A comparison study: Applying segmentation to array CGH data for downstream analyses

Bioinformatics

Volumn 21, Issue 22, 2005, Pages 4084-4091

  Willenbrock, Hanni ^a   Fridlyand, Jane ^b  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCURACY; ARTICLE; CHROMOSOME; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; GENE MUTATION; GENE STRUCTURE; GENETIC ANALYSIS; GENOME; HUMAN; INTERMETHOD COMPARISON; MOUTH CARCINOMA; PREDICTION; PRIORITY JOURNAL; SIMULATION; SQUAMOUS CELL CARCINOMA; STATISTICAL ANALYSIS;

EID: 27944455289     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti677     Document Type: Article

References (18)

1. Bauer,D.F. (1972) Constructing confidence sets using rank statistics. J. Am. Stat. Assoc., 67, 687-690.
2. Daruwala,R.S. et al. (2004) A versatile statistical analysis algorithm to detect genome copy number variation. Proc. Natl. Acad. Sci. USA, 101, 16292-16297.
3. Dudoit,S. et al. (2002) Comparison of discrimination methods for the classification of tumors using gene expression data. J. Am. Stat. Assoc., 97, 77-87.
4. Fridlyand,J. et al. (2004) Hidden Markov models approach to the analysis of array CGH data. J. Multivar. Anal., 90, 132.
5. Hodgson,G. et al. (2001) Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas. Nat. Genet., 29, 459-464.
6. Hsu,L. et al. (2005) Denoising array-based comparative genomic hybridization data using wavelets. Biostatistics, 6, 211-226.
7. Hupe,P. et al. (2004) Analysis of array CGH data: From signal ratio to gain and loss of DNA regions. Bioinformatics, 20, 3413-3422.
8. Lai,W.R. et al. (2005) Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics, 21, 3763-3770.
9. Myers,C.L. et al. (2004) Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics, 20, 3533-3543.
10. Nakao,K. et al. (2004) High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis, 25, 1345-1357.
11. Olshen,A.B. et al. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557-572.
12. Picard,F. et al. (2005) A statistical approach for array CGH data analysis. BMC Bioinformatics, 6, 27.
13. Pinkel,D. and Albertson,D.G. (2005) Array comparative genomic hybridization and its applications in cancer. Nat. Genet., 37 (suppl), S11-S17.
14. Snijders,A.M. et al. (2005) Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma. Oncogene, 24, 2432-4242.
15. Veltman,J.A. et al. (2003) Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Res., 63, 2872-2880.
16. Wang,P. et al. (2005) A method for calling gains and losses in array CGH data. Biostatistics, 6, 45-58.
17. Westfall,P.H. and Young,S.S. (1993) Resampling-based Multiple Testing: Examples and Methods for P-value Adjustment. Wiley, NY.
18. Zhao,X. et al. (2004) An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res., 64, 3060-3071.