Classification of arrayCGH data using fused SVM

Bioinformatics

Volumn 24, Issue 13, 2008, Pages

  Rapaport, Franck ^a,b   Barillot, Emmanuel ^a,b   Vert, Jean Philippe ^a,b  

^a INSERM   (France)

^b PSL RESEARCH UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCURACY; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BLADDER CANCER; CANCER CLASSIFICATION; COMPARATIVE GENOMIC HYBRIDIZATION; CORRELATION ANALYSIS; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE NUMBER; GENE STRUCTURE; GENETIC ALGORITHM; GENETIC MARKER; GENETIC VARIABILITY; HUMAN; PRIORITY JOURNAL; PROGNOSIS; SUPPORT VECTOR MACHINE; UVEA MELANOMA;

BACTERIA (MICROORGANISMS);

COMPUTER AIDED DIAGNOSIS; DISEASES; GENE EXPRESSION; INTELLIGENT SYSTEMS; MOLECULAR BIOLOGY; SUPERVISED LEARNING; SUPPORT VECTOR MACHINES;

BACTERIAL ARTIFICIAL CHROMOSOMES; CLASSIFICATION METHODS; COMPARATIVE GENOMIC HYBRIDIZATIONS; DIAGNOSIS AND PROGNOSIS; DISCRIMINATIVE FEATURES; GENE EXPRESSION PROFILES; SPATIAL ORGANIZATION; SUPERVISED CLASSIFICATION;

CLASSIFICATION (OF INFORMATION);

EID: 46249091578     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn188     Document Type: Article

References (37)

1. Blaveri,E. et al. (2005) Bladder cancer stage and outcome by array-based comparative genomic, hybridization. Clin. Cancer Res., 11, 7012-7022.
2. Boser,B.E. et al. (1992) A training algorithm for optimal margin classifiers. In COLT '92: Proceedings of the fifth annual workshop on Computational learning theory, New York, NY, USA. ACM, pp. 144-152.
3. Bown,N. et al. (2001) 17q gain in neuroblastoma predicts adverse clinical outcome. U.K. cancer cytogenetics group and the U.K. children's cancer study group. Med. Pediatr. Oncol., 36, 14-19.
4. Boyd,S. and Vandenberghe,L. (2004) Convex Optimization. Cambridge University Press, New York, NY, USA.
5. Chen,S.S. et al. (1998) Atomic decomposition by basis pursuit. SIAM J. Sci. Comput., 20, 33-61.
6. Chin,S.F. et al. (2006) Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers. Oncogene, 26, 1959-1970.
7. Corson,T.W. et al. (2005) Kif14 is a candidate oncogene in the 1q minimal region of genomic gain in multiple cancers. Oncogene, 24, 4741-4753.
8. Cortes,C. and Vapnik,V. (1995) Support vector networks. Machine Learning, 20, 273-297.
9. Efron,F et al. (2004) Least angle regression. Ann. Stat., 32, 407-499.
10. Genkin,A. et al. (2007) Large-scale Bayesian logistic regression for text categorization. Technometrics, 49, 291-304.
11. Gershon,D. (2005) DNA microarrays: More than gene expression. Nature 437, 1195-1198.
12. Hanahan,D. and Weinberg,R.A. (2000) The hallmarks of cancer. Cell, 100, 57-10.
13. Idbaih,A. et al. (2007) BAC array CGH distinguishes mutually exclusive alterations that define clinicogenetic subtypes of gliomas. Int. J. Cancer.
14. Jones,C. et al. (2004) Molecular cytogenetic idenfification of subgroups of grade III invasive ductal breast carcinomas with different clinical outcomes. Clin. Cancer Res., 10, 5988-5997.
15. Krishnapuram,B. et al. (2004) A Bayesian approach to joint feature selection and classifier design. IEEE Trans. Pattern Anal. Mach. Intell., 26, 1105-11.
16. Krishnapuram,B. et al. (2005) Sparse multinomial logistic regression: Fast algorithms and generalization bounds. IEEE Transactions on Pattern Analysis and Machine Intelligence, 27, 957-968.
17. Land,S.R. and Friedman,J.H. (1996) Variable fusion: A new adaptive signal regression method. Technical Report.
18. Lastowska,M. et al. (1997) Comparative genomic hybridization study of primary neuroblastoma tumors. united kingdom children's cancer study group. Genes Chromosomes Cancer, 18, 162-169.
19. O'Hagan,R.C. et al. (2003) Array comparative genome hybridization for tumor classification and gene discovery in mouse models of malignant melanoma. Cancer Res., 63, 5352-5356.
20. Parrella,P. et al. (2003) Fine mapping of chromosome 3 in uveal melanoma: Identification of a minimal region of deletion on chromosomal arm 3p25.1-p25.2. Cancer Res., 63, 8507-8510.
21. Pinkel,D. et al. (1998) High resolution analysis of DNA copy number variation using comparaive genomic hybridization to microarrays. Nat. Genet., 20, 207-211.
22. Shing,D.C. et al. (2003) FUS/ERG gene fusions in Ewing's tumors. Cancer Res., 63, 4568-4576.
23. Speicher,M. et al. (1994) Chromosomal gains and losses in uveal melanomas detected by comparative genomic hybridization. Cancer Res. 54, 3817-23.
24. Stransky,N. et al. (2006) Regional copy number-independent deregulation of transcription in cancer. Nat. Genet., 38, 1386-1396.
25. Sturm,J. (1999) Using SeDuMi 1.02, a MATLAB toolbox for optimization over symmetric cones. Optimization Methods and Software, 11-12 625-653. Special issue on Interior Point Methods (CD supplement with software).
26. Tibshirani,R. (1996) Regression shrinkage and selection via the lasso. J Roy. Statist. Soc. B., 58, 267-288.
27. Tibshirani,R. (1997) The lasso method for variable selection in the Cox model. Stat. Med., 16, 385-395.
28. Tibshirani,R. and Wang,P. (2007) Spatial smoothing and hot spot detection for CGH data using the fused lasso. Biostatistics.
29. Tibshirani,R. et al. (2005) Sparsity and smoothness via the fused lasso. J. Roy. Statist. Soc. B., 67, 91-108. available at http://ideas.repec.org/a/bla/jorssb/v67y2005ilp91-108.html.
30. Trolet,J. et al. (2008) Genomic profiling and identification of high nsk tumors in uveal melanoma by array-CGH analysis of primary tumors and liver metastases. submitted to Cancer Res.
31. Tschentscher,F. et al. (2001) Partial deletions of the long and short arm of chromosome 3 point to two tumor suppressor genes in uveal melanoma. Cancer Res., 61, 3439-3442.
32. van Beers,E. and Nederlof,P. (2006) Array-CGH and breast cancer. Breast Cancer Res., 8, 210.
33. Van Roy,N. et al. (2002) Localization of the 17q breakpoint of a constitutional 1;17 translocation in a patient with neuroblastoma within a 25-kb segment located between the accn1 and tlk2 genes and near the distal breakpoints of two microdeletions in neurofibromatosis type 1 patients. Genes, Chromosomes Cancer, 35, 113-120.
34. Vapnik,V.N. (1998) Statistical Learning Theory. Wiley.
35. Waldman,F.M. et al. (1991) Centromeric copy number of chromosome 7 is strongly correlated with tumor grade and labeling index in human bladder cancer. Cancer Res., 51, 3807-3813.
36. Yao,J. et al. (2006) Combined cDNA Array Comparative Genomic Hybridization and Serial Analysis of Gene Expression Analysis of Breast Tumor Progression. Cancer Res., 66, 4065-4078.
37. Zhu,J. et al. (2004) 1-norm support vector machines. In Thrun,S. (eds), Adv. Neural. Inform. Process Syst., volume 16, MIT Press, Cambridge, MA.