METABRIC

The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (CNVs, SNPs) and acquired somatic copy number aberrations (CNAs) were associated with expression in 40% of genes, although the landscape was dominated by cis and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP, and MAP2K4. Unsupervised analysis of paired DNA/RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, ER-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration 0152hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the 0152CNA-devoid sub-group and a Basal-specific chromosome 5 deletion-driven mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic copy number aberrations on the transcriptome.

Type: Other
Archiver: EGA European Genome-Phenome Archive

10 Datasets 206 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00010000162	Illumina HT 12 IDATS	Illumina HT 12	-
EGAD00010000164	Affymetrix 6.0 CEL files	Affymetrix SNP 6.0	-
EGAD00010000210	Normalized expression data; discovery set	Illumina HT 12	1
EGAD00010000211	Normalized expression data; validation set	Illumina HT 12	-
EGAD00010000212	Normalized expression data; normals	Illumina HT 12	-
EGAD00010000213	Segmented (CBS) copy number aberrations (CNA); discovery set	Affymetrix SNP 6.0	-
EGAD00010000214	Segmented (CBS) copy number variants (CNV); discovery set	Affymetrix SNP 6.0	-
EGAD00010000215	Segmented (CBS) copy number aberrations (CNA); validation set	Affymetrix SNP 6.0	-
EGAD00010000216	Segmented (CBS) copy number variants (CNV); validation set	Affymetrix SNP 6.0	-
EGAD00010000217	Segmented (HMM) copy number aberrations (CNA); discovery set	Affymetrix SNP 6.0	-

Publications	Citations
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S, METABRIC Group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale AL, Brenton JD, Tavaré S, Caldas C, Aparicio S. Nature 486: 2012 346-352	3049
Regulation of mRNA expression in breast cancer - a cis-tematic trans-action. Verhaak RG, Mills GB. Breast Cancer Res 14: 2012 322	0
Improving breast cancer survival analysis through competition-based multidimensional modeling. Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA. PLoS Comput Biol 9: 2013 e1003047	50
The molecular diversity of Luminal A breast tumors. Ciriello G, Sinha R, Hoadley KA, Jacobsen AS, Reva B, Perou CM, Sander C, Schultz N. Breast Cancer Res Treat 141: 2013 409-420	69
The breast cancer oncogene EMSY represses transcription of antimetastatic microRNA miR-31. Viré E, Curtis C, Davalos V, Git A, Robson S, Villanueva A, Vidal A, Barbieri I, Aparicio S, Esteller M, Caldas C, Kouzarides T. Mol Cell 53: 2014 806-818	37
Systematic assessment of prognostic gene signatures for breast cancer shows distinct influence of time and ER status. Zhao X, Rødland EA, Sørlie T, Vollan HK, Russnes HG, Kristensen VN, Lingjærde OC, Børresen-Dale AL. BMC Cancer 14: 2014 211	17
Information content and analysis methods for multi-modal high-throughput biomedical data. Ray B, Henaff M, Ma S, Efstathiadis E, Peskin ER, Picone M, Poli T, Aliferis CF, Statnikov A. Sci Rep 4: 2014 4411	12
Seven In Absentia Homolog 2 (SIAH2) downregulation is associated with tamoxifen resistance in MCF-7 breast cancer cells. Interiano RB, Yang J, Harris AL, Davidoff AM. J Surg Res 190: 2014 203-209	6
Breast cancer prognosis predicted by nuclear receptor-coregulator networks. Doan TB, Eriksson NA, Graham D, Funder JW, Simpson ER, Kuczek ES, Clyne C, Leedman PJ, Tilley WD, Fuller PJ, Muscat GE, Clarke CL. Mol Oncol 8: 2014 998-1013	10
Hypomethylation of the MMP7 promoter and increased expression of MMP7 distinguishes the basal-like breast cancer subtype from other triple-negative tumors. Sizemore ST, Sizemore GM, Booth CN, Thompson CL, Silverman P, Bebek G, Abdul-Karim FW, Avril S, Keri RA. Breast Cancer Res Treat 146: 2014 25-40	20
Validation of the prognostic gene portfolio, ClinicoMolecular Triad Classification, using an independent prospective breast cancer cohort and external patient populations. Wang DY, Done SJ, Mc Cready DR, Leong WL. Breast Cancer Res 16: 2014 R71	5
Predicting response and survival in chemotherapy-treated triple-negative breast cancer. Prat A, Lluch A, Albanell J, Barry WT, Fan C, Chacón JI, Parker JS, Calvo L, Plazaola A, Arcusa A, Seguí-Palmer MA, Burgues O, Ribelles N, Rodriguez-Lescure A, Guerrero A, Ruiz-Borrego M, Munarriz B, López JA, Adamo B, Cheang MC, Li Y, Hu Z, Gulley ML, Vidal MJ, Pitcher BN, Liu MC, Citron ML, Ellis MJ, Mardis E, Vickery T, Hudis CA, Winer EP, Carey LA, Caballero R, Carrasco E, Martín M, Perou CM, Alba E. Br J Cancer 111: 2014 1532-1541	54
Molecular features and survival outcomes of the intrinsic subtypes within HER2-positive breast cancer. Prat A, Carey LA, Adamo B, Vidal M, Tabernero J, Cortés J, Parker JS, Perou CM, Baselga J. J Natl Cancer Inst 106: 2014 dju152	88
Cancer progression modeling using static sample data. Sun Y, Yao J, Nowak NJ, Goodison S. Genome Biol 15: 2014 440	13
Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Ali HR, Rueda OM, Chin SF, Curtis C, Dunning MJ, Aparicio SA, Caldas C. Genome Biol 15: 2014 431	93
Acquired convergence of hormone signaling in breast cancer: ER and PR transition from functionally distinct in normal breast to predictors of metastatic disease. Hilton HN, Doan TB, Graham JD, Oakes SR, Silvestri A, Santucci N, Kantimm S, Huschtscha LI, Ormandy CJ, Funder JW, Simpson ER, Kuczek ES, Leedman PJ, Tilley WD, Fuller PJ, Muscat GE, Clarke CL. Oncotarget 5: 2014 8651-8664	18
Hypoxia promotes stem cell phenotypes and poor prognosis through epigenetic regulation of DICER. van den Beucken T, Koch E, Chu K, Rupaimoole R, Prickaerts P, Adriaens M, Voncken JW, Harris AL, Buffa FM, Haider S, Starmans MHW, Yao CQ, Ivan M, Ivan C, Pecot CV, Boutros PC, Sood AK, Koritzinsky M, Wouters BG. Nat Commun 5: 2014 5203	127
Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53. Quigley D, Silwal-Pandit L, Dannenfelser R, Langerød A, Vollan HK, Vaske C, Siegel JU, Troyanskaya O, Chin SF, Caldas C, Balmain A, Børresen-Dale AL, Kristensen V. Mol Cancer Res 13: 2015 493-501	37
A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation. Burleigh A, McKinney S, Brimhall J, Yap D, Eirew P, Poon S, Ng V, Wan A, Prentice L, Annab L, Barrett JC, Caldas C, Eaves C, Aparicio S. Breast Cancer Res 17: 2015 4	15
APOBEC3B expression in breast cancer reflects cellular proliferation, while a deletion polymorphism is associated with immune activation. Cescon DW, Haibe-Kains B, Mak TW. Proc Natl Acad Sci U S A 112: 2015 2841-2846	86
Decreased <i>BECN1</i> mRNA Expression in Human Breast Cancer is Associated with Estrogen Receptor-Negative Subtypes and Poor Prognosis. Tang H, Sebti S, Titone R, Zhou Y, Isidoro C, Ross TS, Hibshoosh H, Xiao G, Packer M, Xie Y, Levine B. EBioMedicine 2: 2015 255-263	63
Polymorphism at 19q13.41 Predicts Breast Cancer Survival Specifically after Endocrine Therapy. Khan S, Fagerholm R, Rafiq S, Tapper W, Aittomäki K, Liu J, Blomqvist C, Eccles D, Nevanlinna H. Clin Cancer Res 21: 2015 4086-4096	9
MicroRNA profiling of the pubertal mouse mammary gland identifies miR-184 as a candidate breast tumour suppressor gene. Phua YW, Nguyen A, Roden DL, Elsworth B, Deng N, Nikolic I, Yang J, Mcfarland A, Russell R, Kaplan W, Cowley MJ, Nair R, Zotenko E, O'Toole S, Tan SX, James DE, Clark SJ, Kouros-Mehr H, Swarbrick A. Breast Cancer Res 17: 2015 83	31
The Discovery of Novel Biomarkers Improves Breast Cancer Intrinsic Subtype Prediction and Reconciles the Labels in the METABRIC Data Set. Milioli HH, Vimieiro R, Riveros C, Tishchenko I, Berretta R, Moscato P. PLoS One 10: 2015 e0129711	13
IDEA: Integrated Drug Expression Analysis-Integration of Gene Expression and Clinical Data for the Identification of Therapeutic Candidates. Ung MH, Varn FS, Cheng C. CPT Pharmacometrics Syst Pharmacol 4: 2015 415-425	3
An integrated network platform for contextual prioritization of drugs and pathways. Segura-Cabrera A, Singh N, Komurov K. Mol Biosyst 11: 2015 2850-2859	4
An ecological measure of immune-cancer colocalization as a prognostic factor for breast cancer. Maley CC, Koelble K, Natrajan R, Aktipis A, Yuan Y. Breast Cancer Res 17: 2015 131	45
Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer. Liu C, Srihari S, Lal S, Gautier B, Simpson PT, Khanna KK, Ragan MA, Lê Cao KA. Mol Oncol 10: 2016 179-193	16
p21-activated kinase group II small compound inhibitor GNE-2861 perturbs estrogen receptor alpha signaling and restores tamoxifen-sensitivity in breast cancer cells. Zhuang T, Zhu J, Li Z, Lorent J, Zhao C, Dahlman-Wright K, Strömblad S. Oncotarget 6: 2015 43853-43868	26
Iroquois homeobox 2 suppresses cellular motility and chemokine expression in breast cancer cells. Werner S, Stamm H, Pandjaitan M, Kemming D, Brors B, Pantel K, Wikman H. BMC Cancer 15: 2015 896	8
Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis. Wassef M, Rodilla V, Teissandier A, Zeitouni B, Gruel N, Sadacca B, Irondelle M, Charruel M, Ducos B, Michaud A, Caron M, Marangoni E, Chavrier P, Le Tourneau C, Kamal M, Pasmant E, Vidaud M, Servant N, Reyal F, Meseure D, Vincent-Salomon A, Fre S, Margueron R. Genes Dev 29: 2015 2547-2562	52
YAP enhances the pro-proliferative transcriptional activity of mutant p53 proteins. Di Agostino S, Sorrentino G, Ingallina E, Valenti F, Ferraiuolo M, Bicciato S, Piazza S, Strano S, Del Sal G, Blandino G. EMBO Rep 17: 2016 188-201	114
Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles. Varn FS, Andrews EH, Mullins DW, Cheng C. Nat Commun 7: 2016 10248	32
Iteratively refining breast cancer intrinsic subtypes in the METABRIC dataset. Milioli HH, Vimieiro R, Tishchenko I, Riveros C, Berretta R, Moscato P. BioData Min 9: 2016 2	8
Microenvironmental Heterogeneity Parallels Breast Cancer Progression: A Histology-Genomic Integration Analysis. Natrajan R, Sailem H, Mardakheh FK, Arias Garcia M, Tape CJ, Dowsett M, Bakal C, Yuan Y. PLoS Med 13: 2016 e1001961	57
Predicting chemoinsensitivity in breast cancer with 'omics/digital pathology data fusion. Savage RS, Yuan Y. R Soc Open Sci 3: 2016 140501	5
Oncogenic mTOR signalling recruits myeloid-derived suppressor cells to promote tumour initiation. Welte T, Kim IS, Tian L, Gao X, Wang H, Li J, Holdman XB, Herschkowitz JI, Pond A, Xie G, Kurley S, Nguyen T, Liao L, Dobrolecki LE, Pang L, Mo Q, Edwards DP, Huang S, Xin L, Xu J, Li Y, Lewis MT, Wang T, Westbrook TF, Rosen JM, Zhang XH. Nat Cell Biol 18: 2016 632-644	116
Germline APOBEC3B deletion is associated with breast cancer risk in an Asian multi-ethnic cohort and with immune cell presentation. Wen WX, Soo JS, Kwan PY, Hong E, Khang TF, Mariapun S, Lee CS, Hasan SN, Rajadurai P, Yip CH, Mohd Taib NA, Teo SH. Breast Cancer Res 18: 2016 56	29
Activation of the orphan receptor GPR55 by lysophosphatidylinositol promotes metastasis in triple-negative breast cancer. Andradas C, Blasco-Benito S, Castillo-Lluva S, Dillenburg-Pilla P, Diez-Alarcia R, Juanes-García A, García-Taboada E, Hernando-Llorente R, Soriano J, Hamann S, Wenners A, Alkatout I, Klapper W, Rocken C, Bauer M, Arnold N, Quintanilla M, Megías D, Vicente-Manzanares M, Urigüen L, Gutkind JS, Guzmán M, Pérez-Gómez E, Sánchez C. Oncotarget 7: 2016 47565-47575	28
Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers. Tishchenko I, Milioli HH, Riveros C, Moscato P. PLoS One 11: 2016 e0158259	9
Genome-wide association study in East Asians identifies two novel breast cancer susceptibility loci. Han MR, Long J, Choi JY, Low SK, Kweon SS, Zheng Y, Cai Q, Shi J, Guo X, Matsuo K, Iwasaki M, Shen CY, Kim MK, Wen W, Li B, Takahashi A, Shin MH, Xiang YB, Ito H, Kasuga Y, Noh DY, Matsuda K, Park MH, Gao YT, Iwata H, Tsugane S, Park SK, Kubo M, Shu XO, Kang D, Zheng W. Hum Mol Genet 25: 2016 3361-3371	20
Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia. Haider S, McIntyre A, van Stiphout RG, Winchester LM, Wigfield S, Harris AL, Buffa FM. Genome Biol 17: 2016 140	44
Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer. Hu Z, Mao JH, Curtis C, Huang G, Gu S, Heiser L, Lenburg ME, Korkola JE, Bayani N, Samarajiwa S, Seoane JA, Dane MA, Esch A, Feiler HS, Wang NJ, Hardwicke MA, Laquerre S, Jackson J, W Wood K, Weber B, Spellman PT, Aparicio S, Wooster R, Caldas C, Gray JW. Breast Cancer Res 18: 2016 70	8
A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers. Ferrari A, Vincent-Salomon A, Pivot X, Sertier AS, Thomas E, Tonon L, Boyault S, Mulugeta E, Treilleux I, MacGrogan G, Arnould L, Kielbassa J, Le Texier V, Blanché H, Deleuze JF, Jacquemier J, Mathieu MC, Penault-Llorca F, Bibeau F, Mariani O, Mannina C, Pierga JY, Trédan O, Bachelot T, Bonnefoi H, Romieu G, Fumoleau P, Delaloge S, Rios M, Ferrero JM, Tarpin C, Bouteille C, Calvo F, Gut IG, Gut M, Martin S, Nik-Zainal S, Stratton MR, Pauporté I, Saintigny P, Birnbaum D, Viari A, Thomas G. Nat Commun 7: 2016 12222	68
Association between EZH2 expression, silencing of tumor suppressors and disease outcome in solid tumors. Wassef M, Michaud A, Margueron R. Cell Cycle 15: 2016 2256-2262	9
Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer. Bailey SD, Desai K, Kron KJ, Mazrooei P, Sinnott-Armstrong NA, Treloar AE, Dowar M, Thu KL, Cescon DW, Silvester J, Yang SY, Wu X, Pezo RC, Haibe-Kains B, Mak TW, Bedard PL, Pugh TJ, Sallari RC, Lupien M. Nat Genet 48: 2016 1260-1266	45
Application of pharmacologically induced transcriptomic profiles to interrogate PI3K-Akt-mTOR pathway activity associated with cancer patient prognosis. Ung MH, Wang GL, Varn FS, Cheng C. Oncotarget 7: 2016 84142-84154	2
HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status. Weitsman G, Barber PR, Nguyen LK, Lawler K, Patel G, Woodman N, Kelleher MT, Pinder SE, Rowley M, Ellis PA, Purushotham AD, Coolen AC, Kholodenko BN, Vojnovic B, Gillett C, Ng T. Oncotarget 7: 2016 51012-51026	13
Comprehensive functional analysis of the tousled-like kinase 2 frequently amplified in aggressive luminal breast cancers. Kim JA, Tan Y, Wang X, Cao X, Veeraraghavan J, Liang Y, Edwards DP, Huang S, Pan X, Li K, Schiff R, Wang XS. Nat Commun 7: 2016 12991	32
Functional redundancy between Apc and Apc2 regulates tissue homeostasis and prevents tumorigenesis in murine mammary epithelium. Daly CS, Shaw P, Ordonez LD, Williams GT, Quist J, Grigoriadis A, Van Es JH, Clevers H, Clarke AR, Reed KR. Oncogene 36: 2017 1793-1803	19
Reduced mRNA expression levels of NFE2L2 are associated with poor outcome in breast cancer patients. Wolf B, Goebel G, Hackl H, Fiegl H. BMC Cancer 16: 2016 821	12
PIM1 kinase regulates cell death, tumor growth and chemotherapy response in triple-negative breast cancer. Brasó-Maristany F, Filosto S, Catchpole S, Marlow R, Quist J, Francesch-Domenech E, Plumb DA, Zakka L, Gazinska P, Liccardi G, Meier P, Gris-Oliver A, Cheang MC, Perdrix-Rosell A, Shafat M, Noël E, Patel N, McEachern K, Scaltriti M, Castel P, Noor F, Buus R, Mathew S, Watkins J, Serra V, Marra P, Grigoriadis A, Tutt AN. Nat Med 22: 2016 1303-1313	108
Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer. Wang Y, Mark KM, Ung MH, Kettenbach A, Miller T, Xu W, Cheng W, Xia T, Cheng C. Genome Med 8: 2016 114	2
Unique epigenetic gene profiles define human breast cancers with poor prognosis. Peña-Llopis S, Wan Y, Martinez ED. Oncotarget 7: 2016 85819-85831	8
Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome. Andrews E, Wang Y, Xia T, Cheng W, Cheng C. PLoS Comput Biol 13: 2017 e1005340	5
Integrin-β4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells. Bierie B, Pierce SE, Kroeger C, Stover DG, Pattabiraman DR, Thiru P, Liu Donaher J, Reinhardt F, Chaffer CL, Keckesova Z, Weinberg RA. Proc Natl Acad Sci U S A 114: 2017 E2337-E2346	148
A prosurvival DNA damage-induced cytoplasmic interferon response is mediated by end resection factors and is limited by Trex1. Erdal E, Haider S, Rehwinkel J, Harris AL, McHugh PJ. Genes Dev 31: 2017 353-369	95
Large-scale gene network analysis reveals the significance of extracellular matrix pathway and homeobox genes in acute myeloid leukemia: an introduction to the Pigengene package and its applications. Foroushani A, Agrahari R, Docking R, Chang L, Duns G, Hudoba M, Karsan A, Zare H. BMC Med Genomics 10: 2017 16	20
Basal-like breast cancer: molecular profiles, clinical features and survival outcomes. Milioli HH, Tishchenko I, Riveros C, Berretta R, Moscato P. BMC Med Genomics 10: 2017 19	40
Cadherins Associate with Distinct Stem Cell-Related Transcription Factors to Coordinate the Maintenance of Stemness in Triple-Negative Breast Cancer. Yang C, Zhao X, Cui N, Liang Y. Stem Cells Int 2017: 2017 5091541	16
miR-424(322)/503 is a breast cancer tumor suppressor whose loss promotes resistance to chemotherapy. Rodriguez-Barrueco R, Nekritz EA, Bertucci F, Yu J, Sanchez-Garcia F, Zeleke TZ, Gorbatenko A, Birnbaum D, Ezhkova E, Cordon-Cardo C, Finetti P, Llobet-Navas D, Silva JM. Genes Dev 31: 2017 553-566	57
Regulatory network of GATA3 in pediatric acute lymphoblastic leukemia. Hou Q, Liao F, Zhang S, Zhang D, Zhang Y, Zhou X, Xia X, Ye Y, Yang H, Li Z, Wang L, Wang X, Ma Z, Zhu Y, Ouyang L, Wang Y, Zhang H, Yang L, Xu H, Shu Y. Oncotarget 8: 2017 36040-36053	7
Transcriptional response profiles of paired tumor-normal samples offer novel perspectives in pan-cancer analysis. Hu S, Yuan H, Li Z, Zhang J, Wu J, Chen Y, Shi Q, Ren W, Shao N, Ying X. Oncotarget 8: 2017 41334-41347	14
Predicting Outcomes of Hormone and Chemotherapy in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Study by Biochemically-inspired Machine Learning. Mucaki EJ, Baranova K, Pham HQ, Rezaeian I, Angelov D, Ngom A, Rueda L, Rogan PK. F1000Res 5: 2016 2124	10
The mutant p53-ID4 complex controls VEGFA isoforms by recruiting lncRNA MALAT1. Pruszko M, Milano E, Forcato M, Donzelli S, Ganci F, Di Agostino S, De Panfilis S, Fazi F, Bates DO, Bicciato S, Zylicz M, Zylicz A, Blandino G, Fontemaggi G. EMBO Rep 18: 2017 1331-1351	54
Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity. Dannenfelser R, Nome M, Tahiri A, Ursini-Siegel J, Vollan HKM, Haakensen VD, Helland Å, Naume B, Caldas C, Børresen-Dale AL, Kristensen VN, Troyanskaya OG. Oncotarget 8: 2017 57121-57133	18
A role for Tau protein in maintaining ribosomal DNA stability and cytidine deaminase-deficient cell survival. Bou Samra E, Buhagiar-Labarchède G, Machon C, Guitton J, Onclercq-Delic R, Green MR, Alibert O, Gazin C, Veaute X, Amor-Guéret M. Nat Commun 8: 2017 693	18
Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology. Mechanic LE, Lindström S, Daily KM, Sieberts SK, Amos CI, Chen HS, Cox NJ, Dathe M, Feuer EJ, Guertin MJ, Hoffman J, Liu Y, Moore JH, Myers CL, Ritchie MD, Schildkraut J, Schumacher F, Witte JS, Wang W, Williams SM, U4C Challenge Participants, U4C Challenge Data Contributors, Gillanders EM. PLoS Genet 13: 2017 e1006945	1
A novel approach for data integration and disease subtyping. Nguyen T, Tagett R, Diaz D, Draghici S. Genome Res 27: 2017 2025-2039	56
Transcription factor c-Myb inhibits breast cancer lung metastasis by suppression of tumor cell seeding. Knopfová L, Biglieri E, Volodko N, Masařík M, Hermanová M, Glaus Garzón JF, Dúcka M, Kučírková T, Souček K, Šmarda J, Beneš P, Borsig L. Oncogene 37: 2018 1020-1030	9
Cancer cell line specific co-factors modulate the FOXM1 cistrome. Wang Y, Ung MH, Xia T, Cheng W, Cheng C. Oncotarget 8: 2017 76498-76515	7
Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer. Wang Y, Ung MH, Cantor S, Cheng C. Sci Rep 7: 2017 15742	7
Age, estrogen, and immune response in breast adenocarcinoma and adjacent normal tissue. Quigley DA, Tahiri A, Lüders T, Riis MH, Balmain A, Børresen-Dale AL, Bukholm I, Kristensen V. Oncoimmunology 6: 2017 e1356142	17
Immune Checkpoint Molecules on Tumor-Infiltrating Lymphocytes and Their Association with Tertiary Lymphoid Structures in Human Breast Cancer. Solinas C, Garaud S, De Silva P, Boisson A, Van den Eynden G, de Wind A, Risso P, Rodrigues Vitória J, Richard F, Migliori E, Noël G, Duvillier H, Craciun L, Veys I, Awada A, Detours V, Larsimont D, Piccart-Gebhart M, Willard-Gallo K. Front Immunol 8: 2017 1412	48
Identification of cancer genes that are independent of dominant proliferation and lineage programs. Selfors LM, Stover DG, Harris IS, Brugge JS, Coloff JL. Proc Natl Acad Sci U S A 114: 2017 E11276-E11284	12
Mechanical cues control mutant p53 stability through a mevalonate-RhoA axis. Ingallina E, Sorrentino G, Bertolio R, Lisek K, Zannini A, Azzolin L, Severino LU, Scaini D, Mano M, Mantovani F, Rosato A, Bicciato S, Piccolo S, Del Sal G. Nat Cell Biol 20: 2018 28-35	63
miR-105/93-3p promotes chemoresistance and circulating miR-105/93-3p acts as a diagnostic biomarker for triple negative breast cancer. Li HY, Liang JL, Kuo YL, Lee HH, Calkins MJ, Chang HT, Lin FC, Chen YC, Hsu TI, Hsu TI, Hsiao M, Ger LP, Lu PJ. Breast Cancer Res 19: 2017 133	66
Therapeutically targeting tumor microenvironment-mediated drug resistance in estrogen receptor-positive breast cancer. Shee K, Yang W, Hinds JW, Hampsch RA, Varn FS, Traphagen NA, Patel K, Cheng C, Jenkins NP, Kettenbach AN, Demidenko E, Owens P, Faber AC, Golub TR, Straussman R, Miller TW. J Exp Med 215: 2018 895-910	28
MYC-driven epigenetic reprogramming favors the onset of tumorigenesis by inducing a stem cell-like state. Poli V, Fagnocchi L, Fasciani A, Cherubini A, Mazzoleni S, Ferrillo S, Miluzio A, Gaudioso G, Vaira V, Turdo A, Gaggianesi M, Chinnici A, Lipari E, Bicciato S, Bosari S, Todaro M, Zippo A. Nat Commun 9: 2018 1024	66
Capture Hi-C identifies putative target genes at 33 breast cancer risk loci. Baxter JS, Leavy OC, Dryden NH, Maguire S, Johnson N, Fedele V, Simigdala N, Martin LA, Andrews S, Wingett SW, Assiotis I, Fenwick K, Chauhan R, Rust AG, Orr N, Dudbridge F, Haider S, Fletcher O. Nat Commun 9: 2018 1028	51
Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort. Mukherjee A, Russell R, Chin SF, Liu B, Rueda OM, Ali HR, Turashvili G, Mahler-Araujo B, Ellis IO, Aparicio S, Caldas C, Provenzano E. NPJ Breast Cancer 4: 2018 5	18
Recurrent copy number alterations in young women with breast cancer. Chi C, Murphy LC, Hu P. Oncotarget 9: 2018 11541-11558	7
Applications of Bayesian network models in predicting types of hematological malignancies. Agrahari R, Foroushani A, Docking TR, Chang L, Duns G, Hudoba M, Karsan A, Zare H. Sci Rep 8: 2018 6951	22
A Comprehensive cis-eQTL Analysis Revealed Target Genes in Breast Cancer Susceptibility Loci Identified in Genome-wide Association Studies. Guo X, Lin W, Bao J, Cai Q, Pan X, Bai M, Yuan Y, Shi J, Sun Y, Han MR, Wang J, Liu Q, Wen W, Li B, Long J, Chen J, Zheng W. Am J Hum Genet 102: 2018 890-903	39
SIK2 attenuates proliferation and survival of breast cancer cells with simultaneous perturbation of MAPK and PI3K/Akt pathways. Zohrap N, Saatci Ö, Ozes B, Coban I, Atay HM, Battaloglu E, Şahin Ö, Bugra K. Oncotarget 9: 2018 21876-21892	13
Cancer Cells Co-opt the Neuronal Redox-Sensing Channel TRPA1 to Promote Oxidative-Stress Tolerance. Takahashi N, Chen HY, Harris IS, Stover DG, Selfors LM, Bronson RT, Deraedt T, Cichowski K, Welm AL, Mori Y, Mills GB, Brugge JS. Cancer Cell 33: 2018 985-1003.e7	96
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