Ximmer: a system for improving accuracy and consistency of CNV calling from exome data

  1. Simon P Sadedin
  2. Justine A Ellis
  3. Seth L Masters
  4. Alicia Oshlack

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Abstract

Background

While exome and targeted next-generation DNA sequencing are primarily used for detecting single nucleotide changes and small indels, detection of copy number variants (CNVs) can provide highly valuable additional information from the data. Although there are dozens of exome CNV detection methods available, these are often difficult to use, and accuracy varies unpredictably between and within datasets.

Findings

We present Ximmer, a tool that supports an end-to-end process for evaluating, tuning, and running analysis methods for detection of CNVs in germline samples. Ximmer includes a simulation framework, implementations of several commonly used CNV detection methods, and a visualization and curation tool that together enable interactive exploration and quality control of CNV results. Using Ximmer, we comprehensively evaluate CNV detection on four datasets using five different detection methods. We show that application of Ximmer can improve accuracy and aid in quality control of CNV detection results. In addition, Ximmer can be used to run analyses and explore CNV results in exome data.

Conclusions

Ximmer offers a comprehensive tool and method for applying and improving accuracy of CNV detection methods for exome data.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giy112

    Simon P Sadedin 1Bioinformatics, Murdoch Childrens Research Institute, Royal Children's Hospital Flemington Road, Parkville, Victoria 3052 AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJustine A Ellis 2Genes Environment & Complex Disease, Murdoch Childrens Research Institute, Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052 Australia3Department of Paediatrics, University of Melbourne, Victoria 3010 Australia4Centre for Social and Early Emotional Development, Faculty of Health, Deakin University, Burwood, Victoria 3125 AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Justine A EllisSeth L Masters 5Inflamation Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAlicia Oshlack 1Bioinformatics, Murdoch Childrens Research Institute, Royal Children's Hospital Flemington Road, Parkville, Victoria 3052 Australia6Department of BioScience, University of Melbourne, Parkville 3050, AustraliaFind this author on Google ScholarFind this author on PubMedSearch for this author on this site

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giy112 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101340 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101341 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101342 Reviewer 4: http://dx.doi.org/10.5524/REVIEW.101343 Reviewer 5: http://dx.doi.org/10.5524/REVIEW.101345

  2. Version published to 10.1093/gigascience/giy112
  3. Version published to 10.1101/260927v1 on bioRxiv