Benefits of biomarker selection and clinico-pathological covariate inclusion in breast cancer prognostic models

Breast Cancer Research

Volumn 12, Issue 5, 2010, Pages

  Parisi, Fabio ^a,b,c   González, Ana M ^a,d   Nadler, Yasmine ^b   Camp, Robert L ^b   Rimm, David L ^b   Kluger, Harriet M ^b,c   Kluger, Yuval ^a,b,c  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c YALE CANCER CENTER   (United States)

^d UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; ESTROGEN RECEPTOR; MESSENGER RNA; PROGESTERONE RECEPTOR; TAMOXIFEN; TUMOR MARKER;

ARTICLE; ASSAY; BREAST CANCER; CANCER ADJUVANT THERAPY; CANCER PATIENT; COHORT ANALYSIS; DIAGNOSTIC TEST ACCURACY STUDY; EPIFLUORESCENCE MICROSCOPE; FOLLOW UP; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; MULTIVARIATE ANALYSIS; NOTTINGHAM PROGNOSTIC INDEX; PROGNOSIS; PROPORTIONAL HAZARDS MODEL; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; RECEIVER OPERATING CHARACTERISTIC; REGRESSION ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TISSUE MICROARRAY; VALIDATION STUDY; BREAST TUMOR; FEMALE; GENE EXPRESSION; PATHOLOGY;

BREAST NEOPLASMS; FEMALE; GENE EXPRESSION; HUMANS; PROGNOSIS; PROPORTIONAL HAZARDS MODELS; ROC CURVE; TUMOR MARKERS, BIOLOGICAL;

EID: 78650871508     PISSN: 14655411     EISSN: 1465542X     Source Type: Journal    
DOI: 10.1186/bcr2633     Document Type: Article

References (33)

1. Ross JS, Hatzis C, Symmans WF, Pusztai L, Hortobagyi GN. Commercialized multigene predictors of clinical outcome for breast cancer. Oncologist 2008, 13:477-493. 10.1634/theoncologist.2007-0248, 18515733.
2. Paik S. Methods for gene expression profiling in clinical trials of adjuvant breast cancer therapy. Clin Cancer Res 2006, 12:1019s-1023s. 10.1158/1078-0432.CCR-05-2296, 16467119.
3. Paik S. Development and clinical utility of a 21-gene recurrence score prognostic assay in patients with early breast cancer treated with tamoxifen. Oncologist 2007, 12:631-635. 10.1634/theoncologist.12-6-631, 17602054.
4. Paik S, Kim CY, Song YK, Kim WS. Technology insight: application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer. Nat Clin Pract Oncol 2005, 2:246-254. 10.1038/ncponc0171, 16264960.
5. 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. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med 2004, 351:2817-2826. 10.1056/NEJMoa041588, 15591335.
6. Paik S, Tang G, Shak S, Kim C, Baker J, Kim W, Cronin M, Baehner FL, Watson D, Bryant J, Costantino JP, Geyer CE, Wickerham DL, Wolmark N. Gene expression and benefit of chemotherapy in women with node-negative, estrogen receptor-positive breast cancer. J Clin Oncol 2006, 24:3726-3734. 10.1200/JCO.2005.04.7985, 16720680.
7. Bueno-de-Mesquita JM, Linn SC, Keijzer R, Wesseling J, Nuyten DS, van Krimpen C, Meijers C, de Graaf PW, Bos MM, Hart AA, Rutgers EJ, Peterse JL, Halfwerk H, de Groot R, Pronk A, Floore AN, Glas AM, Van't Veer LJ, van de Vijver MJ. Validation of 70-gene prognosis signature in node-negative breast cancer. Breast Cancer Res Treat 2009, 117(3):483-495. 10.1007/s10549-008-0191-2, 18819002.
8. Buyse M, Loi S, van't Veer L, Viale G, Delorenzi M, Glas AM, d'Assignies MS, Bergh J, Lidereau R, Ellis P, Harris A, Bogaerts J, Therasse P, Floore A, Amakrane M, Piette F, Rutgers E, Sotiriou C, Cardoso F, Piccart MJ. 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. 10.1093/jnci/djj329, 16954471.
9. Cronin M, Pho M, Dutta D, Stephans JC, Shak S, Kiefer MC, Esteban JM, Baker JB. Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am J Pathol 2004, 164:35-42. 1602211, 14695316.
10. Camp RL, Chung GG, Rimm DL. Automated subcellular localization and quantification of protein expression in tissue microarrays. Nat Med 2002, 8:1323-1327. 10.1038/nm791, 12389040.
11. Camp RL, Dolled-Filhart M, King BL, Rimm DL. Quantitative analysis of breast cancer tissue microarrays shows that both high and normal levels of HER2 expression are associated with poor outcome. Cancer Res 2003, 63:1445-1448.
12. Dolled-Filhart M, McCabe A, Giltnane J, Cregger M, Camp RL, Rimm DL. Quantitative in situ analysis of beta-catenin expression in breast cancer shows decreased expression is associated with poor outcome. Cancer Res 2006, 66:5487-5494. 10.1158/0008-5472.CAN-06-0100, 16707478.
13. Kluger HM, Dolled-Filhart M, Rodov S, Kacinski BM, Camp RL, Rimm DL. Macrophage colony-stimulating factor-1 receptor expression is associated with poor outcome in breast cancer by large cohort tissue microarray analysis. Clin Cancer Res 2004, 10:173-177. 10.1158/1078-0432.CCR-0699-3, 14734466.
14. Nadler Y, Camp RL, Giltnane JM, Moeder C, Rimm DL, Kluger HM, Kluger Y. Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer. Breast Cancer Res 2008, 10:R35. 10.1186/bcr1998, 2397537, 18430249.
15. Nadler Y, Camp RL, Schwartz C, Rimm DL, Kluger HM, Kluger Y. Expression of Aurora A (but not Aurora B) is predictive of survival in breast cancer. Clin Cancer Res 2008, 14:4455-4462. 10.1158/1078-0432.CCR-07-5268, 18628459.
16. Nadler Y, González AM, Camp RL, Rimm DL, Kluger HM, Kluger Y. Growth factor receptor-bound protein-7 (GRB7) as a prognostic marker and therapeutic target in breast cancer. Ann Oncol 2010, 21:466-473. 10.1093/annonc/mdp346, 19717535.
17. Giltnane JM, Moeder CB, Camp RL, Rimm DL. Quantitative multiplexed analysis of ErbB family coexpression for primary breast cancer prognosis in a large retrospective cohort. Cancer 2009, 115:2400-2409. 10.1002/cncr.24277, 2756449, 19330842.
18. Dudoit S, van der Laan MJ. Asymptotics of cross-validated risk estimation in estimator selection and performance assessment. Statistical Methodology 2005, 2(2):131-154.
19. Statnikov A, Tsamardinos I, Dosbayev Y, Aliferis CF. GEMS: a system for automated cancer diagnosis and biomarker discovery from microarray gene expression data. Int J Med Inform 2005, 74:491-503. 10.1016/j.ijmedinf.2005.05.002, 15967710.
20. Scheffer T. Error estimation and model selection. 1999, Technischen Universita t Berlin, School of Computer Science.
21. Heagerty P, Zheng Y. Survival model predictive accuracy and ROC curves. Biometrics 2005, 61:92-105. 10.1111/j.0006-341X.2005.030814.x, 15737082.
22. Heagerty PJ, Lumley T, Pepe MS. Time-dependent ROC curves for censored survival data and a diagnostic marker. Biometrics 2000, 56:337-344. 10.1111/j.0006-341X.2000.00337.x, 10877287.
23. Haibe-Kains B, Desmedt C, Sotiriou C, Bontempi G. A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?. Bioinformatics 2008, 24:2200-2208. 10.1093/bioinformatics/btn374, 2553442, 18635567.
24. Zheng Z, Chen T, Li X, Haura E, Sharma A, Bepler G. DNA synthesis and repair genes RRM1 and ERCC1 in lung cancer. N Engl J Med 2007, 356:800-808. 10.1056/NEJMoa065411, 17314339.
25. Metro G, Zheng Z, Fabi A, Schell M, Antoniani B, Mottolese M, Monteiro AN, Vici P, Lara Rivera S, Boulware D, Cognetti F, Bepler G. In situ protein expression of RRM1, ERCC1, and BRCA1 in metastatic breast cancer patients treated with gemcitabine-based chemotherapy. Cancer Invest 28:172-180. 10.3109/07357900903095722, 19968494.
26. Akita H, Zheng Z, Takeda Y, Kim C, Kittaka N, Kobayashi S, Marubashi S, Takemasa I, Nagano H, Dono K, Nakamori S, Monden M, Mori M, Doki Y, Bepler G. Significance of RRM1 and ERCC1 expression in resectable pancreatic adenocarcinoma. Oncogene 2009, 28:2903-2909. 10.1038/onc.2009.158, 19543324.
27. Zheng Z, Li X, Schell MJ, Chen T, Boulware D, Robinson L, Sommers E, Bepler G. Thymidylate synthase in situ protein expression and survival in stage I nonsmall-cell lung cancer. Cancer 2008, 112:2765-2773. 10.1002/cncr.23491, 18442042.
28. Aitken SJ, Thomas JS, Langdon SP, Harrison DJ, Faratian D. Quantitative analysis of changes in ER, PR and HER2 expression in primary breast cancer and paired nodal metastases. Ann Oncol 2010, 21:1254-1261. 10.1093/annonc/mdp427, 19858088.
29. Mercier I, Casimiro MC, Zhou J, Wang C, Plymire C, Bryant KG, Daumer KM, Sotgia F, Bonuccelli G, Witkiewicz AK, Lin J, Tran TH, Milliman J, Frank PG, Jasmin JF, Rui H, Pestell RG, Lisanti MP. Genetic ablation of caveolin-1 drives estrogen-hypersensitivity and the development of DCIS-like mammary lesions. Am J Pathol 2009, 174:1172-1190. 10.2353/ajpath.2009.080882, 2671351, 19342371.
30. Millar EK, Dean JL, McNeil CM, O'Toole SA, Henshall SM, Tran T, Lin J, Quong A, Comstock CE, Witkiewicz A, Musgrove EA, Rui H, Lemarchand L, Setiawan VW, Haiman CA, Knudsen KE, Sutherland RL, Knudsen ES. Cyclin D1b protein expression in breast cancer is independent of cyclin D1a and associated with poor disease outcome. Oncogene 2009, 28:1812-1820. 10.1038/onc.2009.13, 19287456.
31. Faratian D, Goltsov A, Lebedeva G, Sorokin A, Moodie S, Mullen P, Kay C, Um IH, Langdon S, Goryanin I, Harrison DJ. Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab. Cancer Res 2009, 69:6713-6720. 10.1158/0008-5472.CAN-09-0777, 19638581.
32. Kolesar J, Huang W, Eickhoff J, Hahn K, Alberti D, Attia S, Schelman W, Holen K, Traynor A, Ivy P, Wilding G. Evaluation of mRNA by Q-RTPCR and protein expression by AQUA of the M2 subunit of ribonucleotide reductase (RRM2) in human tumors. Cancer Chemother Pharmacol 2009, 64:79-86. 10.1007/s00280-008-0845-0, 18941749.
33. Goldstein LJ, Gray R, Badve S, Childs BH, Yoshizawa C, Rowley S, Shak S, Baehner FL, Ravdin PM, Davidson NE, Sledge GW, Perez EA, Shulman LN, Martino S, Sparano JA. Prognostic utility of the 21-gene assay in hormone receptor-positive operable breast cancer compared with classical clinicopathologic features. J Clin Oncol 2008, 26:4063-4071. 10.1200/JCO.2007.14.4501, 2654377, 18678838.