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Title: Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays
Authors: Dellinger, A.E.
Saw, S.-M. 
Goh, L.K. 
Seielstad, M.
Young, T.L. 
Li, Y.-J.
Issue Date: 8-Feb-2010
Citation: Dellinger, A.E., Saw, S.-M., Goh, L.K., Seielstad, M., Young, T.L., Li, Y.-J. (2010-02-08). Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Research 38 (9) : e105-. ScholarBank@NUS Repository.
Abstract: Determination of copy number variants (CNVs) inferred in genome wide single nucleotide polymorphism arrays has shown increasing utility in genetic variant disease associations. Several CNV detection methods are available, but differences in CNV call thresholds and characteristics exist. We evaluated the relative performance of seven methods: circular binary segmentation, CNVFinder, cnvPartition, gain and loss of DNA, Nexus algorithms, PennCNV and QuantiSNP. Tested data included real and simulated Illumina HumHap 550 data from the Singapore cohort study of the risk factors for Myopia (SCORM) and simulated data from Affymetrix 6.0 and platformindependent distributions. The normalized singleton ratio (NSR) is proposed as a metric for parameter optimization before enacting full analysis. We used 10 SCORM samples for optimizing parameter settings for each method and then evaluated method performance at optimal parameters using 100 SCORM samples. The statistical power, false positive rates, and receiver operating characteristic (ROC) curve residuals were evaluated by simulation studies. Optimal parameters, as determined by NSR and ROC curve residuals, were consistent across datasets. QuantiSNP outperformed other methods based on ROC curve residuals over most datasets. Nexus Rank and SNPRank have low specificity and high power. Nexus Rank calls oversized CNVs. PennCNV detects one of the fewest numbers of CNVs. © The Author(s) 2010.
Source Title: Nucleic Acids Research
ISSN: 03051048
DOI: 10.1093/nar/gkq040
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