik-Zainal
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge; Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, UK
| | - G Chenevix-Trench
- Cancer Genetics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - N Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD.
| | - P T Simpson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD.
| |
Collapse
|