The ICR96 exon CNV validation series: a resource for orthogonal assessment of exon CNV calling in NGS data

Abstract

Detection of deletions and duplications of whole exons (exon CNVs) is a key requirement of genetic testing. Accurate detection of this variant type has proved very challenging in targeted next-generation sequencing (NGS) data, particularly if only a single exon is involved. Many different NGS exon CNV calling methods have been developed over the last five years. Such methods are usually evaluated using simulated and/or in-house data due to a lack of publicly-available datasets with orthogonally generated results. This hinders tool comparisons, transparency and reproducibility. To provide a community resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. 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 or 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 type of exon CNV to detect. The FASTQ files for the ICR96 exon CNV validation series can be accessed through the European-Genome phenome Archive (EGA) under the accession number EGAS00001002428.

SavvyCNV: genome-wide CNV calling from off-target reads

“…To evaluate the performance of SavvyCNV at calling CNVs from on-target data we used the ICR96 validation series(19). ICR96 is a set of 96 samples sequenced using a small targeted sequencing panel (TruSight Cancer Panel v2, 100 genes), with exon CNVs detected independently using MLPA (25 single-exon CNVs, 43 multi-exon CNVs, and 1752 normal copy number genes).…”

“…The ICR96 data set (19) was used to benchmark on-target CNV calling. This data set consists of 96 samples sequenced on a targeted panel where the truth set of CNVs is based on 68 positive and 1752 negative MLPA tests.…”

Benchmark of tools for CNV detection from NGS panel data in a genetic diagnostics context

“…The dataset ICR96 exon CNV validation series (Mahamdallie et al, 2017) was downloaded from the European Genome-phenome Archive (EGA) (EGAD00001003335) and contained 96 samples captured with TruSight Cancer Panel v2 (100 genes) and sequenced in a single HiSeq lane with 101-base pairedend reads. panelcnDataset (Povysil et al, 2017) was also downloaded from EGA (EGAS00001002481) and had 170 samples captured using TruSight Cancer Panel (94 genes, Illumina) and sequenced on a MiSeq instrument with 151-base paired-end reads.…”

Validation of an ultra-fast CNV calling tool for Next Generation Sequencing data using MLPA-verified copy number alterations

“…The ICR96 dataset includes two separate library enrichment pools (Mahamdallie et al 2017) that have different coverage characteristics. When we examine coverage depths of samples from either pool 1 or pool2, we observe better correlations as compared to samples from both pools ( Figure S3A).…”