Design of a multi-signature ensemble classifier predicting neuroblastoma patients' outcome

BMC Bioinformatics

Volumn 13, Issue SUPPL.4, 2012, Pages

  Cornero, Andrea ^a   Acquaviva, Massimo ^a   Fardin, Paolo ^a   Versteeg, Rogier ^b   Schramm, Alexander ^c   Eva, Alessandra ^a   Bosco, Maria C ^a   Blengio, Fabiola ^a   Barzaghi, Sara ^a   Varesio, Luigi ^a  

^a G GASLINI INSTITUTE   (Italy)

^b UNIVERSITY OF AMSTERDAM   (Netherlands)

^c UNIVERSITY HOSPITAL ESSEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION ALGORITHM; DISCRIMINATING POWER; ENSEMBLE APPROACHES; ENSEMBLE CLASSIFIERS; GENE EXPRESSION PROFILES; GENE EXPRESSION SIGNATURES; GENE SIGNATURES; GENOMIC ANALYSIS; HIGHLY ACCURATE; KAPLAN-MEIER; MULTI-SIGNATURE; NEUROBLASTOMAS; NUMERIC VALUES; OUTCOME PREDICTION; PREDICTIVE TOOLS; PROGNOSTIC MARKERS; SOLID TUMORS; SURVIVAL CURVES; SYMPATHETIC NERVOUS SYSTEMS;

ALGORITHMS; DECISION TABLES; FORECASTING; GENE EXPRESSION; PATIENT TREATMENT; TUMORS;

CRYPTOGRAPHY;

ALGORITHM; ARTICLE; ARTIFICIAL NEURAL NETWORK; GENE EXPRESSION PROFILING; GENETICS; HUMAN; INFANT; MORTALITY; NEUROBLASTOMA; PROGNOSIS; RISK ASSESSMENT; TREATMENT OUTCOME;

ALGORITHMS; GENE EXPRESSION PROFILING; HUMANS; INFANT; NEURAL NETWORKS (COMPUTER); NEUROBLASTOMA; PROGNOSIS; RISK ASSESSMENT; TREATMENT OUTCOME;

EID: 84864951415     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-S4-S13     Document Type: Article

References (50)

1. De Preter K, Vandesompele J, Heimann P, Yigit N, Beckman S, Schramm A, Eggert A, Stallings R, Benoit Y, Renard M, De Paepe A, Laureys G, Pahlman S, Speleman F. Human fetal neuroblast and neuroblastoma transcriptome analysis confirms neuroblast origin and highlights neuroblastoma candidate genes. Genome Biology 2006, 7:R84. 10.1186/gb-2006-7-9-r84, 1794547, 16989664.
2. Haupt R, Garaventa A, Gambini C, Parodi S, Cangemi G, Casale F, Viscardi E, Bianchi M, Prete A, Jenkner A, Luksch R, Di Cataldo A, Favre C, D'Angelo P, Zanazzo GA, Arcamone G, Izzi GC, Gigliotti AR, Pastore G, De Bernardi B. Improved survival of children with neuroblastoma between 1979 and 2005: a report of the Italian Neuroblastoma Registry. J Clin Oncol 2010, 28:2331-2338. 10.1200/JCO.2009.24.8351, 20351331.
3. Doroshow JH. Selecting systemic cancer therapy one patient at a time: is there a role for molecular profiling of individual patients with advanced solid tumors?. J Clin Oncol 2010, 28:4869-4871. 10.1200/JCO.2010.31.1472, 20921466.
4. Wei J, Greer B, Westermann F, Steinberg S, Son C, Chen Q, Whiteford C, Bilke S, Krasnoselsky A, Cenacchi N, Catchpoole D, Berthold F, Schwab M, Khan J. Prediction of clinical outcome using gene expression profiling and artificial neural networks for patients with neuroblastoma. Cancer Res 2004, 64:6883-6891. 10.1158/0008-5472.CAN-04-0695, 1298184, 15466177.
5. Schramm A, Schulte JH, Klein-Hitpass L, Havers W, Sieverts H, Berwanger B, Christiansen H, Warnat P, Brors B, Eils J, Eils R, Eggert A. Prediction of clinical outcome and biological characterization of neuroblastoma by expression profiling. Oncogene 2005, 24:7902-7912. 10.1038/sj.onc.1208936, 16103881.
6. Ohira M, Oba S, Nakamura Y, Isogai E, Kaneko S, Nakagawa A, Hirata T, Kubo H, Goto T, Yamada S. Expression profiling using a tumor-specific cDNA microarray predicts the prognosis of intermediate risk neuroblastomas. Cancer Cell 2005, 7:337-350. 10.1016/j.ccr.2005.03.019, 15837623.
7. Oberthuer A, Berthold F, Warnat P, Hero B, Kahlert Y, Spitz R, Ernestus K, Konig R, Haas S, Eils R, Schwab M, Brors B, Westermann F, Fischer M. Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification. J Clin Oncol 2006, 24:5070-5078. 10.1200/JCO.2006.06.1879, 17075126.
8. Fischer M, Oberthuer A, Brors B, Kahlert Y, Skowron M, Voth H, Warnat P, Ernestus K, Hero B, Berthold F. Differential expression of neuronal genes defines subtypes of disseminated neuroblastoma with favorable and unfavorable outcome. Clin Cancer Res 2006, 12:5118-5128. 10.1158/1078-0432.CCR-06-0985, 16951229.
9. Vermeulen J, De Preter K, Naranjo A, Vercruysse L, Van Roy N, Hellemans J, Swerts K, Bravo S, Scaruffi P, Tonini GP, De Bernardi B, Noguera R, Piqueras M, Canete A, Castel V, Janoueix-Lerosey I, Delattre O, Schleiermacher G, Michon J, Combaret V, Fischer M, Oberthuer A, Ambros PF, Beiske K, Benard J, Marques B, Rubie H, Kohler J, Potschger U, Ladenstein R, Hogarty MD, McGrady P, London WB, Laureys G, Speleman F, Vandesompele J. Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study. Lancet Oncol 2009, 10:663-671. 10.1016/S1470-2045(09)70154-8, 3045079, 19515614.
10. De Preter K, Vermeulen J, Brors B, Delattre O, Eggert A, Fischer M, Janoueix-Lerosey I, Lavarino C, Maris JM, Mora J, Nakagawara A, Oberthuer A, Ohira M, Schleiermacher G, Schramm A, Schulte JH, Wang Q, Westermann F, Speleman F, Vandesompele J. Accurate Outcome Prediction in Neuroblastoma across Independent Data Sets Using a Multigene Signature. Clin Cancer Res 2010, 16:1532-1541. 10.1158/1078-0432.CCR-09-2607, 20179214.
11. Fardin P, Barla A, Mosci S, Rosasco L, Verri A, Varesio L. The l1-l2 regularization framework unmasks the hypoxia signature hidden in the transcriptome of a set of heterogeneous neuroblastoma cell lines. BMC Genomics 2009, 10:474. 10.1186/1471-2164-10-474, 2768750, 19832978.
12. Fardin P, Barla A, Mosci S, Rosasco L, Verri A, Versteeg R, Caron HN, Molenaar JJ, Ora I, Eva A, Puppo M, Varesio L. A biology-driven approach identifies the hypoxia gene signature as a predictor of the outcome of neuroblastoma patients. Molecular Cancer 2010, 9:185. 10.1186/1476-4598-9-185, 2908582, 20624283.
13. Haibe-Kains B, Desmedt C, Piette F, Buyse M, Cardoso F, Van't Veer L, Piccart M, Bontempi G, Sotiriou C. Comparison of prognostic gene expression signatures for breast cancer. BMC Genomics 2008, 9:394. 10.1186/1471-2164-9-394, 2533026, 18717985.
14. Tan AC, Gilbert D. Ensemble machine learning on gene expression data for cancer classification. Appl Bioinformatics 2003, 2:S75-S83.
15. Abeel T, Helleputte T, Van de PY, Dupont P, Saeys Y. Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics 2010, 26:392-398. 10.1093/bioinformatics/btp630, 19942583.
16. Xu L, Tan AC, Winslow RL, Geman D. Merging microarray data from separate breast cancer studies provides a robust prognostic test. BMC Bioinformatics 2008, 9:125. 10.1186/1471-2105-9-125, 2409450, 18304324.
17. Nuyten DS, Hastie T, Chi JT, Chang HY, van de Vijver MJ. Combining biological gene expression signatures in predicting outcome in breast cancer: An alternative to supervised classification. Eur J Cancer 2008, 44:2319-2329. 10.1016/j.ejca.2008.07.015, 18715778.
18. Fan C, Prat A, Parker JS, Liu Y, Carey LA, Troester MA, Perou CM. Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures. BMC Med Genomics 2011, 4:3. 10.1186/1755-8794-4-3, 3025826, 21214954.
19. Heck JE, Ritz B, Hung RJ, Hashibe M, Boffetta P. The epidemiology of neuroblastoma: a review. Paediatr Perinat Epidemiol 2009, 23:125-143. 10.1111/j.1365-3016.2008.00983.x, 19159399.
20. Asgharzadeh S, Pique-Regi R, Sposto R, Wang H, Yang Y, Shimada H, Matthay K, Buckley J, Ortega A, Seeger R. Prognostic significance of gene expression profiles of metastatic neuroblastomas lacking MYCN gene amplification. J Natl Cancer Inst 2006, 98:1193-1203. 10.1093/jnci/djj330, 16954472.
21. Benard J, Raguenez G, Kauffmann A, Valent A, Ripoche H, Joulin V, Job B, Danglot G, Cantais S, Robert T, Terrier-Lacombe MJ, Chassevent A, Koscielny S, Fischer M, Berthold F, Lipinski M, Tursz T, Dessen P, Lazar V, Valteau-Couanet D. MYCN-non-amplified metastatic neuroblastoma with good prognosis and spontaneous regression: A molecular portrait of stage 4S. Molecular Oncology 2008, 2:261-271. 10.1016/j.molonc.2008.07.002, 19383347.
22. Chen QR, Song YK, Yu LR, Wei JS, Chung JY, Hewitt SM, Veenstra TD, Khan J. Global genomic and proteomic analysis identifies biological pathways related to high-risk neuroblastoma. J Proteome Res 2010, 9:373-382. 10.1021/pr900701v, 2801773, 19921788.
23. Di Pietro C, Ragusa M, Barbagallo D, Duro LR, Guglielmino MR, Majorana A, Angelica R, Scalia M, Statello L, Salito L, Tomasello L, Pernagallo S, Valenti S, D'Agostino V, Triberio P, Tandurella I, Palumbo GA, La Cava P, Cafiso V, Bertuccio T, Santagati M, Li DG, Lanzafame S, Di Raimondo F, Stefani S, Mishra B, Purrello M. The apoptotic machinery as a biological complex system: analysis of its omics and evolution, identification of candidate genes for fourteen major types of cancer, and experimental validation in CML and neuroblastoma. BMC Med Genomics 2009, 2:20. 10.1186/1755-8794-2-20, 2683874, 19402918.
24. Fransson S, Martinsson T, Ejeskar K. Neuroblastoma tumors with favorable and unfavorable outcomes: Significant differences in mRNA expression of genes mapped at 1p36.2. Genes Chromosomes Cancer 2007, 46:45-52. 10.1002/gcc.20387, 17044048.
25. Fredlund E, Ringner M, Maris JM, Pahlman S. High Myc pathway activity and low stage of neuronal differentiation associate with poor outcome in neuroblastoma. PNAS 2008, 105:14094-14099. 10.1073/pnas.0804455105, 2544584, 18780787.
26. Hahn CK, Ross KN, Warrington IM, Mazitschek R, Kanegai CM, Wright RD, Kung AL, Golub TR, Stegmaier K. Expression-based screening identifies the combination of histone deacetylase inhibitors and retinoids for neuroblastoma differentiation. Proc Natl Acad Sci USA 2008, 105:9751-9756. 10.1073/pnas.0710413105, 2474517, 18607002.
27. Shimada A, Hirato J, Kuroiwa M, Kikuchi A, Hanada R, Wakai K, Hayashi Y. Expression of KIT and PDGFR is associated with a good prognosis in neuroblastoma. Pediatr Blood Cancer 2008, 50:213-217. 10.1002/pbc.21288, 17941064.
28. Oe T, Sasayama T, Nagashima T, Muramoto M, Yamazaki T, Morikawa N, Okitsu O, Nishimura S, Aoki T, Katayama Y, Kita Y. Differences in gene expression profile among SH-SY5Y neuroblastoma subclones with different neurite outgrowth responses to nerve growth factor. J Neurochem 2005, 94:1264-1276. 10.1111/j.1471-4159.2005.03273.x, 15992370.
29. McArdle L, McDermott M, Purcell R, Grehan D, O'Meara A, Breatnach F, Catchpoole D, Culhane AC, Jeffery I, Gallagher WM, Stallings RL. Oligonucleotide microarray analysis of gene expression in neuroblastoma displaying loss of chromosome 11q. Carcinogenesis 2004, 25:1599-1609. 10.1093/carcin/bgh173, 15090470.
30. Nevo I, Oberthuer A, Botzer E, Sagi-Assif O, Maman S, Pasmanik-Chor M, Kariv N, Fischer M, Yron I, Witz IP. Gene-expression-based analysis of local and metastatic neuroblastoma variants reveals a set of genes associated with tumor progression in neuroblastoma patients. Int J Cancer 2010, 126:1570-1581.
31. Nevo I, Sagi-Assif O, Meshel T, Geminder H, Goldberg-Bittman L, Ben Menachem S, Shalmon B, Goldberg I, Ben Baruch A, Witz IP. The tumor microenvironment: CXCR4 is associated with distinct protein expression patterns in neuroblastoma cells. Immunol Lett 2004, 92:163-169. 10.1016/j.imlet.2003.10.019, 15081541.
32. Agathanggelou A, Bieche I, Ahmed-Choudhury J, Nicke B, Dammann R, Baksh S, Gao B, Minna JD, Downward J, Maher ER, Latif F. Identification of novel gene expression targets for the Ras association domain family 1 (RASSF1A) tumor suppressor gene in non-small cell lung cancer and neuroblastoma. Cancer Res 2003, 63:5344-5351.
33. de Ruijter AJ, Meinsma RJ, Bosma P, Kemp S, Caron HN, van Kuilenburg AB. Gene expression profiling in response to the histone deacetylase inhibitor BL1521 in neuroblastoma. Exp Cell Res 2005, 309:451-467. 10.1016/j.yexcr.2005.06.024, 16084510.
34. Janoueix-Lerosey I, Novikov E, Monteiro M, Gruel N, Schleiermacher G, Loriod B, Nguyen C, Delattre O. Gene expression profiling of 1p35-36 genes in neuroblastoma. Oncogene 2004, 23:5912-5922. 10.1038/sj.onc.1207784, 15195138.
35. Fredlund E, Ovenberger M, Borg K, Pahlman S. Transcriptional adaptation of neuroblastoma cells to hypoxia. Biochem Biophys Res Commun 2008, 366:1054-1060. 10.1016/j.bbrc.2007.12.074, 18155155.
36. Ho R, Minturn JE, Hishiki T, Zhao H, Wang Q, Cnaan A, Maris J, Evans AE, Brodeur GM. Proliferation of human neuroblastomas mediated by the epidermal growth factor receptor. Cancer Res 2005, 65:9868-9875. 10.1158/0008-5472.CAN-04-2426, 16267010.
37. Molenaar JJ, Ebus ME, Koster J, van Sluis P, van Noesel CJ, Versteeg R, Caron HN. Cyclin D1 and CDK4 activity contribute to the undifferentiated phenotype in neuroblastoma. Cancer Res 2008, 68:2599-2609. 10.1158/0008-5472.CAN-07-5032, 18413728.
38. Blum AL, Langley P. Selection of relevant features and examples in machine learning. Artif Intell 1997, 97:245-271.
39. Sandoval JA, Eppstein AC, Hoelz DJ, Klein PJ, Linebarger JH, Turner KE, Rescorla FJ, Hickey RJ, Malkas LH, Schmidt CM. Proteomic analysis of neuroblastoma subtypes in response to mitogen-activated protein kinase inhibition: profiling multiple targets of cancer kinase signaling. J Surg Res 2006, 134:61-67. 10.1016/j.jss.2006.02.011, 16650873.
40. Schramm A, Mierswa I, Kaderali L, Morik K, Eggert A, Schulte JH. Reanalysis of neuroblastoma expression profiling data using improved methodology and extended follow-up increases validity of outcome prediction. Cancer Lett 2009, 282:55-62. 10.1016/j.canlet.2009.02.052, 19349112.
41. Schramm A, Vandesompele J, Schulte JH, Dreesmann S, Kaderali L, Brors B, Eils R, Speleman F, Eggert A. Translating expression profiling into a clinically feasible test to predict neuroblastoma outcome. Clin Cancer Res 2007, 13:1459-1465. 10.1158/1078-0432.CCR-06-2032, 17332289.
42. Schulte JH, Lim S, Schramm A, Friedrichs N, Koster J, Versteeg R, Ora I, Pajtler K, Klein-Hitpass L, Kuhfittig-Kulle S, Metzger E, Schule R, Eggert A, Buettner R, Kirfel J. Lysine-specific demethylase 1 is strongly expressed in poorly differentiated neuroblastoma: implications for therapy. Cancer Res 2009, 69:2065-2071.
43. Warnat P, Oberthuer A, Fischer M, Westermann F, Eils R, Brors B. Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes. BMC Cancer 2007, 7:89. 10.1186/1471-2407-7-89, 1904223, 17531100.
44. Hall M, Eibe F, Holmes G, Pfahringer B, Reutemann P, Witten IH. The WEKA Data Mining Software: An Update: SIGKDD Explorations 2009,
45. Wang SL, Li X, Zhang S, Gui J, Huang DS. Tumor classification by combining PNN classifier ensemble with neighborhood rough set based gene reduction. Comput Biol Med 2010, 40:179-189. 10.1016/j.compbiomed.2009.11.014, 20044083.
46. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotech 2010, 28:827-838.
47. Qiu P, Gentles AJ, Plevritis SK. Discovering biological progression underlying microarray samples. PLoS Comput Biol 2011, 7:e1001123. 10.1371/journal.pcbi.1001123, 3077357, 21533210.
48. Ohtaki M, Otani K, Hiyama K, Kamei N, Satoh K, Hiyama E. A robust method for estimating gene expression states using Affymetrix microarray probe level data. BMC Bioinformatics 2010, 11:183. 10.1186/1471-2105-11-183, 2873532, 20380745.
49. R2 repository. , http://r2.amc.nl
50. BIT-neuroblastoma Biobank of the Gaslini Institute. , http://www.gaslini.org/servizi/notizie/notizie_homepage.aspx