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January 29, 2019; 92 (5) Article

Diagnostic yield of genetic tests in epilepsy

A meta-analysis and cost-effectiveness study

Iván Sánchez Fernández, Tobias Loddenkemper, Marina Gaínza-Lein, Beth Rosen Sheidley, Annapurna Poduri
First published January 4, 2019, DOI: https://doi.org/10.1212/WNL.0000000000006850
Iván Sánchez Fernández
From the Epilepsy Genetics Program (B.R.S., A.P.), Division of Epilepsy and Clinical Neurophysiology (I.S.F., T.L., M.G.-L., B.R.S., A.P.), Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Child Neurology (I.S.F.), Hospital Sant Joan de Déu, Universidad de Barcelona, Spain; and Facultad de Medicina (M.G.-L.), Universidad Austral de Chile, Valdivia.
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Tobias Loddenkemper
From the Epilepsy Genetics Program (B.R.S., A.P.), Division of Epilepsy and Clinical Neurophysiology (I.S.F., T.L., M.G.-L., B.R.S., A.P.), Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Child Neurology (I.S.F.), Hospital Sant Joan de Déu, Universidad de Barcelona, Spain; and Facultad de Medicina (M.G.-L.), Universidad Austral de Chile, Valdivia.
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Marina Gaínza-Lein
From the Epilepsy Genetics Program (B.R.S., A.P.), Division of Epilepsy and Clinical Neurophysiology (I.S.F., T.L., M.G.-L., B.R.S., A.P.), Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Child Neurology (I.S.F.), Hospital Sant Joan de Déu, Universidad de Barcelona, Spain; and Facultad de Medicina (M.G.-L.), Universidad Austral de Chile, Valdivia.
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Beth Rosen Sheidley
From the Epilepsy Genetics Program (B.R.S., A.P.), Division of Epilepsy and Clinical Neurophysiology (I.S.F., T.L., M.G.-L., B.R.S., A.P.), Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Child Neurology (I.S.F.), Hospital Sant Joan de Déu, Universidad de Barcelona, Spain; and Facultad de Medicina (M.G.-L.), Universidad Austral de Chile, Valdivia.
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Annapurna Poduri
From the Epilepsy Genetics Program (B.R.S., A.P.), Division of Epilepsy and Clinical Neurophysiology (I.S.F., T.L., M.G.-L., B.R.S., A.P.), Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Child Neurology (I.S.F.), Hospital Sant Joan de Déu, Universidad de Barcelona, Spain; and Facultad de Medicina (M.G.-L.), Universidad Austral de Chile, Valdivia.
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Diagnostic yield of genetic tests in epilepsy
A meta-analysis and cost-effectiveness study
Iván Sánchez Fernández, Tobias Loddenkemper, Marina Gaínza-Lein, Beth Rosen Sheidley, Annapurna Poduri
Neurology Jan 2019, 92 (5) e418-e428; DOI: 10.1212/WNL.0000000000006850

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Abstract

Objective To compare the cost-effectiveness of genetic testing strategies in patients with epilepsy of unknown etiology.

Methods This meta-analysis and cost-effectiveness study compared strategies involving 3 genetic tests: chromosomal microarray (CMA), epilepsy panel (EP) with deletion/duplication testing, and whole-exome sequencing (WES) in a cost-effectiveness model, using “no genetic testing” as a point of comparison.

Results Twenty studies provided information on the diagnostic yield of CMA (8 studies), EP (9 studies), and WES (6 studies). The diagnostic yield was highest for WES: 0.45 (95% confidence interval [CI]: 0.33–0.57) (0.32 [95% CI: 0.22–0.44] adjusting for potential publication bias), followed by EP: 0.23 (95% CI: 0.18–0.29), and CMA: 0.08 (95% CI: 0.06–0.12). The most cost-effective test was WES with an incremental cost-effectiveness ratio (ICER) of $15,000/diagnosis. However, after adjusting for potential publication bias, the most cost-effective test was EP (ICER: $15,848/diagnosis) followed by WES (ICER: $34,500/diagnosis). Among combination strategies, the most cost-effective strategy was WES, then if nondiagnostic, EP, then if nondiagnostic, CMA (ICER: $15,336/diagnosis), although adjusting for potential publication bias, the most cost-effective strategy was EP ± CMA ± WES (ICER: $18,385/diagnosis). While the cost-effectiveness of individual tests and testing strategies overlapped, CMA was consistently less cost-effective than WES and EP.

Conclusion WES and EP are the most cost-effective genetic tests for epilepsy. Our analyses support, for a broad population of patients with unexplained epilepsy, starting with these tests. Although less expensive, CMA has lower yield, and its use as the first-tier test is thus not supported from a cost-effectiveness perspective.

Glossary

CI=
confidence interval;
CMA=
chromosomal microarray;
CNV=
copy number variation;
EP=
epilepsy panel;
ICER=
incremental cost-effectiveness ratio;
WES=
whole-exome sequencing

Footnotes

  • Go to Neurology.org/N for full disclosures. Funding information and disclosures deemed relevant by the authors, if any, are provided at the end of the article.

  • Supplementary data: GitHub: github.com/IvanSanchezFernandez/CostEffectivenessGeneticTests and at Zenodo: zenodo.org/badge/latestdoi/138793909.

  • Patient Page page e523

  • Received April 8, 2018.
  • Accepted in final form August 30, 2018.
  • © 2019 American Academy of Neurology
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