Enter Note Done

Session


Keywords: Immune system; Identification of disease genes; Molecular pathophysiology; Variant calling11; Bioinformatics

Authors:
J.A. SoRelle 1; C.A. Wysocki 2; J.Y. Park 1,4; G. Gotway 3,4

Affiliations:
1) Pathology, University of Texas Southwestern Medical Center, Dallas, Texas.; 2) Internal Medicine, Division of Allergy and Immunology, University of Texas Southwestern Medical Center, Dallas, Texas.; 3) Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.; 4) Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, Dallas.


Introduction: Next-generation sequencing (NGS) testing has become a common diagnostic tool for evaluating pediatric patients with immune disorders. NGS testing can comprehensively identify gene variants of interest; however, determining the clinical significance of novel variants is challenging. Advances in publicly available databases and standardized interpretation criteria have improved the clinical interpretation of variants. However, the utility of re-interpreting previously reported NGS immune tests has not been systematically evaluated. In this study, we identify the frequency and significance of variant reclassification from previously reported NGS immune gene panels.
Methods: All NGS immune gene panel reports sent out from a tertiary-care pediatric hospital were retrospectively reviewed (July 2012 to July 2018). Reports were from multiple reference laboratories, and included genes for severe combined immunodeficiency, primary ciliary dyskinesia, and autoimmune and lymphoproliferative syndrome. Previously reported variants were first screened using population (gnomAD, 1000 Genomes phase 3) and clinical (ClinVar) databases. Any variant marked for having a high population frequency (>1%) or a conflicting report in ClinVar was 1) flagged then 2) reinterpreted using ACMG variant classification criteria.
Results: 120 patients were previously tested yielding 110 variants in 62 patients. Of the 110 variants, 36% were pathogenic or likely-pathogenic (P-LP n=40), and 64% were variants of uncertain significance (VUS n=71). 15% (n=6) of the P-LP variants were reclassified; variants were downgraded to VUS (n=5, CYBB, DOCK8, FOXN1, MBD5), or B-LB (n=1, CFTR). Of the 71 VUS, 27% (n=19) were reclassified downward in significance (B-LB), and none were upgraded to clinically significant (P-LP). Overall, 23 of 120 patients (19%) were impacted by variant reclassification.
Conclusions: Based on our single institution experience, a large proportion of variant classifications were revised (21%; 25/120). These reclassifications impacted 19% of patients (23/120). A clinically significant reclassification (P-LP to VUS or benign) occurred in 15% of patients with a diagnostic variant. In addition, many reclassified VUS were downgraded. Overall, these findings indicate that all P-LP and VUS variants from previously reported NGS tests should be routinely reviewed and reanalyzed.