Clinical Variant Reclassification in Hereditary Disease Genetic Testing

Abstract

Importance: Because accurate and consistent classification of DNA sequence variants is fundamental to germline genetic testing, understanding patterns of initial variant classification (VC) and subsequent reclassification from large-scale, empirical data can help improve VC methods, promote equity among race, ethnicity, and ancestry (REA) groups, and provide insights to inform clinical practice.

Objectives: To measure the degree to which initial VCs met certainty thresholds set by professional guidelines and quantify the rates of, the factors associated with, and the impact of reclassification among more than 2 million variants.

Design, setting, and participants: This cohort study used clinical multigene panel and exome sequencing data from diagnostic testing for hereditary disorders, carrier screening, or preventive genetic screening from individuals for whom genetic testing was performed between January 1, 2015, and June 30, 2023.

Exposure: DNA variants were classified into 1 of 5 categories: benign, likely benign, variant of uncertain significance (VUS), likely pathogenic, or pathogenic.

Main outcomes and measures: The main outcomes were accuracy of classifications, rates and directions of reclassifications, evidence contributing to reclassifications, and their impact across different clinical areas and REA groups. One-way analysis of variance followed by post hoc pairwise Tukey honest significant difference tests were used to analyze differences among means, and pairwise Pearson χ2 tests with Bonferroni corrections were used to compare categorical variables among groups.

Results: The cohort comprised 3 272 035 individuals (median [range] age, 44 [0-89] years; 2 240 506 female [68.47%] and 1 030 729 male [31.50%]; 216 752 Black [6.62%]; 336 414 Hispanic [10.28%]; 1 804 273 White [55.14%]). Among 2 051 736 variants observed over 8 years in this cohort, 94 453 (4.60%) were reclassified. Some variants were reclassified more than once, resulting in 105 172 total reclassification events. The majority (64 752 events [61.65%]) were changes from VUS to either likely benign, benign, likely pathogenic, or pathogenic categories. An additional 37.66% of reclassifications (39 608 events) were gains in classification certainty to terminal categories (ie, likely benign to benign and likely pathogenic to pathogenic). Only a small fraction (663 events [0.63%]) moved toward less certainty, or very rarely (61 events [0.06%]) were classification reversals. When normalized by the number of individuals tested, VUS reclassification rates were higher among specific underrepresented REA populations (Ashkenazi Jewish, Asian, Black, Hispanic, Pacific Islander, and Sephardic Jewish). Approximately one-half of VUS reclassifications (37 074 of 64 840 events [57.18%]) resulted from improved use of data from computational modeling.

Conclusions and relevance: In this cohort study of individuals undergoing genetic testing, the empirically estimated accuracy of pathogenic, likely pathogenic, benign, and likely benign classifications exceeded the certainty thresholds set by current VC guidelines, suggesting the need to reevaluate definitions of these classifications. The relative contribution of various strategies to resolve VUS, including emerging machine learning-based computational methods, RNA analysis, and cascade family testing, provides useful insights that can be applied toward further improving VC methods, reducing the rate of VUS, and generating more definitive results for patients.

Figure 1.. Direction and Sources of Evidence for Variant of Uncertain Significance (VUS) Reclassifications

A, Final classification for variants that were initially classified as VUS. B, Three broad categories provided additional evidence to support reclassifications: improved use of available data (black), data obtained organically from internal and external sources (dark gray), and data actively generated by additional testing (light gray). C, Final classification of variants initially classified as VUS, stratified by the level of evidence toward pathogenic and benign available at the time of initial classification. Each horizontal bar represents different categories of summarized evidence scores (eg, a collection of variants where the combined score = 1); individual evidence supporting pathogenic or benign classifications are captured using a numeric point-based system with scores between −5 and 5 at 0.5 point intervals, with a higher score indicating more evidence supporting pathogenic and a lower score indicating more evidence supporting benign. Scores between −3 and 4 (not inclusive) are classified as VUS. B indicates benign; LB, likely benign; LP, likely pathogenic; ML, machine learning; P, pathogenic.

Figure 2.. Variant of Uncertain Significance (VUS) Reclassification Rates and Classification Reversal Rates

A, Cumulative VUS reclassifications over time. B, Cumulative VUS reclassifications over time normalized by the total number of VUS. C, Time to VUS reclassification. D, The combined rate of classification reversals and reclassifications to VUS among all reclassifications decreased 4-fold by the end of the study period. B indicates benign; LB, likely benign; LP, likely pathogenic; P, pathogenic.

Figure 3.. Patterns of Variant of Uncertain Significance (VUS) Reclassifications in Race, Ethnicity, and Ancestry (REA) Groups

A, Trends in cumulative VUS reclassifications among REA groups over the study period. B-C, Normalized VUS reclassification rates among REA groups at the end of the study period. In panel C, the bars represent the 95% CI of the mean reclassified VUS per patient in each ethnicity group. ^aP < .001 vs the comparison group (White).