Ultra-Low Level Somatic Mutations and Structural Variations in Focal Cortical Dysplasia Type II
- Authors
- Kim, Ja Hye; Park, Ji-Hyung; Lee, Junehawk; Park, Jung Woo; Kim, Hyun Jung; Chang, Won Seok; Kim, Dong-Seok; Ju, Young Seok; Aronica, Eleonora; Lee, Jeong Ho
- Issue Date
- Jun-2023
- Publisher
- John Wiley & Sons Inc.
- Citation
- Annals of Neurology, v.93, no.6, pp 1082 - 1093
- Pages
- 12
- Indexed
- SCIE
SCOPUS
- Journal Title
- Annals of Neurology
- Volume
- 93
- Number
- 6
- Start Page
- 1082
- End Page
- 1093
- URI
- https://scholarworks.korea.ac.kr/kumedicine/handle/2021.sw.kumedicine/62551
- DOI
- 10.1002/ana.26609
- ISSN
- 0364-5134
1531-8249
- Abstract
- Objective
Brain somatic mutations in mTOR pathway genes are a major genetic etiology of focal cortical dysplasia type II (FCDII). Despite a greater ability to detect low-level somatic mutations in the brain by deep sequencing and analytics, about 40% of cases remain genetically unexplained.
Methods
We included 2 independent cohorts consisting of 21 patients with mutation-negative FCDII without apparent mutations on conventional deep sequencing of bulk brain. To find ultra-low level somatic variants or structural variants, we isolated cells exhibiting phosphorylation of the S6 ribosomal protein (p-S6) in frozen brain tissues using fluorescence-activated cell sorting (FACS). We then performed deep whole-genome sequencing (WGS; >90×) in p-S6+ cells in a cohort of 11 patients with mutation-negative. Then, we simplified the method to whole-genome amplification and target gene sequencing of p-S6+ cells in independent cohort of 10 patients with mutation-negative followed by low-read depth WGS (10×).
Results
We found that 28.6% (6 of 21) of mutation-negative FCDII carries ultra-low level somatic mutations (less than 0.2% of variant allele frequency [VAF]) in mTOR pathway genes. Our method showed ~34 times increase of the average mutational burden in FACS mediated enrichment of p-S6+ cells (average VAF = 5.84%) than in bulky brain tissues (average VAF = 0.17%). We found that 19% (4 of 21) carried germline structural variations in GATOR1 complex undetectable in whole exome or targeted gene sequencing.
Conclusions
Our method facilitates the detection of ultra-low level somatic mutations, in specifically p-S6+ cells, and germline structural variations and increases the genetic diagnostic rate up to ~80% for the entire FCDII cohort. ANN NEUROL 2023
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- Appears in
Collections - 1. Basic Science > Department of Anatomy > 1. Journal Articles
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