20 Years of Cardiogenetics in the Netherlands location:Amsterdam date:4 December 2015
In inherited primary arrhythmia syndromes (PAS) and cardiomyopathies (CMP) the yield of genetic testing varies between 20% and 75% in different diseases. These numbers are mainly derived from studies evaluating only the most frequently affected genes. We evaluated the additional yield of NGS based panel testing in PAS and CMP patients and determined if genetic retesting was worthwhile in previously genotype negative – phenotype positive probands.
Patients with a clear phenotype who remained genotype-negative after genetic analysis of the main genes implicated in their specific phenotype were selected. NGS allowed us to design and validate a panel of 75 PAS and CMP susceptibility genes for targeted capture and massive parallel sequencing. Variant interpretation and classification was done according to a stringent scoring system implementing different in-silico analyses, population frequencies and paralogous and orthologous conservation. Sanger sequencing was performed to confirm the presence of class 3 (VOUS), class 4 (probably pathogenic) and class 5 (pathogenic) variants. Co-segregation was done if DNA and clinical data from family members were available.
96 patients were included: 25 with LQTS, 8 with BrS, 5 with CPVT, 7 with idiopathic VF, 42 with HCM, 8 with DCM and 1 with ARVC. A total of 42 variants of class 3, 4 or 5 were identified. Co-segregation was performed on 21 variants. Three class 3/4 variants were downgraded to a benign variant due to lack of co-segregation. In contrast, 12 were upgraded to class 4 or 5 after critical evaluation of the literature or co-segregation analysis. In total, 22 class 3 variants and 17 mutations (class 4/5 variants) in 16 patients were identified, resulting in a genetic yield of 17% (14% in CMP and 20% in PAS). The initial detection failures had several causes: detection of a mutation in a new gene in 8 patients, not reported variant by an external lab in 3, allelic dropout with DHPLC in 2, functional reclassification in 1, heterozygous calling with sequencing failed in 1 and a wrong initial diagnosis in 1.
Genetic retesting in clinically overt PAS and CMP cases, who were genotype-negative with older scanning techniques, resulted in an additional genetic diagnosis in up to 17% of the cases. This clearly supports genetic retesting with NGS based panels.