A Single-Center Reevaluation and Reanalysis of Copy Number Variants of Uncertain Significance Detected by Chromosome Microarray From Consecutive Pediatric Patients
Laboratory Genetics and Genomics
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Primary Categories:
- Laboratory Genetics
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Secondary Categories:
- Laboratory Genetics
Introduction:
Over the past decade, chromosomal microarray analysis (CMA) for the evaluation of genomic copy number imbalances in clinical laboratories has grown rapidly. However, inconsistencies in copy number variant (CNV) classifications across laboratories have persisted, particularly prior to the implementation of the 2020 American College of Medical Genetics and Genomics (ACMG) guidelines, which introduced a more rigorous, evidence-based approach aimed at reducing inter-laboratory discrepancies. As genetic knowledge advances and ACMG guidelines evolve, the ACMG recommends periodic reevaluation and reanalysis of genomic test results, including CMA, to ensure accurate and consistent variant classification. To date, few studies have assessed the clinical value of systematic CNV reevaluation under the latest ACMG guidelines, leaving no consensus on the optimal timing to initiate CNV reevaluation and detailed recommendations for reevaluation methods. In this study, we investigated the clinical utility and necessity of systematic reevaluation of CNV of uncertain significance (CNVus), which account for approximately 10-15% of reported CNV and present a persistent challenge in medical genetics. Additionally, we evaluated the role of genome sequencing (GS) in CNV reevaluation, especially for intragenic CNV, and aimed to provide evidence to support detailed guideline development.
Methods:
This laboratory-initiated retrospective study reviewed 5,277 consecutive pediatric CMA cases from the Yale Clinical Cytogenetics Laboratory (2010-2022). CNVus were reevaluated following the 2020 ACMG/ClinGen guidelines for CNV interpretation. GS was subsequently applied to reanalyze cases where CNVus were reclassified to pathogenic or likely pathogenic (p/lpCNV).
Results:
The CNVus detection rate in our laboratory is 9.1%, and 567 CNVus from 480 pediatric cases were reevaluated, with a reclassification rate of 7.3% (35 in 480 cases). Eight CNVus in 8 cases (1.7%; 8/480) were reclassified to p/lpCNV, primarily due to updates in public resources such as ClinGen Dosage Sensitivity and new evidence in medical literature. Twenty-seven CNVus in 27 cases (5.6%; 27/480) were reclassified to benign or likely benign, largely due to new DGV Gold information. Intragenic CNV accounted for 75% (6/8) of the CNVus reclassified as p/lpCNV, and GS further enhanced their reclassification by precisely characterizing the breakpoints and ruling out additional causative genetic variants. Additionally, our data showed that the reclassification rate is not constant over the years, with the majority of reclassified CNVus (97%; 34/35) from tests conducted more than three years prior, and 77% (27/35) from tests performed over 5 years ago. This suggests that reevaluating CNVus every 3-5 years is a feasible and effective approach.
Conclusion:
This study demonstrated the clinical utility and necessity of periodic CNVus reevaluation and highlighted the role of GS in enhancing CNV interpretation. Our data suggested an optimal reevaluation interval of 3-5 years, and provided evidence to support the development of standardized guidelines by professional organizations.
Over the past decade, chromosomal microarray analysis (CMA) for the evaluation of genomic copy number imbalances in clinical laboratories has grown rapidly. However, inconsistencies in copy number variant (CNV) classifications across laboratories have persisted, particularly prior to the implementation of the 2020 American College of Medical Genetics and Genomics (ACMG) guidelines, which introduced a more rigorous, evidence-based approach aimed at reducing inter-laboratory discrepancies. As genetic knowledge advances and ACMG guidelines evolve, the ACMG recommends periodic reevaluation and reanalysis of genomic test results, including CMA, to ensure accurate and consistent variant classification. To date, few studies have assessed the clinical value of systematic CNV reevaluation under the latest ACMG guidelines, leaving no consensus on the optimal timing to initiate CNV reevaluation and detailed recommendations for reevaluation methods. In this study, we investigated the clinical utility and necessity of systematic reevaluation of CNV of uncertain significance (CNVus), which account for approximately 10-15% of reported CNV and present a persistent challenge in medical genetics. Additionally, we evaluated the role of genome sequencing (GS) in CNV reevaluation, especially for intragenic CNV, and aimed to provide evidence to support detailed guideline development.
Methods:
This laboratory-initiated retrospective study reviewed 5,277 consecutive pediatric CMA cases from the Yale Clinical Cytogenetics Laboratory (2010-2022). CNVus were reevaluated following the 2020 ACMG/ClinGen guidelines for CNV interpretation. GS was subsequently applied to reanalyze cases where CNVus were reclassified to pathogenic or likely pathogenic (p/lpCNV).
Results:
The CNVus detection rate in our laboratory is 9.1%, and 567 CNVus from 480 pediatric cases were reevaluated, with a reclassification rate of 7.3% (35 in 480 cases). Eight CNVus in 8 cases (1.7%; 8/480) were reclassified to p/lpCNV, primarily due to updates in public resources such as ClinGen Dosage Sensitivity and new evidence in medical literature. Twenty-seven CNVus in 27 cases (5.6%; 27/480) were reclassified to benign or likely benign, largely due to new DGV Gold information. Intragenic CNV accounted for 75% (6/8) of the CNVus reclassified as p/lpCNV, and GS further enhanced their reclassification by precisely characterizing the breakpoints and ruling out additional causative genetic variants. Additionally, our data showed that the reclassification rate is not constant over the years, with the majority of reclassified CNVus (97%; 34/35) from tests conducted more than three years prior, and 77% (27/35) from tests performed over 5 years ago. This suggests that reevaluating CNVus every 3-5 years is a feasible and effective approach.
Conclusion:
This study demonstrated the clinical utility and necessity of periodic CNVus reevaluation and highlighted the role of GS in enhancing CNV interpretation. Our data suggested an optimal reevaluation interval of 3-5 years, and provided evidence to support the development of standardized guidelines by professional organizations.