PatternCNV: A versatile tool for detecting copy number changes from exome sequencing data

Chen Wang, Jared M. Evans, Aditya V. Bhagwate, Naresh Prodduturi, Vivekananda Sarangi, Mridu Middha, Hugues Sicotte, Peter T. Vedell, Steven Hart, Gavin R. Oliver, Jean-Pierre Kocher, Matthew J. Maurer, Anne J Novak, Susan L Slager, James R Cerhan, Yan Asmann

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

Results: We developed a novel method named PatternCNV, which (i) accounts for the read coverage variations between exons while leveraging the consistencies of this variability across different samples; (ii) reduces alignment BAM files to WIG format and therefore greatly accelerates computation; (iii) incorporates multiple QC measures designed to identify outlier samples and batch effects; and (iv) provides a variety of visualization options including chromosome, gene and exon-level views of CNVs, along with a tabular summarization of the exon-level CNVs. Compared with other CNV-calling algorithms using data from a lymphoma exome-seq study, PatternCNV has higher sensitivity and specificity.

Availability and implementation: The software for PatternCNV is implemented using Perl and R, and can be used in Mac or Linux environments. Software and user manual are available at http://bioinformaticstools.mayo.edu/research/patterncnv/, and R package at https://github.com/topsoil/patternCNV/.

Motivation: Exome sequencing (exome-seq) data, which are typically used for calling exonic mutations, have also been utilized in detecting DNA copy number variations (CNVs). Despite the existence of several CNV detection tools, there is still a great need for a sensitive and an accurate CNV-calling algorithm with built-in QC steps, and does not require a paired reference for each sample.

Original languageEnglish (US)
Pages (from-to)2678-2680
Number of pages3
JournalBioinformatics
Volume30
Issue number18
DOIs
StatePublished - 2014

Fingerprint

Exome
Sequencing
Exons
Software
Chromosomes
DNA Copy Number Variations
DNA
Visualization
Genes
Availability
Lymphoma
Sensitivity and Specificity
Mutation
Research
Summarization
Linux
Outlier
Batch
Chromosome
Specificity

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

PatternCNV : A versatile tool for detecting copy number changes from exome sequencing data. / Wang, Chen; Evans, Jared M.; Bhagwate, Aditya V.; Prodduturi, Naresh; Sarangi, Vivekananda; Middha, Mridu; Sicotte, Hugues; Vedell, Peter T.; Hart, Steven; Oliver, Gavin R.; Kocher, Jean-Pierre; Maurer, Matthew J.; Novak, Anne J; Slager, Susan L; Cerhan, James R; Asmann, Yan.

In: Bioinformatics, Vol. 30, No. 18, 2014, p. 2678-2680.

Research output: Contribution to journalArticle

Wang, C, Evans, JM, Bhagwate, AV, Prodduturi, N, Sarangi, V, Middha, M, Sicotte, H, Vedell, PT, Hart, S, Oliver, GR, Kocher, J-P, Maurer, MJ, Novak, AJ, Slager, SL, Cerhan, JR & Asmann, Y 2014, 'PatternCNV: A versatile tool for detecting copy number changes from exome sequencing data', Bioinformatics, vol. 30, no. 18, pp. 2678-2680. https://doi.org/10.1093/bioinformatics/btu363
Wang, Chen ; Evans, Jared M. ; Bhagwate, Aditya V. ; Prodduturi, Naresh ; Sarangi, Vivekananda ; Middha, Mridu ; Sicotte, Hugues ; Vedell, Peter T. ; Hart, Steven ; Oliver, Gavin R. ; Kocher, Jean-Pierre ; Maurer, Matthew J. ; Novak, Anne J ; Slager, Susan L ; Cerhan, James R ; Asmann, Yan. / PatternCNV : A versatile tool for detecting copy number changes from exome sequencing data. In: Bioinformatics. 2014 ; Vol. 30, No. 18. pp. 2678-2680.
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