title: Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death.
abstract: BACKGROUND
  Conditions associated with sudden cardiac arrest/death (SCA/D) in youth often have a genetic etiology. While SCA/D is uncommon, a pro-active family screening approach may identify these inherited structural and electrical abnormalities prior to symptomatic events and allow appropriate surveillance and treatment. This study investigated the diagnostic utility of exome sequencing (ES) by evaluating the capture and coverage of genes related to SCA/D.
  
  
  METHODS
  Samples from 102 individuals (13 with known molecular etiologies for SCA/D, 30 individuals without known molecular etiologies for SCA/D and 59 with other conditions) were analyzed following exome capture and sequencing at an average read depth of 100X. Reads were mapped to human genome GRCh37 using Novoalign, and post-processing and analysis was done using Picard and GATK. A total of 103 genes (2,190 exons) related to SCA/D were used as a primary filter. An additional 100 random variants within the targeted genes associated with SCA/D were also selected and evaluated for depth of sequencing and coverage. Although the primary objective was to evaluate the adequacy of depth of sequencing and coverage of targeted SCA/D genes and not for primary diagnosis, all patients who had SCA/D (known or unknown molecular etiologies) were evaluated with the project's variant analysis pipeline to determine if the molecular etiologies could be successfully identified.
  
  
  RESULTS
  The majority of exons (97.6 %) were captured and fully covered on average at minimum of 20x sequencing depth. The proportion of unique genomic positions reported within poorly covered exons remained small (4 %). Exonic regions with less coverage reflect the need to enrich these areas to improve coverage. Despite limitations in coverage, we identified 100 % of cases with a prior known molecular etiology for SCA/D, and analysis of an additional 30 individuals with SCA/D but no known molecular etiology revealed a diagnostic answer in 5/30 (17 %). We also demonstrated 95 % of 100 randomly selected reported variants within our targeted genes would have been picked up on ES based on our coverage analysis.
  
  
  CONCLUSIONS
  ES is a helpful clinical diagnostic tool for SCA/D given its potential to successfully identify a molecular diagnosis, but clinicians should be aware of limitations of available platforms from technical and diagnostic perspectives.
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. lim@email.chop.edu.|Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA. lim@email.chop.edu.
authors.forename: Mindy H
authors.initials: MH
authors.lastname: Li
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. AbrudanP@email.chop.edu.|Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA. AbrudanP@email.chop.edu.
authors.forename: Jenica L
authors.initials: JL
authors.lastname: Abrudan
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. DulikM@email.chop.edu.|Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA. DulikM@email.chop.edu.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Dulik
authors.affiliation: Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. sassona@email.chop.edu.
authors.forename: Ariella
authors.initials: A
authors.lastname: Sasson
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. joshua.s.brunton@gmail.com.|Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA. joshua.s.brunton@gmail.com.
authors.forename: Joshua
authors.initials: J
authors.lastname: Brunton
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. JayaramanV1@email.chop.edu.|Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA. JayaramanV1@email.chop.edu.
authors.forename: Vijayakumar
authors.initials: V
authors.lastname: Jayaraman
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. dugann@email.chop.edu.|Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. dugann@email.chop.edu.
authors.forename: Noreen
authors.initials: N
authors.lastname: Dugan
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. daniellemhaley@gmail.com.|Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. daniellemhaley@gmail.com.
authors.forename: Danielle
authors.initials: D
authors.lastname: Haley
authors.affiliation: Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. rajagopalanr@email.chop.edu.|Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. rajagopalanr@email.chop.edu.
authors.forename: Ramakrishnan
authors.initials: R
authors.lastname: Rajagopalan
authors.affiliation: Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. biswass1@email.chop.edu.
authors.forename: Sawona
authors.initials: S
authors.lastname: Biswas
authors.affiliation: Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. sarmadym@email.chop.edu.
authors.forename: Mahdi
authors.initials: M
authors.lastname: Sarmady
authors.affiliation: Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. DecheneE@email.chop.edu.|Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. DecheneE@email.chop.edu.
authors.forename: Elizabeth T
authors.initials: ET
authors.lastname: DeChene
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. DEARDORFF@email.chop.edu.|Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA. DEARDORFF@email.chop.edu.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Deardorff
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. Wilkens@email.chop.edu.|Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA. Wilkens@email.chop.edu.
authors.forename: Alisha
authors.initials: A
authors.lastname: Wilkens
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. NoonS@email.chop.edu.|Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA. NoonS@email.chop.edu.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Noon
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. scaranom@email.chop.edu.|Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA. scaranom@email.chop.edu.
authors.forename: Maria I
authors.initials: MI
authors.lastname: Scarano
authors.affiliation: Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. SANTANI@email.chop.edu.|Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. SANTANI@email.chop.edu.
authors.forename: Avni B
authors.initials: AB
authors.lastname: Santani
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. peter.white@cchmc.org.|Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. peter.white@cchmc.org.|Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. peter.white@cchmc.org.|Present address: Department of Pediatrics, Cincinnati Children's Hospital and Medical Center, and Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA. peter.white@cchmc.org.
authors.forename: Peter S
authors.initials: PS
authors.lastname: White
authors.affiliation: Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. penningtonj@email.chop.edu.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Pennington
authors.affiliation: Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. conlinl@email.chop.edu.|Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. conlinl@email.chop.edu.
authors.forename: Laura K
authors.initials: LK
authors.lastname: Conlin
authors.affiliation: Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. SPINNER@email.chop.edu.|Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. SPINNER@email.chop.edu.
authors.forename: Nancy B
authors.initials: NB
authors.lastname: Spinner
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. KRANTZ@email.chop.edu.|Division of Human Genetics, The Children's Hospital of Philadelphia, Abramson Research Center, Room 1012G, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA. KRANTZ@email.chop.edu.
authors.forename: Ian D
authors.initials: ID
authors.lastname: Krantz
authors.affiliation: Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. vetter@email.chop.edu.|Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. vetter@email.chop.edu.
authors.forename: Victoria L
authors.initials: VL
authors.lastname: Vetter
mesh_terms: D000293:Adolescent; D000483:Alleles; D002648:Child; D016757:Death, Sudden, Cardiac; D059472:Exome / Q000235:genetics*; D015894:Genome, Human; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA; D055815:Young Adult