title: Next generation diagnostics in inherited arrhythmia syndromes : a comparison of two approaches.
abstract: Next-generation sequencing (NGS) provides an unprecedented opportunity to assess genetic variation underlying human disease. Here, we compared two NGS approaches for diagnostic sequencing in inherited arrhythmia syndromes. We compared PCR-based target enrichment and long-read sequencing (PCR-LR) with in-solution hybridization-based enrichment and short-read sequencing (Hyb-SR). The PCR-LR assay comprehensively assessed five long-QT genes routinely sequenced in diagnostic laboratories and "hot spots" in RYR2. The Hyb-SR assay targeted 49 genes, including those in the PCR-LR assay. The sensitivity for detection of control variants did not differ between approaches. In both assays, the major limitation was upstream target capture, particular in regions of extreme GC content. These initial experiences with NGS cardiovascular diagnostics achieved up to 89 % sensitivity at a fraction of current costs. In the next iteration of these assays we anticipate sensitivity above 97 % for all LQT genes. NGS assays will soon replace conventional sequencing for LQT diagnostics and molecular pathology.
authors.affiliation: MRC Clinical Sciences Centre, Imperial College London, London, UK. j.ware@imperial.ac.uk
authors.forename: James S
authors.initials: JS
authors.lastname: Ware
authors.forename: Shibu
authors.initials: S
authors.lastname: John
authors.forename: Angharad M
authors.initials: AM
authors.lastname: Roberts
authors.forename: Rachel
authors.initials: R
authors.lastname: Buchan
authors.forename: Sungsam
authors.initials: S
authors.lastname: Gong
authors.forename: Nicholas S
authors.initials: NS
authors.lastname: Peters
authors.forename: David O
authors.initials: DO
authors.lastname: Robinson
authors.forename: Anneke
authors.initials: A
authors.lastname: Lucassen
authors.forename: Elijah R
authors.initials: ER
authors.lastname: Behr
authors.forename: Stuart A
authors.initials: SA
authors.lastname: Cook
mesh_terms: D001145:Arrhythmias, Cardiac / Q000175:diagnosis* / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods*; D000072237:ERG1 Potassium Channel; D051638:Ether-A-Go-Go Potassium Channels / Q000235:genetics; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease; D005820:Genetic Testing / Q000379:methods*; D040941:Heredity; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D007473:Ion Channels / Q000235:genetics*; D051657:KCNQ1 Potassium Channel / Q000235:genetics; D009154:Mutation; D062554:NAV1.5 Voltage-Gated Sodium Channel / Q000235:genetics; D016133:Polymerase Chain Reaction; D024642:Potassium Channels, Voltage-Gated / Q000235:genetics; D011237:Predictive Value of Tests; D019837:Ryanodine Receptor Calcium Release Channel / Q000235:genetics; D012680:Sensitivity and Specificity
chemical_list: D000072237:ERG1 Potassium Channel; D051638:Ether-A-Go-Go Potassium Channels; D005819:Genetic Markers; D007473:Ion Channels; C489622:KCNE1 protein, human; C489619:KCNE2 protein, human; D051657:KCNQ1 Potassium Channel; C496909:KCNQ1 protein, human; D062554:NAV1.5 Voltage-Gated Sodium Channel; D024642:Potassium Channels, Voltage-Gated; D019837:Ryanodine Receptor Calcium Release Channel; C568320:SCN5A protein, human