Development of a comprehensive analysis pipeline for next-generation sequencers using the R

• Project/Area Number: 21K15702
• Research Category: Grant-in-Aid for Early-Career Scientists
• Allocation Type: Multi-year Fund
• Review Section: Basic Section 52020:Neurology-related
• Research Institution: Kagoshima University
• Principal Investigator: Ando Masahiro 鹿児島大学, 鹿児島大学病院, 特任助教 (60896976)
• Project Period (FY): 2021-04-01 – 2023-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2022: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2021: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: 次世代シークエンサー / Charcot-Marie-Tooth / 脊髄小脳変性症 / R言語 / 解析パイプライン / エクソーム解析 / Bioinformatics

Outline of Research at the Start

次世代シークエンサーによる網羅的遺伝子解析技術の拡大により, より多くの症例において原因遺伝子変異の同定が可能となっている．しかし, ACMGガイドラインに基づいた病原性判定には, 複数のコントロールデータベースとの比較や, コンピューターを用いた変異の機能解析を複数行うことなどが必要とされており, その判定を1サンプルあたり数万もの変異が検出されるWESデータに対して行うのは, 非常に煩雑である. そのため, WESデータを含めた網羅的遺伝子ゲノムデータの解析にあたり, 全ての変異に対して自動的に情報付けを行うプログラムを作成し, 解析を効率化するシステムを構築する.

Outline of Final Research Achievements

This study efficiently performed a comprehensive genetic diagnosis of inherited peripheral neuropathy and spinocerebellar degeneration (target resequencing and whole exome analysis using next-generation sequencers) using our analysis pipeline. Epidemiological, clinical, and genetic characteristics of the 2695 CMT patients analyzed to date have been summarized and reported in scientific papers. In a scientific paper, we also identified many previously reported genes and reported the clinical and genetic characteristics of the PTRH2, SLC12A6, NEFH, and POLR3B genes.

Academic Significance and Societal Importance of the Research Achievements

全エクソーム解析データから原因遺伝子を同定するためにはその膨大な数の変異をそれぞれ病原性判定する必要がある．しかし既知の病原性変異であるかの確認やACMGガイドラインにそった解析 (複数のコントロールデータベースとの比較や複数のin silico analysisなど)は非常に煩雑である．本研究ではRを用いた解析パイプラインを構築し, 病原性判定を自動化するとともに, 多数の症例を横断的に解析を可能とした．本研究の成果は，本邦の遺伝性神経疾患患者の遺伝子診断を確定する効率的な解析手法を構築したことであり, 遺伝子診断が確定することで病態解明や治療法開発にも寄与する．

Research Products

• [Journal Article] The first case of infantile-onset multisystem neurologic, endocrine, and pancreatic disease caused by novel PTRH2 mutation in Japan (2022)
  • Author(s): Ando Masahiro、Higuchi Yujiro、Takeuchi Mika、Hashiguchi Akihiro、Takashima Hiroshi
  • Journal Title: Neurological Sciences Volume: 43 Issue: 3 Pages: 2133-2136
  • DOI: 10.1007/s10072-021-05817-8
  • Peer Reviewed
• [Journal Article] An NEFH founder mutation causes broad phenotypic spectrum in multiple Japanese families (2022)
  • Author(s): Ando Masahiro、Higuchi Yujiro、Okamoto Yuji、Yuan Junhui、Yoshimura Akiko、Takei Jun、Taniguchi Takaki、Hiramatsu Yu、Sakiyama Yusuke、Hashiguchi Akihiro、Matsuura Eiji、Nakagawa Hiroto、Sonoda Ken、Yamashita Toru、Tamura Akiko、Terasawa Hideo、Mitsui Jun、Ishiura Hiroyuki、Tsuji Shoji、Takashima Hiroshi
  • Journal Title: Journal of Human Genetics Volume: - Issue: 7 Pages: 399-403
  • DOI: 10.1038/s10038-022-01019-y
  • Peer Reviewed
• [Journal Article] Novel de novo POLR3B mutations responsible for demyelinating Charcot-Marie-Tooth disease in Japan (2022)
  • Author(s): Ando Masahiro、Higuchi Yujiro、Yuan Jun‐Hui、Yoshimura Akiko、Kitao Ruriko、Morimoto Takehiko、Taniguchi Takaki、Takeuchi Mika、Takei Jun、Hiramatsu Yu、Sakiyama Yusuke、Hashiguchi Akihiro、Okamoto Yuji、Mitsui Jun、Ishiura Hiroyuki、Tsuji Shoji、Takashima Hiroshi
  • Journal Title: Annals of Clinical and Translational Neurology Volume: 9 Issue: 5 Pages: 747-755
  • DOI: 10.1002/acn3.51555
  • Peer Reviewed / Open Access
• [Journal Article] Novel heterozygous variants of SLC12A6 in Japanese families with Charcot-Marie-Tooth disease. (2022)
  • Author(s): Ando Masahiro、Higuchi Yujiro、Yuan Junhui、Yoshimura Akiko、Taniguchi Takaki、Takei Jun、Takeuchi Mika、Hiramatsu Yu、Shimizu Fumitaka、Kubota Masaya、Takeshima Akari、et al.
  • Journal Title: Annals of Clinical and Translational Neurology Volume: 9 Issue: 7 Pages: 902-911
  • DOI: 10.1002/acn3.51603
  • Peer Reviewed / Open Access
• [Journal Article] Comprehensive Genetic Analyses of Inherited Peripheral Neuropathies in Japan: Making Early Diagnosis Possible (2022)
  • Author(s): Ando Masahiro、Higuchi Yujiro、Yuan Junhui、Yoshimura Akiko、Taniguchi Takaki、Kojima Fumikazu、Noguchi Yutaka、Hobara Takahiro、Takeuchi Mika、Takei Jun、Hiramatsu Yu、Sakiyama Yusuke、Hashiguchi Akihiro、Okamoto Yuji、Mitsui Jun、Ishiura Hiroyuki、Tsuji Shoji、Takashima Hiroshi
  • Journal Title: Biomedicines Volume: 10 Issue: 7 Pages: 1546-1546
  • DOI: 10.3390/biomedicines10071546
  • Peer Reviewed / Open Access
• [Journal Article] Genetic and clinical features of cerebellar ataxia with RFC1 biallelic repeat expansions in Japan (2022)
  • Author(s): Ando Masahiro、Higuchi Yujiro、Yuan Junhui H.、Yoshimura Akiko、Higashi Shuntaro、Takeuchi Mika、Hobara Takahiro、Kojima Fumikazu、Noguchi Yutaka、Takei Jun、Hiramatsu Yu、Nozuma Satoshi、Sakiyama Yusuke、Hashiguchi Akihiro、Matsuura Eiji、Okamoto Yuji、Nagai Masahiro、Takashima Hiroshi
  • Journal Title: Frontiers in Neurology Volume: 13 Pages: 952493-952493
  • DOI: 10.3389/fneur.2022.952493
  • Peer Reviewed / Open Access
• [Journal Article] Elderly patients with suspected Charcot-Marie-Tooth disease should be tested for the TTR gene for effective treatments (2022)
  • Author(s): Taniguchi Takaki、Ando Masahiro、Okamoto Yuji、Yoshimura Akiko、Higuchi Yujiro、Hashiguchi Akihiro、Matsuda Nozomu、Yamamoto Mamoru、Dohi Eisuke、Takahashi Makoto、Yoshino Masanao、Nomura Taichi、Matsushima Masaaki、Yabe Ichiro、Sanpei Yui、Ishiura Hiroyuki、Mitsui Jun、Nakagawa Masanori、Tsuji Shoji、Takashima Hiroshi
  • Journal Title: Journal of Human Genetics Volume: - Issue: 6 Pages: 353-362
  • DOI: 10.1038/s10038-021-01005-w
  • Peer Reviewed / Open Access
• [Journal Article] Complex hereditary peripheral neuropathies caused by novel variants in mitochondrial-related nuclear genes (2022)
  • Author(s): Hiramatsu Yu、Okamoto Yuji、Yoshimura Akiko、Yuan Jun-Hui、Ando Masahiro、Higuchi Yujiro、Hashiguchi Akihiro、Matsuura Eiji、Takashima Hiroshi et al.
  • Journal Title: Journal of Neurology Volume: - Issue: 8 Pages: 4129-4140
  • DOI: 10.1007/s00415-022-11026-w
  • Peer Reviewed / Open Access
• [Journal Article] Prevalence of Fragile X-Associated Tremor/Ataxia Syndrome in Patients with Cerebellar Ataxia in Japan (2021)
  • Author(s): Higuchi Yujiro、Ando Masahiro、Yoshimura Akiko、Hakotani Satoshi、Koba Yuki、Sakiyama Yusuke、Hiramatsu Yu、Tashiro Yuichi、Maki Yoshimitsu、Hashiguchi Akihiro、Yuan Junhui、Okamoto Yuji、Matsuura Eiji、Takashima Hiroshi
  • Journal Title: The Cerebellum Volume: - Issue: 5 Pages: 851-860
  • DOI: 10.1007/s12311-021-01323-x
  • Peer Reviewed
• [Presentation] 南九州地域を中心とした小脳性運動失調症におけるRFC1遺伝子解析 (2022)
  • Author(s): 安藤匡宏
  • Organizer: 第63回日本神経学会学術総会
• [Presentation] 南九州地域を中心とした小脳性運動失調症におけるRFC1遺伝子解析 (2022)
  • Author(s): 安藤匡宏
  • Organizer: 令和3年度運動失調班 班会議
• [Presentation] Charcot-Marie-Tooth病における次世代シークエンサーを用いたcopy number variation解析 (2021)
  • Author(s): 安藤匡宏
  • Organizer: 第62回日本神経学会学術大会