Virtual CGH: Prediction of novel regions of chromosomal alterations in tumor from gene expression profiling

Huimin Geng, Javeed Iqbal, Xutao Deng, Wing C. Chan, Hesham H Ali

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

1 Citation (Scopus)

Abstract

The identification of genetic alterations using array Comparative Genomic Hybridization (CGH) would provide important insights into the mechanisms of tumorogenesis. High resolution array CGH are very expensive and the experiment require a separate sample, therefore, we developed a computational method for predicting gains and losses of genomic DNA segments based on mRNA expression profiles of tumor cell lines, and called this method a Virtual CGH (vCGH) predictor. VCGH is performed through a novel algorithm in which each chromosomal segment is evaluated by the gene transcriptional profiles. The calculation yields a log of odds (LOD) score for each chromosomal segment and this likelihood-based score is used to predict the correlation between mRNA expression patterns and DNA copy number alterations. By aligning all regions of gains and losses from multiple cell lines we can identify minimal common regions of gains and losses which may contain potential oncogenes or tumor suppressors. This method can be used to screen transcriptional profiles of other malignancies for the identification of DNA segmental loss or gain.

Original languageEnglish (US)
Title of host publicationProceedings of the 40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07
DOIs
StatePublished - Dec 1 2007
Event40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07 - Big Island, HI, United States
Duration: Jan 3 2007Jan 6 2007

Publication series

NameProceedings of the Annual Hawaii International Conference on System Sciences
ISSN (Print)1530-1605

Conference

Conference40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07
CountryUnited States
CityBig Island, HI
Period1/3/071/6/07

Fingerprint

Gene expression
Tumors
DNA
Cells
Computational methods
Genes
Experiments
Messenger RNA

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Geng, H., Iqbal, J., Deng, X., Chan, W. C., & Ali, H. H. (2007). Virtual CGH: Prediction of novel regions of chromosomal alterations in tumor from gene expression profiling. In Proceedings of the 40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07 [4076629] (Proceedings of the Annual Hawaii International Conference on System Sciences). https://doi.org/10.1109/HICSS.2007.604

Virtual CGH : Prediction of novel regions of chromosomal alterations in tumor from gene expression profiling. / Geng, Huimin; Iqbal, Javeed; Deng, Xutao; Chan, Wing C.; Ali, Hesham H.

Proceedings of the 40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07. 2007. 4076629 (Proceedings of the Annual Hawaii International Conference on System Sciences).

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

Geng, H, Iqbal, J, Deng, X, Chan, WC & Ali, HH 2007, Virtual CGH: Prediction of novel regions of chromosomal alterations in tumor from gene expression profiling. in Proceedings of the 40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07., 4076629, Proceedings of the Annual Hawaii International Conference on System Sciences, 40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07, Big Island, HI, United States, 1/3/07. https://doi.org/10.1109/HICSS.2007.604
Geng H, Iqbal J, Deng X, Chan WC, Ali HH. Virtual CGH: Prediction of novel regions of chromosomal alterations in tumor from gene expression profiling. In Proceedings of the 40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07. 2007. 4076629. (Proceedings of the Annual Hawaii International Conference on System Sciences). https://doi.org/10.1109/HICSS.2007.604
Geng, Huimin ; Iqbal, Javeed ; Deng, Xutao ; Chan, Wing C. ; Ali, Hesham H. / Virtual CGH : Prediction of novel regions of chromosomal alterations in tumor from gene expression profiling. Proceedings of the 40th Annual Hawaii International Conference on System Sciences 2007, HICSS'07. 2007. (Proceedings of the Annual Hawaii International Conference on System Sciences).
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