Development of a normalization algorithm for array comparative genomic hybridization

Sher Singh, Hung I.Harry Chen, Fang Han Hsu, Mong Hsun Tsai, Eric Y. Chuang, Yidong Chen

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

Abstract

Genomic instability is one of fundamental factors in tumorigenesis and tumor progression. Many studies have demonstrated that copy-number abnormalities at the DNA level are important in the pathogenesis of cancer. Array Comparative Genomic Hybridization (aCGH), developed based on expression microarray technology, can reveal the chromosomal aberrations in segmental copy at a high-resolution. However, due to the nature of aCGH, many standard expression data processing tools, such as data normalization, often failed to yield satisfactory results. The proposed study demonstrated a novel aCGH normalization procedure, which provides an accurate aCGH data normalization by utilizing the dependency of neighboring probe measurements in aCGH experiments. To facilitate the study, we have developed a Hidden Markov Model (HMM) to simulate a series of aCGH experiment with random DNA copy number alteration. Furthermore, based on this new development, we will establish a user-friendly web system in order to provide convenient aCGH analysis.

Original languageEnglish
Title of host publication2006 IEEE International Workshop on Genomic Signal Processing and Statstics, GENSIPS 2006
Pages49-50
Number of pages2
DOIs
Publication statusPublished - 2006 Dec 1
Event2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006 - College Station, TX, United States
Duration: 2006 May 282006 May 30

Publication series

Name2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006

Other

Other2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006
CountryUnited States
CityCollege Station, TX
Period06/5/2806/5/30

Fingerprint

Comparative Genomics
Comparative Genomic Hybridization
Normalization
DNA
Hidden Markov models
Microarrays
Aberrations
Tumors
Experiments
Genomic Instability
Aberration
Progression
Microarray
Chromosome Aberrations
Markov Model
Experiment
Genomics
Tumor
Neoplasms
Cancer

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computational Theory and Mathematics
  • Computer Vision and Pattern Recognition
  • Statistics and Probability

Cite this

Singh, S., Chen, H. I. H., Hsu, F. H., Tsai, M. H., Chuang, E. Y., & Chen, Y. (2006). Development of a normalization algorithm for array comparative genomic hybridization. In 2006 IEEE International Workshop on Genomic Signal Processing and Statstics, GENSIPS 2006 (pp. 49-50). [4161771] (2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006). https://doi.org/10.1109/GENSIPS.2006.353150

Development of a normalization algorithm for array comparative genomic hybridization. / Singh, Sher; Chen, Hung I.Harry; Hsu, Fang Han; Tsai, Mong Hsun; Chuang, Eric Y.; Chen, Yidong.

2006 IEEE International Workshop on Genomic Signal Processing and Statstics, GENSIPS 2006. 2006. p. 49-50 4161771 (2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006).

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

Singh, S, Chen, HIH, Hsu, FH, Tsai, MH, Chuang, EY & Chen, Y 2006, Development of a normalization algorithm for array comparative genomic hybridization. in 2006 IEEE International Workshop on Genomic Signal Processing and Statstics, GENSIPS 2006., 4161771, 2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006, pp. 49-50, 2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006, College Station, TX, United States, 06/5/28. https://doi.org/10.1109/GENSIPS.2006.353150
Singh S, Chen HIH, Hsu FH, Tsai MH, Chuang EY, Chen Y. Development of a normalization algorithm for array comparative genomic hybridization. In 2006 IEEE International Workshop on Genomic Signal Processing and Statstics, GENSIPS 2006. 2006. p. 49-50. 4161771. (2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006). https://doi.org/10.1109/GENSIPS.2006.353150
Singh, Sher ; Chen, Hung I.Harry ; Hsu, Fang Han ; Tsai, Mong Hsun ; Chuang, Eric Y. ; Chen, Yidong. / Development of a normalization algorithm for array comparative genomic hybridization. 2006 IEEE International Workshop on Genomic Signal Processing and Statstics, GENSIPS 2006. 2006. pp. 49-50 (2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006).
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