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Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays.

Publication ,  Journal Article
Dellinger, AE; Saw, S-M; Goh, LK; Seielstad, M; Young, TL; Li, Y-J
Published in: Nucleic Acids Res
May 2010

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 platform-independent 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.

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Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

May 2010

Volume

38

Issue

9

Start / End Page

e105

Location

England

Related Subject Headings

  • Polymorphism, Single Nucleotide
  • Oligonucleotide Array Sequence Analysis
  • Myopia
  • Male
  • Humans
  • Female
  • Developmental Biology
  • DNA Copy Number Variations
  • Computer Simulation
  • Algorithms
 

Citation

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Dellinger, A. E., Saw, S.-M., Goh, L. K., Seielstad, M., Young, T. L., & Li, Y.-J. (2010). Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res, 38(9), e105. https://doi.org/10.1093/nar/gkq040
Dellinger, Andrew E., Seang-Mei Saw, Liang K. Goh, Mark Seielstad, Terri L. Young, and Yi-Ju Li. “Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays.Nucleic Acids Res 38, no. 9 (May 2010): e105. https://doi.org/10.1093/nar/gkq040.
Dellinger AE, Saw S-M, Goh LK, Seielstad M, Young TL, Li Y-J. Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res. 2010 May;38(9):e105.
Dellinger, Andrew E., et al. “Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays.Nucleic Acids Res, vol. 38, no. 9, May 2010, p. e105. Pubmed, doi:10.1093/nar/gkq040.
Dellinger AE, Saw S-M, Goh LK, Seielstad M, Young TL, Li Y-J. Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res. 2010 May;38(9):e105.
Journal cover image

Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

May 2010

Volume

38

Issue

9

Start / End Page

e105

Location

England

Related Subject Headings

  • Polymorphism, Single Nucleotide
  • Oligonucleotide Array Sequence Analysis
  • Myopia
  • Male
  • Humans
  • Female
  • Developmental Biology
  • DNA Copy Number Variations
  • Computer Simulation
  • Algorithms