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Precise detection of low-level somatic mutation in resected epilepsy brain tissue

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Abstract

Low-level somatic mutations have been shown to be the major genetic etiology of intractable epilepsy. The extents thereof, however, have yet to be systematically and accurately explored in a large cohort of resected epilepsy brain tissues. Moreover, clinically useful and precise analysis tools for detecting low-level somatic mutations from unmatched formalin-fixed paraffin-embedded (FFPE) brain samples, the most clinically relevant samples, are still lacking. In total, 446 tissues samples from 232 intractable epilepsy patients with various brain pathologies were analyzed using deep sequencing (average read depth, 1112x) of known epilepsy-related genes (up to 28 genes) followed by confirmatory site-specific amplicon sequencing. Pathogenic mutations were discovered in 31.9% (74 of 232) of the resected epilepsy brain tissues and were recurrently found in only eight major focal epilepsy genes, including AKT3, DEPDC5, MTOR, PIK3CA, TSC1, TSC2, SCL35A2, and BRAF. Somatic mutations, two-hit mutations, and germline mutations accounted for 22.0% (51), 0.9% (2), and 9.1% (21) of the patients with intractable epilepsy, respectively. The majority of pathogenic somatic mutations (62.3%, 33 of 53) had a low variant allelic frequency of less than 5%. The use of deep sequencing replicates in the eight major focal epilepsy genes robustly increased PPVs to 50–100% and sensitivities to 71–100%. In an independent FCDII cohort of only unmatched FFPE brain tissues, deep sequencing replicates in the eight major focal epilepsy genes identified pathogenic somatic mutations in 33.3% (5 of 15) of FCDII individuals (similar to the genetic detecting rate in the entire FCDII cohort) without any false-positive calls. Deep sequencing replicates of major focal epilepsy genes in unmatched FFPE brain tissues can be used to accurately and efficiently detect low-level somatic mutations, thereby improving overall patient care by enriching genetic counseling and informing treatment decisions.

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Acknowledgements

This work was supported by grants from the Suh Kyungbae Foundation (to J.H.L.), the National Research Foundation of Korea (NRF) grant funded by the Korea government, Ministry of Science and ICT (No. 2019R1A3B2066619 to J.H.L), Korean Health Technology R&D Project, Ministry of Health & Welfare, Republic of Korea (H15C3143 and H16C0415 to J.H.L.; HI15C1601 and HI18C0586 to H.C.K.), and Netherlands Organisation for Health Research and Development (ZonMW, Programma Translationeel Onderzoek, Project number: 95105004; AE, CM to E.A.).

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Author notes

  1. Dong Seok Kim, Hoon-Chul Kang, and Jeong Ho Lee contributed equally to this article.

Authors and Affiliations

  1. Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea

    Nam Suk Sim, Woo Kyeong Kim, Hyun Yong Koh & Jeong Ho Lee

  2. Department of Pediatrics, Pusan National University Children’s Hospital, Pusan National University School of Medicine, Yangsan, Republic of Korea

    Ara Ko

  3. Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea

    Ara Ko

  4. Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea

    Se Hoon Kim

  5. Department of Neurosurgery, Pediatric Neurosurgery, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea

    Ju Seong Kim, Kyu-Won Shim & Dong Seok Kim

  6. Department of (Neuro) Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands

    Eleonora Aronica & Caroline Mijnsbergen

  7. Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands

    Eleonora Aronica

  8. Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands

    Wim G. M. Spliet

  9. Division of Pediatric Neurology, Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children’s Hospital, Seoul, Republic of Korea

    Heung Dong Kim, Joon Soo Lee & Hoon-Chul Kang

  10. Epilepsy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea

    Heung Dong Kim, Joon Soo Lee & Hoon-Chul Kang

Authors
  1. Nam Suk Sim
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  2. Ara Ko
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  3. Woo Kyeong Kim
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Contributions

NSS and JHL organized the project, and NSS performed genetic studies. SHK performed pathological study. NSS performed data analysis and bioinformatics analysis. DSK, KS, and JSK performed surgeries and collected patient samples. HK, AK, HDK, and JSL managed patient information. EA, CM, and WGMS collected patient samples, patient information, and tissue samples. NSS, WKK and HYK managed tissue samples and sequencing data. NSS and JHL wrote the manuscript. DSK, HK, and JHL led the project and oversaw the manuscript preparation.

Corresponding authors

Correspondence to Hoon-Chul Kang or Jeong Ho Lee.

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Conflict of interest

J.H.L is a co-founder of SoVarGen, Inc., which seeks to develop new diagnostics and therapeutics for brain disorders. The remaining authors declare no competing financial interests.

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Sim, N.S., Ko, A., Kim, W.K. et al. Precise detection of low-level somatic mutation in resected epilepsy brain tissue. Acta Neuropathol 138, 901–912 (2019). https://doi.org/10.1007/s00401-019-02052-6

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