Generation of an algorithm based on minimal gene sets to clinically subtype triple negative breast cancer patients

BMC Cancer

Volumn 16, Issue 1, 2016, Pages

  Ring, Brian Z ^a   Hout, David R ^b   Morris, Stephan W ^b   Lawrence, Kasey ^b   Schweitzer, Brock L ^b   Bailey, Daniel B ^b   Lehmann, Brian D ^c   Pietenpol, Jennifer A ^c   Seitz, Robert S ^b  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b Insight Genetics   (United States)

^c VANDERBILT INGRAM CANCER CENTER   (United States)

Author keywords

Biomarkers; Breast cancer; Statistical analysis; Translational oncology

Indexed keywords

CYCLOPHOSPHAMIDE; DOXORUBICIN; IXABEPILONE; PACLITAXEL;

ARTICLE; CLASSIFICATION ALGORITHM; CONTROLLED STUDY; DRUG RESPONSE; FEMALE; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ALGORITHM; HUMAN; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; PROCESS DEVELOPMENT; TREATMENT OUTCOME; TRIPLE NEGATIVE BREAST CANCER; VALIDATION STUDY; ADULT; ALGORITHM; BIOLOGICAL MODEL; GENETICS; NEOADJUVANT THERAPY; PATHOLOGY; PREDICTIVE VALUE; PROGNOSIS; RETROSPECTIVE STUDY; TRIPLE NEGATIVE BREAST NEOPLASMS;

ADULT; ALGORITHMS; FEMALE; GENE EXPRESSION; HUMANS; MODELS, GENETIC; NEOADJUVANT THERAPY; PREDICTIVE VALUE OF TESTS; PROGNOSIS; RETROSPECTIVE STUDIES; TREATMENT OUTCOME; TRIPLE NEGATIVE BREAST NEOPLASMS;

EID: 84975722457     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/s12885-016-2198-0     Document Type: Article

References (31)

1. Dent R, Trudeau M, Pritchard KI, Hanna WM, Kahn HK, Sawka CA, Lickley LA, Rawlinson E, Sun P, Narod SA. Triple-negative breast cancer: clinical features and patterns of recurrence. Clin Cancer Res. 2007;13(15 Pt 1):4429-34.
2. Liedtke C, Mazouni C, Hess KR, André F, Tordai A, Mejia JA, Symmans WF, et al. Response to neoadjuvant therapy and long-term survival in patients with triple-negative breast cancer. J Clin Oncol. 2008;26(8):1275-81.
3. Wang-Lopeza Q, Chalabia N, Abriala C, Radosevic-Robina N, Durandoa X, Mouret-Reyniera MA, et al. Can pathologic complete response (pCR) be used as a surrogate marker of survival after neoadjuvant therapy for breast cancer? Crit Rev Oncol Hematol. 2015;95:88-104.
4. Guidance for industry: pathological complete response in neoadjuvant treatment of high-risk early-stage breast cancer: use as an endpoint to support accelerated approval. http://www.fda.gov/downloads/drugs/guidancecomplianceregulatoryinformation/guidances/ucm305501.pdf.
5. Gyorffy B, Hatzis C, Sanft T, Hofstatter E, Aktas B, Pusztai L. Multigene prognostic tests in breast cancer: past, present, future. Breast Cancer Res. 2015;17(1):514.
6. Van Cutsem E, Lenz HJ, Kohne CH, Heinemann V, Tejpar S, Melezinek I, Beier F, Stroh C, Rougier P, van Krieken JH et al. Fluorouracil, leucovorin, and irinotecan plus cetuximab treatment and RAS mutations in colorectal cancer. J Clin Oncol. 2015;33(7):692-700.
7. Rosell R, Carcereny E, Gervais R, Vergnenegre A, Massuti B, Felip E, Palmero R, Garcia-Gomez R, Pallares C, Sanchez JM et al. Erlotinib versus standard chemotherapy as first-line treatment for European patients with advanced EGFR mutation-positive non-small-cell lung cancer (EURTAC): a multicentre, open-label, randomised phase 3 trial. Lancet Oncol. 2012;13(3):239-46.
8. Solomon BJ, Mok T, Kim DW, Wu YL, Nakagawa K, Mekhail T, Felip E, Cappuzzo F, Paolini J, Usari T et al. First-line crizotinib versus chemotherapy in ALK-positive lung cancer. N Engl J Med. 2014;371(23):2167-77.
9. Perou CM, Sorlie 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.
10. Bertucci F, Finetti P, Cervera N, Esterni B, Hermitte F, Viens P, Birnbaum D. How basal are triple-negative breast cancers? Int J Cancer. 2008;123(1):236-40.
11. 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 Invest. 2011;121(7):2750-67.
12. Masuda H, Baggerly KA, Wang Y, Zhang Y, Gonzalez-Angulo AM, Meric-Bernstam F, Valero V, Lehmann BD, Pietenpol JA, Hortobagyi GN et al. Differential response to neoadjuvant chemotherapy among 7 triple-negative breast cancer molecular subtypes. Clin Cancer Res. 2013;19(19):5533-40.
13. Weigelt B, Peterse JL, van 't Veer LJ. Breast cancer metastasis: markers and models. Nat Rev Cancer. 2005;5(8):591-602.
14. 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 U S A. 2006;103(15):5923-8.
15. Pochet N, De Smet F, Suykens JA, De Moor BL. Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction. Bioinformatics. 2004;20(17):3185-95.
16. Lee G, Rodriguez C, Madabhushi A. Investigating the efficacy of nonlinear dimensionality reduction schemes in classifying gene and protein expression studies. IEEE/ACM Trans Comput Biol Bioinform. 2008;5(3):368-84.
17. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545-50.
18. Gruber S, Van der Laan M. tmle: an R package for targeted maximum likelihood estimation. J Stat Softw. 2012;51(12):35.
19. Liaw A, Wiener M. Classification and regression by random forest. R News. 2002;2(3):18-22.
20. Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw. 2010;33(1):1-22.
21. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, et al. ClueGO: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091-3. doi: 10.1093/bioinformatics/btp101.
22. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498-504.
23. Denkert C, von Minckwitz G, Brase JC, Sinn BV, Gade S, Kronenwett R, Pfitzner BM, Salat C, Loi S, Schmitt WD, et al. Tumor-infiltrating lymphocytes and response to neoadjuvant chemotherapy with or without carboplatin in human epidermal growth factor receptor 2-positive and triple-negative primary breast cancers. J Clin Oncol. 2014;33:983-91.
24. Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A. 2002;99(10):6567-72.
25. Goldstein AS, Huang J, Guo C, Garraway IP, Witte ON. Identification of a cell of origin for human prostate cancer. Science. 2010;329(5991):568-71.
26. Horak CE, Pusztai L, Xing G, Trifan OC, Saura C, Tseng LM, Chan S, Welcher R, Liu D. Biomarker analysis of neoadjuvant doxorubicin/cyclophosphamide followed by ixabepilone or paclitaxel in early-stage breast cancer. Clin Cancer Res. 2013;19(6):1587-95.
27. Morales JC, Li L, Fattah FJ, Dong Y, Bey EA, Patel M, Gao J, Boothman DA. Review of Poly (ADP-ribose) Polymerase (PARP) mechanisms of action and rationale for targeting in cancer and other diseases. Crit Rev Eukaryot Gene Expr. 2014;24(1):15-28.
28. Carey LA, Dees EC, Sawyer L, Gatti L, Moore DT, Collichio F, Ollila DW, Sartor CI, Graham ML, Perou CM. The triple negative paradox: primary tumor chemosensitivity of breast cancer subtypes. Clin Cancer Res. 2007;13(8):2329-34.
29. Nahleh Z. Neoadjuvant chemotherapy for "triple negative" breast cancer: a review of current practice and future outlook. Med Oncol. 2010;27(2):531-9. doi: 10.1007/s12032-009-9244-6. Epub 2009 Jun 10. Review.
30. Cameron D, Brown J, Dent R, Jackisch C, Mackey J, Pivot X, Steger GG, Suter TM, et al. Adjuvant bevacizumab-containing therapy in triple-negative breast cancer (BEATRICE): primary results of a randomised, phase 3 trial. Lancet Oncol. 2013;14(10):933-42.
31. Carey LA, Rugo HS, Marcom PK, Mayer EL, Esteva FJ, Ma CX, Liu MC, Storniolo AM, et al. TBCRC 001: randomized phase II study of cetuximab in combination with carboplatin in stage IV triple-negative breast cancer. J Clin Oncol. 2012;30(21):2615-23.