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

^*Corresponding author for this work

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

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
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 - 2009
Externally published	Yes
Event	2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009 - Washington, D.C., United States Duration: 01 11 2009 → 04 11 2009

Publication series

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

Conference

Conference	2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009
Country/Territory	United States
City	Washington, D.C.
Period	01/11/09 → 04/11/09

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10.1109/BIBM.2009.57

Cite this

@inproceedings{e4d515f60a3c4833b2814c022e629bc5,

title = "Analyzing DNA copy number changes using fused margin regression",

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.",

author = "Yuanjian Feng and Guoqiang Yu and Wang, {Tian Li} and Shih, {Ie Ming} and Yue Wang",

year = "2009",

doi = "10.1109/BIBM.2009.57",

language = "英语",

isbn = "9780769538853",

series = "2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009",

pages = "388--391",

booktitle = "2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009",

note = "2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009 ; Conference date: 01-11-2009 Through 04-11-2009",

}

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, 01/11/09. https://doi.org/10.1109/BIBM.2009.57

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 › peer-review

TY - GEN

T1 - Analyzing DNA copy number changes using fused margin regression

AU - Feng, Yuanjian

AU - Yu, Guoqiang

AU - Wang, Tian Li

AU - Shih, Ie Ming

AU - Wang, Yue

PY - 2009

Y1 - 2009

N2 - 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.

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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DO - 10.1109/BIBM.2009.57

M3 - 会议稿件

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SN - 9780769538853

T3 - 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009

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BT - 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009

T2 - 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009

Y2 - 1 November 2009 through 4 November 2009

ER -

Analyzing DNA copy number changes using fused margin regression

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