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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants
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Copy Number Variants of Uncertain Significance by Chromosome Microarray Analysis from Consecutive Pediatric Patients:

Wenjiao Li1, Xiaolei Xie1,2, Hongyan Chai1

  • 1Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.

Genes
|August 28, 2025
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Summary

Periodic reevaluation of copy number variants of uncertain significance (CNVus) and whole genome sequencing (WGS) reanalysis can improve diagnostic yield. This study highlights the clinical impact of reclassifying CNVus, supporting standardized laboratory practices for better patient outcomes.

Keywords:
chromosomal microarray analysis (CMA)copy number variants of uncertain significance (CNVus)reanalysisreclassificationreevaluationwhole genome sequencing (WGS)

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Area of Science:

  • Genetics and Genomics
  • Clinical Cytogenetics
  • Diagnostic Technologies

Background:

  • Copy number variants of uncertain significance (CNVus) pose diagnostic challenges in clinical genetics.
  • Chromosome microarray analysis (CMA) is a primary tool for detecting CNVus, necessitating reevaluation strategies.

Purpose of the Study:

  • To systematically reevaluate reported CNVus using current guidelines.
  • To assess the diagnostic value and clinical impact of reclassifying CNVus through reanalysis, including whole genome sequencing (WGS).
  • To evaluate the utility of periodic reevaluation and WGS reanalysis for CNVus.

Main Methods:

  • Retrospective review of 5277 pediatric cases analyzed by CMA over 13 years.
  • Reevaluation of all reported CNVus according to ACMG/ClinGen guidelines.
  • Reanalysis by WGS for selected CNVus to confirm reclassification.

Main Results:

  • Of 567 reported CNVus in 480 cases (9.1%), 5.6% were reclassified.
  • 4 CNVus (0.8%) were reclassified to pathogenic/likely pathogenic (pCNVs/lpCNVs).
  • 23 CNVus (4.8%) were reclassified to benign/likely benign (bCNVs/lbCNVs).
  • WGS refined breakpoints and excluded other genetic variants in selected cases.

Conclusions:

  • Periodic reevaluation (every 3-5 years) of CNVus has diagnostic value.
  • Reanalysis by WGS aids in the accurate reclassification of CNVus.
  • Standardized laboratory reevaluation and reanalysis protocols are supported by these findings.