Statistical issues in the analysis of the array CGH data

J. Fridlyand, A. Snijders, D. Pinkel, D. Albertson, Ajay Jain

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 derangement 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 as well as to associate them with known biological markers. To utilize the spatial coherence between nearby clones, we use unsupervised Hidden Markov Models approach. The clones are partitioned into the states which represent underlying copy number of the group of clones. The method is demonstrated on the two cell line datasets with known copy number alterations for one of them. The biological conclusions drawn from the analyses are discussed.

Original languageEnglish (US)
Title of host publicationProceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages407-408
Number of pages2
ISBN (Print)0769520006, 9780769520001
DOIs
StatePublished - 2003
Event2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003 - Stanford, United States
Duration: Aug 11 2003Aug 14 2003

Other

Other2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003
CountryUnited States
CityStanford
Period8/11/038/14/03

Fingerprint

Microarrays
Tumors
Hidden Markov models
Genes
Cells

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Computer Science Applications

Cite this

Fridlyand, J., Snijders, A., Pinkel, D., Albertson, D., & Jain, A. (2003). Statistical issues in the analysis of the array CGH data. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003 (pp. 407-408). [1227347] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CSB.2003.1227347

Statistical issues in the analysis of the array CGH data. / Fridlyand, J.; Snijders, A.; Pinkel, D.; Albertson, D.; Jain, Ajay.

Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 407-408 1227347.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Fridlyand, J, Snijders, A, Pinkel, D, Albertson, D & Jain, A 2003, Statistical issues in the analysis of the array CGH data. in Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003., 1227347, Institute of Electrical and Electronics Engineers Inc., pp. 407-408, 2nd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, Stanford, United States, 8/11/03. https://doi.org/10.1109/CSB.2003.1227347
Fridlyand J, Snijders A, Pinkel D, Albertson D, Jain A. Statistical issues in the analysis of the array CGH data. In Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc. 2003. p. 407-408. 1227347 https://doi.org/10.1109/CSB.2003.1227347
Fridlyand, J. ; Snijders, A. ; Pinkel, D. ; Albertson, D. ; Jain, Ajay. / Statistical issues in the analysis of the array CGH data. Proceedings of the 2003 IEEE Bioinformatics Conference, CSB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. pp. 407-408
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