A diagnostic gene profile for molecular subtyping of breast cancer associated with treatment response


Classification of breast cancer into molecular subtypes maybe important for the proper selection of therapy, as tumors with seemingly similar histopathological features can have strikingly different clinical outcomes. Herein, we report the development of a molecular subtyping profile (BluePrint), that enables rationalization in patient selection for either chemotherapy or endocrine therapy prescription. An 80-Gene Molecular Subtyping Profile (BluePrint) was developed using 200 breast cancer patient specimens and confirmed on four independent validation cohorts (n = 784). Additionally, the profile was tested as a predictor of chemotherapy response in 133 breast cancer patients, treated with T/FAC neoadjuvant chemotherapy. BluePrint classification of a patient cohort that was treated with neoadjuvant chemotherapy (n = 133) shows improved distribution of pathological Complete Response (pCR), among molecular subgroups compared with local pathology: 56% of the patients had a pCR in the Basal-type subgroup, 3% in the MammaPrint Low-risk, Luminal-type subgroup, 11% in the MammaPrint High-risk, Luminal-type subgroup, and 50% in the HER2-type subgroup. The group of genes identifying Luminal-type breast cancer is highly enriched for genes having an Estrogen Receptor binding site proximal to the promoter-region, suggesting that these genes are direct targets of the Estrogen Receptor. Implementation of this profile may improve the clinical management of breast cancer patients, by enabling the selection of patients who are most likely to benefit from either chemotherapy or from endocrine therapy.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4


  1. 1.

    Rakha EA, Elsheikh SE, Aleskandarany MA, Habashi HO, Green AR, Powe DG, El-Sayed ME, Benhasouna A, Brunet JS, Akslen LA, Evans AJ, Blamey R, Reis-Filho JS, Foulkes WD, Ellis IO (2009) Triple-negative breast cancer: distinguishing between basal and nonbasal subtypes. Clin Cancer Res 15(7):2302–2310

    PubMed  Article  CAS  Google Scholar 

  2. 2.

    Carey LA, Dees EC, Sawyer L, Gatti L, Moore DT, Collichio F, Ollila DW, Sartor CI, Graham ML, Perou CM (2007) The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin Cancer Res 13:2329–2334

    PubMed  Article  CAS  Google Scholar 

  3. 3.

    Nielsen TO, Hsu FD, Jensen K, Cheang M, Karaca G, Hu Z, Hernandez-Boussard T, Livasy C, Cowan D, Dressler L, Akslen LA, Ragaz J, Gown AM, Gilks CB, van de Rijn M, Perou CM (2004) Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clin Cancer Res 10:5367–5374

    PubMed  Article  CAS  Google Scholar 

  4. 4.

    Kauraniemi P, Kallioniemi A (2006) Activation of multiple cancer-associated genes at the ERBB2 amplicon in breast cancer. Endocr Relat Cancer 13:39–49

    PubMed  Article  CAS  Google Scholar 

  5. 5.

    Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lønning PE, Børresen-Dale AL, Brown PO, Botstein D (2000) Molecular portraits of human breast tumours. Nature 406:747–752

    PubMed  Article  CAS  Google Scholar 

  6. 6.

    Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Eystein Lønning P, Børresen-Dale AL (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 98:10869–10874

    PubMed  Article  CAS  Google Scholar 

  7. 7.

    Rouzier R, Perou CM, Symmans WF, Ibrahim N, Cristofanilli M, Anderson K, Hess KR, Stec J, Ayers M, Wagner P, Morandi P, Fan C, Rabiul I, Ross JS, Hortobagyi GN, Pusztai L (2005) Breast cancer molecular subtypes respond differently to preoperative chemotherapy. Clin Cancer Res 11(16):5678–5685

    PubMed  Article  CAS  Google Scholar 

  8. 8.

    Liedtke C, Mazouni C, Hess KR, André F, Tordai A, Mejia JA, Symmans WF, Gonzalez-Angulo AM, Hennessy B, Green M, Cristofanilli M, Hortobagyi GN, Pusztai L (2008) Response to neoadjuvant therapy and long-term survival in patients with triple-negative breast cancer. J Clin Oncol 26(8):1275–1281

    PubMed  Article  Google Scholar 

  9. 9.

    Rakha EA, Reis-Filho JS, Ellis IO (2008) Basal-like breast cancer: a critical review. J Clin Oncol 26:2568–2581

    PubMed  Article  Google Scholar 

  10. 10.

    Liang H, Tan AR (2010) Iniparib, a PARP1 inhibitor for the potential treatment of cancer, including triple-negative breast cancer. Drugs 13(9):646–656

    CAS  Google Scholar 

  11. 11.

    Sotiriou C, Pusztai L (2009) Gene-expression signatures in breast cancer. N Engl J Med 360(8):790–800

    PubMed  Article  CAS  Google Scholar 

  12. 12.

    Cheang MC, Chia SK, Voduc D, Gao D, Leung S, Snider J, Watson M, Davies S, Bernard PS, Parker JS, Perou CM, Ellis MJ, Nielsen TO (2009) Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. J Natl Cancer Inst 101(10):736–750

    PubMed  Article  CAS  Google Scholar 

  13. 13.

    Livasy CA, Karaca G, Nanda R, Tretiakova MS, Olopade OI, Moore DT, Perou CM (2006) Phenotypic evaluation of the basal-like subtype of invasive breast carcinoma. Mod Pathol 19(2):264–271

    PubMed  Article  CAS  Google Scholar 

  14. 14.

    Roepman P, Horlings HM, Krijgsman O, Kok M, Bueno-de-Mesquita JM, Bender R, Linn SC, Glas AM, van de Vijver MJ (2009) Microarray-based determination of ER, PR and HER2 receptor status in breast cancer. Clin Cancer Res 15(22):7004–7011

    Article  Google Scholar 

  15. 15.

    van ‘t Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Bernards R, Friend SH (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530–536

    PubMed  Article  Google Scholar 

  16. 16.

    Paik S, Shak S, Tang G, Kim C, Baker J, Cronin M, Baehner FL, Walker MG, Watson D, Park T, Hiller W, Fisher ER, Wickerham DL, Bryant J, Wolmark N (2004) A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 351(27):2817–2826

    PubMed  Article  CAS  Google Scholar 

  17. 17.

    van de Vijver MJ, He YD, van ‘t Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R (2002) A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347:1999–2009

    PubMed  Article  Google Scholar 

  18. 18.

    Kok M, Koornstra RH, Mook S, Hauptmann M, Fles R, Glas AM, Jansen MP, Berns EM, Linn SC and Van’t Veer LJ. Additional value of the 70-gene prognosis profile and levels of ER and PR in the prediction of outcome in tamoxifen-treated ER-positive breast cancer. 2011 (submitted)

  19. 19.

    Bueno-de-Mesquita JM, van Harten WH, Retel VP, van’t Veer LJ, van Dam FS, Karsenberg K, Douma KF, van Tinteren H, Peterse JL, Wesseling J, Wu TS, Atsma D, Rutgers EJ, Brink G, Floore AN, Glas AM, Roumen RM, Bellot FE, van Krimpen C, Rodenhuis S, van de Vijver MJ, Linn SC (2007) Use of 70-gene signature to predict prognosis of patients with node-negative breast cancer: a prospective community-based feasibility study (RASTER). Lancet Oncol 8(12):1079–1087

    PubMed  Article  CAS  Google Scholar 

  20. 20.

    Pawitan Y, Bjöhle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Holmberg L, Huang F, Klaar S, Liu ET, Miller L, Nordgren H, Ploner A, Sandelin K, Shaw PM, Smeds J, Skoog L, Wedrén S, Bergh J (2005) Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res 7(6):R953–R964

    PubMed  Article  CAS  Google Scholar 

  21. 21.

    Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, Bergh J (2005) An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci USA 102:13550–13555

    PubMed  Article  CAS  Google Scholar 

  22. 22.

    Hess KR, Anderson K, Symmans WF, Valero V, Ibrahim N, Mejia JA, Booser D, Theriault RL, Buzdar AU, Dempsey PJ, Rouzier R, Sneige N, Ross JS, Vidaurre T, Gómez HL, Hortobagyi GN, Pusztai L (2006) Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and Fluorouracil, Doxorubicin, and Cyclophosphamide in breast cancer. J Clin Oncol 24(26):4236–4244

    PubMed  Article  CAS  Google Scholar 

  23. 23.

    McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, Clark GM (2005) Statistics Subcommittee of the NCI-EORTC Working Group on Cancer Diagnostics. Reporting recommendations for tumor marker prognostic studies. J Clin Oncol 23(36):9067–9072. Epub 2005 Sep 19

    PubMed  Article  Google Scholar 

  24. 24.

    Roepman P, Jassem J, Smit EF, Muley T, Niklinski J, van de Velde T, Witteveen AT, Rzyman W, Floore A, Burgers S, Giaccone G, Meister M, Dienemann H, Skrzypski M, Kozlowski M, Mooi WJ, van Zandwijk N (2009) An immune response enriched 72-gene prognostic profile for early-stage non-small-cell lung cancer. Clin Cancer Res 15(1):284–290

    PubMed  Article  CAS  Google Scholar 

  25. 25.

    Glas AM, Kersten MJ, Delahaye LJ, Witteveen AT, Kibbelaar RE, Velds A, Wessels LF, Joosten P, Kerkhoven RM, Bernards R, van Krieken JH, Kluin PM, van’tVeer LJ, de Jong D (2005) Gene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment. Blood 105(1):301–307

    PubMed  Article  CAS  Google Scholar 

  26. 26.

    Ross-Innes CS, Stark R, Holmes KA, Schmidt D, Spyrou C, Russell R, Massie CE, Vowler SL, Eldridge M, Carroll JS (2010) Cooperative interaction between retinoic acid receptor-alpha and estrogen receptor in breast cancer. Genes Dev 24(2):171–182

    PubMed  Article  CAS  Google Scholar 

  27. 27.

    Kapp AV, Tibshirani R (2007) Are clusters found in one data set present in another dataset? Biostatistics 8(1):9–31

    PubMed  Article  Google Scholar 

  28. 28.

    Parker JS, Mullins M, Cheang MC, Leung S, Voduc D, Vickery T, Davies S, Fauron C, He X, Hu Z, Quackenbush JF, Stijleman IJ, Palazzo J, Marron JS, Nobel AB, Mardis E, Nielsen TO, Ellis MJ, Perou CM, Bernard PS (2009) Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 27(8):1160–1167

    PubMed  Article  Google Scholar 

  29. 29.

    Fan C, Oh DS, Wessels L, Weigelt B, Nuyten DS, Nobel AB, van’t Veer LJ, Perou CM (2006) Concordance among gene-expression-based predictors for breast cancer. N Engl J Med 355(6):560–569

    PubMed  Article  CAS  Google Scholar 

  30. 30.

    Kapp AV, Jeffrey SS, Langerød A, Børresen-Dale AL, Han W, Noh DY, Bukholm IR, Nicolau M, Brown PO, Tibshirani R (2007) Discovery and validation of breast cancer subtypes. BMC Genomics 8(1):101

    Article  Google Scholar 

  31. 31.

    Pusztai L, Mazouni C, Anderson K, Wu Y, Symmans WF (2006) Molecular classification of breast cancer: limitations and potential. Oncologist 11(8):868–877

    PubMed  Article  CAS  Google Scholar 

  32. 32.

    Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462(7269):58–64

    PubMed  Article  CAS  Google Scholar 

  33. 33.

    Sotiriou C, Desmedt C (2006) Gene expression profiling in breast cancer. Ann Oncol 17(Suppl 10):x259–x262

    PubMed  Article  Google Scholar 

  34. 34.

    Goldhirsch A, Ingle JN, Gelber RD, Coates AS, Thürlimann B, Senn HJ (2009) Panel members. Thresholds for therapies: highlights of the St Gallen International Expert Consensus on the primary therapy of early breast cancer 2009. Ann Oncol 20(8):1319–1329

    PubMed  Article  CAS  Google Scholar 

  35. 35.

    Bertucci F, Finetti P, Cervera N, Esterni B, Hermitte F, Viens P, Birnbaum D (2008) How basal are triple-negative breast cancers? Int J Cancer 123(1):236–240

    PubMed  Article  CAS  Google Scholar 

  36. 36.

    Rakha EA, Reis-Filho JS, Ellis IO (2008) Basal-like breast cancer: a critical review. J Clin Oncol 26(15):2568–2581

    PubMed  Article  Google Scholar 

  37. 37.

    Fisher B, Bryant J, Wolmark N, Mamounas E, Brown A, Fisher ER, Wickerham DL, Begovic M, DeCillis A, Robidoux A, Margolese RG, Cruz AB Jr, Hoehn JL, Lees AW, Dimitrov NV, Bear HD (1998) Effect of preoperative chemotherapy on the outcome of women with operable breast cancer. J Clin Oncol 16(8):2672–2685

    PubMed  CAS  Google Scholar 

  38. 38.

    Kuerer HM, Newman LA, Smith TL, Ames FC, Hunt KK, Dhingra K, Theriault RL, Singh G, Binkley SM, Sneige N, Buchholz TA, Ross MI, McNeese MD, Buzdar AU, Hortobagyi GN, Singletary SE (1999) Clinical course of breast cancer patients with complete pathologic primary tumor and axillary lymph node response to doxorubicin-based neoadjuvant chemotherapy. J Clin Oncol 17(2):460–469

    PubMed  CAS  Google Scholar 

  39. 39.

    Rastogi P, Anderson SJ, Bear HD, Geyer CE, Kahlenberg MS, Robidoux A, Margolese RG, Hoehn JL, Vogel VG, Dakhil SR, Tamkus D, King KM, Pajon ER, Wright MJ, Robert J, Paik S, Mamounas EP, Wolmark N (2008) Preoperative chemotherapy: updates of National Surgical Adjuvant Breast and Bowel Project Protocols B-18 and B-27. J Clin Oncol 26(5):778–785

    PubMed  Article  Google Scholar 

  40. 40.

    Straver ME, Glas AM, Hannemann J, Wesseling J, van de Vijver MJ, Rutgers EJ, Vrancken Peeters MJ, van Tinteren H, Van’t Veer LJ, Rodenhuis S (2010) The 70-gene signature as a response predictor for neoadjuvant chemotherapy in breast cancer. Breast Cancer Res Treat 119(3):551–558

    PubMed  Article  Google Scholar 

  41. 41.

    Weigelt B, Mackay A, A’hern R, Natrajan R, Tan DS, Dowsett M, Ashworth A, Reis-Filho JS (2010) Breast cancer molecular profiling with single sample predictors: a retrospective analysis. Lancet Oncol 11(4):339–349

    PubMed  Article  CAS  Google Scholar 

Download references


The authors thank Rob Pover, Maurice Pater, and Arenda Schuurman for sample and microarray processing; Cor Lieftink and Bram Gerritsen for statistical advice, and Lisette Stork-Sloots and Laura van ‘t Veer for fruitful discussions and helpful suggestions.

Conflicts of interest

RAB is employed by Agendia Inc, all other authors, except WZ and JC, are employed by Agendia BV.

Author information



Corresponding author

Correspondence to Annuska M. Glas.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Krijgsman, O., Roepman, P., Zwart, W. et al. A diagnostic gene profile for molecular subtyping of breast cancer associated with treatment response. Breast Cancer Res Treat 133, 37–47 (2012). https://doi.org/10.1007/s10549-011-1683-z

Download citation


  • Breast cancer
  • Estrogen receptor
  • Molecular subtyping
  • Luminal
  • Basal
  • HER2