The role of molecular analysis in breast cancer

References

• Reis-Filho J S, Simpson P T, Gale T, Lakhani S R. The molecular genetics of breast cancer: the contribution of comparative genomic hybridization. Pathol Res Pract 2005; 201: 713–725
   PubMed Web of Science ®Google Scholar
• Simpson P T, Reis-Filho J S, Gale T, Lakhani S R. Molecular evolution of breast cancer. J Pathol 2005; 205: 248–254
   PubMed Web of Science ®Google Scholar
• Nahta R, Esteva F J. Trastuzumab: triumphs and tribulations. Oncogene 2007; 26: 3637–3643
   PubMed Web of Science ®Google Scholar
• Perou C M, Sorlie T, Eisen M B, et al. Molecular portraits of human breast tumours. Nature 2000; 406: 747–752
   PubMed Web of Science ®Google Scholar
• Sorlie T, Perou C M, Tibshirani R, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001; 98: 10869–10874
   PubMed Web of Science ®Google Scholar
• Brenton J D, Carey L A, Ahmed A A, Caldas C. Molecular classification and molecular forecasting of breast cancer: ready for clinical application?. J Clin Oncol 2005; 23: 7350–7360
   PubMed Web of Science ®Google Scholar
• Reis-Filho J S, Westbury C, Pierga J Y. The impact of expression profiling on prognostic and predictive testing in breast cancer. J Clin Pathol 2006; 59: 225–231
   PubMed Web of Science ®Google Scholar
• Sorlie T, Tibshirani R, Parker J, et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 2003; 100: 8418–8423
   PubMed Web of Science ®Google Scholar
• Geyer C E, Forster J, Lindquist D, et al. Lapatinib plus capecitabine for HER2-positive advanced breast cancer. N Engl J Med 2006; 355: 2733–2743
   PubMed Web of Science ®Google Scholar
• Joensuu H, Kellokumpu-Lehtinen P L, Bono P, et al. Adjuvant docetaxel or vinorelbine with or without trastuzumab for breast cancer. N Engl J Med 2006; 354: 809–820
   PubMed Web of Science ®Google Scholar
• Piccart-Gebhart M J, Procter M, Leyland-Jones B, et al. Trastuzumab after adjuvant chemotherapy in HER2-positive breast cancer. N Engl J Med 2005; 353: 1659–1672
   PubMed Web of Science ®Google Scholar
• Romond E H, Perez E A, Bryant J, et al. Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. N Engl J Med 2005; 353: 1673–1684
   PubMed Web of Science ®Google Scholar
• Slamon D J, Leyland-Jones B, Shak S, et al. Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N Engl J Med 2001; 344: 783–792
   PubMed Web of Science ®Google Scholar
• Rouzier R, Perou C M, Symmans W F, et al. Breast cancer molecular subtypes respond differently to preoperative chemotherapy. Clin Cancer Res 2005; 11: 5678–5685
   PubMed Web of Science ®Google Scholar
• Abd El-Rehim D M, Pinder S E, Paish C E, et al. Expression of luminal and basal cytokeratins in human breast carcinoma. J Pathol 2004; 203: 661–671
   PubMed Web of Science ®Google Scholar
• Gusterson B A, Ross D T, Heath V J, Stein T. Basal cytokeratins and their relationship to the cellular origin and functional classification of breast cancer. Breast Cancer Res 2005; 7: 143–148
   PubMed Web of Science ®Google Scholar
• Nielsen T O, Hsu F D, Jensen K, et al. Immunohistochemical and clinical characterization of the basal-like subtype of invasive breast carcinoma. Clin Cancer Res 2004; 10: 5367–5374
   PubMed Web of Science ®Google Scholar
• Rakha E A, Putti T C, Abd El-Rehim D M, et al. Morphological and immunophenotypic analysis of breast carcinomas with basal and myoepithelial differentiation. J Pathol 2006; 208: 495–506
   PubMed Web of Science ®Google Scholar
• Savage K, Lambros M B, Robertson D, et al. Caveolin 1 is overexpressed and amplified in a subset of basal-like and metaplastic breast carcinomas: a morphologic, ultrastructural, immunohistochemical, and in situ hybridization analysis. Clin Cancer Res 2007; 13: 90–101
   PubMed Web of Science ®Google Scholar
• Savage K, Leung S, Todd S K, et al. Distribution and significance of caveolin 2 expression in normal breast and invasive breast cancer: an immunofluorescence and immunohistochemical analysis. Breast Cancer Res Treat 2008; 110: 245–256
   PubMed Web of Science ®Google Scholar
• Turner N C, Reis-Filho J S. Basal-like breast cancer and the BRCA1 phenotype. Oncogene 2006; 25: 5846–5853
   PubMed Web of Science ®Google Scholar
• van de Rijn M, Perou C M, Tibshirani R, et al. Expression of cytokeratins 17 and 5 identifies a group of breast carcinomas with poor clinical outcome. Am J Pathol 2002; 161: 1991–1996
   PubMed Web of Science ®Google Scholar
• Fulford L G, Easton D F, Reis-Filho J S, et al. Specific morphological features predictive for the basal phenotype in grade 3 invasive ductal carcinoma of breast. Histopathology 2006; 49: 22–34
   PubMed Web of Science ®Google Scholar
• Livasy C A, Karaca G, Nanda R, et al. Phenotypic evaluation of the basal-like subtype of invasive breast carcinoma. Mod Pathol 2006; 19: 264–271
   PubMed Web of Science ®Google Scholar
• Reis-Filho J S, Milanezi F, Steele D, et al. Metaplastic breast carcinomas are basal-like tumours. Histopathology 2006; 49: 10–21
   PubMed Web of Science ®Google Scholar
• Turner N C, Reis-Filho J S, Russell A M, et al. BRCA1 dysfunction in sporadic basal-like breast cancer. Oncogene 2007; 26: 2126–2132
   PubMed Web of Science ®Google Scholar
• Liu X, Holstege H, van der Gulden H, et al. Somatic loss of BRCA1 and p53 in mice induces mammary tumors with features of human BRCA1-mutated basal-like breast cancer. Proc Natl Acad Sci USA 2007; 104: 12111–12116
   PubMed Web of Science ®Google Scholar
• McCarthy A, Savage K, Gabriel A, et al. A mouse model of basal-like breast carcinoma with metaplastic elements. J Pathol 2007; 211: 389–398
   PubMed Web of Science ®Google Scholar
• Dairkee S H, Mayall B H, Smith H S, Hackett A J. Monoclonal marker that predicts early recurrence of breast cancer. Lancet 1987; 1: 514
   PubMed Web of Science ®Google Scholar
• Gould V E, Koukoulis G K, Jansson D S, et al. Coexpression patterns of vimentin and glial filament protein with cytokeratins in the normal, hyperplastic, and neoplastic breast. Am J Pathol 1990; 137: 1143–1155
   PubMed Web of Science ®Google Scholar
• Malzahn K, Mitze M, Thoenes M, Moll R. Biological and prognostic significance of stratified epithelial cytokeratins in infiltrating ductal breast carcinomas. Virchows Arch 1998; 433: 119–129
   PubMed Web of Science ®Google Scholar
• Murad T M, Scharpelli D G. The ultrastructure of medullary and scirrhous mammary duct carcinoma. Am J Pathol 1967; 50: 335–360
   PubMed Web of Science ®Google Scholar
• Santini D, Ceccarelli C, Taffurelli M, Pileri S, Marrano D. Differentiation pathways in primary invasive breast carcinoma as suggested by intermediate filament and biopathological marker expression. J Pathol 1996; 179: 386–391
   PubMed Web of Science ®Google Scholar
• Kreike B, van Kouwenhove M, Horlings H, et al. Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas. Breast Cancer Res 2007; 9: R65
   PubMed Web of Science ®Google Scholar
• Banerjee S, Reis-Filho J S, Ashley S, et al. Basal-like breast carcinomas: clinical outcome and response to chemotherapy. J Clin Pathol 2006; 59: 729–735
   PubMed Web of Science ®Google Scholar
• Rakha E A, El-Sayed M E, Green A R, et al. Prognostic markers in triple-negative breast cancer. Cancer 2007; 109: 25–32
   PubMed Web of Science ®Google Scholar
• Rakha E A, Tan D S, Foulkes W D, et al. Are triple-negative tumours and basal-like breast cancer synonymous?. Breast Cancer Res 2007; 9: 404, author reply 405
   PubMed Web of Science ®Google Scholar
• Cheang M C, Voduc D, Bajdik C, et al. Basal-like breast cancer defined by five biomarkers has superior prognostic value than triple-negative phenotype. Clin Cancer Res 2008; 14: 1368–1376
   PubMed Web of Science ®Google Scholar
• Bertucci F, Finetti P, Cervera N, et al. How basal are triple-negative breast cancers?. Int J Cancer 2008; 123: 236–240
   PubMed Web of Science ®Google Scholar
• Calza S, Hall P, Auer G, et al. Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients. Breast Cancer Res 2006; 8: R34
   PubMed Web of Science ®Google Scholar
• Jumppanen M, Gruvberger-Saal S, Kauraniemi P, et al. Basal-like phenotype is not associated with patient survival in estrogen-receptor-negative breast cancers. Breast Cancer Res 2007; 9: R16
   PubMed Web of Science ®Google Scholar
• Tan D S, Marchio C, Jones R L, et al. Triple negative breast cancer: molecular profiling and prognostic impact in adjuvant anthracycline-treated patients. Breast Cancer Res Treat 2008; 111: 27–44
   PubMed Web of Science ®Google Scholar
• Parker J, Mullins M, Cheang M C, et al. A supervised risk predictor of breast cancer based on biological subtypes. J Clin Oncol 2008; 26: (in press)
   Web of Science ®Google Scholar
• Perreard L, Fan C, Quackenbush J F, et al. Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay. Breast Cancer Res 2006; 8: R23
   PubMed Web of Science ®Google Scholar
• Rakha E A, Reis-Filho J S, Ellis I O. Basal-like breast cancer: a critical review. J Clin Oncol 2008; 26: 2568–2581
   PubMed Web of Science ®Google Scholar
• Abd El-Rehim D M, Ball G, Pinder S E, et al. High-throughput protein expression analysis using tissue microarray technology of a large well-characterised series identifies biologically distinct classes of breast cancer confirming recent cDNA expression analyses. Int J Cancer 2005; 116: 340–350
   PubMed Web of Science ®Google Scholar
• Fulford L G, Reis-Filho J S, Ryder K, et al. Basal-like grade III invasive ductal carcinoma of the breast: patterns of metastasis and long-term survival. Breast Cancer Res 2007; 9: R4
   PubMed Web of Science ®Google Scholar
• Carey L A, Dees E C, Sawyer L, et al. The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin Cancer Res 2007; 13: 2329–2334
   PubMed Web of Science ®Google Scholar
• Dent R, Trudeau M, Pritchard K I, et al. Triple-negative breast cancer: clinical features and patterns of recurrence. Clin Cancer Res 2007; 13: 4429–4434
   PubMed Web of Science ®Google Scholar
• Liedtke C, Mazouni C, Hess K R, et al. Response to neoadjuvant therapy and long-term survival in patients with triple-negative breast cancer. J Clin Oncol 2008; 26: 1275–1281
   PubMed Web of Science ®Google Scholar
• Jones C, Ford E, Gillett C, et al. Molecular cytogenetic identification of subgroups of grade III invasive ductal breast carcinomas with different clinical outcomes. Clin Cancer Res 2004; 10: 5988–5997
   PubMed Web of Science ®Google Scholar
• Honeth G, Bendahl P O, Ringner M, et al. The CD44+/CD24- phenotype is enriched in basal-like breast tumors. Breast Cancer Res 2008; 10: R53
   PubMed Web of Science ®Google Scholar
• Wright M H, Calcagno A M, Salcido C D, et al. Brca1 breast tumors contain distinct CD44+/CD24- and CD133+ cells with cancer stem cell characteristics. Breast Cancer Res 2008; 10: R10
   PubMed Web of Science ®Google Scholar
• Krag D, Weaver D, Ashikaga T, et al. The sentinel node in breast cancer—a multicenter validation study. N Engl J Med 1998; 339: 941–946
   PubMed Web of Science ®Google Scholar
• Veronesi U, Paganelli G, Galimberti V, et al. Sentinel-node biopsy to avoid axillary dissection in breast cancer with clinically negative lymph-nodes. Lancet 1997; 349: 1864–1867
   PubMed Web of Science ®Google Scholar
• Rutgers E J. Sentinel node biopsy: interpretation and management of patients with immunohistochemistry-positive sentinel nodes and those with micrometastases. J Clin Oncol 2008; 26: 698–702
   PubMed Web of Science ®Google Scholar
• Viale G, Maiorano E, Mazzarol G, et al. Histologic detection and clinical implications of micrometastases in axillary sentinel lymph nodes for patients with breast carcinoma. Cancer 2001; 92: 1378–1384
   PubMed Web of Science ®Google Scholar
• Eifel P, Axelson J A, Costa J, et al. National Institutes of Health Consensus Development Conference Statement: adjuvant therapy for breast cancer, November 1–3, 2000. J Natl Cancer Inst 2001; 93: 979–989
   PubMed Web of Science ®Google Scholar
• Goldhirsch A, Wood W C, Gelber R D, et al. Meeting highlights: updated international expert consensus on the primary therapy of early breast cancer. J Clin Oncol 2003; 21: 3357–3365
   PubMed Web of Science ®Google Scholar
• van't Veer L J, Dai H, van de Vijver M J, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002; 415: 530–536
   PubMed Web of Science ®Google Scholar
• Buyse M, Loi S, van't Veer L, et al. Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J Natl Cancer Inst 2006; 98: 1183–1192
   PubMed Web of Science ®Google Scholar
• van de Vijver M J, He Y D, van't Veer L J, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002; 347: 1999–2009
   PubMed Web of Science ®Google Scholar
• Wang Y, Klijn J G, Zhang Y, et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005; 365: 671–679
   PubMed Web of Science ®Google Scholar
• Dunkler D, Michiels S, Schemper M. Gene expression profiling: does it add predictive accuracy to clinical characteristics in cancer prognosis?. Eur J Cancer 2007; 43: 745–751
   PubMed Web of Science ®Google Scholar
• Eden P, Ritz C, Rose C, Ferno M, Peterson C. ‘Good Old’ clinical markers have similar power in breast cancer prognosis as microarray gene expression profilers. Eur J Cancer 2004; 40: 1837–1841
   PubMed Web of Science ®Google Scholar
• Lu X, Lu X, Wang Z C, et al. Predicting features of breast cancer with gene expression patterns. Breast Cancer Res Treat 2008; 108: 191–201
   PubMed Web of Science ®Google Scholar
• Fan C, Oh D S, Wessels L, et al. Concordance among gene-expression-based predictors for breast cancer. N Engl J Med 2006; 355: 560–569
   PubMed Web of Science ®Google Scholar
• Sotiriou C, Piccart M J. Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care?. Nat Rev Cancer 2007; 7: 545–553
   PubMed Web of Science ®Google Scholar
• Ioannidis J P. Microarrays and molecular research: noise discovery?. Lancet 2005; 365: 454–455
   PubMed Web of Science ®Google Scholar
• Michiels S, Koscielny S, Hill C. Interpretation of microarray data in cancer. Br J Cancer 2007; 96: 1155–1158
   PubMed Web of Science ®Google Scholar
• Ein-Dor L, Zuk O, Domany E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 2006; 103: 5923–5928
   PubMed Web of Science ®Google Scholar
• Simon R. Roadmap for developing and validating therapeutically relevant genomic classifiers. J Clin Oncol 2005; 23: 7332–7341
   PubMed Web of Science ®Google Scholar
• Simon R, Radmacher M D, Dobbin K, McShane L M. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003; 95: 14–18
   PubMed Web of Science ®Google Scholar
• Shi L, Reid L H, Jones W D, et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006; 24: 1151–1161
   PubMed Web of Science ®Google Scholar
• Ravo M, Mutarelli M, Ferraro L, et al. Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays. Lab Invest 2008; 88: 430–440
   PubMed Web of Science ®Google Scholar
• Paik S, Shak S, Tang G, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004; 351: 2817–2826
   PubMed Web of Science ®Google Scholar
• Esteva F J, Sahin A A, Cristofanilli M, et al. Prognostic role of a multigene reverse transcriptase-PCR assay in patients with node-negative breast cancer not receiving adjuvant systemic therapy. Clin Cancer Res 2005; 11: 3315–3319
   PubMed Web of Science ®Google Scholar
• Mina L, Soule S E, Badve S, et al. Predicting response to primary chemotherapy: gene expression profiling of paraffin-embedded core biopsy tissue. Breast Cancer Res Treat 2007; 103: 197–208
   PubMed Web of Science ®Google Scholar
• Flanagan M B, Dabbs D J, Brufsky A M, Beriwal S, Bhargava R. Histopathologic variables predict Oncotype DX recurrence score. Mod Pathol 2008; 21: 1255–1261
   PubMed Web of Science ®Google Scholar
• Pusztai L, Cristofanilli M, Paik S. New generation of molecular prognostic and predictive tests for breast cancer. Semin Oncol 2007; 34: S10–S16
   PubMed Web of Science ®Google Scholar
• Rosai J. Why microscopy will remain a cornerstone of surgical pathology. Lab Invest 2007; 87: 403–408
   PubMed Web of Science ®Google Scholar
• Ma X J, Salunga R, Tuggle J T, et al. Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci USA 2003; 100: 5974–5979
   PubMed Web of Science ®Google Scholar
• Elston C W, Ellis I O. Pathological prognostic factors in breast cancer. I. The value of histological grade in breast cancer: experience from a large study with long-term follow-up. Histopathology 1991; 19: 403–410
   PubMed Web of Science ®Google Scholar
• Robbins P, Pinder S, de Klerk N, et al. Histological grading of breast carcinomas: a study of interobserver agreement. Hum Pathol 1995; 26: 873–879
   PubMed Web of Science ®Google Scholar
• Sotiriou C, Wirapati P, Loi S, et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 2006; 98: 262–272
   PubMed Web of Science ®Google Scholar
• Desmedt C, Sotiriou C. Proliferation: the most prominent predictor of clinical outcome in breast cancer. Cell Cycle 2006; 5: 2198–2202
   PubMed Web of Science ®Google Scholar
• Loi S, Haibe-Kains B, Desmedt C, et al. Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. J Clin Oncol 2007; 25: 1239–1246
   PubMed Web of Science ®Google Scholar
• Ivshina A V, George J, Senko O, et al. Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Cancer Res 2006; 66: 10292–10301
   PubMed Web of Science ®Google Scholar
• Ma X J, Salunga R, Dahiya S, et al. A five-gene molecular grade index and HOXB13:IL17BR are complementary prognostic factors in early stage breast cancer. Clin Cancer Res 2008; 14: 2601–2608
   PubMed Web of Science ®Google Scholar
• Andre F, Mazouni C, Hortobagyi G N, Pusztai L. DNA arrays as predictors of efficacy of adjuvant/neoadjuvant chemotherapy in breast cancer patients: current data and issues on study design. Biochim Biophys Acta 2006; 1766: 197–204
   PubMed Web of Science ®Google Scholar
• Andre F, Pusztai L. Molecular classification of breast cancer: implications for selection of adjuvant chemotherapy. Nat Clin Pract Oncol 2006; 3: 621–632
   PubMedGoogle Scholar
• Tordai A, Wang J, Andre F, et al. Evaluation of biological pathways involved in chemotherapy response in breast cancer. Breast Cancer Res 2008; 10: R37
   PubMed Web of Science ®Google Scholar
• Loi S, Haibe-Kains B, Desmedt C, et al. Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics 2008; 9: 239
   PubMed Web of Science ®Google Scholar
• Ma X J, Wang Z, Ryan P D, et al. A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell 2004; 5: 607–616
   PubMed Web of Science ®Google Scholar
• Reid J F, Lusa L, De Cecco L, et al. Limits of predictive models using microarray data for breast cancer clinical treatment outcome. J Natl Cancer Inst 2005; 97: 927–930
   PubMed Web of Science ®Google Scholar
• Goetz M P, Suman V J, Ingle J N, et al. A two-gene expression ratio of homeobox 13 and interleukin-17B receptor for prediction of recurrence and survival in women receiving adjuvant tamoxifen. Clin Cancer Res 2006; 12: 2080–2087
   PubMed Web of Science ®Google Scholar
• Ma X J, Hilsenbeck S G, Wang W, et al. The HOXB13:IL17BR expression index is a prognostic factor in early-stage breast cancer. J Clin Oncol 2006; 24: 4611–4619
   PubMed Web of Science ®Google Scholar
• Hudis C A. Trastuzumab—mechanism of action and use in clinical practice. N Engl J Med 2007; 357: 39–51
   PubMed Web of Science ®Google Scholar
• Harris L N, You F, Schnitt S J, et al. Predictors of resistance to preoperative trastuzumab and vinorelbine for HER2-positive early breast cancer. Clin Cancer Res 2007; 13: 1198–1207
   PubMed Web of Science ®Google Scholar
• Muss H B, Thor A D, Berry D A, et al. c-erbB-2 expression and response to adjuvant therapy in women with node-positive early breast cancer. N Engl J Med 1994; 330: 1260–1266
   PubMed Web of Science ®Google Scholar
• Paik S, Bryant J, Park C, et al. erbB-2 and response to doxorubicin in patients with axillary lymph node-positive, hormone receptor-negative breast cancer. J Natl Cancer Inst 1998; 90: 1361–1370
   PubMed Web of Science ®Google Scholar
• Wang J C. DNA topoisomerases. Annu Rev Biochem 1996; 65: 635–692
   PubMed Web of Science ®Google Scholar
• Arriola E, Marchio C, Tan D S, et al. Genomic analysis of the HER2/TOP2A amplicon in breast cancer and breast cancer cell lines. Lab Invest 2008; 88: 491–503
   PubMed Web of Science ®Google Scholar
• Arriola E, Rodriguez-Pinilla S M, Lambros M B, et al. Topoisomerase II alpha amplification may predict benefit from adjuvant anthracyclines in HER2 positive early breast cancer. Breast Cancer Res Treat 2007; 106: 181–189
   PubMed Web of Science ®Google Scholar
• Hicks D G, Yoder B J, Pettay J, et al. The incidence of topoisomerase II-alpha genomic alterations in adenocarcinoma of the breast and their relationship to human epidermal growth factor receptor-2 gene amplification: a fluorescence in situ hybridization study. Hum Pathol 2005; 36: 348–356
   PubMed Web of Science ®Google Scholar
• Jarvinen T A, Tanner M, Barlund M, Borg A, Isola J. Characterization of topoisomerase II alpha gene amplification and deletion in breast cancer. Genes Chromosomes Cancer 1999; 26: 142–150
   PubMed Web of Science ®Google Scholar
• Orlando L, Del Curto B, Gandini S, et al. Topoisomerase IIalpha gene status and prediction of pathological complete remission after anthracycline-based neoadjuvant chemotherapy in endocrine non-responsive Her2/neu-positive breast cancer. Breast 2008; 17: 506–511
   PubMed Web of Science ®Google Scholar
• Tanner M, Isola J, Wiklund T, et al. Topoisomerase IIalpha gene amplification predicts favorable treatment response to tailored and dose-escalated anthracycline-based adjuvant chemotherapy in HER-2/neu-amplified breast cancer: Scandinavian Breast Group Trial 9401. J Clin Oncol 2006; 24: 2428–2436
   PubMed Web of Science ®Google Scholar
• Allinen M, Beroukhim R, Cai L, et al. Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell 2004; 6: 17–32
   PubMed Web of Science ®Google Scholar
• Beck A H, Espinosa I, Gilks C B, van de Rijn M, West R B. The fibromatosis signature defines a robust stromal response in breast carcinoma. Lab Invest 2008; 88: 591–601
   PubMed Web of Science ®Google Scholar
• Bergamaschi A, Tagliabue E, Sorlie T, et al. Extracellular matrix signature identifies breast cancer subgroups with different clinical outcome. J Pathol 2008; 214: 357–367
   PubMed Web of Science ®Google Scholar
• Casey T, Bond J, Tighe S, et al. Molecular signatures suggest a major role for stromal cells in development of invasive breast cancer. Breast Cancer Res Treat 2008; Mar 29, Epub ahead of print
   Google Scholar
• Finak G, Bertos N, Pepin F, et al. Stromal gene expression predicts clinical outcome in breast cancer. Nat Med 2008; 14: 518–527
   PubMed Web of Science ®Google Scholar
• Weigelt B, Bissell M J. Unraveling the microenvironmental influences on the normal mammary gland and breast cancer. Semin Cancer Biol 2008; 18: 311–321
   PubMed Web of Science ®Google Scholar
• West R B, Nuyten D S, Subramanian S, et al. Determination of stromal signatures in breast carcinoma. PLoS Biol 2005; 3: e187
   PubMed Web of Science ®Google Scholar
• Hu M, Yao J, Carroll D K, et al. Regulation of in situ to invasive breast carcinoma transition. Cancer Cell 2008; 13: 394–406
   PubMed Web of Science ®Google Scholar
• Jones C, Mackay A, Grigoriadis A, et al. Expression profiling of purified normal human luminal and myoepithelial breast cells: identification of novel prognostic markers for breast cancer. Cancer Res 2004; 64: 3037–3045
   PubMed Web of Science ®Google Scholar
• Teschendorff A E, Miremadi A, Pinder S E, Ellis I O, Caldas C. An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer. Genome Biol 2007; 8: R157
   PubMed Web of Science ®Google Scholar
• Tan D S, Lambros M B, Natrajan R, Reis-Filho J S. Getting it right: designing microarray (and not ‘microawry’) comparative genomic hybridization studies for cancer research. Lab Invest 2007; 87: 737–754
   PubMed Web of Science ®Google Scholar
• Bergamaschi A, Kim Y H, Wang P, et al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 2006; 45: 1033–1040
   PubMed Web of Science ®Google Scholar
• Hicks J, Krasnitz A, Lakshmi B, et al. Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 2006; 16: 1465–1479
   PubMed Web of Science ®Google Scholar
• Chin K, DeVries S, Fridlyand J, et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006; 10: 529–541
   PubMed Web of Science ®Google Scholar
• Vogelstein B, Fearon E R, Hamilton S R, et al. Genetic alterations during colorectal-tumor development. N Engl J Med 1988; 319: 525–532
   PubMed Web of Science ®Google Scholar
• Buerger H, Otterbach F, Simon R, et al. Comparative genomic hybridization of ductal carcinoma in situ of the breast-evidence of multiple genetic pathways. J Pathol 1999; 187: 396–402
   PubMed Web of Science ®Google Scholar
• Buerger H, Otterbach F, Simon R, et al. Different genetic pathways in the evolution of invasive breast cancer are associated with distinct morphological subtypes. J Pathol 1999; 189: 521–526
   PubMed Web of Science ®Google Scholar
• Roylance R, Gorman P, Harris W, et al. Comparative genomic hybridization of breast tumors stratified by histological grade reveals new insights into the biological progression of breast cancer. Cancer Res 1999; 59: 1433–1436
   PubMed Web of Science ®Google Scholar
• Stange D E, Radlwimmer B, Schubert F, et al. High-resolution genomic profiling reveals association of chromosomal aberrations on 1q and 16p with histologic and genetic subgroups of invasive breast cancer. Clin Cancer Res 2006; 12: 345–352
   PubMed Web of Science ®Google Scholar
• Cleton-Jansen A M, Buerger H, Haar N, et al. Different mechanisms of chromosome 16 loss of heterozygosity in well- versus poorly differentiated ductal breast cancer. Genes Chromosomes Cancer 2004; 41: 109–116
   PubMed Web of Science ®Google Scholar
• Waldman F M, DeVries S, Chew K L, et al. Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences. J Natl Cancer Inst 2000; 92: 313–320
   PubMedGoogle Scholar
• Allred D C, Wu Y, Mao S, et al. Ductal carcinoma in situ and the emergence of diversity during breast cancer evolution. Clin Cancer Res 2008; 14: 370–378
   PubMed Web of Science ®Google Scholar
• Weigelt B, Horlings H, Kreike B, et al. Refinement of breast cancer classification by molecular characterization of histological special types. J Pathol 2008; 216: 141–150
   PubMed Web of Science ®Google Scholar
• Kumar R, Neilsen P M, Crawford J, et al. FBXO31 is the chromosome 16q24.3 senescence gene, a candidate breast tumor suppressor, and a component of an SCF complex. Cancer Res 2005; 65: 11304–11313
   PubMed Web of Science ®Google Scholar
• Rakha E A, Green A R, Powe D G, Roylance R, Ellis I O. Chromosome 16 tumor-suppressor genes in breast cancer. Genes Chromosomes Cancer 2006; 45: 527–535
   PubMed Web of Science ®Google Scholar
• van Wezel T, Lombaerts M, van Roon E H, et al. Expression analysis of candidate breast tumour suppressor genes on chromosome 16q. Breast Cancer Res 2005; 7: R998–1004
   PubMed Web of Science ®Google Scholar
• Cleton-Jansen A M. E-cadherin and loss of heterozygosity at chromosome 16 in breast carcinogenesis: different genetic pathways in ductal and lobular breast cancer?. Breast Cancer Res 2002; 4: 5–8
   PubMed Web of Science ®Google Scholar
• Vos C B, Cleton-Jansen A M, Berx G, et al. E-cadherin inactivation in lobular carcinoma in situ of the breast: an early event in tumorigenesis. Br J Cancer 1997; 76: 1131–1133
   PubMed Web of Science ®Google Scholar
• Droufakou S, Deshmane V, Roylance R, et al. Multiple ways of silencing E-cadherin gene expression in lobular carcinoma of the breast. Int J Cancer 2001; 92: 404–408
   PubMed Web of Science ®Google Scholar
• Sarrio D, Moreno-Bueno G, Hardisson D, et al. Epigenetic and genetic alterations of APC and CDH1 genes in lobular breast cancer: relationships with abnormal E-cadherin and catenin expression and microsatellite instability. Int J Cancer 2003; 106: 208–215
   PubMed Web of Science ®Google Scholar
• Jacobs T W, Pliss N, Kouria G, Schnitt S J. Carcinomas in situ of the breast with indeterminate features: role of E-cadherin staining in categorization. Am J Surg Pathol 2001; 25: 229–236
   PubMed Web of Science ®Google Scholar
• Maluf H M. Differential diagnosis of solid carcinoma in situ. Semin Diagn Pathol 2004; 21: 25–31
   PubMed Web of Science ®Google Scholar
• Nishizaki T, Chew K, Chu L, et al. Genetic alterations in lobular breast cancer by comparative genomic hybridization. Int J Cancer 1997; 74: 513–517
   PubMed Web of Science ®Google Scholar
• Palacios J, Sarrio D, Garcia-Macias M C, et al. Frequent E-cadherin gene inactivation by loss of heterozygosity in pleomorphic lobular carcinoma of the breast. Mod Pathol 2003; 16: 674–678
   PubMed Web of Science ®Google Scholar
• Reis-Filho J S, Simpson P T, Jones C, et al. Pleomorphic lobular carcinoma of the breast: role of comprehensive molecular pathology in characterization of an entity. J Pathol 2005; 207: 1–13
   PubMed Web of Science ®Google Scholar
• Simpson P, Reis-Filho J, Lambros M, et al. Molecular profiling pleomorphic lobular carcinomas of the breast: evidence for a common molecular genetic pathway with classic lobular carcinomas. J Pathol 2008; 215: 231–244
   PubMed Web of Science ®Google Scholar
• Boecker W, Buerger H, Schmitz K, et al. Ductal epithelial proliferations of the breast: a biological continuum? Comparative genomic hybridization and high-molecular-weight cytokeratin expression patterns. J Pathol 2001; 195: 415–421
   PubMed Web of Science ®Google Scholar
• Boecker W, Moll R, Dervan P, et al. Usual ductal hyperplasia of the breast is a committed stem (progenitor) cell lesion distinct from atypical ductal hyperplasia and ductal carcinoma in situ. J Pathol 2002; 198: 458–467
   PubMed Web of Science ®Google Scholar
• O'Connell P. Genetic and cytogenetic analyses of breast cancer yield different perspectives of a complex disease. Breast Cancer Res Treat 2003; 78: 347–357
   PubMed Web of Science ®Google Scholar
• Simpson P T, Gale T, Reis-Filho J S, et al. Columnar cell lesions of the breast: the missing link in breast cancer progression? A morphological and molecular analysis. Am J Surg Pathol 2005; 29: 734–746
   PubMed Web of Science ®Google Scholar
• Jones C, Nonni A V, Fulford L, et al. CGH analysis of ductal carcinoma of the breast with basaloid/myoepithelial cell differentiation. Br J Cancer 2001; 85: 422–427
   PubMed Web of Science ®Google Scholar
• Abdel-Fatah T M, Powe D G, Hodi Z, et al. High frequency of coexistence of columnar cell lesions, lobular neoplasia, and low grade ductal carcinoma in situ with invasive tubular carcinoma and invasive lobular carcinoma. Am J Surg Pathol 2007; 31: 417–426
   PubMed Web of Science ®Google Scholar
• Tognon C, Knezevich S R, Huntsman D, et al. Expression of the ETV6-NTRK3 gene fusion as a primary event in human secretory breast carcinoma. Cancer Cell 2002; 2: 367–376
   PubMed Web of Science ®Google Scholar
• Diallo R, Schaefer K L, Bankfalvi A, et al. Secretory carcinoma of the breast: a distinct variant of invasive ductal carcinoma assessed by comparative genomic hybridization and immunohistochemistry. Hum Pathol 2003; 34: 1299–1305
   PubMed Web of Science ®Google Scholar
• Diallo R, Tognon C, Knezevich S R, Sorensen P, Poremba C. Secretory carcinoma of the breast: a genetically defined carcinoma entity. Verh Dtsch Ges Pathol 2003; 87: 193–203
   PubMedGoogle Scholar
• Makretsov N, He M, Hayes M, et al. A fluorescence in situ hybridization study of ETV6-NTRK3 fusion gene in secretory breast carcinoma. Genes Chromosomes Cancer 2004; 40: 152–157
   PubMed Web of Science ®Google Scholar
• Reis-Filho J S, Natrajan R, Vatcheva R, et al. Is acinic cell carcinoma a variant of secretory carcinoma? A FISH study using ETV6 ‘split apart’ probes. Histopathology 2008; 52: 840–846
   PubMed Web of Science ®Google Scholar
• Lakhani S R, Jacquemier J, Sloane J P, et al. Multifactorial analysis of differences between sporadic breast cancers and cancers involving BRCA1 and BRCA2 mutations. J Natl Cancer Inst 1998; 90: 1138–1145
   PubMedGoogle Scholar
• Honrado E, Benitez J, Palacios J. The molecular pathology of hereditary breast cancer: genetic testing and therapeutic implications. Mod Pathol 2005; 18: 1305–1320
   PubMed Web of Science ®Google Scholar
• Tan D S, Marchio C, Reis-Filho J S. Hereditary breast cancer: from molecular pathology to tailored therapies. J Clin Pathol 2008; 61: 1073–1082
   PubMed Web of Science ®Google Scholar
• Lakhani S R, Van De Vijver M J, Jacquemier J, et al. The pathology of familial breast cancer: predictive value of immunohistochemical markers estrogen receptor, progesterone receptor, HER-2, and p53 in patients with mutations in BRCA1 and BRCA2. J Clin Oncol 2002; 20: 2310–2318
   PubMed Web of Science ®Google Scholar
• Lakhani S R, Reis-Filho J S, Fulford L, et al. Prediction of BRCA1 status in patients with breast cancer using estrogen receptor and basal phenotype. Clin Cancer Res 2005; 11: 5175–5180
   PubMed Web of Science ®Google Scholar
• Foulkes W D, Stefansson I M, Chappuis P O, et al. Germline BRCA1 mutations and a basal epithelial phenotype in breast cancer. J Natl Cancer Inst 2003; 95: 1482–1485
   PubMed Web of Science ®Google Scholar
• Marchio C, Iravani M, Natrajan R, et al. Genomic and immunophenotypical characterization of pure micropapillary carcinomas of the breast. J Pathol 2008; 215: 398–410
   PubMed Web of Science ®Google Scholar
• Weinstein I B. Cancer. Addiction to oncogenes—the Achilles heal of cancer. Science 2002; 297: 63–64
   PubMed Web of Science ®Google Scholar
• Weinstein I B, Joe A K. Mechanisms of disease: Oncogene addiction—a rationale for molecular targeting in cancer therapy. Nat Clin Pract Oncol 2006; 3: 448–457
   PubMedGoogle Scholar