Atlas-CNV: a validated approach to call single-exon CNVs in the eMERGESeq gene panel

Genet Med. 2019 Sep;21(9):2135-2144. doi: 10.1038/s41436-019-0475-4. Epub 2019 Mar 20.


Purpose: To provide a validated method to confidently identify exon-containing copy-number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs.

Methods: DNA sequence coverage data are normalized within each sample and subsequently exonic CNVs are identified in a batch of samples, when the target log2 ratio of the sample to the batch median exceeds defined thresholds. The quality of exonic CNV calls is assessed by C-scores (Z-like scores) using thresholds derived from gold standard samples and simulation studies. We integrate an ExonQC threshold to lower FDR and compare performance with alternate software (VisCap).

Results: Thirteen CNVs were used as a truth set to validate Atlas-CNV and compared with VisCap. We demonstrated FDR reduction in validation, simulation, and 10,926 eMERGESeq samples without sensitivity loss. Sixty-four multiexon and 29 single-exon CNVs with high C-scores were assessed by Multiplex Ligation-dependent Probe Amplification (MLPA).

Conclusion: Atlas-CNV is validated as a method to identify exonic CNVs in targeted sequencing data generated in the clinical laboratory. The ExonQC and C-score assignment can reduce FDR (identification of targets with high variance) and improve calling accuracy of single-exon CNVs respectively. We propose guidelines and criteria to identify high confidence single-exon CNVs.

Keywords: Atlas-CNV; CNV; copy-number variation; single-exon deletion duplication; targeted gene panel clinical sequencing.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • DNA Copy Number Variations / genetics*
  • Exons / genetics*
  • Genome, Human / genetics*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Sequence Analysis, DNA
  • Software*