Meta-analysis of gene expression profiles related to relapse-free survival in 1,079 breast cancer patients

Breast Cancer Research and Treatment

Volumn 118, Issue 3, 2009, Pages 433-441

  Györffy, Balazs ^a,b   Schäfer, Reinhold ^c  

^a SEMMELWEIS UNIVERSITY   (Hungary)

^b HARVARD MIT DIVISION OF HEALTH SCIENCES AND TECHNOLOGY   (United States)

^c CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

Bioinformatics; Breast cancer prognosis; Gene expression signature; Microarray

Indexed keywords

ARTICLE; BREAST CANCER; CANCER EPIDEMIOLOGY; CANCER PATIENT; CANCER RELAPSE; CLINICAL TRIAL; CONTROL GROUP; DISEASE FREE SURVIVAL; FOLLOW UP; GENE EXPRESSION PROFILING; HUMAN; KAPLAN MEIER METHOD; META ANALYSIS; MICROARRAY ANALYSIS; PRIORITY JOURNAL; STATISTICAL SIGNIFICANCE; SYSTEMATIC REVIEW;

BREAST NEOPLASMS; DATABASES, GENETIC; DISEASE-FREE SURVIVAL; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; KAPLAN-MEIERS ESTIMATE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; PROGNOSIS; TUMOR MARKERS, BIOLOGICAL;

EID: 70449553671     PISSN: 01676806     EISSN: 15737217     Source Type: Journal    
DOI: 10.1007/s10549-008-0242-8     Document Type: Article

References (41)

1. P Surowiak V Materna B Gyorffy, et al. 2006 Multivariate analysis of oestrogen receptor alpha, pS2, metallothionein and CD24 expression in invasive breast cancers Br J Cancer 95 339 346 10.1038/sj.bjc.6603254 10.1038/sj.bjc.6603254 1:CAS:528:DC%2BD28Xnsl2hsr8%3D 16892043 (Pubitemid 44187595)
2. T Sorlie CM Perou R Tibshirani, et al. 2001 Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications Proc Natl Acad Sci USA 98 10869 10874 10.1073/pnas.191367098 10.1073/pnas.191367098 1:CAS:528:DC%2BD3MXntVGmsbo%3D 11553815 (Pubitemid 32878711)
3. C Sotiriou P Wirapati S Loi, et al. 2006 Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis J Natl Cancer Inst 98 262 272 1:CAS:528:DC%2BD28Xhs1Skt74%3D 16478745
4. Z Hu C Fan DS Oh, et al. 2006 The molecular portraits of breast tumors are conserved across microarray platforms BMC Genomics 7 96 10.1186/1471-2164-7- 96 10.1186/1471-2164-7-96 16643655 (Pubitemid 43786485)
5. AV Ivshina J George O Senko, et al. 2006 Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer Cancer Res 66 10292 10301 10.1158/0008-5472.CAN-05-4414 10.1158/0008-5472.CAN-05-4414 1:CAS:528:DC%2BD28XhtFGjsrjM 17079448 (Pubitemid 44799747)
6. OW Petersen PE Hoyer DB van 1987 Frequency and distribution of estrogen receptor-positive cells in normal, nonlactating human breast tissue Cancer Res 47 5748 5751 1:STN:280:DyaL1c%2Fis1OnsQ%3D%3D 3664479
7. T Kuukasjarvi J Kononen H Helin, et al. 1996 Loss of estrogen receptor in recurrent breast cancer is associated with poor response to endocrine therapy J Clin Oncol 14 2584 2589 1:CAS:528:DyaK28XlvVGisL0%3D 8823339
8. S Gruvberger M Ringner Y Chen, et al. 2001 Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns Cancer Res 61 5979 5984 1:CAS:528:DC%2BD3MXmt12ktrw%3D 11507038
9. S Paik S Shak G Tang, et al. 2004 A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer N Engl J Med 351 2817 2826 10.1056/NEJMoa041588 10.1056/NEJMoa041588 1:CAS:528:DC%2BD2MXhslymsw%3D%3D 15591335 (Pubitemid 40051905)
10. S Loi B Haibe-Kains C Desmedt, et al. 2007 Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade J Clin Oncol 25 1239 1246 10.1200/JCO.2006.07.1522 10.1200/JCO.2006.07.1522 1:CAS:528:DC%2BD2sXkvFyms7w%3D 17401012 (Pubitemid 46640570)
11. DS Oh MA Troester J Usary, et al. 2006 Estrogen-regulated genes predict survival in hormone receptor-positive breast cancers J Clin Oncol 24 1656 1664 10.1200/JCO.2005.03.2755 10.1200/JCO.2005.03.2755 1:CAS:528:DC%2BD28XksVKgtL0%3D 16505416 (Pubitemid 46622136)
12. M West C Blanchette H Dressman, et al. 2001 Predicting the clinical status of human breast cancer by using gene expression profiles Proc Natl Acad Sci USA 98 11462 11467 10.1073/pnas.201162998 10.1073/pnas.201162998 1:CAS:528:DC%2BD3MXnt1yqu7w%3D 11562467 (Pubitemid 32928751)
13. DF Ransohoff 2004 Rules of evidence for cancer molecular-marker discovery and validation Nat Rev Cancer 4 309 314 10.1038/nrc1322 10.1038/nrc1322 1:CAS:528:DC%2BD2cXis1Gmt7g%3D 15057290
14. M Buyse S Loi L van't Veer, et al. 2006 Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer J Natl Cancer Inst 98 1183 1192 1:CAS:528:DC%2BD28Xps1yjtLw%3D 16954471
15. S Michiels S Koscielny C Hill 2005 Prediction of cancer outcome with microarrays: a multiple random validation strategy Lancet 365 488 492 10.1016/S0140-6736(05)17866-0 10.1016/S0140-6736(05)17866-0 1:CAS:528: DC%2BD2MXhtlSgt7s%3D 15705458 (Pubitemid 40215731)
16. JP Ioannidis 2005 Microarrays and molecular research: noise discovery? Lancet 365 454 455 15705441
17. A Naderi AE Teschendorff NL Barbosa-Morais, et al. 2007 A gene-expression signature to predict survival in breast cancer across independent data sets Oncogene 26 1507 1516 10.1038/sj.onc.1209920 10.1038/sj.onc.1209920 1:CAS:528:DC%2BD2sXit12rs7g%3D 16936776 (Pubitemid 46340809)
18. R Tibshirani T Hastie B Narasimhan, et al. 2002 Diagnosis of multiple cancer types by shrunken centroids of gene expression Proc Natl Acad Sci USA 99 6567 6572 10.1073/pnas.082099299 10.1073/pnas.082099299 1:CAS:528: DC%2BD38XjvFCktbg%3D 12011421 (Pubitemid 34526173)
19. E Bair R Tibshirani 2004 Semi-supervised methods to predict patient survival from gene expression data PLoS Biol 2 E108 10.1371/journal.pbio.0020108 10.1371/journal.pbio.0020108 15094809 (Pubitemid 39234509)
20. M Lauss A Kriegner K Vierlinger, et al. 2008 Consensus genes of the literature to predict breast cancer recurrence Breast Cancer Res Treat 110 235 244 10.1007/s10549-007-9716-3 10.1007/s10549-007-9716-3 17899371 (Pubitemid 351793872)
21. M Gormley W Dampier A Ertel, et al. 2007 Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets BMC Bioinformatics 8 415 10.1186/1471-2105-8-415 10.1186/1471-2105-8-415 17963508
22. EE Ntzani JP Ioannidis 2003 Predictive ability of DNA microarrays for cancer outcomes and correlates: an empirical assessment Lancet 362 1439 1444 10.1016/S0140-6736(03)14686-7 10.1016/S0140-6736(03)14686-7 1:CAS:528: DC%2BD3sXos1Cns78%3D 14602436 (Pubitemid 37352879)
23. R Simon MD Radmacher K Dobbin, et al. 2003 Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification J Natl Cancer Inst 95 14 18 1:CAS:528:DC%2BD3sXitlOntrY%3D 12509396 (Pubitemid 36124291)
24. S Dudoit J Fridlyand T Speed 2002 Comparison of discrimination methods for the classification of tumors using gene expression data J Am Stat Assoc 97 77 87 10.1198/016214502753479248 10.1198/016214502753479248 1:CAS:528: DC%2BD28Xht1SqtL7I
25. L Shi LH Reid WD Jones, et al. 2006 The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nat Biotechnol 24 1151 1161 10.1038/nbt1239 10.1038/nbt1239 1:CAS:528:DC%2BD28XptlSlsb4%3D 16964229 (Pubitemid 44359727)
26. Y Pawitan J Bjohle L Amler, et al. 2005 Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts Breast Cancer Res 7 R953 R964 10.1186/bcr1325 10.1186/bcr1325 1:CAS:528:DC%2BD2MXht1WmsrjM 16280042
27. YX Wang JGM Klijn Y Zhang, et al. 2005 Gene-expression pro-files to predict distant metastasis of lymph-node-negative primary breast cancer Lancet 365 671 679 1:CAS:528:DC%2BD2MXhsVOitLk%3D 15721472
28. LD Miller J Smeds J George, et al. 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 10.1073/pnas.0506230102 10.1073/pnas.0506230102 1:CAS:528:DC%2BD2MXhtVygtr7I 16141321 (Pubitemid 41420886)
29. C Desmedt F Piette S Loi, et al. 2007 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 13 3207 3214 10.1158/1078-0432.CCR-06-2765 10.1158/1078-0432.CCR-06-2765 1:CAS:528: DC%2BD2sXmtVajur0%3D 17545524 (Pubitemid 46944903)
30. LJ van 't Veer H Dai MJ van de Vijver, et al. 2002 Gene expression profiling predicts clinical outcome of breast cancer Nature 415 530 536 10.1038/415530a 10.1038/415530a 11823860 (Pubitemid 34130608)
31. MJ van de Vijver YD He LJ van 't Veer, et al. 2002 A gene-expression signature as a predictor of survival in breast cancer N Engl J Med 347 1999 2009 10.1056/NEJMoa021967 10.1056/NEJMoa021967 1:CAS:528:DC%2BD38Xps1Ojt7w%3D 12490681 (Pubitemid 35461656)
32. C Sotiriou SY Neo LM McShane, et al. 2003 Breast cancer classification and prognosis based on gene expression profiles from a population-based study Proc Natl Acad Sci USA 100 10393 10398 10.1073/pnas.1732912100 10.1073/pnas.1732912100 1:CAS:528:DC%2BD3sXntFynsrk%3D 12917485 (Pubitemid 37071889)
33. XJ Ma R Salunga JT Tuggle, et al. 2003 Gene expression profiles of human breast cancer progression Proc Natl Acad Sci USA 100 5974 5979 10.1073/pnas.0931261100 10.1073/pnas.0931261100 1:CAS:528:DC%2BD3sXjvFOlt78%3D 12714683 (Pubitemid 36576916)
34. S Ramaswamy KN Ross ES Lander, et al. 2003 A molecular signature of metastasis in primary solid tumors Nat Genet 33 49 54 10.1038/ng1060 10.1038/ng1060 1:CAS:528:DC%2BD38XpvVeqs7w%3D 12469122 (Pubitemid 36068681)
35. E Huang SH Cheng H Dressman, et al. 2003 Gene expression predictors of breast cancer outcomes Lancet 361 1590 1596 10.1016/S0140-6736(03)13308-9 10.1016/S0140-6736(03)13308-9 1:CAS:528:DC%2BD3sXjs1Wltbo%3D 12747878 (Pubitemid 36578995)
36. JC Chang EC Wooten A Tsimelzon, et al. 2003 Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer Lancet 362 362 369 10.1016/S0140-6736(03)14023-8 10.1016/S0140-6736(03) 14023-8 1:CAS:528:DC%2BD3sXlvFGnsLo%3D 12907009 (Pubitemid 36957839)
37. JA Foekens D Atkins Y Zhang, et al. 2006 Multicenter validation of a gene expression-based prognostic signature in lymph node-negative primary breast cancer J Clin Oncol 24 1665 1671 10.1200/JCO.2005.03.9115 10.1200/JCO.2005.03. 9115 1:CAS:528:DC%2BD28XksVKgtLo%3D 16505412 (Pubitemid 46622137)
38. S Paik G Tang S Shak, et al. 2006 Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer J Clin Oncol 24 3726 3734 10.1200/JCO.2005.04.7985 10.1200/JCO.2005.04. 7985 1:CAS:528:DC%2BD28XpsVaqsrs%3D 16720680 (Pubitemid 46622311)
39. AE Teschendorff A Miremadi SE Pinder, et al. 2007 An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer Genome Biol 8 R157 10.1186/gb-2007-8-8-r157 10.1186/gb-2007-8-8-r157 17683518 (Pubitemid 351891480)
40. JE Korkola E Blaveri S DeVries, et al. 2007 Identification of a robust gene signature that predicts breast cancer outcome in independent data sets BMC Cancer 7 61 10.1186/1471-2407-7-61 10.1186/1471-2407-7-61 17428335 (Pubitemid 46647961)
41. T Sorlie R Tibshirani J Parker, et al. 2003 Repeated observation of breast tumor subtypes in independent gene expression data sets Proc Natl Acad Sci USA 100 8418 8423 10.1073/pnas.0932692100 10.1073/pnas.0932692100 1:CAS:528:DC%2BD3sXlsFGntLk%3D 12829800 (Pubitemid 36842560)