Analyzing DNA copy number changes using fused margin regression

Yuanjian Feng; Guoqiang Yu; Tian Li Wang; Ie Ming Shih; Yue Wang

doi:10.1109/BIBM.2009.57

Analyzing DNA copy number changes using fused margin regression

Yuanjian Feng, Guoqiang Yu, Tian Li Wang, Ie Ming Shih, Yue Wang

School of Medicine

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

DNA copy number change is an important form of structural variations in human genomes. Detecting copy number changes using DNA array data is a challenging task due to high density genomic loci, low signal to noise ratios, and normal tissue contamination. We propose fused margin regression (FMR) method that combines a variable fusion rule and robust ε-insensitive loss criterion to approximate piecewise constant segments of the underlying copy number profile. We tested FMR on both simulation and real CGH and SNP array datasets, and observed competitively improved performance as compared to several widely-adopted existing methods.

Original language	English (US)
Title of host publication	2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009
Pages	388-391
Number of pages	4
DOIs	https://doi.org/10.1109/BIBM.2009.57
State	Published - Dec 1 2009
Event	2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009 - Washington, D.C., United States Duration: Nov 1 2009 → Nov 4 2009

Publication series

Name	2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009

Other

Other	2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009
Country/Territory	United States
City	Washington, D.C.
Period	11/1/09 → 11/4/09

ASJC Scopus subject areas

Artificial Intelligence
Software
Biomedical Engineering
Health Informatics

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10.1109/BIBM.2009.57

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Analyzing DNA copy number changes using fused margin regression. / Feng, Yuanjian; Yu, Guoqiang; Wang, Tian Li et al.
2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009. 2009. p. 388-391 5341749 (2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Feng, Y, Yu, G, Wang, TL , Shih, IM & Wang, Y 2009, Analyzing DNA copy number changes using fused margin regression. in 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009., 5341749, 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009, pp. 388-391, 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009, Washington, D.C., United States, 11/1/09. https://doi.org/10.1109/BIBM.2009.57

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AB - DNA copy number change is an important form of structural variations in human genomes. Detecting copy number changes using DNA array data is a challenging task due to high density genomic loci, low signal to noise ratios, and normal tissue contamination. We propose fused margin regression (FMR) method that combines a variable fusion rule and robust ε-insensitive loss criterion to approximate piecewise constant segments of the underlying copy number profile. We tested FMR on both simulation and real CGH and SNP array datasets, and observed competitively improved performance as compared to several widely-adopted existing methods.

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Analyzing DNA copy number changes using fused margin regression

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