{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T15:17:46Z","timestamp":1792509466159,"version":"4.5.0"},"reference-count":40,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2023,2,8]],"date-time":"2023-02-08T00:00:00Z","timestamp":1675814400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["2019R1A3B2066619"],"award-info":[{"award-number":["2019R1A3B2066619"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF\u20102019H1A2A1077149"],"award-info":[{"award-number":["NRF\u20102019H1A2A1077149"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001321","name":"National Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Annals of Neurology"],"published-print":{"date-parts":[[2023,6]]},"abstract":"<jats:sec><jats:title>Objective<\/jats:title><jats:p>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\u2010level somatic mutations in the brain by deep sequencing and analytics, about 40% of cases remain genetically unexplained.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We included 2 independent cohorts consisting of 21 patients with mutation\u2010negative FCDII without apparent mutations on conventional deep sequencing of bulk brain. To find ultra\u2010low level somatic variants or structural variants, we isolated cells exhibiting phosphorylation of the S6 ribosomal protein (p\u2010S6) in frozen brain tissues using fluorescence\u2010activated cell sorting (FACS). We then performed deep whole\u2010genome sequencing (WGS; &gt;90\u00d7) in p\u2010S6<jats:sup>+<\/jats:sup> cells in a cohort of 11 patients with mutation\u2010negative. Then, we simplified the method to whole\u2010genome amplification and target gene sequencing of p\u2010S6<jats:sup>+<\/jats:sup> cells in independent cohort of 10 patients with mutation\u2010negative followed by low\u2010read depth WGS (10\u00d7).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We found that 28.6% (6 of 21) of mutation\u2010negative FCDII carries ultra\u2010low level somatic mutations (less than 0.2% of variant allele frequency [VAF]<jats:bold>)<\/jats:bold> in mTOR pathway genes. Our method showed ~34 times increase of the average mutational burden in FACS mediated enrichment of p\u2010S6<jats:sup>+<\/jats:sup> cells (average VAF\u00a0=\u00a05.84%) than in bulky brain tissues (average VAF\u00a0=\u00a00.17%). We found that 19% (4 of 21) carried germline structural variations in GATOR1 complex undetectable in whole exome or targeted gene sequencing.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our method facilitates the detection of ultra\u2010low level somatic mutations, in specifically p\u2010S6<jats:sup>+<\/jats:sup> cells, and germline structural variations and increases the genetic diagnostic rate up to ~80% for the entire FCDII cohort. ANN NEUROL 2023;93:1082\u20131093<\/jats:p><\/jats:sec>","DOI":"10.1002\/ana.26609","type":"journal-article","created":{"date-parts":[[2023,1,26]],"date-time":"2023-01-26T12:13:44Z","timestamp":1674735224000},"page":"1082-1093","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["Ultra\u2010Low Level Somatic Mutations and Structural Variations in Focal Cortical Dysplasia Type <scp>II<\/scp>"],"prefix":"10.1002","volume":"93","author":[{"given":"Ja Hye","family":"Kim","sequence":"first","affiliation":[{"name":"Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology (KAIST)  Daejeon Republic of Korea"},{"name":"Department of Pediatrics, Asan Medical Center Children's Hospital University of Ulsan College of Medicine  Seoul Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji\u2010Hyung","family":"Park","sequence":"additional","affiliation":[{"name":"Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology (KAIST)  Daejeon Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junehawk","family":"Lee","sequence":"additional","affiliation":[{"name":"Center for Supercomputing Applications, National Institute of Supercomputing and Networking Korea Institute of Science and Technology Information  Daejeon Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jung Woo","family":"Park","sequence":"additional","affiliation":[{"name":"Center for Supercomputing Applications, National Institute of Supercomputing and Networking Korea Institute of Science and Technology Information  Daejeon Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyun Jung","family":"Kim","sequence":"additional","affiliation":[{"name":"Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology (KAIST)  Daejeon Republic of Korea"},{"name":"Department of Anatomy Korea University College of Medicine  Seoul Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Won Seok","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery Yonsei University College of Medicine  Seoul Republic of Korea"},{"name":"Brain Research Institute Yonsei University College of Medicine  Seoul Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong\u2010Seok","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery Yonsei University College of Medicine  Seoul Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Young Seok","family":"Ju","sequence":"additional","affiliation":[{"name":"Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology (KAIST)  Daejeon Republic of Korea"},{"name":"Genome Insight Inc.  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