効率的大量並行シークエンスによる難治性疾患責任遺伝子同定と疾病病態の解明

2014 Fiscal Year Annual Research Report

• Project/Area Number: 25293235
• Research Institution: Yokohama City University
• Principal Investigator: 三宅 紀子 横浜市立大学, 医学部, 准教授 (40523494)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Keywords: 全エクソームシークエンス / 連鎖解析

Outline of Annual Research Achievements

解析対象疾患（Aicardi症候群、関節弛緩型エーラス・ダンロス症候群、肺リンパ脈管筋腫症、Galloway-Mowat 症候群）の内、本年度までにAicardi症候群は45症例、肺リンパ脈管筋腫症は24症例、Galloway-Mowat 症候群は19家系を集積した。また、新規解析疾患としてステロイド抵抗性ネフローゼ症候群家系27家系を集積した。各疾患の罹患者対し全エクソーム解析を行い、想定される遺伝形式従って候補となるバリアントをリスト化し、2症例以上に共通して変異のある遺伝子に着目して順次Sanger法による確認と、家系内segregationを検証している。Aicardi症候群に関しては、トリオ解析ができない症例（両親検体が得られない、もしくは両親検体が揃わない）も含め、優性遺伝形式（常染色体およびＸ染色体）と劣性遺伝形式の両方を考慮した解析を行ったが、疾患遺伝子の同定には至っていない。それと並行して、典型的な3症例に対し、全ゲノムシークエンスを行い、現在解析を進めている。Galloway-Mowat 症候群に関しては、2家系の連鎖解析で同定された候補領域内のタンパク質翻訳領域を、全エクソーム解析で解析したが病因となる変異を同定しなかった。そこで、連鎖解析を行った2家系の発端者それぞれ1名に対して全ゲノムシークエンスを行い、出てきたバリアントに関して検証を行っているが、今のところ疾患遺伝子の特定には至っていない。

Current Status of Research Progress

2: Research has progressed on the whole more than it was originally planned.

Reason

症例集積は、稀な疾患ながらも連携研究者の協力により着実に集積できている状況にある。エクソーム解析は患者全例で解析が済んでいるが、両親そろっての検体提供が困難な場合もあり、候補遺伝子の絞り込みに時間がかかっている。新規で集積したステロイド抵抗性ネフローゼ症候群家系は両親検体がほぼ全例でそろっており、候補遺伝子の絞り込みが効率的に行うことができている。

Strategy for Future Research Activity

複数症例で共通してvariantを認めた遺伝子に関しては、積極的に両親検体を解析し、家系内segregation、de novoの確認を行う。また、所属する研究室で全エクソームのデータを用いたコピー数検出の解析系が確立できた為、コピー数解析を行い様々なサイズのゲノム異常を網羅的に解析する。それでも候補遺伝子にたどり着けない場合は、典型例で、かつ両親検体が得られる症例から必要に応じて全ゲノム解析を追加して行う。現在入手可能な非翻訳領域における日本人正常コントロールのバリアントデータ等を積極的に利用して、全ゲノム解析を進めたい。また、候補となった遺伝子に対しては、疾患発症メカニズムを明らかにするため分子の特性に応じた機能解析を行う。

Causes of Carryover

疾患遺伝子が同定された場合に必要と見積もっていた費用が想定より少ない購入にとどまったため。

Expenditure Plan for Carryover Budget

次年度使用額分は物品費として使用する。具体的にはゲノム解析に必要なシークエンス試薬、機能解析に必要な抗体やトランスフェクション試薬等、各プロジェクトの進行状況に応じて使用する。

Research Products

• [Journal Article] Mutations in the glutaminyl-tRNA synthetase gene cause early-onset epileptic encephalopathy. (2015)
  • Author(s): Kodera H, Osaka H, Iai M, Aida N, Yamashita A, Tsurusaki Y, Nakashima M, Miyake N, Saitsu H, Matsumoto N.
  • Journal Title: J Hum Genet. Volume: 60 Pages: 97-101
  • DOI: 10.1038/jhg.2014.103.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Late-onset spastic ataxia phenotype in a patient with a homozygous DDHD2 mutation. (2015)
  • Author(s): Doi H, Ushiyama M, Baba T, Tani K, Shiina M, Ogata K, Miyatake S, Fukuda-Yuzawa Y, Tsuji S, Nakashima M, Tsurusaki Y, Miyake N, Saitsu H, Ikeda S, Tanaka F, Matsumoto N, Yoshida K.
  • Journal Title: Sci Rep. Volume: 4 Pages: 7132-7132
  • DOI: 10.1038/srep07132.
  • Peer Reviewed
• [Journal Article] Identification and in vivo functional characterization of novel compound heterozygous BMP1 variants in osteogenesis imperfecta. (2015)
  • Author(s): Cho SY, Asharani PV, Kim OH, Iida A, Miyake N, Matsumoto N, Nishimura G, Ki CS, Hong G, Kim SJ, Sohn YB, Park SW, Lee J, Kwun Y, Carney TJ, Huh R, Ikegawa S, Jin DK.
  • Journal Title: Hum Mutat. Volume: 36 Pages: 191-5
  • DOI: 10.1002/humu.22731.
  • Peer Reviewed
• [Journal Article] Mutations in COG2 encoding a subunit of the conserved oligomeric golgi complex cause a congenital disorder of glycosylation. (2015)
  • Author(s): Kodera H, Ando N, Yuasa I, Wada Y, Tsurusaki Y, Nakashima M, Miyake N, Saitoh S, Matsumoto N, Saitsu H.
  • Journal Title: Clin Genet. Volume: 87 Pages: 455-60.
  • DOI: 10.1111/cge.12417.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] The somatic GNAQ mutation c.548G>A (p.R183Q) is consistently found in Sturge-Weber syndrome. (2014)
  • Author(s): Nakashima M, Miyajima M, Sugano H, Iimura Y, Kato M, Tsurusaki Y, Miyake N, Saitsu H, Arai H, Matsumoto N.
  • Journal Title: J Hum Genet. Volume: 59 Pages: 691-3
  • DOI: 10.1038/jhg.2014.95.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Compound heterozygous BRAT1 mutations cause familial Ohtahara syndrome with hypertonia and microcephaly. (2014)
  • Author(s): Saitsu H, Yamashita S, Tanaka Y, Tsurusaki Y, Nakashima M, Miyake N, Matsumoto N.
  • Journal Title: J Hum Genet. Volume: 59 Pages: 687-90
  • DOI: 10.1038/jhg.2014.91
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Precise detection of chromosomal translocation or inversion breakpoints by whole-genome sequencing. (2014)
  • Author(s): Suzuki T, Tsurusaki Y, Nakashima M, Miyake N, Saitsu H, Takeda S, Matsumoto N.
  • Journal Title: J Hum Genet. Volume: 59 Pages: 649-54
  • DOI: 10.1038/jhg.2014.88.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Cortical cerebellar atrophy' dwindles away in the era of next-generation sequencing. (2014)
  • Author(s): Yoshida K, Miyatake S, Kinoshita T, Doi H, Tsurusaki Y, Miyake N, Saitsu H, Matsumoto N.
  • Journal Title: J Hum Genet. Volume: 59 Pages: 589-90
  • DOI: 10.1038/jhg.2014.75.
  • Peer Reviewed
• [Journal Article] Duplication of the NPHP1 gene in patients with autism spectrum disorder and normal intellectual ability: a case series. (2014)
  • Author(s): Yasuda Y, Hashimoto R, Fukai R, Okamoto N, Hiraki Y, Yamamori H, Fujimoto M, Ohi K, Taniike M, Mohri I, Nakashima M, Tsurusaki Y, Saitsu H, Matsumoto N, Miyake N, Takeda M.
  • Journal Title: Ann Gen Psychiatry. Volume: 13 Pages: 22
  • DOI: 10.1186/s12991-014-0022-2.
  • Peer Reviewed
• [Journal Article] A girl with West syndrome and autistic features harboring a de novo TBL1XR1 mutation. (2014)
  • Author(s): Saitsu H, Tohyama J, Walsh T, Kato M, Kobayashi Y, Lee M, Tsurusaki Y, Miyake N, Goto Y, Nishino I, Ohtake A, King MC, Matsumoto N.
  • Journal Title: J Hum Genet Volume: 59 Pages: 581-3
  • DOI: 10.1038/jhg.2014.71.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Numerous BAF complex genes are mutated in Coffin-Siris syndrome. (2014)
  • Author(s): Miyake N, Tsurusaki Y, Matsumoto N.
  • Journal Title: Am J Med Genet C Semin Med Genet. Volume: 166C Pages: 257-61
  • DOI: 10.1002/ajmg.c.31406.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Coffin-Siris syndrome and related disorders involving components of the BAF (mSWI/SNF) complex: historical review and recent advances using next generation sequencing. (2014)
  • Author(s): Kosho T, Miyake N, Carey JC.
  • Journal Title: Am J Med Genet C Semin Med Genet. Volume: 166C Pages: 241-51.
  • DOI: 10.1002/ajmg.c.31415.
  • Peer Reviewed
• [Journal Article] Cono-spondylar dysplasia: clinical, radiographic, and molecular findings of a previously unreported disorder. (2014)
  • Author(s): Ben-Omran T, Lakhani S, Almureikhi M, Ali R, Takahashi A, Miyake N, Matsumoto N, Ikegawa S, Superti-Furga A, Unger S.
  • Journal Title: Am J Med Genet A. Volume: 164A Pages: 2147-52.
  • DOI: 10.1002/ajmg.a.36632.
  • Peer Reviewed
• [Journal Article] Causative novel PNKP mutations and concomitant PCDH15 mutations in a patient with microcephaly with early-onset seizures and developmental delay syndrome and hearing loss. (2014)
  • Author(s): Nakashima M, Takano K, Osaka H, Aida N, Tsurusaki Y, Miyake N, Saitsu H, Matsumoto N.
  • Journal Title: J Hum Genet. Volume: 59 Pages: 471-4.
  • DOI: 10.1038/jhg.2014.51.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Severe manifestations of hand-foot-genital syndrome associated with a novel HOXA13 mutation. (2014)
  • Author(s): Imagawa E, Kayserili H, Nishimura G, Nakashima M, Tsurusaki Y, Saitsu H,Ikegawa S, Matsumoto N, Miyake N.
  • Journal Title: Am J Med Genet A. Volume: 164A Pages: 2398-402
  • DOI: 10.1002/ajmg.a.36648.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Novel compound heterozygous PIGT mutations caused multiple congenital anomalies-hypotonia-seizures syndrome 3. (2014)
  • Author(s): Nakashima M, Kashii H, Murakami Y, Kato M, Tsurusaki Y, Miyake N, Kubota M, Kinoshita T, Saitsu H, Matsumoto N.
  • Journal Title: Neurogenetics. Volume: 15 Pages: 193-200.
  • DOI: 10.1007/s10048-014-0408-y.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Early onset epileptic encephalopathy caused by de novo SCN8A mutations. (2014)
  • Author(s): Ohba C, Kato M, Takahashi S, Lerman-Sagie T, Lev D, Terashima H, Kubota M, Kawawaki H, Matsufuji M, Kojima Y, Tateno A, Goldberg-Stern H, Straussberg R, Marom D, Leshinsky-Silver E, Nakashima M, Nishiyama K, Tsurusaki Y, Miyake N,Tanaka F, Matsumoto N, Saitsu H.
  • Journal Title: Epilepsia. Volume: 55 Pages: 994-1000.
  • DOI: 10.1111/epi.12668.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] De novo SOX11 mutations cause Coffin-Siris syndrome. (2014)
  • Author(s): Tsurusaki Y, Koshimizu E, Ohashi H, Phadke S, Kou I, Shiina M, Suzuki T, Okamoto N, Imamura S, Yamashita M, Watanabe S, Yoshiura K, Kodera H, Miyatake S, Nakashima M, Saitsu H, Ogata K, Ikegawa S, Miyake N, Matsumoto N.
  • Journal Title: Nat Commun. Volume: 5 Pages: 4011
  • DOI: 10.1038/ncomms5011.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Deep sequencing detects very-low-grade somatic mosaicism in the unaffected mother of siblings with nemaline myopathy. (2014)
  • Author(s): Miyatake S, Koshimizu E, Hayashi YK, Miya K, Shiina M, Nakashima M, Tsurusaki Y, Miyake N, Saitsu H, Ogata K, Nishino I, Matsumoto N.
  • Journal Title: Neuromuscul Disord. Volume: 24 Pages: 642-647
  • DOI: 10.1016/j.nmd.2014.04.002.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Expanding the phenotypic spectrum of TUBB4A-associated hypomyelinating leukoencephalopathies. (2014)
  • Author(s): Miyatake S, Osaka H, Shiina M, Sasaki M, Takanashi J, Haginoya K, Wada T, Morimoto M, Ando N, Ikuta Y, Nakashima M, Tsurusaki Y, Miyake N, Ogata K, Matsumoto N, Saitsu H.
  • Journal Title: Neurology. Volume: 82 Pages: 2230-7
  • DOI: 10.1212/WNL.0000000000000535
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] PIGA mutations cause early-onset epileptic (2014)
  • Author(s): Kato M, Saitsu H, Murakami Y, Kikuchi K, Watanabe S, Iai M, Miya K, Matsuura
  • Journal Title: Neurology. Volume: 82 Pages: 1587-96.
  • DOI: 10.1212/WNL.0000000000000389
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] De novo WDR45 mutation in a patient showing clinically Rett syndrome with childhood iron deposition in brain. (2014)
  • Author(s): Ohba C, Nabatame S, Iijima Y, Nishiyama K, Tsurusaki Y, Nakashima M, Miyake N, Tanaka F, Ozono K, Saitsu H, Matsumoto N.
  • Journal Title: J Hum Genet. Volume: 59 Pages: 292-5.
  • DOI: 10.1038/jhg.2014.18.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] A novel WTX mutation in a female patient with osteopathia striata with cranial sclerosis and hepatoblastoma. (2014)
  • Author(s): Fujita A, Ochi N, Fujimaki H, Muramatsu H, Takahashi Y, Natsume J, Kojima S, Nakashima M, Tsurusaki Y, Saitsu H, Matsumoto N, Miyake N.
  • Journal Title: Am J Med Genet A. Volume: 164A Pages: 998-1002
  • DOI: 10.1002/ajmg.a.36369.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] A de novo 1.4-Mb deletion at 21q22.11 in a boy with developmentaldelay. (2014)
  • Author(s): Fukai R, Hiraki Y, Nishimura G, Nakashima M, Tsurusaki Y, Saitsu H, Matsumoto N, Miyake N.
  • Journal Title: Am J Med Genet A. Volume: 164A Pages: 1021-8.
  • DOI: 10.1002/ajmg.a.36377.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] A novel homozygous YARS2 mutation causessevere myopathy, lactic acidosis, and sideroblastic anemia 2. (2014)
  • Author(s): Nakajima J, Eminoglu TF, Vatansever G, Nakashima M, Tsurusaki Y, Saitsu H,Kawashima H, Matsumoto N, Miyake N.
  • Journal Title: J Hum Genet. Volume: 59 Pages: 229-32.
  • DOI: 10.1038/jhg.2013.143.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] PIGN mutations cause congenitalanomalies, developmental delay, hypotonia, epilepsy, and progressive cerebellaratrophy. (2014)
  • Author(s): Ohba C, Okamoto N, Murakami Y, Suzuki Y, Tsurusaki Y, Nakashima M, Miyake N, Tanaka F, Kinoshita T, Matsumoto N, Saitsu H.
  • Journal Title: Neurogenetics. Volume: 15 Pages: 85-92.
  • DOI: 10.1007/s10048-013-0384-7.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Whole exome sequencing revealed biallelic IFT122 mutations in a family with CED1 and recurrent pregnancy loss. (2014)
  • Author(s): Tsurusaki Y, Yonezawa R, Furuya M, Nishimura G, Pooh RK, Nakashima M, Saitsu H, Miyake N, Saito S, Matsumoto N.
  • Journal Title: Clin Genet. Volume: 85 Pages: 592-4.
  • DOI: 10.1111/cge.12215.
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Coffin-Siris syndrome is a SWI/SNF complex disorder. (2014)
  • Author(s): Tsurusaki Y, Okamoto N, Ohashi H, Mizuno S, Matsumoto N, Makita Y, Fukuda M, Isidor B, Perrier J, Aggarwal S, Dalal AB, Al-Kindy A, Liebelt J, Mowat D,Nakashima M, Saitsu H, Miyake N, Matsumoto N.
  • Journal Title: Clin Genet. Volume: 85 Pages: 548-54.
  • DOI: 10.1111/cge.12225.
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] 歌舞伎症候群における遺伝子変異と表現型の関連. (2014)
  • Author(s): 三宅紀子、輿水江里子、松本直通、新川詔夫.
  • Organizer: 日本人類遺伝学会第59回大会
  • Place of Presentation: タワーホール船堀、（東京都江戸川区）
  • Year and Date: 2014-11-19 – 2014-11-22
• [Presentation] Glycosaminoglycan abnormalities in human bone and connective tissues (2014)
  • Author(s): Miyake N.
  • Organizer: 日本人類遺伝学会第59回大会
  • Place of Presentation: タワーホール船堀、（東京都江戸川区）
  • Year and Date: 2014-11-19 – 2014-11-22
• [Presentation] KMT2D and KDM6A mutations in patients with Kabuki syndrome. (2014)
  • Author(s): Miyake N.
  • Organizer: 日本人類遺伝学会第59回大会
  • Place of Presentation: タワーホール船堀、（東京都江戸川区）
  • Year and Date: 2014-11-19 – 2014-11-22
• [Presentation] メンデル遺伝性疾患における遺伝学的解析の現状と課題。 (2014)
  • Author(s): 三宅紀子
  • Organizer: 第37回日本母体胎児医学会学術集会
  • Place of Presentation: ハウステンボス （長崎県佐世保市）
  • Year and Date: 2014-11-07 – 2014-11-07
  • Invited
• [Presentation] Clinical comparison of Kabuki syndrome with KMT2D and KDM6A mutations. (2014)
  • Author(s): Miyake N, Koshimizu E, Matsumoto N, Niikawa N.
  • Organizer: The 64th Annual Meeting of the American Society of Human Genetics
  • Place of Presentation: San Diego, CA, USA
  • Year and Date: 2014-10-18 – 2014-10-22
• [Presentation] KMT2D and KDM6A mutations in patients with Kabuki syndrome. (2014)
  • Author(s): Miyake N, Koshimizu E, Matsumoto N, Niikawa N.
  • Organizer: The European Human Genetics Conference
  • Place of Presentation: Milan, Italy
  • Year and Date: 2014-05-31 – 2014-06-03
• [Book] 整形・災害外科 (2014)
  • Author(s): 三宅紀子、松本直通
  • Total Pages: 8
  • Publisher: 金原出版株式会社
• [Book] 神経症候群 (2014)
  • Author(s): 今川英里, 三宅紀子, 松本直通
  • Total Pages: 4
  • Publisher: 日本臨牀社
• [Patent(Industrial Property Rights)] コフィン－シリス症候群の検出方法 (2014)
  • Inventor(s): 松本直通・三宅紀子・鶴崎美徳
  • Industrial Property Rights Holder: 横浜市立大学
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 特願2013-552406
  • Filing Date: 2014-07-14