Flexible and accurate detection of genomic copy-number changes from aCGH

PLoS Computational Biology

Volumn 3, Issue 6, 2007, Pages 1115-1122

  Rueda, Oscar M ^a   Díaz Uriarte, Ramón ^a  

^a Centro Nacional de Investigaciones Oncológicas   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN NETWORKS; CLINICAL RESEARCH; DISEASES; GENE THERAPY; GENOME; MONTE CARLO METHODS; UNCERTAINTY ANALYSIS;

COMPARATIVE GENOMIC HYBRIDIZATION DATUM; COMPARATIVE GENOMIC HYBRIDIZATIONS; COMPLEX DISEASE; COPY NUMBER; COPY-NUMBER ALTERATIONS; DNA COPY NUMBERS; GENOMIC DNA; GENOMICS; PATIENT SURVIVALS; REVERSIBLE JUMP;

HIDDEN MARKOV MODELS;

GENOMIC DNA;

ARTICLE; BAYES THEOREM; CANCER; CHROMOSOME; CLINICAL RESEARCH; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DATA ANALYSIS; GENE LOCATION; GENE NUMBER; GENE PROBE; GENOMIC COPY NUMBER ALTERATION; HUMAN; MONTE CARLO METHOD; PROBABILITY; REVERSIBLE JUMP COMPARATIVE GENOMIC HYBRIDIZATION; STATISTICAL ANALYSIS; ALGORITHM; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; CHROMOSOME MAP; DNA MICROARRAY; DNA SEQUENCE; GENE DOSAGE; GENETICS; METHODOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CHROMOSOME MAPPING; GENE DOSAGE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 34347342852     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030122     Document Type: Article

References (54)

1. Pinkel D, Albertson DG (2005) Array comparative genomic hybridization and its applications in cancer. Nat Genet 37 (Supplement): S11-S17.
2. Lockwood WW, Chari R, Chi B, Lam WLa (2006) Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet 14: 139-148.
3. Urban AE, Korbel JO, Selzer R, Richmond T, Hacker A, et al. (2006) High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A 103: 4534-4539.
4. Misra A, Pellarin M, Nigro J, Smirnov I, Moore D, et al. (2005) Array comparative genomic hybridization identifies genetic subgroups in grade 4 human astrocytoma. Clin Cancer Res 11: 2907-2918.
5. Aguirre AJ, Brennan C, Bailey G, Sinha R, Feng B, et al. (2004) High-resolution characterization of the pancreatic adenocarcinoma genome. Proc Natl Acad Sci U S A 101: 9067-9072.
6. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528.
7. Forozan F, Mahlamäki EH, Monni O, Chen Y, Veldman R, et al. (2000) Comparative genomic hybridization analysis of 38 breast cancer cell lines: A basis for interpreting complementary DNA microarray data. Cancer Res 60: 4519-4525.
8. Heiskanen MA, Bittner ML, Chen Y, Khan J, Adler KE, et al. (2000) Detection of gene amplification by genomic hybridization to cDNA microarrays. Cancer Res 60: 799-802.
9. Holzmann K, Kohlhammer H, Schwaenen C, Wessendorf S, Kestler HA, et al. (2004) Genomic DNA-chip hybridization reveals a higher incidence of genomic amplifications in pancreatic cancer than conventional comparative genomic hybridization and leads to the identification of novel candidate genes. Cancer Res 64: 4428-4433.
10. Veltman JA, Fridlyand J, Pejavar S, Olshen AB, Korkola JE, et al. (2003) Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Res 63: 2872-2880.
11. Vogelstein B, Kinzler KW (2004) Cancer genes and the pathways they control. Nat Med 10: 789-799.
12. Pollack JR, Sørlie T, Perou CM, Rees CA, Jeffrey SS, 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 U S A 99: 12963-12968.
13. Ylstra B, van den Ijssel P, Carvalho B, Brakenhoff RH, Meijer GA (2006) BAC to the future! or oligonucleotides: A perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res 34: 445-450.
14. Engler D, Mohaptra G, Louis D, Betensky R (2006) A pseudolikelihood approach for simultaneous analysis of array comparative genomic hybridizations. Biostatistics 7: 399-421.
15. Broët P, Richardson S (2006) Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model. Bioinformatics 22: 911-918.
16. Shah SP, Xuan X, Deleeuw RJ, Khojasteh M, Lam WL, et al. (2006) Integrating copy number polymorphisms into array CGH analysis using a robust HMM. Bioinformatics 22: e431-e439.
17. Hoeting J, Madigan H, Raftery A, Volinsky C (1999) Bayesian model averaging: A tutorial. Stat Sci 14: 382-417.
18. Marioni JC, Thorne NP, Tavaré S (2006) BioHMM: A heterogeneous hidden Markov model for segmenting array CGH data. Bioinformatics 22: 1144-1146.
19. Fridlyand J, Snijders AM, Pinkel D, Albertson DGa (2004) Hidden Markov models approach to the analysis of array CGH data. J Multivariate Anal 90: 132-153.
20. Lai WRR, Johnson MDD, Kucherlapati R, Park PJJ (2005) Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data. Bioinformatics 21: 3763-3770.
21. Huang T, Wu B, Lizardi P, Zhao H (2005) Detection of DNA copy number alterations using penalized least squares regression. Bioinformatics 21: 3811-3817.
22. Daruwala RS, Rudra A, Ostrer H, Lucito R, Wigler M, et al. (2004) A versatile statistical analysis algorithm to detect genome copy number variation. Proc Natl Acad Sci U S A 101: 16292-16297.
23. Hupé P, Stransky N, Thiery JP, Radvanyi F, Barillot E (2004) Analysis of array CGH data: From signal ratio to gain and loss of DNA regions. Bioinformatics 20: 3413-3422.
24. Olshen AB, Venkatraman ES, Lucito R, Wigler M (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5: 557-572.
25. Price TS, Regan R, Mott R, Hedman A, Honey B, et al. (2005) SW-array: A dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res 33: 3455-3464.
26. Hsu L, Self SG, Grove D, Randolph T, Wang K, et al. (2005) Denoising array-based comparative genomic hybridization data using wavelets. Biostatistics 6: 211-226.
27. Lingjaerde OC, Baumbusch LO, Liestøl K, Glad IK, Borresen-Dale AL (2005) CGH-explorer: A program for analysis of array-CGH data. Bioinformatics 21: 821-822.
28. Picard F, Robin S, Lavielle M, Vaisse C, Daudin JJ (2005) A statistical approach for array CGH data analysis. BMC Bioinformatics 6: 27.
29. Cappé O, Moulines E, Ryden T (2005) Inference in hidden Markov models (Springer series in statistics). New York: Springer. 652 p.
30. Green P (1995) Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82: 711-732.
31. Willenbrock H, Fridlyand J (2005) A comparison study: Applying segmentation to array CGH data for downstream analyses. Bioinformatics 21: 4084-4091.
32. Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, et al. (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29: 263-264.
33. Raftery AE, Zheng Y (2003) Discussion: Performance of bayesian model averaging. J Am Statist Assoc 98: 931-938.
34. Rouveirol C, Stransky N, Hupé P, La Rosa P, Viara E, et al. (2006) Computation of recurrent minimal genomic alterations from array-CGH data. Bioinformatics 22: 2066-2073.
35. Diskin SJ, Eck T, Greshock J, Mosse YPP, Naylor T, et al. (2006) STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res 16: 1149-1158.
36. Misra A, Pellarin M, Nigro J, Smirnov I, Moore D, et al. (2005) Array comparative genomic hybridization identifies genetic subgroups in grade 4 human astrocytoma. Clin Cancer Res 11: 2907-2918.
37. Tonon G, Wong KK, Maulik G, Brennan C, Feng B, et al. (2005) High-resolution genomic profiles of human lung cancer. Proc Natl Acad Sci U S A 102: 9625-9630.
38. Albertson DG, Pinkel D (2003) Genomic microarrays in human genetic disease and cancer. Hum Mol Genet 12: R145-R152.
39. Bergamaschi A, Kim YH, Wang P, Sørlie T, Hernandez-Boussard T, et al. (2006) Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 45: 1033-1040.
40. van Beers EH, Nederlof PM (2006) Array-CGH and breast cancer. Breast Cancer Res 8: 210.
41. Yao J, Weremowicz S, Feng B, Gentleman RC, Marks JR, 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.
42. Habermann JKK, Paulsen U, Roblick UJJ, Upender MBB, McShane LMM, et al. (2007) Stage-specific alterations of the genome, transcriptome, and proteome during colorectal carcinogenesis. Genes Chromosomes Cancer 46: 10-26.
43. Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, et al. (2006) Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther 5: 853-867.
44. Parmigiani G, Garrett E, Anbazhaghan R, Gabrielson E (2002) A statistical framework for expression-based molecular classification in cancer. J R Stat Soc Ser B Stat Methodol 64: 717-736.
45. Garrett E, Parmigiani G (2003) POE: Statistical methods for qualitative analysis of gene expression. In: Parmigi ani G, Garrett ES, Irizarry RA, Zeger SL, editors. The analysis of gene expression data: Methods and software. New York: Springer. pp. 362-387.
46. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.
47. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853.
48. Kirshner S (2005) Modeling of multivariate time series using hidden Markov models [dissertation]. Irvine (California): University of California Irvine. Available: http://www.datalab.uci.edu/papers/kirshner_thesis.pdf. Accessed 22 May 2007.
49. Hughes PJ, Guttorp P, Charles PS (1999) A nonhomogeneous hidden Markov model for precipitation. Northwest Research Center for Statistics and the Environment. Available: http://www.nrcse.washington.edu/pdf/trs04_hgc.pdf. Accessed 22 May 2007.
50. Richardson S, Green PJ (1997) On Bayesian analysis of mixtures with an unknown number of components. J R Stat Soc Ser B Stat Methodol 59: 731-792.
51. Robert C, Ryden T, Titterington D (2000) Bayesian inference in hidden Markov models through reversible jump Markov chain Monte Carlo. J R Stat Soc Ser B Stat Methodol 62: 57-75.
52. Brooks SP, Giudici P, Roberts GO (2003) Efficient construction of reversible jump Markov chain Monte Carlo proposal distributions. J R Stat Soc Ser B Stat Methodol 65: 3-39.
53. Brooks S, Gelman A (1998) General methods for monitoring convergence of iterative simulations. J Comput Graph Statist 7: 434-455.
54. R Development Core Team (2006) R: A language and environment for statistical computing. R Foundation for Statistical Computing. Available: http://www.R-project.org. Accessed 22 May 2007.