Epilepsy is the most common neurological disorder of childhood and is associated with substantial morbidity. Identifying the genetic causes underlying epilepsy is critical for precision diagnosis, developing precision therapies, and improving outcomes. Children with nonacquired (unexplained) epilepsy are presumed to have genetic causes. Genome sequencing (GS) has the potential to identify pathogenic variants detectable by other genetic testing approaches (eg, chromosomal microarray, gene panels, and exome sequencing [ES]) and novel pathogenic variants uniquely detectable by GS. Because most cases of epilepsy in children remain unsolved after ES and there have been limited studies of GS for this population,^1-3 we sought to examine the yield and utility of GS after nondiagnostic ES in pediatric epilepsy.

This cohort study was approved by the Boston Children’s Hospital institutional review board and reported per the reporting guideline. Participants or their guardians provided written informed consent. Between August 2018 and May 2023, we recruited patients with unexplained epilepsy and available biological parents. For cases remaining genetically unsolved after research and/or clinical ES,⁴ we performed research GS and comprehensive analyses through the Children’s Rare Disease Collaborative.⁵ Raw sequencing data were aligned to the hg38 genome using DRAGEN v3.9.3 (Illumina) and analyzed using various computational workflows. The diagnostic yield of GS was calculated as the percentage of participants with diagnostic or likely diagnostic genetic findings. The unique diagnostic yield of GS was calculated as the percentage of participants with diagnostic or likely diagnostic genetic findings that required GS (eMethods in Supplement 1).

We enrolled 125 participants (58 female [46%]) with nondiagnostic ES and a median age at seizure onset of 3 years (IQR, 1-8 years), including 44 (35%) with developmental and epileptic encephalopathies (DEEs) (Table). GS identified diagnostic genetic findings in 5 and likely diagnostic genetic findings in 4 individuals, for a diagnostic yield of 7.2% (9 of 125). This included 4 of 44 individuals (9.1%) with DEE and 5 of 81 (6.2%) with non-DEE. Of the 9 solved cases, 7 (78%) required GS for variant detection and could not be solved by current ES methods: 3 difficult-to-sequence coding variants (in IRF2BPL, PRRT2, SYNGAP1), a small copy number variant (exonic deletion in MECP2), and 3 noncoding variants (promoter deletion in PHF21A, noncoding exon variant in noncoding RNA RNU4-2, intronic variant in SCN1A poison exon) (Figure). Thus, the unique diagnostic yield of GS was 5.6% (7 of 125). This included 4 of 4 solved cases with DEE (100%), for a unique yield of GS of 9.1% (4 of 44), and 3 of 5 solved cases with non-DEE (60%), for a unique yield of GS of 3.7% (3 of 81). The additional 2 findings were a deletion including part of SMARCC2 detectable using current ES methods and a variant in CDK19 recognized as mosaic in the father. The median length of the diagnostic odyssey was 6 years (range, 3-17 years) for the 9 participants with diagnostic or likely diagnostic genetic findings. For 4 participants, the findings had clinical utility (impact on evaluation, treatment, and/or prognosis); for 3, the findings allowed the families to access etiology-specific research studies; and for 5, the findings allowed the families to access etiology-specific foundations or support groups.

Our findings demonstrate that GS can identify genetic diagnoses not detectable by ES in pediatric epilepsy, supporting implementation of GS as a future first-line genetic test in epilepsy care, especially for DEE phenotypes.⁶ The additional yield of GS is comparable to the total yield of CMA in epilepsy.³ We expect the yield of GS to continue to increase as sequencing costs decrease and as we learn more about noncoding regions. Our cohort is limited to largely White and non-Hispanic participants referred for research GS from a single referral center. Future studies of GS and its cost-effectiveness in larger and more diverse epilepsy cohorts will further inform optimal implementation of GS in epilepsy care.

Accepted for Publication: August 21, 2024.

Published Online: October 21, 2024. doi:10.1001/jamaneurol.2024.3582

Corresponding Author: Annapurna Poduri, MD, MPH, Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA 02115 (annapurna.poduri@childrens.harvard.edu).

Author Contributions: Drs D’Gama and Poduri 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.

Concept and design: D’Gama, Shao, Sheidley, Rockowitz, Poduri.

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

Drafting of the manuscript: D’Gama, Shao, Poduri.

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

Statistical analysis: D’Gama, Shao, H. Y. Koh.

Obtained funding: D’Gama, H. Y. Koh, Poduri.

Administrative, technical, or material support: H. Y. Koh, Davis, Oby, Urzua, Sheidley, Rockowitz, Poduri.

Supervision: Sheidley, Rockowitz, Poduri.

Conflict of Interest Disclosures: None reported.

Funding/Support: This study was supported by the Boston Children’s Hospital Children’s Rare Disease Collaborative and the Robinson Fund for Transformative Research in Epilepsy. Dr D’Gama was supported by grant T32 HD098061 from the National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health and Human Development, the Hearst Foundation Fellowship from Harvard Medical School, and Boston Children’s Hospital Office of Faculty Development/Basic & Clinical Translational Research Executive Committees Faculty Career Development Fellowship.

Role of the Funder/Sponsor: The funders 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.

Data Sharing Statement: See Supplement 2.

Additional Contributions: We thank the participants and their families who participated in this study. We thank the Boston Children’s Hospital (BCH) clinicians who referred participants to this study, including Christelle Moufawad El Achkar, MD (Department of Neurology, BCH and Harvard Medical School [HMS]), Chellamani Harini, MD (Department of Neurology, BCH and HMS), Phillip L. Pearl, MD (Division of Epilepsy and Clinical Neurophysiology, BCH; Department of Neurology, HMS), and Jurriaan M. Peters, MD, PhD (Department of Neurology, BCH and HMS). We thank Courtney E. French, PhD (Children’s Rare Disease Collaborative [CRDC], BCH) and Piotr Sliz, PhD (CRDC and Division of Molecular Medicine, BCH; Departments of Pediatrics and Biological Chemistry and Molecular Pharmacology, HMS) for assistance with data management and review of the manuscript. None of the contributors were compensated for their work.