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

Nam Suk Sim, Ara Ko, Woo Kyeong Kim, Se Hoon Kim, Ju Seong Kim, Kyu Won Shim, Eleonora Aronica, Caroline Mijnsbergen, Wim G.M. Spliet, Hyun Yong Koh, Heung Dong Kim, Joon Soo Lee, Dong Seok Kim, Hoon Chul Kang, Jeong Ho Lee

Research output: Contribution to journalArticle

2 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)901-912
Number of pages12
JournalActa Neuropathologica
Volume138
Issue number6
DOIs
Publication statusPublished - 2019 Dec 1

Fingerprint

Epilepsy
Tonic-Clonic Epilepsy
High-Throughput Nucleotide Sequencing
Mutation
Partial Epilepsy
Brain
Paraffin
Formaldehyde
Genes
Germ-Line Mutation
Genetic Counseling
Patient Care
Pathology
Drug Resistant Epilepsy

All Science Journal Classification (ASJC) codes

  • Pathology and Forensic Medicine
  • Clinical Neurology
  • Cellular and Molecular Neuroscience

Cite this

Sim, N. S., Ko, A., Kim, W. K., Kim, S. H., Kim, J. S., Shim, K. W., ... Lee, J. H. (2019). Precise detection of low-level somatic mutation in resected epilepsy brain tissue. Acta Neuropathologica, 138(6), 901-912. https://doi.org/10.1007/s00401-019-02052-6
Sim, Nam Suk ; Ko, Ara ; Kim, Woo Kyeong ; Kim, Se Hoon ; Kim, Ju Seong ; Shim, Kyu Won ; Aronica, Eleonora ; Mijnsbergen, Caroline ; Spliet, Wim G.M. ; Koh, Hyun Yong ; Kim, Heung Dong ; Lee, Joon Soo ; Kim, Dong Seok ; Kang, Hoon Chul ; Lee, Jeong Ho. / Precise detection of low-level somatic mutation in resected epilepsy brain tissue. In: Acta Neuropathologica. 2019 ; Vol. 138, No. 6. pp. 901-912.
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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.",
author = "Sim, {Nam Suk} and Ara Ko and Kim, {Woo Kyeong} and Kim, {Se Hoon} and Kim, {Ju Seong} and Shim, {Kyu Won} and Eleonora Aronica and Caroline Mijnsbergen and Spliet, {Wim G.M.} and Koh, {Hyun Yong} and Kim, {Heung Dong} and Lee, {Joon Soo} and Kim, {Dong Seok} and Kang, {Hoon Chul} and Lee, {Jeong Ho}",
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Sim, NS, Ko, A, Kim, WK, Kim, SH, Kim, JS, Shim, KW, Aronica, E, Mijnsbergen, C, Spliet, WGM, Koh, HY, Kim, HD, Lee, JS, Kim, DS, Kang, HC & Lee, JH 2019, 'Precise detection of low-level somatic mutation in resected epilepsy brain tissue', Acta Neuropathologica, vol. 138, no. 6, pp. 901-912. https://doi.org/10.1007/s00401-019-02052-6

Precise detection of low-level somatic mutation in resected epilepsy brain tissue. / Sim, Nam Suk; Ko, Ara; Kim, Woo Kyeong; Kim, Se Hoon; Kim, Ju Seong; Shim, Kyu Won; Aronica, Eleonora; Mijnsbergen, Caroline; Spliet, Wim G.M.; Koh, Hyun Yong; Kim, Heung Dong; Lee, Joon Soo; Kim, Dong Seok; Kang, Hoon Chul; Lee, Jeong Ho.

In: Acta Neuropathologica, Vol. 138, No. 6, 01.12.2019, p. 901-912.

Research output: Contribution to journalArticle

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T1 - Precise detection of low-level somatic mutation in resected epilepsy brain tissue

AU - Sim, Nam Suk

AU - Ko, Ara

AU - Kim, Woo Kyeong

AU - Kim, Se Hoon

AU - Kim, Ju Seong

AU - Shim, Kyu Won

AU - Aronica, Eleonora

AU - Mijnsbergen, Caroline

AU - Spliet, Wim G.M.

AU - Koh, Hyun Yong

AU - Kim, Heung Dong

AU - Lee, Joon Soo

AU - Kim, Dong Seok

AU - Kang, Hoon Chul

AU - Lee, Jeong Ho

PY - 2019/12/1

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N2 - 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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