Weigelt B, Baehner FL, Reis-Filho JS. The contribution of gene expression profiling to breast cancer classification, prognostication and prediction: a retrospective of the last decade. J Pathol. 2010; 220(2):263–80. doi:http://dx.doi.org/10.1002/path.2648.
CAS
PubMed
Google Scholar
Sotiriou C, Piccart MJ. Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care?Nat Rev Cancer. 2007; 7(7):545–53.
Article
CAS
PubMed
Google Scholar
Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, et al. Molecular portraits of human breast tumours. Nature. 2000; 406(6797):747–52.
Article
CAS
PubMed
Google Scholar
Wang X, Markowetz F, De Sousa E Melo F, Medema JP, Vermeulen L. Dissecting cancer heterogeneity – an unsupervised classification approach. Int J Biochem Cell Biol. 2013; 45(11):2574–9.
Article
CAS
PubMed
Google Scholar
Weigelt B, Mackay A, A’hern R, Natrajan R, Tan DSP, Dowsett M, Ashworth A, Reis-Filho JS. Breast cancer molecular profiling with single sample predictors: a retrospective analysis. Lancet Oncol. 2010; 11(4):339–49.
Article
CAS
PubMed
Google Scholar
Sørlie T, Tibshirani R, Parker J, Hastie T, Marron J, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci. 2003; 100(14):8418–23.
Article
PubMed
PubMed Central
Google Scholar
Hu Z, Fan C, Oh DS, Marron J, He X, Qaqish BF, Livasy C, Carey LA, Reynolds E, Dressler L, et al. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics. 2006; 7:96.
Article
PubMed
PubMed Central
Google Scholar
Parker JS, Mullins M, Cheang MCU, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol. 2009; 27(8):1160–7.
Article
PubMed
PubMed Central
Google Scholar
Perou CM, Parker JS, Prat A, Ellis MJ, Bernard PS. Clinical implementation of the intrinsic subtypes of breast cancer. Lancet Oncol. 2010; 11(8):718–9.
Article
PubMed
Google Scholar
Sørlie T, Borgan E, Myhre S, Vollan HK, Russnes H, Zhao X, Nilsen G, Lingjærde OC, Børresen-Dale AL, Rødland E. The importance of gene-centring microarray data. Lancet Oncol. 2010; 11(8):719–20.
Article
PubMed
Google Scholar
Weigelt B, Mackay A, A’hern R, Natrajan R, Tan DSP, Dowsett M, Ashworth A, Reis-Filho JS. Reflection and reaction, authors’ reply breast cancer molecular profiling with single sample predictors: a retrospective analysis. Lancet Oncol. 2010; 11(8):720–1.
Article
Google Scholar
Haibe-Kains B, Desmedt C, Loi S, Culhane AC, Bontempi G, Quackenbush J, Sotiriou C. A three-gene model to robustly identify breast cancer molecular subtypes. J Natl Cancer Inst. 2012; 104(4):311–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G, Delorenzi M, Piccart M, Sotiriou C. Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res. 2008; 14(16):5158–65.
Article
CAS
PubMed
Google Scholar
Goldhirsch A, Wood W, Coates A, Gelber R, Thürlimann B, Senn HJ, et al. Strategies for subtypes - dealing with the diversity of breast cancer: highlights of the St Gallen International Expert Consensus on the Primary Therapy of Early Breast Cancer 2011. Ann Oncol. 2011; 22(8):1736–47.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kapp AV, Jeffrey SS, Langerod A, Borresen-Dale A, Han W, Noh DY, Bukholm I, Nicolau M, Brown PO, Tibshirani R. Discovery and validation of breast cancer subtypes. BMC Genomics. 2006; 7:231.
Article
PubMed
PubMed Central
Google Scholar
Pusztai L, Mazouni C, Anderson K, Wu Y, Symmans WF. Molecular classification of breast cancer: limitations and potential. The Oncologist. 2006; 11(8):868–77.
Article
CAS
PubMed
Google Scholar
McCall MN, Bolstad BM, Irizarry RA. Frozen robust multiarray analysis (fRMA). Biostatistics. 2010; 11(2):242–53.
Article
PubMed
PubMed Central
Google Scholar
Guiu S, Michiels S, Andre F, Cortes J, Denkert C, Di Leo A, Hennessy B, Sorlie T, Sotiriou C, Turner N, et al. Molecular subclasses of breast cancer: how do we define them? the IMPAKT 2012 Working Group Statement. Ann Oncol. 2012; 23(12):2997–3006.
Article
CAS
PubMed
Google Scholar
Mackay A, Weigelt B, Grigoriadis A, Kreike B, Tan DSP, Dowsett M, Ashworth A, Reis-Filho JS. Microarray-based class discovery for molecular classification of breast cancer: analysis of interobserver agreement. J Natl Cancer Inst. 2011; 103(8):662–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cohen J. A coefficient of agreement for nominal scales. Educ Psychol Meas. 1960; 20(1):37–46.
Article
Google Scholar
Guedj M, Marisa L, De Reynies A, Orsetti B, Schiappa R, Bibeau F, MacGrogan G, Lerebours F, Finetti P, Longy M, Bertheau P, et al. A refined molecular taxonomy of breast cancer. Oncogene. 2012; 31(9):1196–206.
Article
CAS
PubMed
Google Scholar
Lusa L, McShane LM, Reid JF, De Cecco L, Ambrogi F, Biganzoli E, Gariboldi M, Pierotti MA. Challenges in projecting clustering results across gene expression profiling datasets. J Natl Cancer Inst. 2007; 99(22):1715–23.
Article
CAS
PubMed
Google Scholar
Tibshirani R, Walther G. Cluster validation by prediction strength. J Comput Graph Stat. 2005; 14(3):511–28.
Article
Google Scholar
Wirapati P, Sotiriou C, Kunkel S, Farmer P, Pradervand S, Haibe-Kains B, Desmedt C, et al. Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Res. 2008; 10(4):65.
Article
Google Scholar
Zhao X, Rødland EA, Tibshirani R, Plevritis S. Molecular subtyping for clinically defined breast cancer subgroups. Breast Cancer Res. 2015; 27(1):29.
Article
Google Scholar
Paquet ER, Hallett MT. Absolute assignment of breast cancer intrinsic molecular subtype. J Natl Cancer Inst. 2015; 107(1):357.
Article
PubMed
Google Scholar
Alexe G, Dalgin GS, Ramaswamy R, DeLisi C, Bhanot G. Data perturbation independent diagnosis and validation of breast cancer subtypes using clustering and patterns. Cancer Informat. 2006; 2:243–74.
CAS
Google Scholar
Prat A, Ellis MJ, Perou CM. Practical implications of gene-expression-based assays for breast oncologists. Nat Rev Clin Oncol. 2011; 9(1):48–57.
Article
PubMed
PubMed Central
Google Scholar
Prat A, Parker JS, Karginova O, Fan C, Livasy C, Herschkowitz JI, He X, Perou CM, et al. Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res. 2010; 12(5):68.
Article
Google Scholar
Lehmann BD, Bauer JA, Chen X, Sanders ME, Chakravarthy AB, Shyr Y, Pietenpol JA. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Investig. 2011; 121(7):2750.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koboldt D, Fulton R, McLellan M, Schmidt H, Kalicki-Veizer J, Mc Michael J, Fulton L, Dooling D, Ding L, Mardis E, et al. Comprehensive molecular portraits of human breast tumours. Nature. 2012; 490(7418):61–70.
Article
CAS
Google Scholar
Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012; 486(7403):346–52.
CAS
PubMed
PubMed Central
Google Scholar
Ali HR, Rueda OM, Chin SF, Curtis C, Dunning MJ, Aparicio S, Caldas C. Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biol. 2014; 15:8.
Article
Google Scholar
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002; 30(1):207–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, et al. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003; 31(1):68–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Y, Klijn JGM, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. The Lancet. 2005; 365(9460):671–9.
Article
CAS
Google Scholar
Yu JX, Sieuwerts AM, Zhang Y, Martens J, Smid M, Klijn J, Wang Y, Foekens JA. Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer. BMC Cancer. 2007; 7:182.
Article
PubMed
PubMed Central
Google Scholar
Prat A, Parker J, Perou C. Guide to Intrinsic Subtypes. https://genome.unc.edu/pubsup/breastGEO/GuidetoIntrinsicSubtyping9-6-10.pdf. Accessed 15 May 2016.
Richardson AL, Wang ZC, De Nicolo A, Lu X, Brown M, Miron A, Liao X, Iglehart JD, Livingston DM, Ganesan S. X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell. 2006; 9(2):121–32.
Article
CAS
PubMed
Google Scholar
Li Y, Zou L, Li Q, Haibe-Kains B, Tian R, Li Y, Desmedt C, Sotiriou C, Szallasi Z, Iglehart JD, et al. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nat Med. 2010; 16(2):214–8.
Article
PubMed
PubMed Central
Google Scholar
Lu X, Lu X, Wang ZC, Iglehart JD, Zhang X, Richardson AL. Predicting features of breast cancer with gene expression patterns. Breast Cancer Res Treat. 2008; 108(2):191–201.
Article
CAS
PubMed
Google Scholar
Bos PD, Xiang HFZ, Nadal C, Shu W, Gomis RR, Nguyen DX, Minn AJ, van de Vijver MJ, Gerald WL, Foekens JA, et al. Genes that mediate breast cancer metastasis to the brain. Nature. 2009; 459(7249):1005–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dedeurwaerder S, Desmedt C, Calonne E, Singha SK, Haibe-Kains B, Defrance M, Michiels S, Volkmar M, Deplus R, Luciani J, et al. DNA methylation profiling reveals a predominant immune component in breast cancers. EMBO Mol Med. 2011; 3:726–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kao KJ, Chang KM, Hsu HC, Huang A. Correlation of microarray-based breast cancer molecular subtypes and clinical outcomes: implications for treatment optimization. BMC Cancer. 2011; 11:143.
Article
PubMed
PubMed Central
Google Scholar
Sabatier R, Finetti P, Cervera N, Lambaudie E, Esterni B, Mamessier E, Tallet A, Chabannon C, Extra JM, Jacquemier J, et al. A gene expression signature identifies two prognostic subgroups of basal breast cancer. Breast Cancer Res Treat. 2011; 126(2):407–20.
Article
CAS
PubMed
Google Scholar
Symmans WF, Hatzis C, Sotiriou C, Andre F, Peintinger F, Regitnig P, Daxenbichler G, Desmedt C, Domont J, Marth C, et al. Genomic index of sensitivity to endocrine therapy for breast cancer. J Clin Oncol. 2010; 28(27):4111–9.
Article
PubMed
PubMed Central
Google Scholar
Desmedt C, Piette F, Loi S, Wang Y, Lallemand F, Haibe-Kains B, Viale G, Delorenzi M, Zhang Y, d’Assignies MS, et al. Strong time dependence of the 76-Gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Clin Cancer Res. 2007; 13(11):3207–14.
Article
CAS
PubMed
Google Scholar
Farmer P, Bonnefoi H, Becette V, Tubiana-Hulin M, Fumoleau P, Larsimont D, MacGrogan G, Bergh J, Cameron D, Goldstein D, et al. Identification of molecular apocrine breast tumours by microarray analysis. Oncogene. 2005; 24(9):4660–71.
Article
CAS
PubMed
Google Scholar
Schmidt M, Bohm D, von Torne C, Steiner E, Puhl A, Pilch H, Lehr HA, Hengstler JG, Kolbl H, Gehrmann M. The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Res. 2008; 68(13):5405–13.
Article
CAS
PubMed
Google Scholar
Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, et al. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci. 2005; 102(38):13550–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pawitan Y, Bjohle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Holmberg L, Huang F, Klaar S, et al. Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res. 2005; 7(6):953–64.
Article
Google Scholar
Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 2010; 28(8):827–38.
Article
CAS
PubMed
Google Scholar
Popovici V, Chen W, Gallas BG, Hatzis C, Shi W, Samuelson FW, Nikolsky Y, Tsyganova M, Ishkin A, Nikolskaya T, et al. Effect of training-sample size and classification difficulty on the accuracy of genomic predictors. Breast Cancer Res. 2010; 12(1):5.
Article
Google Scholar
Minn AJ, Gupta GP, Siegel PM, Bos PD, Shu W, Giri DD, Viale A, Olshen AB, Gerald WL, Massagué J. Genes that mediate breast cancer metastasis to lung. Nature. 2005; 436(7050):518–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haibe-Kains B, Desmedt C, Rothé F, Piccart M, Sotiriou C, Bontempi G. A fuzzy gene expression-based computational approach improves breast cancer prognostication. Genome Biol. 2010; 11(2):18.
Article
Google Scholar
Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, et al. Gene exression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst. 2006; 98(4):262–72.
Article
CAS
PubMed
Google Scholar
Haibe-Kains B, Desmedt C, Rothe F, Piccart M, Sotiriou C, Bontempi G. A fuzzy gene expression-based computational approach improves breast cancer prognostication. Genome Biol. 2010; 11(2):18.
Article
Google Scholar