CNV detection in targeted NGS panel data

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.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 4 Publications

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Dataset ID	Description	Technology	Samples
EGAD00001003400	We present targeted NGS panel data from 170 samples that were processed using the TruSightTM 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.	Illumina MiSeq	170

Publications	Citations
panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics. Povysil G, Tzika A, Vogt J, Haunschmid V, Messiaen L, Zschocke J, Klambauer G, Hochreiter S, Wimmer K. Hum Mutat 38: 2017 889-897	47
Evaluation of CNV detection tools for NGS panel data in genetic diagnostics. Moreno-Cabrera JM, Del Valle J, Castellanos E, Feliubadaló L, Pineda M, Brunet J, Serra E, Capellà G, Lázaro C, Gel B. Eur J Hum Genet 28: 2020 1645-1655	50
BRACNAC: A <i>BRCA1</i> and <i>BRCA2</i> Copy Number Alteration Caller from Next-Generation Sequencing Data. Kechin A, Boyarskikh U, Borobova V, Khrapov E, Subbotin S, Filipenko M. Int J Mol Sci 24: 2023 16630	0
Detection of germline CNVs from gene panel data: benchmarking the state of the art. Munté E, Roca C, Del Valle J, Feliubadaló L, Pineda M, Gel B, Castellanos E, Rivera B, Cordero D, Moreno V, Lázaro C, Moreno-Cabrera JM. Brief Bioinform 26: 2024 bbae645	0