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CNV detection in targeted NGS panel data

ABSTRACT: The aim of this study was to compare copy-number-variation (CNV) detection methods for targeted NGS panel data in a clinical diagnostic setting. We present targeted NGS panel data from 170 samples that were processed using the TruSight(TM) Cancer (TSC) panel (Illumina, San Diego, CA, USA), which targets 94 genes and 284 SNPs associated with a predisposition towards cancer. The samples are enriched for CNVs in the genes of interest. All CNVs have previously been assessed with MLPA and can therefore be considered as confirmed.

PROVIDER: EGAS00001002481 | EGA |

REPOSITORIES: EGA

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panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics.

Povysil Gundula G Tzika Antigoni A Vogt Julia J Haunschmid Verena V Messiaen Ludwine L Zschocke Johannes J Klambauer Günter G Hochreiter Sepp S Wimmer Katharina K

Human mutation 20170516 7

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 (QC), incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. U ...[more]

PMID: 28449315

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