Introduction

Only a few large systematic studies have evaluated the impact of copy number variants (CNVs) on common diseases. Several million individuals have been genotyped on single nucleotide variation arrays, which could be used for genome-wide CNVs association studies. However, CNV calls remain prone to false positives and only empirical filtering strategies exist in the literature. To overcome this issue, we defined a new quality score (QS) estimating the probability of a CNV called by PennCNV to be confirmed by other software.Out-of-sample comparison showed that the correlation between the consensus CNV status and the QS is twice as high as it is for any previously proposed CNV filters. ROC curves displayed an AUC higher than 0.8 and simulations showed an increase up to 20% in statistical power when using QS in comparison to other filtering strategies. Superior performance was confirmed also for alternative consensus CNV definition and through improving known CNV-trait associations.http://goo.gl/T6yuFM CONTACT: zoltan.kutalik@unil.ch or aurelien@mace@unil.chSupplementary information: Supplementary data are available at Bioinformatics online.

Publications

  1. New quality measure for SNP array based CNV detection.
    Cite this
    Macé A, Tuke MA, Beckmann JS, Lin L, Jacquemont S, Weedon MN, Reymond A, Kutalik Z, 2016-11-01 - Bioinformatics (Oxford, England)

Credits

  1. A Macé
    Developer

    Institute of Social and Preventive Medicine, University Hospital of Lausanne, Switzerland

  2. M A Tuke
    Developer

    Genetics of Complex Traits, University of Exeter Medical School

  3. J S Beckmann
    Developer

    Swiss Institute of Bioinformatics, Lausanne, Switzerland

  4. L Lin
    Developer

    Division of Cardiology, Geneva University Hospital, Switzerland

  5. S Jacquemont
    Developer

    Service de Génétique Médicale, Centre Universitaire Hospitalier Vaudois, Switzerland

  6. M N Weedon
    Developer

    Genetics of Complex Traits, University of Exeter Medical School

  7. A Reymond
    Developer

    Center for Integrative Genomics, University for Lausanne, Switzerland

  8. Z Kutalik
    Investigator

    Institute of Social and Preventive Medicine, University Hospital of Lausanne, Switzerland

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Summary
AccessionBT000167
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionSwitzerland
Submitted ByZ Kutalik