Valérie Chanavat1, Alexandre Janin2, Gilles Millat3. 1. Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France; NGS Sequencing Platform for Molecular Diagnosis, Hospices Civils de Lyon, Lyon, France. 2. Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France; Université de Lyon, Lyon F-69003, France; Université Lyon 1, Lyon, France. 3. Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France; NGS Sequencing Platform for Molecular Diagnosis, Hospices Civils de Lyon, Lyon, France; Université de Lyon, Lyon F-69003, France; Université Lyon 1, Lyon, France. Electronic address: gilles.millat@chu-lyon.fr.
Abstract
BACKGROUND: Cardiomyopathies and arrhythmia syndromes are common genetic cardiac diseases that account for a significant number of sudden cardiac death (SCD) cases. METHODS: NGS workflow based on a panel of 95 genes was developed on Illumina NextSeq500™ sequencer for sequencing prevalent SCD-causing genes. A cohort of 90 patients (56 genotype-positive, 27 genotype-negative and 7 new cases) was screened to evaluate this strategy in terms of sensitivity, specificity, practicability and cost. In silico analysis were performed using a pipeline based on NextGENe® software and a personalized Sophia Genetics pipeline. RESULTS: Using our panel custom, 100% of targeted sequences were efficiently covered and all previously identified genetic variants were readily detected. Applied to 27 genotype-negative patients, this molecular strategy allowed the identification of pathogenic or likely pathogenic variants into 12 cases. It confirmed the involvement of HCN4 mutations in the combined bradycardia–myocardial non-compaction phenotype, and also suggested, for the first time, the involvement of PKP2, usually associated with arrhythmogenic right ventricular dysplasia, in ventricular non-compaction. CONCLUSION: This NGS approach is a fast, cheap, sensitive and high-throughput mutation detection method that is ready to be deployed in clinical laboratories and would provide new insights on physiopathology of SCD, more particularly of cardiomyopathies and arrhythmia syndromes.
BACKGROUND:Cardiomyopathies and arrhythmia syndromes are common genetic cardiac diseases that account for a significant number of sudden cardiac death (SCD) cases. METHODS: NGS workflow based on a panel of 95 genes was developed on Illumina NextSeq500™ sequencer for sequencing prevalent SCD-causing genes. A cohort of 90 patients (56 genotype-positive, 27 genotype-negative and 7 new cases) was screened to evaluate this strategy in terms of sensitivity, specificity, practicability and cost. In silico analysis were performed using a pipeline based on NextGENe® software and a personalized Sophia Genetics pipeline. RESULTS: Using our panel custom, 100% of targeted sequences were efficiently covered and all previously identified genetic variants were readily detected. Applied to 27 genotype-negative patients, this molecular strategy allowed the identification of pathogenic or likely pathogenic variants into 12 cases. It confirmed the involvement of HCN4 mutations in the combined bradycardia–myocardial non-compaction phenotype, and also suggested, for the first time, the involvement of PKP2, usually associated with arrhythmogenic right ventricular dysplasia, in ventricular non-compaction. CONCLUSION: This NGS approach is a fast, cheap, sensitive and high-throughput mutation detection method that is ready to be deployed in clinical laboratories and would provide new insights on physiopathology of SCD, more particularly of cardiomyopathies and arrhythmia syndromes.
Authors: Samuel Chauveau; Alexandre Janin; Marianne Till; Elodie Morel; Philippe Chevalier; Gilles Millat Journal: HeartRhythm Case Rep Date: 2017-10-20
Authors: Job A J Verdonschot; Els K Vanhoutte; Godelieve R F Claes; Apollonia T J M Helderman-van den Enden; Janneke G J Hoeijmakers; Debby M E I Hellebrekers; Amber de Haan; Imke Christiaans; Ronald H Lekanne Deprez; Hanne M Boen; Emeline M van Craenenbroeck; Bart L Loeys; Yvonne M Hoedemaekers; Carlo Marcelis; Marlies Kempers; Esther Brusse; Jaap I van Waning; Annette F Baas; Dennis Dooijes; Folkert W Asselbergs; Daniela Q C M Barge-Schaapveld; Pieter Koopman; Arthur van den Wijngaard; Stephane R B Heymans; Ingrid P C Krapels; Han G Brunner Journal: Hum Mutat Date: 2020-03-20 Impact factor: 4.878