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

Abstract

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.

Authors:
 [1];  [2];  [3];  [2];  [2];  [2];  [2];  [4];  [2];  [2];  [5];  [2];  [6];  [7];  [8];  [9];  [10];  [9];  [3];  [11] more »;  [12];  [13];  [14];  [2];  [15];  [16];  [2];  [17];  [6];  [2];  [18];  [19];  [2];  [20];  [21];  [22];  [19];  [20];  [2];  [2];  [2];  [2];  [2];  [23];  [24];  [25];  [2];  [2];  [6];  [26];  [6];  [27];  [2];  [2];  [28];  [2];  [29];  [12];  [30];  [30];  [31];  [2];  [32];  [14];  [33];  [34];  [35];  [14];  [3];  [22];  [15];  [36];  [37];  [2];  [38];  [16];  [39];  [28];  [40];  [8];  [7];  [18];  [6];  [9];  [41];  [20];  [42];  [2] « less
+ Show Author Affiliations
  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)
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1255873
Report Number(s):
LA-UR-15-24625
Journal ID: ISSN 0028-0836
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
Journal Name: Nature (London); Journal Volume: 534; Journal Issue: 7605; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biological Science

Citation Formats

Nik-Zainal, Serena, Davies, Helen, Staaf, Johan, Ramakrishna, Manasa, Glodzik, Dominik, Zou, Xueqing, Martincorena, Inigo, Alexandrov, Ludmil B., Martin, Sancha, Wedge, David C., Van Loo, Peter, Ju, Young Seok, Smid, Marcel, Brinkman, Arie B., Morganella, Sandro, Aure, Miriam R., Lingjærde, Ole Christian, Langerod, Anita, Ringner, Markus, Ahn, Sung -Min, Boyault, Sandrine, Brock, Jane E., Broeks, Annegien, Butler, Adam, Desmedt, Christine, Dirix, Luc, Dronov, Serge, Fatima, Aquila, Foekens, John A., Gerstung, Moritz, Hooijer, Gerrit K. J., Jang, Se Jin, Jones, David R., Kim, Hyung -Yong, King, Tari A., Krishnamurthy, Savitri, Lee, Hee Jin, Lee, Jeong -Yeon, Li, Yilong, McLaren, Stuart, Menzies, Andrew, Mustonen, Ville, O’Meara, Sarah, Pauporte, Iris, Pivot, Xavier, Purdie, Colin A., Raine, Keiran, Ramakrishnan, Kamna, Rodríguez-Gonzalez, F. German, Romieu, Gilles, Sieuwerts, Anieta M., Simpson, Peter T., Shepherd, Rebecca, Stebbings, Lucy, Stefansson, Olafur A., Teague, Jon, Tommasi, Stefania, Treilleux, Isabelle, Van den Eynden, Gert G., Vermeulen, Peter, Vincent-Salomon, Anne, Yates, Lucy, Caldas, Carlos, Veer, Laura van’t, Tutt, Andrew, Knappskog, Stian, Tan, Benita Kiat Tee, Jonkers, Jos, Borg, Ake, Ueno, Naoto T., Sotiriou, Christos, Viari, Alain, Futreal, P. Andrew, Campbell, Peter J., Span, Paul N., Van Laere, Steven, Lakhani, Sunil R., Eyfjord, Jorunn E., Thompson, Alastair M., Birney, Ewan, Stunnenberg, Hendrik G., van de Vijver, Marc J., Martens, John W. M., Borresen-Dale, Anne -Lise, Richardson, Andrea L., Kong, Gu, Thomas, Gilles, and Stratton, Michael R. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. United States: N. p., 2016. Web. doi:10.1038/nature17676.
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Nik-Zainal, Serena, Davies, Helen, Staaf, Johan, Ramakrishna, Manasa, Glodzik, Dominik, Zou, Xueqing, Martincorena, Inigo, Alexandrov, Ludmil B., Martin, Sancha, Wedge, David C., Van Loo, Peter, Ju, Young Seok, Smid, Marcel, Brinkman, Arie B., Morganella, Sandro, Aure, Miriam R., Lingjærde, Ole Christian, Langerod, Anita, Ringner, Markus, Ahn, Sung -Min, Boyault, Sandrine, Brock, Jane E., Broeks, Annegien, Butler, Adam, Desmedt, Christine, Dirix, Luc, Dronov, Serge, Fatima, Aquila, Foekens, John A., Gerstung, Moritz, Hooijer, Gerrit K. J., Jang, Se Jin, Jones, David R., Kim, Hyung -Yong, King, Tari A., Krishnamurthy, Savitri, Lee, Hee Jin, Lee, Jeong -Yeon, Li, Yilong, McLaren, Stuart, Menzies, Andrew, Mustonen, Ville, O’Meara, Sarah, Pauporte, Iris, Pivot, Xavier, Purdie, Colin A., Raine, Keiran, Ramakrishnan, Kamna, Rodríguez-Gonzalez, F. German, Romieu, Gilles, Sieuwerts, Anieta M., Simpson, Peter T., Shepherd, Rebecca, Stebbings, Lucy, Stefansson, Olafur A., Teague, Jon, Tommasi, Stefania, Treilleux, Isabelle, Van den Eynden, Gert G., Vermeulen, Peter, Vincent-Salomon, Anne, Yates, Lucy, Caldas, Carlos, Veer, Laura van’t, Tutt, Andrew, Knappskog, Stian, Tan, Benita Kiat Tee, Jonkers, Jos, Borg, Ake, Ueno, Naoto T., Sotiriou, Christos, Viari, Alain, Futreal, P. Andrew, Campbell, Peter J., Span, Paul N., Van Laere, Steven, Lakhani, Sunil R., Eyfjord, Jorunn E., Thompson, Alastair M., Birney, Ewan, Stunnenberg, Hendrik G., van de Vijver, Marc J., Martens, John W. M., Borresen-Dale, Anne -Lise, Richardson, Andrea L., Kong, Gu, Thomas, Gilles, & Stratton, Michael R. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. United States. https://doi.org/10.1038/nature17676
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Nik-Zainal, Serena, Davies, Helen, Staaf, Johan, Ramakrishna, Manasa, Glodzik, Dominik, Zou, Xueqing, Martincorena, Inigo, Alexandrov, Ludmil B., Martin, Sancha, Wedge, David C., Van Loo, Peter, Ju, Young Seok, Smid, Marcel, Brinkman, Arie B., Morganella, Sandro, Aure, Miriam R., Lingjærde, Ole Christian, Langerod, Anita, Ringner, Markus, Ahn, Sung -Min, Boyault, Sandrine, Brock, Jane E., Broeks, Annegien, Butler, Adam, Desmedt, Christine, Dirix, Luc, Dronov, Serge, Fatima, Aquila, Foekens, John A., Gerstung, Moritz, Hooijer, Gerrit K. J., Jang, Se Jin, Jones, David R., Kim, Hyung -Yong, King, Tari A., Krishnamurthy, Savitri, Lee, Hee Jin, Lee, Jeong -Yeon, Li, Yilong, McLaren, Stuart, Menzies, Andrew, Mustonen, Ville, O’Meara, Sarah, Pauporte, Iris, Pivot, Xavier, Purdie, Colin A., Raine, Keiran, Ramakrishnan, Kamna, Rodríguez-Gonzalez, F. German, Romieu, Gilles, Sieuwerts, Anieta M., Simpson, Peter T., Shepherd, Rebecca, Stebbings, Lucy, Stefansson, Olafur A., Teague, Jon, Tommasi, Stefania, Treilleux, Isabelle, Van den Eynden, Gert G., Vermeulen, Peter, Vincent-Salomon, Anne, Yates, Lucy, Caldas, Carlos, Veer, Laura van’t, Tutt, Andrew, Knappskog, Stian, Tan, Benita Kiat Tee, Jonkers, Jos, Borg, Ake, Ueno, Naoto T., Sotiriou, Christos, Viari, Alain, Futreal, P. Andrew, Campbell, Peter J., Span, Paul N., Van Laere, Steven, Lakhani, Sunil R., Eyfjord, Jorunn E., Thompson, Alastair M., Birney, Ewan, Stunnenberg, Hendrik G., van de Vijver, Marc J., Martens, John W. M., Borresen-Dale, Anne -Lise, Richardson, Andrea L., Kong, Gu, Thomas, Gilles, and Stratton, Michael R. Mon . "Landscape of somatic mutations in 560 breast cancer whole-genome sequences". United States. https://doi.org/10.1038/nature17676. https://www.osti.gov/servlets/purl/1255873.
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@article{osti_1255873,
title = {Landscape of somatic mutations in 560 breast cancer whole-genome sequences},
author = {Nik-Zainal, Serena and Davies, Helen and Staaf, Johan and Ramakrishna, Manasa and Glodzik, Dominik and Zou, Xueqing and Martincorena, Inigo and Alexandrov, Ludmil B. and Martin, Sancha and Wedge, David C. and Van Loo, Peter and Ju, Young Seok and Smid, Marcel and Brinkman, Arie B. and Morganella, Sandro and Aure, Miriam R. and Lingjærde, Ole Christian and Langerod, Anita and Ringner, Markus and Ahn, Sung -Min and Boyault, Sandrine and Brock, Jane E. and Broeks, Annegien and Butler, Adam and Desmedt, Christine and Dirix, Luc and Dronov, Serge and Fatima, Aquila and Foekens, John A. and Gerstung, Moritz and Hooijer, Gerrit K. J. and Jang, Se Jin and Jones, David R. and Kim, Hyung -Yong and King, Tari A. and Krishnamurthy, Savitri and Lee, Hee Jin and Lee, Jeong -Yeon and Li, Yilong and McLaren, Stuart and Menzies, Andrew and Mustonen, Ville and O’Meara, Sarah and Pauporte, Iris and Pivot, Xavier and Purdie, Colin A. and Raine, Keiran and Ramakrishnan, Kamna and Rodríguez-Gonzalez, F. German and Romieu, Gilles and Sieuwerts, Anieta M. and Simpson, Peter T. and Shepherd, Rebecca and Stebbings, Lucy and Stefansson, Olafur A. and Teague, Jon and Tommasi, Stefania and Treilleux, Isabelle and Van den Eynden, Gert G. and Vermeulen, Peter and Vincent-Salomon, Anne and Yates, Lucy and Caldas, Carlos and Veer, Laura van’t and Tutt, Andrew and Knappskog, Stian and Tan, Benita Kiat Tee and Jonkers, Jos and Borg, Ake and Ueno, Naoto T. and Sotiriou, Christos and Viari, Alain and Futreal, P. Andrew and Campbell, Peter J. and Span, Paul N. and Van Laere, Steven and Lakhani, Sunil R. and Eyfjord, Jorunn E. and Thompson, Alastair M. and Birney, Ewan and Stunnenberg, Hendrik G. and van de Vijver, Marc J. and Martens, John W. M. and Borresen-Dale, Anne -Lise and Richardson, Andrea L. and Kong, Gu and Thomas, Gilles and Stratton, Michael R.},
abstractNote = {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.},
doi = {10.1038/nature17676},
journal = {Nature (London)},
number = 7605,
volume = 534,
place = {United States},
year = {Mon May 02 00:00:00 EDT 2016},
month = {Mon May 02 00:00:00 EDT 2016}
}
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    Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation
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    The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact
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    Molecular features of premenopausal breast cancers in Latin American women: pilot results from the PRECAMA study
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    Comprehensive Genomic Characterization of Breast Tumors with BRCA1 and BRCA2 Mutations
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    Genomic aberration based molecular signatures efficiently characterize homologous recombination deficiency in prostate cancer
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    Recurrent intragenic rearrangements of EGFR and BRAF in soft tissue tumors of infants.
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    Somatic mutations reveal asymmetric cellular dynamics in the early human embryo.
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    • Ju, Young Seok; Martincorena, Inigo; Gerstung, Moritz
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    Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome.
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    The repertoire of mutational signatures in human cancer
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    Pan-cancer analysis of whole genomes.
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    • Consortium, ICGC/TCGA Pan-Cancer Analysis Of Whole Genomes
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    PARP Inhibitors as a Therapeutic Agent for Homologous Recombination Deficiency in Breast Cancers
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    Genomic patterns of progression in smoldering multiple myeloma
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    The therapeutic significance of mutational signatures from DNA repair deficiency in cancer
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    A unified haplotype-based method for accurate and comprehensive variant calling
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    High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants
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    Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes
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    The Ras-related gene ERAS is involved in human and murine breast cancer
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    Journey’s end: the quest for BRCA-like hereditary breast cancer genes is nearly over
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    Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference
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    Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses
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    Computational approaches for discovery of mutational signatures in cancer.
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    Validating the concept of mutational signatures with isogenic cell models.
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    Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.
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    Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma
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    GDNF and the RET Receptor in Cancer: New Insights and Therapeutic Potential
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    Breast Cancer Stem Cells as Drivers of Tumor Chemoresistance, Dormancy and Relapse: New Challenges and Therapeutic Opportunities
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    Fine-mapping of 150 breast cancer risk regions identifies 191 likely target genes
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    In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data
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    Cross comparison and prognostic assessment of breast cancer multigene signatures in a large population-based contemporary clinical series
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    Learning mutational signatures and their multidimensional genomic properties with TensorSignatures
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    Feasibility and utility of a panel testing for 114 cancer‐associated genes in a clinical setting: A hospital‐based study
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    Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations
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    Tumor sequencing is useful to refine the analysis of germline variants in unexplained high-risk breast cancer families
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    The Landscape of Somatic Genetic Alterations in Breast Cancers From ATM Germline Mutation Carriers.
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    Homologous recombination DNA repair defects in PALB2-associated breast cancers.
    text, January 2019

    • Li, Anqi; Geyer, Felipe C.; Blecua, Pedro
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    HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
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    Butler enables rapid cloud-based analysis of thousands of human genomes.
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    • Yakneen, Sergei; Waszak, Sebastian M.; Group, PCAWG Technical Working
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    Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.
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    • Cortés-Ciriano, Isidro; Lee, Jake June-Koo; Xi, Ruibin
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    Single peptides and combination modalities for triple negative breast cancer
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    Breast Cancer Heterogeneity: Roles in Tumorigenesis and Therapeutic Implications
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    Discovery of naturally occurring ESR1 mutations in breast cancer cell lines modelling endocrine resistance
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    Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors
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    Piercing the dark matter: bioinformatics of long-range sequencing and mapping
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    Effects of short indels on protein structure and function in human genomes
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    Imaging mass cytometry and multiplatform genomics define the phenogenomic landscape of breast cancer
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    Cancer Target Gene Screening: a web application for breast cancer target gene screening using multi-omics data analysis
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    Detecting presence of mutational signatures in cancer with confidence
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    Hidden Markov Models Lead to Higher Resolution Maps of Mutation Signature Activity in Cancer
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    • Genome Medicine
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    Epigenetic dysregulation underpins tumorigenesis in a cutaneous tumor syndrome
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    • Davies, Helen R.; Hodgson, Kirsty; Schwalbe, Edward
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    Aneuploidy and deregulated DNA damage response define haploinsufficiency in breast tissues of BRCA2 mutation carriers
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    Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer
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    Next Generation Sequencing of Circulating Cell-Free DNA for Evaluating Mutations and Gene Amplification in Metastatic Breast Cancer
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    A practical guide for mutational signature analysis in hematological malignancies
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    Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome
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    Compromised BRCA1-PALB2 interaction is associated with breast cancer risk.
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    Pan-cancer analysis of whole genomes
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    Recurrent hotspot mutations in HRAS Q61 and PI3K-AKT pathway genes as drivers of breast adenomyoepitheliomas
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    miRNA expression changes during the course of neoadjuvant bevacizumab and chemotherapy treatment in breast cancer
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    Tumor suppressor MCPH1 regulates gene expression profiles related to malignant conversion and chromosomal assembly
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    • Tervasmäki, Anna; Mantere, Tuomo; Eshraghi, Leila
    • International Journal of Cancer, Vol. 145, Issue 8
    • DOI: 10.1002/ijc.32234

    Germline variants and somatic mutation signatures of breast cancer across populations of African and European ancestry in the US and Nigeria
    journal, June 2019

    • Wang, Shengfeng; Pitt, Jason J.; Zheng, Yonglan
    • International Journal of Cancer, Vol. 145, Issue 12
    • DOI: 10.1002/ijc.32498

    Prevalence of BRCA1 and BRCA2 gene mutations in Chinese patients with high‐risk breast cancer
    journal, April 2019

    • Wang, Xiaozhen; Liu, Haimeng; Maimaitiaili, Amina
    • Molecular Genetics & Genomic Medicine, Vol. 7, Issue 6
    • DOI: 10.1002/mgg3.677

    Genomic characteristics of trastuzumab-resistant Her2-positive metastatic breast cancer
    journal, February 2017

    • de Oliveira Taveira, Mateus; Nabavi, Sheida; Wang, Yuker
    • Journal of Cancer Research and Clinical Oncology, Vol. 143, Issue 7
    • DOI: 10.1007/s00432-017-2358-x

    Histone methyltransferases regulate the transcriptional expression of ERα and the proliferation of tamoxifen-resistant breast cancer cells
    journal, January 2020

    Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy
    journal, August 2016

    • Zhang, Weiguo; Mao, Jian-Hua; Zhu, Wei
    • Nature Communications, Vol. 7, Issue 1
    • DOI: 10.1038/ncomms12619

    Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration
    journal, September 2016

    • Smid, Marcel; Rodríguez-González, F. Germán; Sieuwerts, Anieta M.
    • Nature Communications, Vol. 7, Issue 1
    • DOI: 10.1038/ncomms12910

    Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B
    journal, December 2016

    • Shi, Ke; Carpenter, Michael A.; Banerjee, Surajit
    • Nature Structural & Molecular Biology, Vol. 24, Issue 2
    • DOI: 10.1038/nsmb.3344

    Comprehensive detection of recurring genomic abnormalities: a targeted sequencing approach for multiple myeloma
    journal, December 2019

    • Yellapantula, Venkata; Hultcrantz, Malin; Rustad, Even H.
    • Blood Cancer Journal, Vol. 9, Issue 12
    • DOI: 10.1038/s41408-019-0264-y

    BRCA1/2 testing: therapeutic implications for breast cancer management
    journal, June 2018

    Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development
    journal, February 2019

    • Dorssers, Lambert C. J.; Gillis, Ad J. M.; Stoop, Hans
    • British Journal of Cancer, Vol. 120, Issue 4
    • DOI: 10.1038/s41416-019-0381-1

    Genomic patterns of progression in smoldering multiple myeloma
    journal, August 2018

    The therapeutic significance of mutational signatures from DNA repair deficiency in cancer
    journal, August 2018

    Clonal replacement and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy
    journal, February 2019

    • Caswell-Jin, Jennifer L.; McNamara, Katherine; Reiter, Johannes G.
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-019-08593-4

    Breast cancer quantitative proteome and proteogenomic landscape
    journal, April 2019

    • Johansson, Henrik J.; Socciarelli, Fabio; Vacanti, Nathaniel M.
    • Nature Communications, Vol. 10, Issue 1
    • DOI: 10.1038/s41467-019-09018-y

    Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets
    journal, July 2019

    Detailed modeling of positive selection improves detection of cancer driver genes
    journal, July 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

    Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study
    journal, September 2019

    Evaluation of site-specific homologous recombination activity of BRCA1 by direct quantitation of gene editing efficiency
    journal, February 2019

    Co-regulated gene expression of splicing factors as drivers of cancer progression
    journal, April 2019

    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

    • Vallon-Christersson, Johan; Häkkinen, Jari; Hegardt, Cecilia
    • Scientific Reports, Vol. 9, Issue 1
    • DOI: 10.1038/s41598-019-48570-x

    Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors
    journal, February 2017

    • Marotta, Michael; Onodera, Taku; Johnson, Jeffrey
    • Scientific Reports, Vol. 7, Issue 1
    • DOI: 10.1038/srep41921

    Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes
    journal, August 2019

    • Agarwal, Ipsita; Przeworski, Molly
    • Proceedings of the National Academy of Sciences, Vol. 116, Issue 36
    • DOI: 10.1073/pnas.1900714116

    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

    • Mandelker, Diana; Kumar, Rahul; Pei, Xin
    • JNCI Cancer Spectrum, Vol. 3, Issue 2
    • DOI: 10.1093/jncics/pkz027

    The BioGRID interaction database: 2017 update
    journal, December 2016

    • Chatr-aryamontri, Andrew; Oughtred, Rose; Boucher, Lorrie
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw1102

    Rev1 is a base excision repair enzyme with 5′-deoxyribose phosphate lyase activity
    journal, September 2016

    • Prasad, Rajendra; Poltoratsky, Vladimir; Hou, Esther W.
    • Nucleic Acids Research, Vol. 44, Issue 22
    • DOI: 10.1093/nar/gkw869

    Short inverted repeats contribute to localized mutability in human somatic cells
    journal, August 2017

    • Zou, Xueqing; Morganella, Sandro; Glodzik, Dominik
    • Nucleic Acids Research, Vol. 45, Issue 19
    • DOI: 10.1093/nar/gkx731

    Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures
    journal, May 2018

    • Lee, Jongkeun; Lee, Andy Jinseok; Lee, June-Koo
    • Nucleic Acids Research, Vol. 46, Issue W1
    • DOI: 10.1093/nar/gky406

    WITER: a powerful method for estimation of cancer-driver genes using a weighted iterative regression modelling background mutation counts
    journal, July 2019

    • Jiang, Lin; Zheng, Jingjing; Kwan, Johnny S. H.
    • Nucleic Acids Research, Vol. 47, Issue 16
    • DOI: 10.1093/nar/gkz566

    Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks
    posted_content, April 2017

    • Atak, Zeynep Kalender; Imrichova, Hana; Svetlichnyy, Dmitry
    • bioRxiv
    • DOI: 10.1101/130641

    Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability
    journal, May 2018

    • Jing, Anqi; Vizeacoumar, Frederick S.; Parameswaran, Sreejit
    • npj Systems Biology and Applications
    • DOI: 10.1101/333633

    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

    • Law, Emily K.; Sieuwerts, Anieta M.; LaPara, Kelly
    • Science Advances, Vol. 2, Issue 10
    • DOI: 10.1126/sciadv.1601737

    Interchromosomal Translocations as a Means to Map Chromosome Territories in Breast Cancer
    journal, January 2019

    Identification of coding and non-coding mutational hotspots in cancer genomes
    journal, January 2017

    Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls
    journal, June 2017

    • Buckley, Alexandra R.; Standish, Kristopher A.; Bhutani, Kunal
    • BMC Genomics, Vol. 18, Issue 1
    • DOI: 10.1186/s12864-017-3770-y

    Up-regulation of ceRNA TINCR by SP1 contributes to tumorigenesis in breast cancer
    journal, April 2018

    CoMutPlotter: a web tool for visual summary of mutations in cancer cohorts
    journal, July 2019

    Comprehensive evaluation of methods to assess overall and cell-specific immune infiltrates in breast cancer
    journal, December 2019

    • Nederlof, Iris; De Bortoli, Davide; Bareche, Yacine
    • Breast Cancer Research, Vol. 21, Issue 1
    • DOI: 10.1186/s13058-019-1239-4

    Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity
    journal, September 2016

    Integrative analysis of genomic alterations in triple-negative breast cancer in association with homologous recombination deficiency
    journal, June 2017

    High expression of the vacuole membrane protein 1 (VMP1) is a potential marker of poor prognosis in HER2 positive breast cancer
    journal, August 2019

    Transcriptional regulation of normal human mammary cell heterogeneity and its perturbation in breast cancer
    journal, January 2019

    Reviewing the characteristics of BRCA and PALB2-related cancers in the precision medicine era
    journal, January 2019

    • Macedo, Gabriel S.; Alemar, Barbara; Ashton-Prolla, Patricia
    • Genetics and Molecular Biology, Vol. 42, Issue 1 suppl 1
    • DOI: 10.1590/1678-4685-gmb-2018-0104

    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

    • Encinas, Giselly; Sabelnykova, Veronica Y.; de Lyra, Eduardo Carneiro
    • Oncotarget, Vol. 9, Issue 32
    • DOI: 10.18632/oncotarget.25123

    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

    • McVeigh, Terri P.; Kerin, Michael J.
    • Breast Cancer: Targets and Therapy, Vol. Volume 9
    • DOI: 10.2147/bctt.s109847

    ‘Omics Approaches to Explore the Breast Cancer Landscape
    journal, January 2020

    • Parsons, Joseph; Francavilla, Chiara
    • Frontiers in Cell and Developmental Biology, Vol. 7
    • DOI: 10.3389/fcell.2019.00395

    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

    • Panchy, Nicholas; Azeredo-Tseng, Cassandra; Luo, Michael
    • Frontiers in Oncology, Vol. 9
    • DOI: 10.3389/fonc.2019.01479

    GDNF and the RET Receptor in Cancer: New Insights and Therapeutic Potential
    journal, January 2019

    CNV Detection from Circulating Tumor DNA in Late Stage Non-Small Cell Lung Cancer Patients
    journal, November 2019

    Targeting DNA Replication Stress for Cancer Therapy
    journal, August 2016

    Breast Cancer Brain Metastases: Clonal Evolution in Clinical Context
    journal, January 2017

    • Saunus, Jodi; McCart Reed, Amy; Lim, Zhun
    • International Journal of Molecular Sciences, Vol. 18, Issue 1
    • DOI: 10.3390/ijms18010152

    Non-Coding RNAs in Breast Cancer: Intracellular and Intercellular Communication
    journal, December 2018

    Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage
    journal, August 2016

    • Stork, Caroline Townsend; Bocek, Michael; Crossley, Madzia P.
    • eLife, Vol. 5
    • DOI: 10.7554/elife.17548

    A sequential Monte Carlo algorithm for inference of subclonal structure in cancer
    text, January 2019

    • Ogundijo, Oyetunji Enoch; Zhu, Kaiyi; Wang, Xiaodong
    • Columbia University
    • DOI: 10.7916/d8-cj4c-q275
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