Yield of the RYR2 Genetic Test in Suspected Catecholaminergic Polymorphic Ventricular Tachycardia and Implications for Test Interpretation

Abstract

Background: Pathogenic RYR2 variants account for ≈60% of clinically definite cases of catecholaminergic polymorphic ventricular tachycardia. However, the rate of rare benign RYR2 variants identified in the general population remains a challenge for genetic test interpretation. Therefore, we examined the results of the RYR2 genetic test among patients referred for commercial genetic testing and examined factors impacting variant interpretability.

Methods: Frequency and location comparisons were made for RYR2 variants identified among 1355 total patients of varying clinical certainty and 60 706 Exome Aggregation Consortium controls. The impact of the clinical phenotype on the yield of RYR2 variants was examined. Six in silico tools were assessed using patient- and control-derived variants.

Results: A total of 18.2% (218/1200) of patients referred for commercial testing hosted rare RYR2 variants, statistically less than the 59% (46/78) yield among clinically definite cases, resulting in a much higher potential genetic false discovery rate among referrals considering the 3.2% background rate of rare, benign RYR2 variants. Exclusion of clearly putative pathogenic variants further complicates the interpretation of the next novel RYR2 variant. Exonic/topologic analyses revealed overrepresentation of patient variants in exons covering only one third of the protein. In silico tools largely failed to show evidence toward enhancement of variant interpretation.

Conclusions: Current expert recommendations have resulted in increased use of RYR2 genetic testing in patients with questionable clinical phenotypes. Using the largest to date catecholaminergic polymorphic ventricular tachycardia patient versus control comparison, this study highlights important variables in the interpretation of variants to overcome the 3.2% background rate that confounds RYR2 variant interpretation.

Keywords: cardiologist; exons; genetic testing; phenotype; uncertainty.

Figure 1.

Yield by Clinical Phenotype. The yield of rare variants (MAF < 1 in 10,000) among patients with a “strong” CPVT phenotype, “possible” CPVT phenotype, or referred for RYR2 genetic testing. The red dotted line represents the 3.2% background rate of rare variants identified in the ExAC exomes. The EPV is provided within the column for each cohort. The p-values for comparisons, indicated by each bar, are provided above the bar. An “*” indicates p < 1.0×10⁻¹⁵ for the comparison to the ExAC background rate of rare variants.

Figure 2.

Age at Genetic Testing. The yield of rare variants among the referral cohort (grouped by age). The red dotted line represents the 3.2% background rate of rare variants identified in the ExAC exomes. The p-values for comparisons, indicated by each bar, are provided above the bar. An “*” indicates p < 0.05 for the comparison to the ExAC background rate of rare variants.

Figure 3.

Rare Variant Yield and Age at Genetic Test over the Life of the Clinically Available RYR2 Genetic Test. Comparing 4 consecutive groups of 300 cases, the bar graph depicts in (A) the yield of rare variants and in (B) the average age at genetic testing. The p-values for comparisons, indicated by each bar, are provided above the bar. The error bars in panel B represent the standard error of the age at genetic testing.

Figure 4.

Occurrence of RYR2 Variants. This bar graph summarizes the distribution of specific rare variants among unrelated cases. The y axis depicts the number of distinct rare RYR2 variants, and the x axis represents the number of unrelated cases.

Figure 5.

Yield of “New” Rare RYR2 Variants by Phenotype. In an effort to identify the yield of “new” rare variants, statistically over-represented variants (ORVs) were removed and the yields were re-calculated for the remaining rare RYR2 variants. The red dotted line represents the 3.2% background rate of rare variants identified in the ExAC exomes. The EPV is provided within the column for each cohort. The p-values for comparisons, indicated by each bar, are provided above the bar. An “*” indicates p < 1.0×10⁻⁶ for the comparison to the ExAC background rate of rare variants.

Figure 6.

Comparison of Yield by Exon. This line chart represents the yield (y-axis) of rare RYR2 variants within each exon (x-axis) of the RYR2 gene. Orange line – yield in referral group, Blue line – yield in the Mayo Clinic/AAMC phenotyped cases (“strong” and “possible” cohorts), Red line – yield in the ExAC exomes. The black bar at the top of the graph the previously identified hotspot regions. Light blue column represent the 21 identified exons.