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Moreno-CabreraJM.pdf (1.28 MB)

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2020-12-01

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cc by (c) Moreno Cabrera et al., 2020
Si us plau utilitzeu sempre aquest identificador per citar o enllaçar aquest document: https://hdl.handle.net/2445/173588

Evaluation of CNV detection tools for NGS panel data in genetic diagnostics

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Recurs relacionat

https://doi.org/10.1038/s41431-020-0675-z

Resum

Although germline copy-number variants (CNVs) are the genetic cause of multiple hereditary diseases, detecting them from targeted next-generation sequencing data (NGS) remains a challenge. Existing tools perform well for large CNVs but struggle with single and multi-exon alterations. The aim of this work is to evaluate CNV calling tools working on gene panel NGS data and their suitability as a screening step before orthogonal confirmation in genetic diagnostics strategies. Five tools (DECoN, CoNVaDING, panelcn.MOPS, ExomeDepth, and CODEX2) were tested against four genetic diagnostics datasets (two in-house and two external) for a total of 495 samples with 231 single and multi-exon validated CNVs. The evaluation was performed using the default and sensitivity-optimized parameters. Results showed that most tools were highly sensitive and specific, but the performance was dataset dependant. When evaluating them in our diagnostics scenario, DECoN and panelcn.MOPS detected all CNVs with the exception of one mosaic CNV missed by DECoN. However, DECoN outperformed panelcn.MOPS specificity achieving values greater than 0.90 when using the optimized parameters. In our in-house datasets, DECoN and panelcn.MOPS showed the highest performance for CNV screening before orthogonal confirmation. Benchmarking and optimization code is freely available at https://github.com/TranslationalBioinformaticsIGTP/CNVbenchmarkeR.

Matèries

Malalties hereditàries, Cèl·lules germinals

Matèries (anglès)

Genetic disorders, Germ cells

Citació

Col·leccions

Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL))

Citació

MORENO CABRERA, José Marcos, et al. Evaluation of CNV detection tools for NGS panel data in genetic diagnostics. European Journal of Human Genetics. 2020. Vol. 28, num. 12, pags. 1645-1655. [consulted: 18 of August of 2026]. Available at: https://hdl.handle.net/2445/173588

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