Dissecting cancer heterogeneity - An unsupervised classification approach

International Journal of Biochemistry and Cell Biology

Volumn 45, Issue 11, 2013, Pages 2574-2579

  Wang, Xin ^a   Markowetz, Florian ^a   De Sousa E Melo, Felipe ^b   Medema, Jan Paul ^b   Vermeulen, Louis ^a,b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b ACADEMIC MEDICAL CENTER   (Netherlands)

Author keywords

Cancer subtypes; Consensus clustering; Gene expression; Personalized medicine; Stratified medicine

Indexed keywords

ARTICLE; BIOINFORMATICS; BRAIN CANCER; BREAST CANCER; CANCER CLASSIFICATION; CLUSTER ANALYSIS; COLORECTAL CANCER; CONSENSUS DEVELOPMENT; GENE EXPRESSION SYSTEM; GENETIC HETEROGENEITY; HUMAN; KIDNEY CANCER; LUNG CANCER; OVARY CANCER; PANCREAS CANCER; STOMACH CANCER; CLASSIFICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; NEOPLASM;

CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC HETEROGENEITY; HUMANS; NEOPLASMS;

EID: 84884184792     PISSN: 13572725     EISSN: 18785875     Source Type: Journal    
DOI: 10.1016/j.biocel.2013.08.014     Document Type: Short Survey

References (42)

1. D. Bell, A. Berchuck, M. Birrer, J. Chien, D.W. Cramer, and F. Dao Integrated genomic analyses of ovarian carcinoma Nature 474 2011 609 615
2. M. Benito, J. Parker, Q. Du, J. Wu, D. Xiang, and C.M. Perou Adjustment of systematic microarray data biases Bioinformatics 20 2004 105 114 (Pubitemid 38094234)
3. A.R. Brannon, A. Reddy, M. Seiler, A. Arreola, D.T. Moore, and R.S. Pruthi Molecular stratification of clear cell renal cell carcinoma by consensus clustering reveals distinct subtypes and survival patterns Genes & Cancer 1 2010 152 163
4. J.-P. Brunet, P. Tamayo, T.R. Golub, and J.P. Mesirov Metagenes and molecular pattern discovery using matrix factorization Proceedings of the National Academy of Science 101 2004 4164 4169 (Pubitemid 38405900)
5. E. Budinska, V. Popovici, S. Tejpar, G. D'Ario, N. Lapique, and K.O. Sikora Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer Journal of Pathology 231 2013 63 76
6. Y.-J. Cho, A. Tsherniak, P. Tamayo, S. Santagata, A. Ligon, and H. Greulich Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome Journal of Clinical Oncology 29 2011 1424 1430
7. E.A. Collisson, A. Sadanandam, P. Olson, W.J. Gibb, M. Truitt, and S. Gu Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy Nature Medicine 17 2011 500 503
8. C.L. Corless, C.M. Barnett, and M.C. Heinrich Gastrointestinal stromal tumours: origin and molecular oncology Nature Reviews Cancer 11 2011 865 878
9. G. Curigliano New drugs for breast cancer subtypes: targeting driver pathways to overcome resistance Cancer Treatment Reviews 38 2012 303 310
10. C. Curtis, S.P. Shah, S.F. Chin, G. Turashvili, O.M. Rueda, and M.J. Dunning The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups Nature 486 2012 346 352
11. A.R. Dabney Classification of microarrays to nearest centroids Bioinformatics 21 2005 4148 4154 (Pubitemid 41672105)
12. F. De Sousa E Melo, L. Vermeulen, E. Fessler, and J.P. Medema Cancer heterogeneity - multifaceted view EMBO Reports 14 2013 686 695
13. F. De Sousa E Melo, X. Wang, M. Jansen, E. Fessler, A. Trinh, and L.P.M.H de Rooij Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions Nature Medicine 19 2013 614 618
14. C. Fan, D.S. Oh, L. Wessels, B. Weigelt, D.S.A. Nuyten, and A.B. Nobel Concordance among gene-expression-based predictors for breast cancer New England Journal of Medicine 355 2006 560 569 (Pubitemid 44200649)
15. D.N. Hayes, S. Monti, G. Parmigiani, C.B. Gilks, K. Naoki, and A. Bhattacharjee Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts Journal of Clinical Oncology 24 2006 5079 5090 (Pubitemid 46631412)
16. W.E. Johnson, C. Li, and A. Rabinovic Adjusting batch effects in microarray expression data using empirical Bayes methods Biostatistics 8 2007 118 127 (Pubitemid 44906106)
17. J.T. Leek, and J.D. Storey Capturing heterogeneity in gene expression studies by surrogate variable analysis PLoS Genetics 3 2007 e161
18. Z. Lei, I.B. Tan, K. Das, N. Deng, H. Zouridis, and S. Pattison Identification of molecular subtypes of gastric cancer with different responses to PI3-kinase inhibitors and 5-fluorouracil Gastroenterology 2013
19. J. Luo, M. Schumacher, A. Scherer, D. Sanoudou, D. Megherbi, and T. Davison A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data Pharmacogenomics Journal 10 2010 278 291
20. L. Marisa, A. de Reyniès, A. Duval, J. Selves, M.P. Gaub, and L. Vescovo Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value PLoS Medicine 10 2013 e1001453
21. M.N. McCall, B.M. Bolstad, and R.A. Irizarry Frozen robust multiarray analysis (fRMA) Biostatistics 11 2010 242 253
22. M.N. McCall, K. Uppal, H.A. Jaffee, M.J. Zilliox, and R.A. Irizarry The gene expression barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes Nucleic Acids Research 39 2011 D1011 D1015
23. S. Monti, P. Tamayo, J. Mesirov, and T. Golub Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data Machine Learning 52 2003 91 118
24. A. Prahallad, C. Sun, S. Huang, F. Di Nicolantonio, R. Salazar, and D. Zecchin Unresponsiveness of colon cancer to BRAF (V600E) inhibition through feedback activation of EGFR Nature 483 2012 100 103
25. P.J. Rousseeuw Silhouettes: a graphical aid to the interpretation and validation of cluster analysis Journal of Computational and Applied Mathematics 20 1987 53 65
26. A. Sadanandam, C.A. Lyssiotis, K. Homicsko, E.A. Collisson, W.J. Gibb, and S. Wullschleger A colorectal cancer classification system that associates cellular phenotype and responses to therapy Nature Medicine 19 2013 619 625
27. G.K. Smyth Limma: linear models for microarray data Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Springer) 2005 397 420
28. T. Sorlie, C.M. Perou, R. Tibshirani, T. Aas, S. Geisler, and H. Johnsen Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications Proceedings of the National Academy of Science 98 2001 10869 10874 (Pubitemid 32878711)
29. T. Sorlie, R. Tibshirani, J. Parker, T. Hastie, J.S. Marron, and A. Nobel Repeated observation of breast tumor subtypes in independent gene expression data sets Proceedings of the National Academy of Science 100 2003 8418 8423 (Pubitemid 36842560)
30. I.B. Tan, T. Ivanova, K.H. Lim, C.W. Ong, N. Deng, and J. Lee Intrinsic subtypes of gastric cancer, based on gene expression pattern, predict survival and respond differently to chemotherapy Gastroenterology 141 2011 476 485 e411
31. T.Z. Tan, Q.H. Miow, R.Y. Huang, M.K. Wong, J. Ye, and J.A. Lau Functional genomics identifies five distinct molecular subtypes with clinical relevance and pathways for growth control in epithelial ovarian cancer EMBO Molecular Medicine 5 2013 1051 1066
32. TCGA Comprehensive molecular characterization of human colon and rectal cancer Nature 487 2012 330 337
33. TCGA Comprehensive molecular portraits of human breast tumours Nature 490 2012 61 70
34. TCGA Comprehensive molecular characterization of clear cell renal cell carcinoma Nature 499 2013 43 49
35. R. Tibshirani, G. Walther, and T. Hastie Estimating the number of clusters in a data set via the gap statistic Journal of the Royal Statistical Society: Series B (Statistical Methodology) 63 2001 411 423
36. R. Tibshirani, T. Hastie, B. Narasimhan, and G. Chu Diagnosis of multiple cancer types by shrunken centroids of gene expression Proceedings of the National Academy of Science 99 2002 6567 6572 (Pubitemid 34526173)
37. R.W. Tothill, A.V. Tinker, J. George, R. Brown, S.B. Fox, and S. Lade Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome Clinical Cancer Research 14 2008 5198 5208
38. V.G. Tusher, R. Tibshirani, and G. Chu Significance analysis of microarrays applied to the ionizing radiation response Proceedings of the National Academy of Science 98 2001 5116 5121 (Pubitemid 32397092)
39. B. Van Ness, C. Ramos, M. Haznadar, A. Hoering, J. Haessler, and J. Crowley Genomic variation in myeloma: design, content, and initial application of the bank on a cure SNP panel to detect associations with progression-free survival BMC Medicine 6 2008 26
40. R.G.W. Verhaak, K.A. Hoadley, E. Purdom, V. Wang, Y. Qi, and M.D. Wilkerson Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1 Cancer Cell 17 2010 98 110
41. M.D. Wilkerson, X. Yin, K.A. Hoadley, Y. Liu, M.C. Hayward, and C.R. Cabanski Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types Clinical Cancer Research 16 2010 4864 4875
42. H. Witt, S.C. Mack, M. Ryzhova, S. Bender, M. Sill, and R. Isserlin Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma Cancer Cell 20 2011 143 157