Signatures of mutational processes in human cancer, Nature, vol.27, issue.7463, pp.415-421, 2013. ,
DOI : 10.1093/bioinformatics/btr354
Sequence analysis of mutations and translocations across breast cancer subtypes, Nature, vol.274, issue.7403, pp.405-409, 2012. ,
DOI : 10.1074/jbc.274.31.21528
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups, Nature, vol.452, pp.346-352, 2012. ,
DOI : 10.1038/nature06757
Mutational Processes Molding the Genomes of 21 Breast Cancers, Cell, vol.149, issue.5, pp.979-993, 2012. ,
DOI : 10.1016/j.cell.2012.04.024
Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype, JNCI: Journal of the National Cancer Institute, vol.107, issue.1, p.357, 2015. ,
DOI : 10.1093/jnci/dju357
A comprehensive catalogue of somatic mutations from a human cancer genome, Nature, vol.19, issue.7278, pp.191-196, 2010. ,
DOI : 10.1016/j.mrfmmm.2004.11.013
The landscape of cancer genes and mutational processes in breast cancer, Nature, vol.135, pp.400-404, 2012. ,
DOI : 10.2307/2344614
Landscape of somatic mutations in 560 breast cancer whole-genome sequences, Nature, vol.14, issue.7605, pp.47-54, 2016. ,
DOI : 10.1093/bioinformatics/btq170
URL : https://hal.archives-ouvertes.fr/hal-01388447
Molecular portraits of human breast tumours, Nature, vol.406, issue.6797, pp.747-752, 2000. ,
DOI : 10.1038/35021093
Subtypes of Breast Cancer Show Preferential Site of Relapse, Cancer Research, vol.68, issue.9, pp.3108-3114, 2008. ,
DOI : 10.1158/0008-5472.CAN-07-5644
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications, Proc. Natl Acad. Sci. USA 98, pp.10869-10874, 2001. ,
DOI : 10.1002/(SICI)1096-9896(199605)179:1<31::AID-PATH523>3.0.CO;2-O
Gene expression profiles and the TP53 mutation status are powerful prognostic markers of breast cancer, Breast Cancer Research, vol.7, issue.S2, p.30, 2007. ,
DOI : 10.1186/bcr1174
High Frequency of TP53 Mutation in BRCA1 and Sporadic Basal-like Carcinomas but not in BRCA1 Luminal Breast Tumors, Cancer Research, vol.69, issue.2, pp.663-671, 2009. ,
DOI : 10.1158/0008-5472.CAN-08-1560
Mutation of GATA3 in human breast tumors, Oncogene, vol.23, issue.46, pp.7669-7678, 2004. ,
DOI : 10.1038/sj.onc.1207966
Characterisation of amplification patterns and target genes at chromosome 11q13 in CCND1-amplified sporadic and familial breast tumours, Breast Cancer Research and Treatment, vol.49, issue.1, pp.583-594, 2012. ,
DOI : 10.1002/gcc.20713
High CCND1 amplification identifies a group of poor prognosis women with estrogen receptor positive breast cancer, International Journal of Cancer, vol.68, pp.355-360, 2010. ,
DOI : 10.1016/S0002-9440(10)65457-0
E-cadherin is a tumour/invasion suppressor gene mutated in human lobular breast cancers, EMBO J, vol.14, pp.6107-6115, 1995. ,
E-cadherin is inactivated in a majority of invasive human lobular breast cancers by truncation mutations throughout its extracellular domain, Oncogene, vol.13, pp.1919-1925, 1996. ,
The rebel angel: mutant p53 as the driving oncogene in breast cancer, Carcinogenesis, vol.33, issue.11, pp.2007-2017, 2012. ,
DOI : 10.1093/carcin/bgs232
CoMEt: a statistical approach to identify combinations of mutually exclusive alterations in cancer ,
Genomic profiling of CHEK2*1100delC-mutated breast carcinomas, BMC Cancer, vol.21, issue.1, 2015. ,
DOI : 10.1093/emboj/cdf506
URL : http://doi.org/10.1186/s12885-015-1880-y
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8???11, Nucleic Acids Research, vol.36, issue.suppl_2, pp.509-512, 2008. ,
DOI : 10.1093/nar/gkn202
Reliable prediction of T-cell epitopes using neural networks with novel sequence representations, Protein Science, vol.13, issue.5, pp.1007-1017, 2003. ,
DOI : 10.1093/oxfordjournals.molbev.a025627
TCR contact residue hydrophobicity is a hallmark of immunogenic CD8 þ T cell epitopes, Proc. Natl Acad. Sci. USA, pp.1754-1762, 2015. ,
Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior, BMC Bioinformatics, vol.10, issue.1, p.394, 2009. ,
DOI : 10.1186/1471-2105-10-394
Gene expression profiling in breast cancer: classification, prognostication, and prediction, The Lancet, vol.378, issue.9805, pp.1812-1823, 2011. ,
DOI : 10.1016/S0140-6736(11)61539-0
Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer, BMC Cancer, vol.356, issue.1, p.182, 2007. ,
DOI : 10.1056/NEJMe068292
c-myc amplification is a better prognostic factor than HER2/neu amplification in primary breast cancer, Cancer Res, vol.52, pp.1107-1113, 1992. ,
c-Myc in breast cancer, Endocrine Related Cancer, vol.7, issue.3, pp.143-164, 2000. ,
DOI : 10.1677/erc.0.0070143
The Clinical Value of Somatic TP53 Gene Mutations in 1,794 Patients with Breast Cancer, Clinical Cancer Research, vol.12, issue.4, pp.1157-1167, 2006. ,
DOI : 10.1158/1078-0432.CCR-05-1029
Somatic mutation load of estrogen receptor-positive breast tumors predicts overall survival: an analysis of genome sequence data, Breast Cancer Research and Treatment, vol.11, issue.6, pp.211-220, 2014. ,
DOI : 10.1186/gb-2010-11-6-r62
Tumor-associated inflammation as a potential prognostic tool in BRCA1/2-associated breast cancer, Human Pathology, vol.46, issue.2, pp.182-190, 2015. ,
DOI : 10.1016/j.humpath.2014.10.020
BRCA2 Mutation-associated Breast Cancers Exhibit a Distinguishing Phenotype Based on Morphology and Molecular Profiles From Tissue Microarrays, The American Journal of Surgical Pathology, vol.31, issue.1, pp.121-128, 2007. ,
DOI : 10.1097/01.pas.0000213351.49767.0f
Neoantigens in cancer immunotherapy, Science, vol.43, issue.D1, pp.69-74, 2015. ,
DOI : 10.1093/nar/gku1075
Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer, Science, vol.105, issue.51, pp.124-128, 2015. ,
DOI : 10.1073/pnas.0810114105
Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma, New England Journal of Medicine, vol.371, issue.23, pp.2189-2199, 2014. ,
DOI : 10.1056/NEJMoa1406498
Cluster analysis and display of genome-wide expression patterns, Proc. Natl Acad. Sci. USA 95, pp.14863-14868, 1998. ,
DOI : 10.1016/0092-8674(81)90326-3
A global test for groups of genes: testing association with a clinical outcome, Bioinformatics, vol.20, issue.1, pp.93-99, 2004. ,
DOI : 10.1093/bioinformatics/btg382
KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.28, issue.1, pp.27-30, 2000. ,
DOI : 10.1093/nar/28.1.27
A simple method for displaying the hydropathic character of a protein, Journal of Molecular Biology, vol.157, issue.1, pp.105-132, 1982. ,
DOI : 10.1016/0022-2836(82)90515-0
Frozen robust multiarray analysis (fRMA), Biostatistics, vol.11, issue.2, pp.242-253, 2010. ,
DOI : 10.1093/biostatistics/kxp059
Adjusting batch effects in microarray expression data using empirical Bayes methods, Biostatistics, vol.8, issue.1, pp.118-127, 2007. ,
DOI : 10.1093/biostatistics/kxj037
URL : https://academic.oup.com/biostatistics/article-pdf/8/1/118/699564/kxj037.pdf
The Icelandic Cancer Registry and from Nijmegen (The Netherlands): Margrete Schlooz-Vries Hanneke van Laarhoven, Fred Sweep and Peter Bult Benita Kiat Tee Tan from the National Cancer Centre Singapore and Singapore General Hospital is thanked for contributing patient samples for this study as are OSBREAC, the Oslo Breast Cancer Research Consortium, the Brisbane Breast Bank, Australia and the Tayside Tissue Bank, Dundee, UK. Finally, we acknowledge all members of the ICGC Breast Cancer Working Group, 14105. ,
were involved in the strategy and supervision of the project ,