DocumentCode :
2501482
Title :
A pipeline for copy number variation detection based on principal component analysis
Author :
Chen, Jiayu ; Liu, Jingyu ; Boutte, David ; Calhoun, Vince D.
Author_Institution :
Electr. Eng. Dept., Univ. of New Mexico, Albuquerque, NM, USA
fYear :
2011
fDate :
Aug. 30 2011-Sept. 3 2011
Firstpage :
6975
Lastpage :
6978
Abstract :
DNA copy number variation (CNV), an important structural variation, is known to be pervasive in the human genome and the determination of CNVs is essential to understanding their potential effects on the susceptibility to diseases. However, CNV detection using SNP array data is challenging due to the low signal-to-noise ratio. In this study, we propose a principal component analysis (PCA) based approach for data correction, and present a novel processing pipeline for reliable CNV detection. Tested data include both simulated and real SNP array datasets. Simulations demonstrate a substantial reduction in the false positive rate of CNV detection after PCA-correction. And we also observe a significant improvement in data quality in real SNP array data after correction.
Keywords :
DNA; biology computing; genomics; pipeline processing; principal component analysis; DNA; PCA; SNP array datasets; copy number variation detection; data correction; human genome; principal component analysis; signal-to-noise ratio; Arrays; Bioinformatics; DNA; Gaussian noise; Genomics; Pipelines; Adult; Analysis of Variance; Computer Simulation; DNA; DNA Copy Number Variations; False Positive Reactions; Female; Genetic Predisposition to Disease; Genome, Human; Genotype; Humans; Male; Normal Distribution; Polymorphism, Single Nucleotide; Principal Component Analysis; Reproducibility of Results; Signal Processing, Computer-Assisted;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Engineering in Medicine and Biology Society, EMBC, 2011 Annual International Conference of the IEEE
Conference_Location :
Boston, MA
ISSN :
1557-170X
Print_ISBN :
978-1-4244-4121-1
Electronic_ISBN :
1557-170X
Type :
conf
DOI :
10.1109/IEMBS.2011.6091763
Filename :
6091763
Link To Document :
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