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Hidden Markov models approach to the analysis of array CGH data

Author

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  • Fridlyand, Jane
  • Snijders, Antoine M.
  • Pinkel, Dan
  • Albertson, Donna G.
  • Jain, A.N.Ajay N.

Abstract

The development of solid tumors is associated with acquisition of complex genetic alterations, indicating that failures in the mechanisms that maintain the integrity of the genome contribute to tumor evolution. Thus, one expects that the particular types of genomic alterations seen in tumors reflect underlying failures in maintenance of genetic stability, as well as selection for changes that provide growth advantage. In order to investigate genomic alterations we are using microarray-based comparative genomic hybridization (array CGH). The computational task is to map and characterize the number and types of copy number alterations present in the tumors, and so define copy number phenotypes and associate them with known biological markers. To utilize the spatial coherence between nearby clones, we use an unsupervised hidden Markov models approach. The clones are partitioned into the states which represent the underlying copy number of the group of clones. The method is demonstrated on the two cell line datasets, one with known copy number alterations. The biological conclusions drawn from the analyses are discussed.

Suggested Citation

  • Fridlyand, Jane & Snijders, Antoine M. & Pinkel, Dan & Albertson, Donna G. & Jain, A.N.Ajay N., 2004. "Hidden Markov models approach to the analysis of array CGH data," Journal of Multivariate Analysis, Elsevier, vol. 90(1), pages 132-153, July.
  • Handle: RePEc:eee:jmvana:v:90:y:2004:i:1:p:132-153
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    References listed on IDEAS

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    1. Hirotugu Akaike, 1969. "Fitting autoregressive models for prediction," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 21(1), pages 243-247, December.
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    1. Salvatore Fasola & Vito M. R. Muggeo & Helmut Küchenhoff, 2018. "A heuristic, iterative algorithm for change-point detection in abrupt change models," Computational Statistics, Springer, vol. 33(2), pages 997-1015, June.
    2. Nancy R. Zhang & David O. Siegmund, 2007. "A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data," Biometrics, The International Biometric Society, vol. 63(1), pages 22-32, March.
    3. A. Gandolfi & M. Benelli & A. Magi & S. Chiti, 2013. "Moment estimation in discrete shifting level model applied to fast array-CGH segmentation," Statistica Neerlandica, Netherlands Society for Statistics and Operations Research, vol. 67(3), pages 227-262, August.
    4. Leighton Pritchard & Hui Liu & Clare Booth & Emma Douglas & Patrice François & Jacques Schrenzel & Peter E Hedley & Paul R J Birch & Ian K Toth, 2009. "Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens," PLOS Computational Biology, Public Library of Science, vol. 5(8), pages 1-17, August.
    5. Yoo-Ah Kim & Stefan Wuchty & Teresa M Przytycka, 2011. "Identifying Causal Genes and Dysregulated Pathways in Complex Diseases," PLOS Computational Biology, Public Library of Science, vol. 7(3), pages 1-13, March.
    6. John Wiedenhoeft & Eric Brugel & Alexander Schliep, 2016. "Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-28, May.
    7. F. Picard & S. Robin & E. Lebarbier & J.-J. Daudin, 2007. "A Segmentation/Clustering Model for the Analysis of Array CGH Data," Biometrics, The International Biometric Society, vol. 63(3), pages 758-766, September.
    8. Oscar M Rueda & Ramón Díaz-Uriarte, 2007. "Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH," PLOS Computational Biology, Public Library of Science, vol. 3(6), pages 1-8, June.
    9. Huixia Judy Wang & Jianhua Hu, 2011. "Identification of Differential Aberrations in Multiple-Sample Array CGH Studies," Biometrics, The International Biometric Society, vol. 67(2), pages 353-362, June.
    10. Xuesong Yu & Timothy W. Randolph & Hua Tang & Li Hsu, 2010. "Detecting Genomic Aberrations Using Products in a Multiscale Analysis," Biometrics, The International Biometric Society, vol. 66(3), pages 684-693, September.
    11. Stacia M. DeSantis & E. Andrés Houseman & Brent A. Coull & David N. Louis & Gayatry Mohapatra & Rebecca A. Betensky, 2009. "A Latent Class Model with Hidden Markov Dependence for Array CGH Data," Biometrics, The International Biometric Society, vol. 65(4), pages 1296-1305, December.
    12. Vincent Guigues, 2012. "Nonparametric multivariate breakpoint detection for the means, variances, and covariances of a discrete time stochastic process," Journal of Nonparametric Statistics, Taylor & Francis Journals, vol. 24(4), pages 857-882, December.
    13. Yu Chuan Tai & Mark N. Kvale & John S. Witte, 2010. "Segmentation and Estimation for SNP Microarrays: A Bayesian Multiple Change-Point Approach," Biometrics, The International Biometric Society, vol. 66(3), pages 675-683, September.
    14. Bérard Caroline & Martin-Magniette Marie-Laure & Brunaud Véronique & Aubourg Sébastien & Robin Stéphane, 2011. "Unsupervised Classification for Tiling Arrays: ChIP-chip and Transcriptome," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-22, November.
    15. Lin Chang-Yun & Lo Yungtai & Ye Kenny Q., 2012. "Genotype Copy Number Variations using Gaussian Mixture Models: Theory and Algorithms," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(5), pages 1-26, October.
    16. Rameen Beroukhim & Ming Lin & Yuhyun Park & Ke Hao & Xiaojun Zhao & Levi A Garraway & Edward A Fox & Ephraim P Hochberg & Ingo K Mellinghoff & Matthias D Hofer & Aurelien Descazeaud & Mark A Rubin & M, 2006. "Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays," PLOS Computational Biology, Public Library of Science, vol. 2(5), pages 1-10, May.
    17. Castro, Bruno M. & Lemes, Renan B. & Cesar, Jonatas & Hünemeier, Tábita & Leonardi, Florencia, 2018. "A model selection approach for multiple sequence segmentation and dimensionality reduction," Journal of Multivariate Analysis, Elsevier, vol. 167(C), pages 319-330.
    18. Love Michael I. & Myšičková Alena & Sun Ruping & Kalscheuer Vera & Vingron Martin & Haas Stefan A., 2011. "Modeling Read Counts for CNV Detection in Exome Sequencing Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-30, November.
    19. repec:jss:jstsof:40:i12 is not listed on IDEAS
    20. Engler David & Shen Yiping & Gusella James & Betensky Rebecca A., 2011. "Comparison of Clinical Subgroup aCGH Profiles through Pseudolikelihood Ratio Tests," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-23, July.
    21. Michael Seifert & André Gohr & Marc Strickert & Ivo Grosse, 2012. "Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana," PLOS Computational Biology, Public Library of Science, vol. 8(1), pages 1-15, January.

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