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Hum Genomics. 2015 Jul 19;9:15. doi: 10.1186/s40246-015-0038-y.

Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death.

Li MH1,2, Abrudan JL3,4, Dulik MC5,6, Sasson A7, Brunton J8,9, Jayaraman V10,11, Dugan N12,13, Haley D14,15, Rajagopalan R16,17, Biswas S18, Sarmady M19, DeChene ET20,21, Deardorff MA22,23, Wilkens A24,25, Noon SE26,27, Scarano MI28,29, Santani AB30,31, White PS32,33,34,35, Pennington J36, Conlin LK37,38, Spinner NB39,40, Krantz ID41,42, Vetter VL43,44.

Author information

1
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. lim@email.chop.edu.
2
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.
3
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. AbrudanP@email.chop.edu.
4
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.
5
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. DulikM@email.chop.edu.
6
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.
7
Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. sassona@email.chop.edu.
8
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. joshua.s.brunton@gmail.com.
9
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.
10
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. JayaramanV1@email.chop.edu.
11
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.
12
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. dugann@email.chop.edu.
13
Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. dugann@email.chop.edu.
14
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. daniellemhaley@gmail.com.
15
Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. daniellemhaley@gmail.com.
16
Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. rajagopalanr@email.chop.edu.
17
Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. rajagopalanr@email.chop.edu.
18
Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. biswass1@email.chop.edu.
19
Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. sarmadym@email.chop.edu.
20
Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. DecheneE@email.chop.edu.
21
Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. DecheneE@email.chop.edu.
22
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. DEARDORFF@email.chop.edu.
23
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.
24
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. Wilkens@email.chop.edu.
25
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.
26
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. NoonS@email.chop.edu.
27
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.
28
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. scaranom@email.chop.edu.
29
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.
30
Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. SANTANI@email.chop.edu.
31
Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. SANTANI@email.chop.edu.
32
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. peter.white@cchmc.org.
33
Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. peter.white@cchmc.org.
34
Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. peter.white@cchmc.org.
35
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.
36
Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. penningtonj@email.chop.edu.
37
Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. conlinl@email.chop.edu.
38
Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. conlinl@email.chop.edu.
39
Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. SPINNER@email.chop.edu.
40
Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. SPINNER@email.chop.edu.
41
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. KRANTZ@email.chop.edu.
42
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.
43
Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. vetter@email.chop.edu.
44
Division of Cardiology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. vetter@email.chop.edu.

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.

PMID:
26187847
PMCID:
PMC4506570
DOI:
10.1186/s40246-015-0038-y
[Indexed for MEDLINE]
Free PMC Article

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