panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics
Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy number variations (CNVs) in addition to single-nucleotide-variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control, incidental findings, and user-friendliness.
We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with 5 state-of-the-art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region-of-interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user-selected genes, thus, avoiding incidental findings. Additionally, panelcn.MOPS offers quality control criteria not only for samples but also for individual ROIs within a sample which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience.
panelcn.MOPS combines high sensitivity and specificity with user-friendliness rendering it highly suitable for routine clinical diagnostics.
Please cite:
Povysil G, Tzika A, Vogt J, et al. panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics. Human Mutation. 2017;38:889–897.
https://doi.org/10.1002/humu.23237
Poster:
panelcn.MOPS R package:
- Available at Bioconductor:
panelcn.mops
- Github:
https://github.com/bioinf-jku/panelcn.mops
Installer for Windows:
- Please contact povysil@bioinf.jku.at
panelcn.MOPS data: