Enhancing rare variant interpretation in inherited arrhythmias through quantitative analysis of 5182 cases from long QT syndrome and Brugada syndrome consortia cohorts and gnomAD population controls

Abstract

Background/Introduction Guidelines for variant interpretation in Mendelian disease set stringent criteria to report a variant as (likely) pathogenic, prioritising control of false positive rate over test sensitivity and diagnostic yield, and require customisation for the specific genetic characteristics of gene-disease dyads. Inherited arrhythmias like long QT syndrome (LQTS) and Brugada syndrome (BrS) are genetically heterogeneous, with missense variants constituting the preponderance of disease-causing variants. Evidence from family segregation or functional assays to confirm pathogenicity are often unavailable or impractical in clinical genetic testing, leading to high rates of variants of uncertain significance and false negative test results. Methods We compared rare variant frequencies from 1847 LQTS (KCNQ1, KCNH2, SCN5A) and 3335 BrS (SCN5A) cases from the International LQTS/BrS Genetics Consortia to population-specific gnomAD data. We propose disease-specific criteria for ACMG/AMP evidence classes – rarity (PM2/BS1 rules) and enrichment of individual (PS4) and domain-specific (PM1) variants in cases over controls. Results Rare SCN5A variant prevalence differed between BrS cases with spontaneous (28.7%) versus induced (15.8%) type 1 Brugada ECG (p=1.3x10–13) and between European (20.8%) and Japanese (8.9%) patients (p=8.8x10–18). Transmembrane regions and specific N-terminus (KCNH2) and C-terminus (KCNQ1/KCNH2) domains were characterised by high enrichment of case variants and >95% probability of pathogenicity. Applying the customised rules, 17.5% of European BrS cases and 73.7% of European LQTS cases had variants classified as (likely) pathogenic, compared to estimated diagnostic yields (case excess over gnomAD) of 19.3%/82.6%. Conclusions Large case/control datasets enable quantitative implementation of ACMG/AMP guidelines and increased sensitivity for inherited arrhythmia genetic testing. Classification of Brugada/LQTS variants Funding Acknowledgement Type of funding source: Foundation. Main funding source(s): Dutch Heart Foundation, Netherlands Organisation for Scientific Research

Arrhythmia Variant Associations and Reclassifications in the eMERGE-III Sequencing Study

“…18 Five variants had different classifications between the 2 sequencing centers (affecting 7 individuals); manual review using ACMG criteria was used to adjudicate these variants (File S3). In addition, 1838 individuals (8.4%) were not heterozygous for any P/LP variant, but were heterozygous for ≥ 1of 1648 ultrarare VUS (gnomAD allele frequency <2.5e-5 25,30 ; Table S1). Self-reported White and non-White individuals had a similar frequency of P/LP variants (0.52% for White individuals versus 0.62% for non-White individuals, P=0.37).…”

“…For example, all 5 of the variants assigned PS3 at the strong level were present in at least 1 eMERGE-III carrier with an extreme or severe phenotype. The updated BS3 and PS3 criteria, and recently published hotspot criteria for the 3 studied genes, as well, 30 were used to reclassify the 52 variants (Table 2, Table S13). Twelve variants were reclassified: 3 VUS→LB, 7 VUS→LP, 1 VUS→P, and 1 LP→P.…”

“…To further decipher these variants' disease risk, we used automated patch clamp recording, a technology that enables the high-throughput electrophysiological study of ion channel variants. 6,9,42 Based on in vitro functional testing and recently published hotspot criteria, 30 we were able to reclassify 12 of 52 examined variants. Future analyses studying even larger cohorts, independently or combined with high-throughput in vitro characterization 6,43 promise to further discern the disease risk of individual ultrarare variants.…”

A rare non-coding enhancer variant inSCN5Acontributes to the high prevalence of Brugada syndrome in Thailand

“…BrS is a cardiac arrhythmia disorder associated with increased risk of sudden death in young adults and characterised by ST-segment elevation in the right precordial leads of the electrocardiogram (ECG) occurring either spontaneously or after challenge with sodium channel blockers like ajmaline 1 . Rare loss-of-function coding variants in SCN5A , encoding the Na v 1.5 sodium channel underlying the cardiac sodium current (I Na ), are found in approximately 20% of European-ancestry BrS cases 2 . Several other genes have been implicated in BrS but were considered to have limited evidence of association by ClinGen re-evaluation and SCN5A remains the only clinically actionable gene 3,4 .…”

Effects of Glucose Fluctuations on Electrocardiogram Readings and the Development of Ventricular Arrhythmia in Diabetic Rats

“…[5] An increasing number of studies have demonstrated that several ECG parameters, including heart rate, P wave, QRS wave duration, T wave, PR segment, RP interval, QT interval, and corrected QT (QTc) interval, credibly reflect the cardiac electrophysiology of the heart. [6–8] Moreover, abnormal ECG parameters in general represent abnormal cardiac electrophysiology. [9] For instance, a prolonged P wave interval represents delayed atrial conduction velocity, indicating an increased risk of atrial fibrillation, [10,11] and a prolonged QTc interval represents an increased dispersion of ventricular repolarization, which may induce malignant arrhythmias including ventricular tachycardia/fibrillation (VT/VF) and sudden death.…”