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Title: Landscape of somatic mutations in 560 breast cancer whole-genome sequences

Journal Article · · Nature (London)
DOI:https://doi.org/10.1038/nature17676· OSTI ID:1255873
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  1. Wellcome Trust Sanger Institute, Cambridge (United Kingdom); Cambridge Univ. Hospitals NHS Foundation Trust, Cambridge (United Kingdom)
  2. Wellcome Trust Sanger Institute, Cambridge (United Kingdom)
  3. Lund Univ., Lund (Sweden)
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wellcome Trust Sanger Institute, Cambridge (United Kingdom)
  5. Wellcome Trust Sanger Institute, Cambridge (United Kingdom); Univ. of Leuven, Leuven (Belgium)
  6. Erasmus Univ. Medical Center, Rotterdam (The Netherlands)
  7. Radboud Univ., Nijmegen (The Netherlands)
  8. Wellcome Trust Genome Campus, Cambridge (United Kingdom)
  9. Oslo Univ. Hospital, Oslo (Norway); Univ. of Oslo, Oslo (Norway)
  10. Univ. of Oslo, Oslo (Norway)
  11. Gachon Univ. Gil Medical Center, Incheon (South Korea)
  12. Centre Leon Berard, Lyon Cedex (France)
  13. Brigham and Women's Hospital, Boston, MA (United States)
  14. The Netherlands Cancer Institute, Amsterdam (The Netherlands)
  15. Univ. Libre de Bruxelles, Brussels (Belgium)
  16. Univ. of Antwerp, Antwerp (Belgium)
  17. Dana-Farber Cancer Institute, Boston, MA (United States)
  18. Academic Medical Center, Amsterdam (The Netherlands)
  19. Ulsan Univ., Ulsan (South Korea)
  20. Hanyang Univ., Seoul (South Korea)
  21. Memorial Sloan Kettering Cancer Center, New York, NY (United States)
  22. The Univ. of Texas MD Anderson Cancer Center, Houston, TX (United States)
  23. Institut National du Cancer, Boulogne-Billancourt (France)
  24. Univ. Hospital of Minjoz, Besancon (France)
  25. Ninewells Hospital and Medical School, Dundee (United Kingdom)
  26. ICM Institut Regional du Cancer, Montpellier (France)
  27. The Univ. of Queensland, Queensland (Australia)
  28. Univ. of Iceland, Reykjavik (Iceland)
  29. IRCCS Istiuto Tumori "Giovanni Paolo II", Bari (Italy)
  30. Univ. of Antwerp, Antwerp (Belgium); GZA Hospitals Sint-Augustinus, Antwerp (Belgium)
  31. Paris Sciences Lettres Univ., Paris Cedex (France)
  32. Univ. of Cambridge, Cambridge (United Kingdom)
  33. King's College London, London (United Kingdom); Breast Cancer Now Toby Robins Research Center, London (United Kingdom)
  34. Univ. of Bergen, Bergen (Norway); Haukeland Univ. Hospital, Bergen (Norway)
  35. Singapore General Hospital (Singapore)
  36. INRIA Grenoble-Rhone-Alpes, Montbonnot-Saint Martin (France); Synergie Lyon Cancer, Lyon Cedex (France)
  37. Wellcome Trust Sanger Institute, Cambridge (United Kingdom); UT MD Anderson Cancer Center, Houston, TX (United States)
  38. Radboud Univ. Medical Center, Nijmegen (The Netherlands)
  39. The Univ. of Queensland, Queensland (Australia); The Royal Brisbane and Women's Hospital, Queensland (Australia)
  40. Ninewells Hospital and Medical School, Dundee (United Kingdom); Univ. of Texas MD Anderson Cancer Center, Houston, TX (United States)
  41. Brigham and Women's Hospital, Boston, MA (United States); Dana-Farber Cancer Institute, Boston, MA (United States)
  42. Synergie Lyon Cancer, Lyon Cedex (France)
+ Show Author Affiliations

Here, we analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC52-06NA25396
OSTI ID:
1255873
Report Number(s):
LA-UR-15-24625
Journal Information:
Nature (London), Vol. 534, Issue 7605; ISSN 0028-0836
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 1314 works
Citation information provided by
Web of Science

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A subgroup of microRNAs defines PTEN-deficient, triple-negative breast cancer patients with poorest prognosis and alterations in RB1, MYC, and Wnt signaling journal January 2019
Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing journal June 2019
SURF: integrative analysis of a compendium of RNA-seq and CLIP-seq datasets highlights complex governing of alternative transcriptional regulation by RNA-binding proteins journal June 2020
Modelling the MYC-driven normal-to-tumour switch in breast cancer journal July 2019
Breaking point: the genesis and impact of structural variation in tumours journal January 2018
De novo mutational signature discovery in tumor genomes using SparseSignatures journal June 2021
Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers journal April 2018
Reviewing the characteristics of BRCA and PALB2-related cancers in the precision medicine era journal January 2019
Computational approaches for discovery of mutational signatures in cancer. text January 2019
Validating the concept of mutational signatures with isogenic cell models. text January 2018
Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. text January 2016
Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma text January 2021
GDNF and the RET Receptor in Cancer: New Insights and Therapeutic Potential journal January 2019
Breast Cancer Stem Cells as Drivers of Tumor Chemoresistance, Dormancy and Relapse: New Challenges and Therapeutic Opportunities journal October 2019
Identifying Biomarkers to Pair with Targeting Treatments within Triple Negative Breast Cancer for Improved Patient Stratification journal November 2019
Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage journal August 2016
ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data: ascatNgs: Identifying Copy-number Alterations from Sequencing Data journal December 2016
Emerging Role of Genomics and Cell-Free DNA in Breast Cancer journal June 2019
Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration journal September 2016
Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations journal March 2018
Prognostic implications of the expression levels of different immunoglobulin heavy chain-encoding RNAs in early breast cancer journal July 2020
Fibroblast growth factor receptors as treatment targets in clinical oncology journal October 2018
The repertoire of mutational signatures in human cancer journal February 2020
Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes journal January 2020
In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data journal June 2019
Cross comparison and prognostic assessment of breast cancer multigene signatures in a large population-based contemporary clinical series journal August 2019
Onco-proteogenomics: Multi-omics level data integration for accurate phenotype prediction journal August 2017
NEAT1-containing paraspeckles: Central hubs in stress response and tumor formation journal October 2016
Next-generation sequencing: from conventional applications to breakthrough genomic analyses and precision oncology journal December 2017
Insights into BRCA Cancer Predisposition from Integrated Germline and Somatic Analyses in 7632 Cancers journal April 2019
An Integrative Framework for Detecting Structural Variations in Cancer Genomes posted_content March 2017
Candidate cancer driver mutations in superenhancers and long-range chromatin interaction networks journal December 2017
Integrated single-nucleotide and structural variation signatures of DNA-repair deficient human cancers posted_content February 2018
Learning mutational signatures and their multidimensional genomic properties with TensorSignatures posted_content June 2020
Feasibility and utility of a panel testing for 114 cancer‐associated genes in a clinical setting: A hospital‐based study journal April 2019
Relation between DNA ionization potentials, single base substitutions and pathogenic variants journal July 2019
Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations journal June 2019
Tumor sequencing is useful to refine the analysis of germline variants in unexplained high-risk breast cancer families journal April 2020
Integrative analysis of genomic alterations in triple-negative breast cancer in association with homologous recombination deficiency journal June 2017
The Landscape of Somatic Genetic Alterations in Breast Cancers From ATM Germline Mutation Carriers. text January 2018
Homologous recombination DNA repair defects in PALB2-associated breast cancers. text January 2019
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. text January 2017
Butler enables rapid cloud-based analysis of thousands of human genomes. text January 2020
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. journalarticle January 2020
A Comparison of DNA Mutation and Copy Number Profiles of Primary Breast Cancers and Paired Brain Metastases for Identifying Clinically Relevant Genetic Alterations in Brain Metastases journal May 2019
Single peptides and combination modalities for triple negative breast cancer journal October 2019
Breast Cancer Heterogeneity: Roles in Tumorigenesis and Therapeutic Implications journal February 2017
A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers journal January 2017
Discovery of naturally occurring ESR1 mutations in breast cancer cell lines modelling endocrine resistance journal November 2017
Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors journal November 2018
Piercing the dark matter: bioinformatics of long-range sequencing and mapping journal March 2018
Detecting the mutational signature of homologous recombination deficiency in clinical samples journal April 2019
Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study journal September 2019
Effects of short indels on protein structure and function in human genomes journal August 2017
Imaging mass cytometry and multiplatform genomics define the phenogenomic landscape of breast cancer journal February 2020
Cancer Target Gene Screening: a web application for breast cancer target gene screening using multi-omics data analysis journal January 2019
Detecting presence of mutational signatures in cancer with confidence journal September 2017
Hidden Markov Models Lead to Higher Resolution Maps of Mutation Signature Activity in Cancer posted_content August 2018
Epigenetic dysregulation underpins tumorigenesis in a cutaneous tumor syndrome posted_content July 2019
Aneuploidy and deregulated DNA damage response define haploinsufficiency in breast tissues of BRCA2 mutation carriers posted_content August 2019
Characterizing the allele- and haplotype-specific copy number landscape of cancer genomes at single-cell resolution with CHISEL journal November 2019
Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer journal April 2018
Coexisting genomic aberrations associated with lymph node metastasis in breast cancer journal April 2018
Novel mutations in actionable breast cancer genes by targeted sequencing in an ethnically homogenous cohort journal September 2019
Chromatin interactome mapping at 139 independent breast cancer risk signals journal January 2020
The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues journal May 2020
Next Generation Sequencing of Circulating Cell-Free DNA for Evaluating Mutations and Gene Amplification in Metastatic Breast Cancer journal February 2017
A practical guide for mutational signature analysis in hematological malignancies text January 2019
Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome text January 2019
Compromised BRCA1-PALB2 interaction is associated with breast cancer risk. text January 2017
Pan-cancer analysis of whole genomes text January 2020
Recurrent hotspot mutations in HRAS Q61 and PI3K-AKT pathway genes as drivers of breast adenomyoepitheliomas text January 2018
Genomic characteristics of trastuzumab-resistant Her2-positive metastatic breast cancer journal February 2017
Tandem Duplications May Supply the Missing Genetic Alterations in Many Triple-Negative Breast and Gynecological Cancers journal August 2018
Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B journal December 2016
Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development journal February 2019
Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy journal February 2019
Breast cancer quantitative proteome and proteogenomic landscape journal April 2019
Tumor diversity and the trade-off between universal cancer tasks journal November 2019
Constitutional variants are not associated with HER2-positive breast cancer: results from the SIGNAL/PHARE clinical cohort journal February 2017
Unique metabolic traits identify CCPAP journal April 2019
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes journal February 2020
Evaluation of site-specific homologous recombination activity of BRCA1 by direct quantitation of gene editing efficiency journal February 2019
Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors journal February 2017
Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes journal August 2019
Complex chromosomal rearrangements by single catastrophic pathogenesis in NUT midline carcinoma journal April 2017
Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers journal July 2019
The Landscape of Somatic Genetic Alterations in Breast Cancers from CHEK2 Germline Mutation Carriers journal April 2019
The BioGRID interaction database: 2017 update journal December 2016
Rev1 is a base excision repair enzyme with 5′-deoxyribose phosphate lyase activity journal September 2016
Short inverted repeats contribute to localized mutability in human somatic cells journal August 2017
Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures journal May 2018
Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability journal May 2018
BATCAVE: Calling somatic mutations with a tumor- and site-specific prior posted_content October 2019
The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer journal October 2016
CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts journal July 2019
Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity journal September 2016
Mutational mechanisms of amplifications revealed by analysis of clustered rearrangements in breast cancers. journalarticle January 2018
Targeted NGS, array-CGH, and patient-derived tumor xenografts for precision medicine in advanced breast cancer: a single-center prospective study journal October 2016
The ubiquitous ‘cancer mutational signature’ 5 occurs specifically in cancers with deleted FHIT alleles journal November 2017
Somatic mutations in early onset luminal breast cancer journal April 2018
Prediction of circRNAs Based on the DNA Methylation-Mediated Feature Sponge Function in Breast Cancer journal June 2019
Clinical use of the Oncotype DX genomic test to guide treatment decisions for patients with invasive breast cancer journal May 2017
‘Omics Approaches to Explore the Breast Cancer Landscape journal January 2020
Computational Methods for Characterizing Cancer Mutational Heterogeneity journal June 2017
Integrative Transcriptomic Analysis Reveals a Multiphasic Epithelial–Mesenchymal Spectrum in Cancer and Non-tumorigenic Cells journal January 2020
CNV Detection from Circulating Tumor DNA in Late Stage Non-Small Cell Lung Cancer Patients journal November 2019
Breast Cancer Brain Metastases: Clonal Evolution in Clinical Context journal January 2017
Diagnostic value of ultrasound combined with magnetic resonance imaging in different stages of breast cancer journal October 2018
BeWith: A Between-Within Method to Discover Relationships between Cancer Modules via Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions text January 2017

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59 BASIC BIOLOGICAL SCIENCES
Biological Science