Development of presumptive diagnostic methods for germ line mosaic variants using low frequency mosaic variants detection technologies

• Project/Area Number: 16K09975
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Pediatrics
• Research Institution: Showa University
• Principal Investigator: Kato Mitsuhiro 昭和大学, 医学部, 教授 (10292434)
• Co-Investigator(Kenkyū-buntansha): 中村 和幸 山形大学, 医学部, 助教 (20436215)
• Project Period (FY): 2016-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2018: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
• Keywords: モザイク変異 / デジタルPCR / 遺伝相談 / de novo / 次世代シーケンサー / de novo変異 / 遺伝子変異 / モザイク / デジタルＰＣＲ / 突然変異 / 生殖細胞 / 診断法

Outline of Final Research Achievements

The frequency of germline mosaic variants varies from disease to disease, and the frequency is often unknown, which is a hindrance to accurate genetic consultation. The purpose of this study is to develop diagnostic methods for low-frequency somatic mosaic variants and contribute to more accurate genetic counseling. We analyzed the causative genes for neurological diseases in children and identified 185 variants in 3 years. Mosaic was confirmed by digital PCR using a sample of a mother whose sample was initially considered to have no variant. A mosaic variant that was overlooked by the Sanger method was confirmed by digital PCR, and the mosaic rate was clarified. Accurate information is critical for genetic counseling in serious diseases, and analysis by Digital PCR would be recommended.

Academic Significance and Societal Importance of the Research Achievements

からだや細胞の一部に変異が起きて、正常と変異が混じった状態をモザイク変異と言います。血液では変異がなくても、精子や卵子などでモザイク変異を起こしていると次の子どもへの遺伝に影響します。私たちは、頻度が少ないモザイク変異の診断法を開発し、より正確な遺伝相談を行うための研究を行いました。小児神経疾患の原因遺伝子解析を行い、3年間で185例の変異をみつけました。両親には一見変異が認められませんでしたが、デジタルPCRという新しい解析手法により、ひとりの母親で5%の変異を確認することができました。重篤な病気の遺伝相談では、正確な情報提供がたいせつであり、デジタルPCRが役立つことを示しました。

Research Products

• [Journal Article] Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy (2019)
  • Author(s): Takata Atsushi、Nakashima Mitsuko、Saitsu Hirotomo、Osaka Hitoshi、Nakamura Kazuyuki、Takeshita Saoko、Sakai Yasunari、Miyake Noriko、Miyatake Satoko、Matsumoto Naomichi
  • Journal Title: Nature Communications Volume: 10 Issue: 1 Pages: 2506-2506
  • DOI: 10.1038/s41467-019-10482-9
  • Peer Reviewed / Open Access
• [Journal Article] A de novo variant in RAC3 causes severe global developmental delay and a middle interhemispheric variant of holoprosencephaly (2019)
  • Author(s): Hiraide Takuya、Kaba Yasui Hikari、Kato Mitsuhiro、Nakashima Mitsuko、Saitsu Hirotomo
  • Journal Title: Journal of Human Genetics Volume: 64 Issue: 11 Pages: 1127-1132
  • DOI: 10.1038/s10038-019-0656-7
  • Peer Reviewed
• [Journal Article] Pathogenic variants of DYNC2H1, KIAA0556, and PTPN11 associated with hypothalamic hamartoma (2019)
  • Author(s): Fujita Atsushi、Higashijima Takefumi、Shirozu Hiroshi、Masuda Hiroshi、Sonoda Masaki、Tohyama Jun、Kato Mitsuhiro、Nakashima Mitsuko、Tsurusaki Yoshinori、Mitsuhashi Satomi、Mizuguchi Takeshi、Takata Atsushi、Miyatake Satoko、Miyake Noriko、Fukuda Masafumi、Kameyama Shigeki、Saitsu Hirotomo、Matsumoto Naomichi
  • Journal Title: Neurology Volume: 93 Issue: 3
  • DOI: 10.1212/wnl.0000000000007774
  • Peer Reviewed
• [Journal Article] Recurrent NUS1 canonical splice donor site mutation in two unrelated individuals with epilepsy, myoclonus, ataxia and scoliosis - a case report (2019)
  • Author(s): Den Kouhei、Kudo Yosuke、Kato Mitsuhiro、Watanabe Kosuke、Doi Hiroshi、Tanaka Fumiaki、Oguni Hirokazu、Miyatake Satoko、Mizuguchi Takeshi、Takata Atsushi、Miyake Noriko、Mitsuhashi Satomi、Matsumoto Naomichi
  • Journal Title: BMC Neurology Volume: 19 Issue: 1 Pages: 253-253
  • DOI: 10.1186/s12883-019-1489-x
  • Peer Reviewed / Open Access
• [Journal Article] De novo variants in CAMK2A and CAMK2B cause neurodevelopmental disorders (2018)
  • Author(s): Akita Tenpei、Aoto Kazushi、Kato Mitsuhiro、Shiina Masaaki、Mutoh Hiroki、Nakashima Mitsuko、Kuki Ichiro、Okazaki Shin、Magara Shinichi、Shiihara Takashi、Yokochi Kenji、Aiba Kaori、Tohyama Jun、Ohba Chihiro、Miyatake Satoko、Miyake Noriko、Ogata Kazuhiro、Fukuda Atsuo、Matsumoto Naomichi、Saitsu Hirotomo
  • Journal Title: Annals of Clinical and Translational Neurology Volume: 5 Issue: 3 Pages: 280-296
  • DOI: 10.1002/acn3.528
  • Peer Reviewed / Open Access
• [Journal Article] A recurrent homozygous NHLRC1 variant in siblings with Lafora disease (2018)
  • Author(s): Araya Nami、Takahashi Yukitoshi、Shimono Masayuki、Fukuda Tomofumi、Kato Mitsuhiro、Nakashima Mitsuko、Matsumoto Naomichi、Saitsu Hirotomo
  • Journal Title: Human Genome Variation Volume: 5 Issue: 1 Pages: 6-9
  • DOI: 10.1038/s41439-018-0015-9
  • Peer Reviewed / Open Access
• [Journal Article] De novo mutations of the ATP6V1A gene cause developmental encephalopathy with epilepsy (2018)
  • Author(s): Fassio Anna、Esposito Alessandro、Kato Mitsuhiro、Saitsu Hirotomo、et al.
  • Journal Title: Brain Volume: 141 Issue: 6 Pages: 1703-1718
  • DOI: 10.1093/brain/awy092
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin?Siris syndrome (2018)
  • Author(s): van der Sluijs PJ, Jansen S, Vergano SA, Adachi-Fukuda M, Alanay Y, AlKindy A, Baban A, Bayat A, Beck-Wodl S, Berry K, Bijlsma EK, Bok LA, Brouwer AFJ, van der Burgt I, Campeau PM, et al.
  • Journal Title: Genetics in Medicine Volume: 未定 Issue: 6 Pages: 1295-1307
  • DOI: 10.1038/s41436-018-0330-z
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Detection of copy number variations in epilepsy using exome data (2018)
  • Author(s): Tsuchida N, Nakashima M, Kato M, Heyman E, Inui T, Haginoya K, Watanabe S, Chiyonobu T, Morimoto M, Ohta M, Kumakura A, Kubota M, Kumagai Y, Hamano SI, Mizuguchi T. et al.
  • Journal Title: Clinical Genetics Volume: 93 Issue: 3 Pages: 577-587
  • DOI: 10.1111/cge.13144
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] De novo variants in SETD1B are associated with intellectual disability, epilepsy and autism (2018)
  • Author(s): Hiraide Takuya、Nakashima Mitsuko、Yamoto Kaori、Fukuda Tokiko、Kato Mitsuhiro、Ikeda Hiroko、Sugie Yoko、Aoto Kazushi、Kaname Tadashi、Nakabayashi Kazuhiko、Ogata Tsutomu、Matsumoto Naomichi、Saitsu Hirotomo
  • Journal Title: Human Genetics Volume: 137 Issue: 1 Pages: 95-104
  • DOI: 10.1007/s00439-017-1863-y
  • Peer Reviewed / Open Access
• [Journal Article] Genetic literacy series: Primer part 2-Paradigm shifts in epilepsy genetics (2018)
  • Author(s): Helbig Ingo、Heinzen Erin L.、Mefford Heather C.、the International League Against Epilepsy Genetics Commission
  • Journal Title: Epilepsia Volume: 59 Issue: 6 Pages: 1138-1147
  • DOI: 10.1111/epi.14193
  • Int'l Joint Research
• [Journal Article] De novo PHACTR1 mutations in West syndrome and their pathophysiological effects (2018)
  • Author(s): Hamada Nanako、Ogaya Shunsuke、Nakashima Mitsuko、Nishijo Takuma、Sugawara Yuji、Iwamoto Ikuko、Ito Hidenori、Maki Yuki、Shirai Kentaro、Baba Shimpei、Maruyama Koichi、Saitsu Hirotomo、Kato Mitsuhiro、Matsumoto Naomichi、Momiyama Toshihiko、Nagata Koh-ichi
  • Journal Title: Brain Volume: 141 Pages: 3098-3114
  • DOI: 10.1093/brain/awy246
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Novel biallelic SZT2 mutations in 3 cases of early-onset epileptic encephalopathy (2017)
  • Author(s): Tsuchida N, Nakashima M, Miyauchi A, Yoshitomi S, Kimizu T, Ganesan V, Teik KW, Ch'ng GS, Kato M, Mizuguchi T, Takata A, Miyatake S, Miyake N, Osaka H, Yamagata T, Nakajima H, Saitsu H, Matsumoto N
  • Journal Title: Clinical Genetics Volume: 93 Issue: 2 Pages: 266-274
  • DOI: 10.1111/cge.13061
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Delineating SPTAN1 associated phenotypes: from isolated epilepsy to encephalopathy with progressive brain atrophy (2017)
  • Author(s): Syrbe S、Harms FL、Parrini E、Montomoli M、Mutze U、Helbig KL、Polster T、Albrecht B、Bernbeck U、van Binsbergen E、Biskup S、Burglen L、Denecke J、Heron B、Heyne H O、Hoffmann GF、Hornemann F、Matsushige T、Matsuura R、Kato M、et al.
  • Journal Title: Brain Volume: 140 Issue: 9 Pages: 2322-2336
  • DOI: 10.1093/brain/awx195
  • Peer Reviewed / Int'l Joint Research
• [Presentation] Genetic role in infantile spasms (2019)
  • Author(s): Kato Mitsuhiro
  • Organizer: 3rd Azalea Festival symposium in Pediatric Neurology
  • Int'l Joint Research / Invited
• [Presentation] STXBP1 Encephalopathy (2019)
  • Author(s): Kato Mitsuhiro
  • Organizer: 3rd Azalea Festival symposium in Pediatric Neurology
  • Int'l Joint Research / Invited
• [Presentation] HECW2 mutation causes periodic attacks of paralysis, intellectual disability and hypotonia (2018)
  • Author(s): Kazuyuki Nakamura, Takahiro Abiko, Takashi Kanbayashi, Mitsuko Nakashima, Hirotomo Saitsu, Naomichi Matsumoto, Mitsuhiro Kato
  • Organizer: 15th International Child Neurology Congress
  • Int'l Joint Research
• [Presentation] De novo variants affecting autoinhibition of Calcium/calmodulin-dependent protein kinase II, cause neurodevelopmental disorders (2018)
  • Author(s): Hirotomo Saitsu, Tenpei Akita, Kazushi Aoto, Mitsuhiro Kato, Masaaki Shiina, Hiroki Mutoh, Mitsuko Nakashima, Ichiro Kuki, Shin Okazaki, Shinichi Magara, Takashi Shiihara, Kenji Yokochi, Kaori Aiba, Jun Tohyama, Chihiro Ohba, Satoko Miyatake, Noriko Miyake, Kazuhiro Ogata, Atsuo Fukuda, Naomichi Matsumoto
  • Organizer: American Society of Human Genetics
  • Int'l Joint Research
• [Presentation] Epileptic spasms in five children carrying WDR45 mutations (2018)
  • Author(s): Taikan Oboshi, Yukitoshi Takahashi, Asako Horino, Yuiti Kimizu, Shinsaku Yoshitomi, Tokito Ymaguchi, Hiroko Ikeda, Hidenobu Otani, Katumi Imai, Hideo Shigematsu, Yushi Inoue, Mitsuhiro Kato
  • Organizer: 19th International Symposium on Severe Infantile Epilepsy Treatment
  • Int'l Joint Research
• [Presentation] Biallelic variants in CNPY3 cause West syndrome with hippocampal malrotation and characteristic fast waves (2018)
  • Author(s): Mitsuhiro Kato, Hiroki Mutoh, Tenpei Akita, Takuma Shibata, Hiroyuki Wakamoto, Hiroko Ikeda, Hiroki Kitaura, Kazushi Aoto, Mitsuko Nakashima, Tianying Wang, Chihiro Ohba, Satoko Miyatake, Noriko Miyake, Akiyoshi Kakita, Kensuke Miyake, Atsuo Fukuda, Naomichi Matsumoto, Hirotomo Saitsu
  • Organizer: 13th European Congress on Epileptology
  • Int'l Joint Research
• [Presentation] Why aetiology matters. (2017)
  • Author(s): Kato Mitsuhiro
  • Organizer: The 32nd International Epilepsy Congress (IEC 2017), Barcelona
  • Int'l Joint Research / Invited
• [Presentation] PROSC mutations feature variable phenotype of early-onset epileptic encephalopathy (2017)
  • Author(s): Hiroshi Shiraku, Mitsuko Nakashima, Saoko Takeshita, Khoo Chai Soon, Muzhirah Haniffa, Ch'ng Gaik Siew, Kazuma Takada, Keisuke Nakajima, Masayasu Ohta, Tohru Okanishi, Sotaro Kanai, Ayataka Fujimoto, Hirotomo Saitsu, Naomichi Matsumoto, Mitsuhiro Kato
  • Organizer: American Epilepsy Society 2017, 71st Annual Meeting: Washington D.C.
  • Int'l Joint Research
• [Presentation] てんかん性脳症の成因―遺伝子診断のup to date― (2017)
  • Author(s): 加藤光広
  • Organizer: 第11回日本てんかん学会関東甲信越地方会：新宿
  • Invited
• [Book] The Causes of Epilepsy: Common and Uncommon Causes in Adults and Children. 2nd ed (2019)
  • Author(s): Kato Mitsuhiro（分担執筆）
  • Total Pages: 1010
  • Publisher: Cambridge University Press