MSMAD: A computationally efficient method for the analysis of noisy array CGH data

Bioinformatics

Volumn 25, Issue 6, 2009, Pages 703-713

  Budinska, Eva ^a   Gelnarova, Eva ^a   Schimek, Michael G ^a,b  

^a MASARYK UNIVERSITY   (Czech Republic)

^b MEDICAL UNIVERSITY OF GRAZ   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CHROMOSOME ABERRATION; COMPARATIVE GENOMIC HYBRIDIZATION; GENOME ANALYSIS; INFORMATION PROCESSING; INTERMETHOD COMPARISON; LUNG NON SMALL CELL CANCER; MATHEMATICAL COMPUTING; MEDIAN SMOOTHING MEDIAN ABSOLUTE DEVIATION METHOD; NOISE; NOISE REDUCTION; NONPARAMETRIC TEST; PRIORITY JOURNAL; SIGNAL NOISE RATIO;

ALGORITHMS; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTATIONAL BIOLOGY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGRAMMING LANGUAGES;

EID: 62549145329     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp022     Document Type: Article

References (36)

1. Andersson,R. et al.. (2008) A segmental maximum a posteriori approach to genome-wide copy number profiling. Bioinformatics, 24, 751-758.
2. Babicka,L. et al.. (2006) Complex chromosomal rearrangements in patients with chronic myeloid leukemia. Cancer Genet. Cytogenet., 168, 22-29.
3. Berrieman,H.K. et al.. (2004) Chromosomal analysis of non-small-cell lung cancer by multicolour fluorescent in situ hybridization. Br. J. Cancer, 90, 900-905.
4. Eilers,P.H.C. and de Menezes,R.X. (2005) Quantile smoothing of array CGH data. Bioinformatics, 21, 1146-1153.
5. Fink,S.R. et al.. (2006) Loss of TP53 is due to rearrangements involving chromosome region 17p10 approximately p12 in chronic lymphocytic leukemia. Cancer Genet. Cytogenet., 167, 177-181.
6. Fridlyand,J. et al.. (2004) Hidden Markov models approach to the analysis of array CGH data. J. Multivariate Anal., 90, 132-153.
7. Garnis,C. et al.. (2006) High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH. Int. J. Cancer, 118, 1556-1564.
8. Guha,S. et al.. (2006) Bayesian Hidden Markov Modeling of Array CGH Data. Harvard University Biostatistics. In Working Paper Series Harvard School of Public Health. The Berkeley Electronic Press. Available at http://www.bepress.com/harvardbiostat/paper24 (last accessed date on 04 February, 2009).
9. Hsu,L. et al.. (2005) Denoising array-based comparative genomic hybridization data using wavelets. Biostatistics, 6, 211-226.
10. Huang,J. et al.. (2007) Robust smooth segmentation approach for array CGH data analysis. Bioinformatics, 23, 2463-2469.
11. Hupé,P. et al.. (2004) Analysis of array CGH data: From signal ratio to gain and loss of DNA regions. Bioinformatics, 20, 3413-3422.
12. Jong,K. et al.. (2003) Chromosomal breakpoint detection in human cancer. In Lecture Notes in ComputerScience, Vol. 2611. Springer-Verlag, Berlin, 54-65.
13. Lai,W.R. et al.. (2005) Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics, 21, 3763-3770.
14. Li,Y. and Zhu,J. (2007) Analysis of array CGH data for cancer studies using fused quantile regression. Bioinformatics, 23, 2470-2476.
15. Marioni,J.C. et al.. (2006) BioHMM: A heterogeneous hidden Markov model for segmenting array CGH data. Bioinformatics, 22, 1144-1146.
16. Nakao,K. et al.. (2004) Highresolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis, 25, 1345-1357.
17. Novak,U. et al.. (2002) A high-resolution allelotype of B-cell chronic lymphocytic leukemia (B-CLL). Blood, 100, 1787-1794.
18. Olshen,A.B. and Ventakraman,E.S. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics, 5, 557-572.
19. Pfeifer,D. et al.. (2007) Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays. Blood, 109: 1202-1210.
20. Picard,F. et al.. (2005) A statistical approach for array CGH data analysis. BMC Bioinformatics, 6, 1-14.
21. Picard,F. et al.. (2007) A segmentation/clustering model for the analysis of array CGH data. Biometrics, 63, 758-766.
22. Pinkel,D. et al.. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet., 20, 207-211.
23. Pollack,J.R. et al.. (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc. Natl Acad. Sci. USA, 99, 12963-12968.
24. R Development Core Team (2007) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. Available at URL http://www.R-project.org. (last accessed date on 04 February, 2009).
25. Schimek,M.G. (1988) A roughness penalty regression approach for statistical graphics. In Edwards,D. and Raun,E. (ed.) COMPSTAT 1988. Proceedings in Computational Statistics. Physica-Verlag, Heidelberg, pp. 37-43.
26. Schwaenen,C. et al.. (2004) Automated array-based genomic profiling in chronic lymphocytic leukemia: Development of a clinical tool and discovery of recurrent genomic alterations. Proc. Natl Acad. Sci. USA. 101, 1039-1044.
27. Shah,S.P. et al.. (2006) Integrating copy number polymorphisms into array CGH analysis using a robust HMM. Bioinformatics, 22 431-439.
28. Solinas-Toldo,S. et al.. (1997) Matrix-based comparative genomic hybridization: Biochips to screen for genomic imbalances. Genes Chromosomes Cancer, 20, 399-407.
29. Snijders,A. et al.. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nature Genet., 29, 263-264.
30. Stjernqvist,S. et al.. (2007) Continuous-index hidden Markov modelling of array CGH copy number data. Bioinformatics, 23, 1006-1014.
31. Tibshirani,R. (1996) Regression shrinkage and selection via the lasso. J. R. Stat. Soc., B 58, 267-288.
32. Tibshirani,R. and Wang,P. (2008) Spatial smoothing and hot spot detection for CGH data using the fused lasso. Biostatistics, 9 18-29.
33. Ventakraman,E.S. and Olshen,A.B. (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 23, 657-663.
34. Wang,P. et al.. (2005) A method for calling gains and losses in array CGH data. Biostatistics, 6, 45-58.
35. Whittaker,E. (1923) On a new method of graduation. Proc. Edinburgh Math. Soc., 41, 63-75.
36. Willenbrock,H. and Fridlyand,J. (2005) A comparison study: Applying segmentation to array CGH data for downstream analyses. Bioinformatics, 21, 4084-4091.