Analyzing DNA copy number changes using fused margin regression

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

Research output: Chapter in Book/Report/Conference proceedingConference 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 languageEnglish (US)
Title of host publication2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009
Pages388-391
Number of pages4
DOIs
StatePublished - 2009
Event2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009 - Washington, D.C., United States
Duration: Nov 1 2009Nov 4 2009

Other

Other2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009
CountryUnited States
CityWashington, D.C.
Period11/1/0911/4/09

Fingerprint

DNA Copy Number Variations
DNA
Signal-To-Noise Ratio
Human Genome
Oligonucleotide Array Sequence Analysis
Single Nucleotide Polymorphism
Signal to noise ratio
Contamination
Fusion reactions
Genes
Tissue

ASJC Scopus subject areas

  • Artificial Intelligence
  • Software
  • Biomedical Engineering
  • Health Informatics

Cite this

Feng, Y., Yu, G., Wang, T-L., Shih, I. M., & Wang, Y. (2009). Analyzing DNA copy number changes using fused margin regression. In 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009 (pp. 388-391). [5341749] https://doi.org/10.1109/BIBM.2009.57

Analyzing DNA copy number changes using fused margin regression. / Feng, Yuanjian; Yu, Guoqiang; Wang, Tian-Li; Shih, Ie Ming; Wang, Yue.

2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009. 2009. p. 388-391 5341749.

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

Feng, Y, Yu, G, Wang, T-L, 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, 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
Feng Y, Yu G, Wang T-L, Shih IM, Wang Y. Analyzing DNA copy number changes using fused margin regression. In 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009. 2009. p. 388-391. 5341749 https://doi.org/10.1109/BIBM.2009.57
Feng, Yuanjian ; Yu, Guoqiang ; Wang, Tian-Li ; Shih, Ie Ming ; Wang, Yue. / Analyzing DNA copy number changes using fused margin regression. 2009 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2009. 2009. pp. 388-391
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