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Evaluation of copy number variant detection from panel-based next-generation sequencing data.

Ruen Yao1,2, Tingting Yu1,2, Yanrong Qing1,2

  • 1Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

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|December 20, 2018
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Summary

Targeted next-generation sequencing (NGS) accurately detects copy number variations (CNVs) on autosomes. Further validation is needed for sex chromosome CNVs, but NGS is suitable for routine clinical use.

Keywords:
chromosomal microarray analysiscopy number variationnext-generation sequencing

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Area of Science:

  • Genomics
  • Molecular Diagnostics

Background:

  • Targeted gene capture and next-generation sequencing (NGS) are cost-effective for small variant detection.
  • The accuracy of copy number variations (CNVs) from panel-based NGS data requires thorough evaluation.

Purpose of the Study:

  • To evaluate the accuracy of CNVs detected using panel-based NGS data.
  • To compare NGS-based CNV detection with established clinical platforms (CMA and MLPA).

Main Methods:

  • Analyzed sequencing data from patients undergoing routine targeted panel testing.
  • Utilized CNVkit to call CNVs from NGS data using read-depth information.
  • Validated NGS-detected CNVs against chromosome microarray analysis (CMA) and multiple ligation-dependent probe amplification (MLPA).

Main Results:

  • NGS detected CNVs over 300 kb with sizes slightly larger (102.3% average) than CMA, improving accuracy with increasing variant size.
  • CNV breakpoints from NGS were highly concordant with CMA (within 2.3% margin).
  • CNVs on sex chromosomes showed lower concordance between NGS and CMA.

Conclusions:

  • Targeted panel sequencing accurately detects autosomal CNVs comparable to CMA.
  • CNVs on sex chromosomes require additional evaluation.
  • Panel-based NGS is supported for routine clinical detection of pathogenic CNVs, excluding sex chromosome and exon-level variants.