TY - GEN
T1 - A pipeline for copy number variation detection based on principal component analysis
AU - Chen, Jiayu
AU - Liu, Jingyu
AU - Boutte, David
AU - Calhoun, Vince D.
PY - 2011
Y1 - 2011
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84864615967&partnerID=8YFLogxK
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U2 - 10.1109/IEMBS.2011.6091763
DO - 10.1109/IEMBS.2011.6091763
M3 - Conference contribution
C2 - 22255943
AN - SCOPUS:84864615967
SN - 9781424441211
T3 - Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS
SP - 6975
EP - 6978
BT - 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011
T2 - 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS 2011
Y2 - 30 August 2011 through 3 September 2011
ER -