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Research Letter |

Diagnostic Yield of Clinical Next-Generation Sequencing Panels for Epilepsy FREE

Jason Wang, MD1; Garrett Gotway, MD, PhD2; Juan M. Pascual, MD, PhD3; Jason Y. Park, MD, PhD1
[+] Author Affiliations
1Department of Pathology, Children’s Medical Center, University of Texas Southwestern Medical Center, Dallas
2Division of Genetics and Metabolism, Department of Pediatrics, Children’s Medical Center, University of Texas Southwestern Medical Center, Dallas
3Rare Brain Disorders Program, Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas
JAMA Neurol. 2014;71(5):650-651. doi:10.1001/jamaneurol.2014.405.
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During the past 2 years, next-generation DNA sequencing (NGS) has become a widespread diagnostic tool in neurology. Several studies have addressed the diagnostic yield and cost of NGS relative to other types of DNA testing. G-banded karyotyping identifies chromosomal aberrations and has a 3% diagnostic yield for unexplained developmental disabilities or other congenital anomalies.1 In comparison, chromosomal microarrays detect gene copy number variations and have a yield of 15% to 20% for the same disorder categories.1 Next-generation DNA sequencing, in the format of whole-exome sequencing (WES), can be diagnostic in 25% of neurogenetic cases.2 Similarly, whole-genome sequencing (WGS) with NGS has a reported diagnostic yield of 27% in children and adults with a broad variety of diseases.3 In contrast to WES and WGS, targeted NGS panels focus on subsets (dozens to hundreds) of genes associated with specific phenotypes. For example, targeted NGS directed at a single disease category, such as congenital glycosylation disorders, has a reported diagnostic yield of 14.8%.4 Given the prevalence of pediatric epilepsy, we set out to critically assess the diagnostic yield of an NGS panel for epilepsy in a pediatric tertiary care hospital.

The University of Texas Southwestern Medical Center institutional review board approved this retrospective study; patient informed consent was waived. We conducted a 1-year retrospective review of all patients with epilepsy treated at our institution who received targeted NGS on peripheral blood by either the 2012 GeneDx Comprehensive (53 genes) or Infantile (38 genes) Epilepsy Gene Panels. The patients’ clinical histories were reviewed to determine the relevance (ie, diagnostic yield) of the targeted NGS test results. In addition, we compared the cost of the targeted NGS panels, subsets of single-gene sequencing tests, and WES (Table).

Table Graphic Jump LocationTable.  Comparison of NGS Panel, WES, and Sanger Sequencing

In 2012, 28 patients were tested using either the GeneDx Comprehensive or the Infantile Epilepsy Gene Panels. Six patients harbored pathogenic or likely pathogenic mutations in 5 epilepsy-associated genes (TCF4, SCN1A, CDKL5, KCNQ2, and POLG) and 11 patients were found to have novel missense variants that were classified as variants of unknown significance in 8 genes (GABRG2, MECP2, PNPO, SCN1A, SCN2A, SCN1B, SLC9A6, and TSC2). All of the pathogenic mutations had been previously characterized as such in the literature; novel variants that were likely pathogenic were reported as variants of unknown significance. The diagnostic yield of these disease-targeted NGS panels was 21.4% (6 of 28 patients), on par with WES or WGS.24 If the GeneDx criteria for prior reporting in diagnosing pathogenicity had been used in a recent study of clinical WES, the WES diagnostic yield would have been only 18%2; therefore, with equivalent reporting criteria, these NGS panel tests for epilepsy would have a superior diagnostic yield compared with WES.

The Comprehensive and Infantile Epilepsy Gene Panels cost $5750 and $4780, respectively. Whole-exome sequencing costs up to $15 129.6 In contrast, examining a subset of 3 commonly tested epilepsy genes by Sanger sequencing (SLC2A1, MECP2, and SCN1A) costs $7300.6 We concluded that there is a cost advantage in the use of NGS technology compared with traditional Sanger sequencing.

Whole-exome sequencing analyzes, with varying quality, more than 20 000 genes, but the Online Mendelian Inheritance in Man and the Human Gene Mutation Database currently include information for 3131 and 6137 genes, respectively.7,8 Indeed, a recent study of WES reporting a diagnostic yield of 25% included 48 novel variants that had not been previously reported.2 In this review of targeted NGS panels for epilepsy, the diagnostic yield was, in aggregate, similar to WES and achieved at a lower cost. In summary, targeted NGS gene panels are a cost-effective alternative to both Sanger sequencing of individual genes and WES for the genetic diagnosis of epilepsy.

Corresponding Author: Jason Wang, MD, Department of Pathology, Children’s Medical Center, 1935 Medical District Dr, Dallas, TX 75235 (jason.wang@utsouthwestern.edu).

Author Contributions: Drs Wang and Park had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis.

Study concept and design: All authors.

Acquisition, analysis, or interpretation of data: All authors.

Drafting of the manuscript: All authors.

Critical revision of the manuscript for important intellectual content: All authors.

Administrative, technical, or material support: All authors.

Study supervision: Pascual, Park.

Conflict of Interest Disclosures: Dr Park is a member of the Scientific Advisory Board of Fujirebio Inc. No other disclosures were reported.

Funding/Support: Drs Pascual and Park are supported by National Institutes of Health Office of Rare Diseases Research: Collaboration, Education, and Test Translation (CETT) program for rare genetic diseases.

Role of the Sponsor: The National Institutes of Health had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

Miller  DT, Adam  MP, Aradhya  S,  et al.  Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010;86(5):749-764.
PubMed   |  Link to Article
Yang  Y, Muzny  DM, Reid  JG,  et al.  Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013;369(16):1502-1511.
PubMed   |  Link to Article
Jacob  HJ, Abrams  K, Bick  DP,  et al.  Genomics in clinical practice: lessons from the front lines. Sci Transl Med.2013;5(194):194cm5.
PubMed   |  Link to Article
Jones  MA, Rhodenizer  D, da Silva  C,  et al.  Molecular diagnostic testing for congenital disorders of glycosylation (CDG): detection rate for single gene testing and next generation sequencing panel testing. Mol Genet Metab. 2013;110(1-2):78-85.
PubMed   |  Link to Article
Michelson  DJ, Shevell  MI, Sherr  EH, Moeschler  JB, Gropman  AL, Ashwal  S.  Evidence report: genetic and metabolic testing on children with global developmental delay: report of the Quality Standards Subcommittee of the American Academy of Neurology and the Practice Committee of the Child Neurology Society. Neurology. 2011;77(17):1629-1635.
PubMed   |  Link to Article
Ambry Genetics. http://www.ambrygen.com. Accessed February 2, 2014.
OMIM gene map statistics.http://www.omim.org/statistics/geneMap. Accessed February 2, 2014.
The Human Gene Mutation database.http://www.hgmd.cf.ac.uk/ac/index.php. Accessed February 2, 2014.

Figures

Tables

Table Graphic Jump LocationTable.  Comparison of NGS Panel, WES, and Sanger Sequencing

References

Miller  DT, Adam  MP, Aradhya  S,  et al.  Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010;86(5):749-764.
PubMed   |  Link to Article
Yang  Y, Muzny  DM, Reid  JG,  et al.  Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013;369(16):1502-1511.
PubMed   |  Link to Article
Jacob  HJ, Abrams  K, Bick  DP,  et al.  Genomics in clinical practice: lessons from the front lines. Sci Transl Med.2013;5(194):194cm5.
PubMed   |  Link to Article
Jones  MA, Rhodenizer  D, da Silva  C,  et al.  Molecular diagnostic testing for congenital disorders of glycosylation (CDG): detection rate for single gene testing and next generation sequencing panel testing. Mol Genet Metab. 2013;110(1-2):78-85.
PubMed   |  Link to Article
Michelson  DJ, Shevell  MI, Sherr  EH, Moeschler  JB, Gropman  AL, Ashwal  S.  Evidence report: genetic and metabolic testing on children with global developmental delay: report of the Quality Standards Subcommittee of the American Academy of Neurology and the Practice Committee of the Child Neurology Society. Neurology. 2011;77(17):1629-1635.
PubMed   |  Link to Article
Ambry Genetics. http://www.ambrygen.com. Accessed February 2, 2014.
OMIM gene map statistics.http://www.omim.org/statistics/geneMap. Accessed February 2, 2014.
The Human Gene Mutation database.http://www.hgmd.cf.ac.uk/ac/index.php. Accessed February 2, 2014.

Correspondence

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