한빛사 논문
Nam Suk Sim1, Ara Ko2,3, Woo Kyeong Kim1, Se Hoon Kim4, Ju Seong Kim5, Kyu-Won Shim5, Eleonora Aronica6,7, Caroline Mijnsbergen6, Wim G. M. Spliet8, Hyun Yong Koh1, Heung Dong Kim9,10, Joon Soo Lee9,10, Dong Seok Kim5, Hoon-Chul Kang9,10,*, Jeong Ho Lee1,*
1Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
2Department of Pediatrics, Pusan National University Children’s Hospital, Pusan National University School of Medicine, Yangsan, Republic of Korea
3Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, Republic of Korea
4Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
5Department of Neurosurgery, Pediatric Neurosurgery, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
6Department of (Neuro) Pathology, Amsterdam NeuroscienceAmsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
7Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands
8Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
9Division of Pediatric Neurology, Department of Pediatrics, Pediatric Epilepsy Clinics, Severance Children’s Hospital, Seoul, Republic of Korea
10Epilepsy Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea
Dong Seok Kim, Hoon-Chul Kang, and Jeong Ho Lee contributed equally to this article.
*To whom correspondence should be addressed.
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.
Keywords : Somatic mutation, Intractable epilepsy, Genetics, Focal cortical dysplasia, Malformation of cortical development
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