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

doi:10.1109/GENSIPS.2006.353150

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

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English
Title of host publication	2006 IEEE International Workshop on Genomic Signal Processing and Statstics, GENSIPS 2006
Pages	49-50
Number of pages	2
DOIs	https://doi.org/10.1109/GENSIPS.2006.353150
Publication status	Published - 2006
Externally published	Yes
Event	2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006 - College Station, TX, United States Duration: 2006 May 28 → 2006 May 30

Publication series

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

Other

Other	2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006
Country/Territory	United States
City	College Station, TX
Period	2006/05/28 → 2006/05/30

ASJC Scopus subject areas

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1109/GENSIPS.2006.353150

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). Article 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 et al.
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 proceeding › Conference 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, 2006/05/28. 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). doi: 10.1109/GENSIPS.2006.353150

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title = "Development of a normalization algorithm for array comparative genomic hybridization",

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.",

author = "Sher Singh and Chen, {Hung I.Harry} and Hsu, {Fang Han} and Tsai, {Mong Hsun} and Chuang, {Eric Y.} and Yidong Chen",

year = "2006",

doi = "10.1109/GENSIPS.2006.353150",

language = "English",

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note = "2006 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2006 ; Conference date: 28-05-2006 Through 30-05-2006",

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AU - Singh, Sher

AU - Chen, Hung I.Harry

AU - Hsu, Fang Han

AU - Tsai, Mong Hsun

AU - Chuang, Eric Y.

AU - Chen, Yidong

PY - 2006

Y1 - 2006

N2 - 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.

AB - 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.

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Development of a normalization algorithm for array comparative genomic hybridization

Abstract

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ASJC Scopus subject areas

UN SDGs

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