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A dataset compiled as a resource a for orthogonal assessment of exon CNV calling in NGS data

The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM and PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs the most difficult exon CNV to detect. The full dataset includes FASTQ files, target BED file, and MLPA results.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001003335 Illumina HiSeq 2500 96
Publications Citations
The ICR96 exon CNV validation series: a resource for orthogonal assessment of exon CNV calling in NGS data.
Wellcome Open Res 2: 2017 35
6
Evaluation of CNV detection tools for NGS panel data in genetic diagnostics.
Eur J Hum Genet 28: 2020 1645-1655
40
isoCNV: in silico optimization of copy number variant detection from targeted or exome sequencing data.
BMC Bioinformatics 22: 2021 530
1
SavvyCNV: Genome-wide CNV calling from off-target reads.
PLoS Comput Biol 18: 2022 e1009940
11
ifCNV: A novel isolation-forest-based package to detect copy-number variations from various targeted NGS datasets.
Mol Ther Nucleic Acids 30: 2022 174-183
2