title: Development of a Comprehensive Sequencing Assay for Inherited Cardiac Condition Genes.
abstract: Inherited cardiac conditions (ICCs) are characterised by marked genetic and allelic heterogeneity and require extensive sequencing for genetic characterisation. We iteratively optimised a targeted gene capture panel for ICCs that includes disease-causing, putatively pathogenic, research and phenocopy genes (n = 174 genes). We achieved high coverage of the target region on both MiSeq (>99.8% at ≥ 20× read depth, n = 12) and NextSeq (>99.9% at ≥ 20×, n = 48) platforms with 100% sensitivity and precision for single nucleotide variants and indels across the protein-coding target on the MiSeq. In the final assay, 40 out of 43 established ICC genes informative in clinical practice achieved complete coverage (100 % at ≥ 20×). By comparison, whole exome sequencing (WES; ∼ 80×), deep WES (∼ 500×) and whole genome sequencing (WGS; ∼ 70×) had poorer performance (88.1, 99.2 and 99.3% respectively at ≥ 20×) across the ICC target. The assay described here delivers highly accurate and affordable sequencing of ICC genes, complemented by accessible cloud-based computation and informatics. See Editorial in this issue (DOI: 10.1007/s12265-015-9667-8 ).
authors.affiliation: National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore.
authors.forename: Chee Jian
authors.initials: CJ
authors.lastname: Pua
authors.affiliation: National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore.
authors.forename: Jaydutt
authors.initials: J
authors.lastname: Bhalshankar
authors.affiliation: Division of Cardiovascular & Metabolic Disorders, Duke-National University of Singapore, 169857, Singapore, Singapore.
authors.forename: Kui
authors.initials: K
authors.lastname: Miao
authors.affiliation: NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London, SW3 6NP, UK.|National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK.
authors.forename: Roddy
authors.initials: R
authors.lastname: Walsh
authors.affiliation: NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London, SW3 6NP, UK.|National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK.
authors.forename: Shibu
authors.initials: S
authors.lastname: John
authors.affiliation: National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore.
authors.forename: Shi Qi
authors.initials: SQ
authors.lastname: Lim
authors.affiliation: National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore.
authors.forename: Kingsley
authors.initials: K
authors.lastname: Chow
authors.affiliation: NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London, SW3 6NP, UK.|National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK.
authors.forename: Rachel
authors.initials: R
authors.lastname: Buchan
authors.affiliation: National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore.
authors.forename: Bee Yong
authors.initials: BY
authors.lastname: Soh
authors.affiliation: National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore.
authors.forename: Pei Min
authors.initials: PM
authors.lastname: Lio
authors.affiliation: National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore.
authors.forename: Jaclyn
authors.initials: J
authors.lastname: Lim
authors.affiliation: National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Schafer
authors.affiliation: Division of Medical Sciences, National Cancer Centre Singapore, 169610, Singapore, Singapore.
authors.forename: Jing Quan
authors.initials: JQ
authors.lastname: Lim
authors.affiliation: Division of Cancer and Stem Cell Biology, Duke-National University of Singapore, 169857, Singapore, Singapore.|SingHealth/Duke-NUS Precision Medicine Institute, National Heart Centre Singapore, 168752, Singapore, Singapore.
authors.forename: Patrick
authors.initials: P
authors.lastname: Tan
authors.affiliation: NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London, SW3 6NP, UK.|National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK.
authors.forename: Nicola
authors.initials: N
authors.lastname: Whiffin
authors.affiliation: NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Foundation Trust and Imperial College London, London, SW3 6NP, UK.|National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Barton
authors.affiliation: National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK.|MRC Clinical Sciences Centre, Imperial College London, London, W12 0NN, UK.
authors.forename: James S
authors.initials: JS
authors.lastname: Ware
authors.affiliation: National Heart Research Institute Singapore, National Heart Centre Singapore, 168752, Singapore, Singapore. stuart.cook@singhealth.com.sg.|Division of Cardiovascular & Metabolic Disorders, Duke-National University of Singapore, 169857, Singapore, Singapore. stuart.cook@singhealth.com.sg.|National Heart and Lung Institute, Imperial College London, London, SW3 6LY, UK. stuart.cook@singhealth.com.sg.|MRC Clinical Sciences Centre, Imperial College London, London, W12 0NN, UK. stuart.cook@singhealth.com.sg.
authors.forename: Stuart A
authors.initials: SA
authors.lastname: Cook
mesh_terms: D000067917:Cloud Computing; D019295:Computational Biology; D004252:DNA Mutational Analysis / Q000379:methods*; D030541:Databases, Genetic; D059472:Exome; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease; D006331:Heart Diseases / Q000175:diagnosis / Q000235:genetics*; D040941:Heredity; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008131:London; D009154:Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011237:Predictive Value of Tests; D012846:Singapore; D057188:Workflow
chemical_list: D005819:Genetic Markers
keywords: Diagnostics; Genetics; Inherited cardiac conditions; Targeted sequencing; Whole exome sequencing; Whole genome sequencing