P500: Reinterpretation of postnatal clinical copy number variants: A practical approach for implementation as a routine laboratory practice (2023)

Introduction: As genetic knowledge increases, clinical laboratories must implement high quality variant interpretation practices, both upon initial patient encounter and also as new information becomes available.While policies and processes for variant-and case-level reinterpretation exist, particularly for sequence variants, there is limited guidance detailing reevaluation processes for copy number variants (CNVs), which are difficult to standardize due to technical limitations and inconsistent classification practices.Here, we provide results and recommendations following a multi-year initiative to implement routine laboratory-and provider-initiated CNV reevaluation processes in an academic reference laboratory setting.Methods: We first developed standardized criteria to identify and prioritize CNVs for reevaluation in accordance with interlaboratory standards and to align with data sharing efforts.ARUP built a chromosomal microarray (CMA) database composed of 10+ years of CNV data to facilitate comprehensive, standardized searches and performed reevaluation of postnatal CNVs from 2011-2021.Processes for initiating internal reviews and responding to external reevaluation requests were also developed and implemented, including establishing criteria for issuing amended reports and recontacting providers.Postnatal cases meeting criteria for submission to public databases were used for the laboratory-initiated process (n=5690).Flagged CNVs overlapped genes with established dosage sensitivity (DS) that are not classified as pathogenic (P) or likely pathogenic (LP), or were "close-match" CNVs with >99% similarity in size and genomic overlap with discordant classifications.All reported CNVs for each flagged case are reevaluated regardless of whether they meet criteria for rereview.Clinically significant reclassifications are defined as a change from variant of uncertain significance (VUS) in either direction, or any two-step reclassifications (eg, likely benign (LB) to P). Amended reports are issued for any clinically significant reclassification, and for all reclassifications resulting from provider requests, regardless of clinical significance.Provider-initiated reevaluations are honored after 1 year of the original report or 1 year from the date of the last reevaluation request and were tracked internally starting in 2018.Results: The laboratory-initiated process identified 548 of 5690 postnatal cases for reevaluation: 65 overlapped established DS genes, 316 were close-match CNVs, and 167 were identified from an index case.To date, 108 (20%) of reevaluated cases representing 32 CNVs (28 unique) have been issued amended reports due to variant reclassification, including 18 (17%) that were upgraded to P or LP and 14 (13%) that were downgraded to LB or B. Provider-initiated requests included 58 unique CNVs, 50 (86%) of which were initially classified as VUS, 11 (19%) of which were subsequently reclassified.Of these, 9 reclassifications were clinically significant (5 upgraded and 4 downgraded); the 2 other CNVs were revised from P to LP or LP to P due to additional information from the provider.The remainder of provider-requested CNV reevaluations (n=47; 81%) remained unchanged.Each CNV reevaluation takes approximately 4-5 hours per case, with an average of 14 provider-initiated requests per year.Conclusion: Increasing expectations placed on laboratories to update CNV interpretations as new evidence emerges, as well as ongoing variant classification discordance, require comprehensive yet efficient methods for identifying and reevaluating CNVs.Our experience establishing processes to reevaluate over 10 years of CMA data and respond to provider requests may inform future best practices for both internal laboratory and provider-response-based CNV reevaluations.Notably, we observed a high frequency of clinically significant CNV reclassifications from our internally initiated reevaluation process providing support for the laboratory to develop practical approaches for variant reevaluation in order to optimize patient care.