Disease-related genome analyses by long-read sequencers
Project/Area Number |
17H01539
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Research Category |
Grant-in-Aid for Scientific Research (A)
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Allocation Type | Single-year Grants |
Section | 一般 |
Research Field |
Human genetics
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Research Institution | Yokohama City University |
Principal Investigator |
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Project Period (FY) |
2017-04-01 – 2020-03-31
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Project Status |
Completed (Fiscal Year 2019)
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Budget Amount *help |
¥42,120,000 (Direct Cost: ¥32,400,000、Indirect Cost: ¥9,720,000)
Fiscal Year 2019: ¥12,090,000 (Direct Cost: ¥9,300,000、Indirect Cost: ¥2,790,000)
Fiscal Year 2018: ¥12,090,000 (Direct Cost: ¥9,300,000、Indirect Cost: ¥2,790,000)
Fiscal Year 2017: ¥17,940,000 (Direct Cost: ¥13,800,000、Indirect Cost: ¥4,140,000)
|
Keywords | ロングリードシーケンス / CNV / リピート異常 / 染色体構造異常 / Chromothripsis / chromothripsis / ゲノム / 遺伝子 / 遺伝学 / 次世代シーケンス解析 / 全ゲノム解析 / SNV |
Outline of Final Research Achievements |
To overcome the low genetic solution rates in the short-read NGS analysis of human rare diseases, we started using long read sequencers such as PacBio Sequel I and II as well as Oxford Nanopore PromethION for whole genome sequencing in unsolved cases who received short read exome sequencing with negative results. We could obtain >20-bp CNVs by using PBSV. We also developed Tandem-Genotypes (Genome Biol 2019) for detecting abnormal repeat regions and dnarrange (medRxiv 2020) for finding genome-wide SVs. Using these tools, we could find a homozygous 12.4-kb deletion involving CLN6 in a PME family (J Hum Genet 2019), a 4.6-kb SAMD12 intronic repeat insertion in a BAFME family (J Hum Genet 2019), a (GGC)n repeat expansion in NOTCH2NLC in familial and sporadic NIID (Nat Genet 2019), and biallelic pathogenic repeat expansion in a CANVAS family (J Hum Genet 2020). We could utilize the long read sequencing in solving unsolved patients by short read sequencing.
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Academic Significance and Societal Importance of the Research Achievements |
ショートリード次世代シーケンス(NGS)での遺伝性疾患の解析では、原因解明率が約30%程度に留まるため、新しい解析手法が期待されている。ロングリードNGSはその有力な候補である。本研究では、ロングリードNGSの新たな解析手法を開発し、その具体的な使用法と具体的な成果を論文に発表している。例えばTandem-Genotypesでロングリード全ゲノムシーケンスデータからリピート伸長を見出した神経核内封入体は、ロングリードNGSの使用法を明示し世界的にも注目され、疾患解明におけるロングリードNGS研究を推進する大きな契機となると考える。
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Report
(4 results)
Research Products
(192 results)
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[Journal Article] Bi-allelic CSF1R Mutations Cause Skeletal Dysplasia of Dysosteosclerosis-Pyle Disease Spectrum and Degenerative Encephalopathy with Brain Malformation2019
Author(s)
Guo L, Bertola DR, Takanohashi A, Saito A, Segawa Y, Yokota T, Ishibashi S, Nishida Y, Yamamoto GL, Franco JFdS, Honjo RS, Kim CA, Musso CM, Timmons M, Pizzino A, Taft RJ, (以下21名省略), Ikegawa S.
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Journal Title
The American Journal of Human Genetics
Volume: 104
Issue: 5
Pages: 925-935
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Peer Reviewed / Int'l Joint Research
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[Journal Article] A frequent variant in the Japanese population determines quasi-Mendelian inheritance of rare retinal ciliopathy.2019
Author(s)
Nikopoulos K, Cisarova K, Quinodoz M, Koskiniemi-Kuendig H, Miyake N, Farinelli P, Rehman AU, Khan MI, Prunotto A, Akiyama M, Kamatani Y, Terao C, Miya F, Ikeda Y, Ueno S, Fuse N, Murakami A, Wada Y, Terasaki H, Sonoda KH, Ishibashi T, Kubo M, Cremers FPM, Kutalik Z, Matsumoto N, Nishiguchi KM, Nakazawa T, Rivolta C.
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Journal Title
Nature Communications
Volume: 10
Issue: 1
Pages: 2884-2884
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[Journal Article] Germline-Activating RRAS2 Mutations Cause Noonan Syndrome2019
Author(s)
Niihori Tetsuya、Nagai Koki、Fujita Atsushi、Ohashi Hirofumi、Okamoto Nobuhiko、Okada Satoshi、Harada Atsuko、Kihara Hirotaka、Arbogast Thomas、Funayama Ryo、Shirota Matsuyuki、Nakayama Keiko、Abe Taiki、Inoue Shin-ichi、Tsai I-Chun、Matsumoto Naomichi、Davis Erica E.、Katsanis Nicholas、Aoki Yoko
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Journal Title
The American Journal of Human Genetics
Volume: 104
Issue: 6
Pages: 1233-1240
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[Journal Article] DNA methylation analysis of multiple imprinted DMRs in Sotos syndrome reveals IGF2-DMR0 as a DNA methylation-dependent, P0 promoter-specific enhancer.2019
Author(s)
Watanabe H, Higashimoto K, Miyake N, Morita S, Horii T, Kimura M, Suzuki T, Maeda T, Hidaka H, Aoki S, Yatsuki H, Okamoto N, Uemura T, Hatada I, Matsumoto N, Soejima H.
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Journal Title
FASEB J.
Volume: 34
Issue: 1
Pages: 960-973
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[Journal Article] Autosomal dominant Alport syndrome due to a COL4A4 mutation with an additional ESPN variant detected by whole-exome analysis2019
Author(s)
Izumi Yuichiro, Hamaguchi Ami, Miura Rei, Nakagawa Terumasa, Nakagawa Miyuki, Saida Ken, Miyake Noriko, Nagayoshi Yu, Kakizoe Yutaka, Miyoshi Taku, Kohda Yukimasa, Misumi Yohei, Matsumoto Naomichi, Ando Yukio, Mukoyama Masashi.
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Journal Title
CEN Case Reports
Volume: 9
Issue: 1
Pages: 59-64
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[Journal Article] KAT6A Syndrome: genotype-phenotype correlation in 76 patients with pathogenic KAT6A variants2018
Author(s)
Kennedy J, Goudie D, Blair E, Chandler K, Joss S, McKay V, Green A, Armstrong R, Lees M, Kamien B, Hopper B, Tan TY, Yap P, Stark Z, Okamoto N, Miyake N, Matsumoto N and others
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Journal Title
Genetics in Medicine
Volume: 21
Issue: 4
Pages: 850-860
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[Journal Article] Mutations in PMPCB Encoding the Catalytic Subunit of the Mitochondrial Presequence Protease Cause Neurodegeneration in Early Childhood2018
Author(s)
Vogtle FN, Brandl B, Larson A, Pendziwiat M, Friederich MW, White SM, Basinger A, Kucukkose C, Muhle H, Jahn JA, Keminer O, Helbig KL, Delto CF, Myketin L, Mossmann D, Burger N, Miyake N, Burnett A, van Baalen A, Lovell MA, Matsumoto N, Walsh M, Yu HC, Shinde DN, Stephani U, Van Hove JLK, Muller FJ, Helbig I.
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Journal Title
The American Journal of Human Genetics
Volume: 102
Issue: 4
Pages: 557-573
DOI
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[Journal Article] A homozygous NOP14 variant is likely to cause recurrent pregnancy loss2018
Author(s)
Suzuki Toshifumi、Behnam Mahdiyeh、Ronasian Firooze、Salehi Mansoor、Shiina Masaaki、Koshimizu Eriko、Fujita Atsushi、Sekiguchi Futoshi、Miyatake Satoko、Mizuguchi Takeshi、Nakashima Mitsuko、Ogata Kazuhiro、Takeda Satoru、Matsumoto Naomichi、Miyake Noriko
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Journal Title
Journal of Human Genetics
Volume: 63
Issue: 4
Pages: 425-430
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[Journal Article] A novel homozygous DPH1 mutation causes intellectual disability and unique craniofacial features.2018
Author(s)
Sekiguchi F, Nasiri J, Sedghi M, Salehi M, Hosseinzadeh M, Okamoto N, Mizuguchi T, Nakashima M, Miyatake S, Takata A, Miyake N#, Matsumoto N# (#: co-correspondence).
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Journal Title
J Hum Genet.
Volume: 63(4)
Issue: 4
Pages: 487-491
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[Journal Article] De novo hotspot variants in CYFIP2 cause early-onset epileptic encephalopathy2018
Author(s)
Nakashima Mitsuko、Kato Mitsuhiro、Aoto Kazushi、Shiina Masaaki、Belal Hazrat、Mukaida Souichi、Kumada Satoko、Sato Atsushi、Zerem Ayelet、Lerman-Sagie Tally、Lev Dorit、Leong Huey Yin、Tsurusaki Yoshinori、Mizuguchi Takeshi、Miyatake Satoko、Miyake Noriko、Ogata Kazuhiro、Saitsu Hirotomo、Matsumoto Naomichi
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Journal Title
Annals of Neurology
Volume: 83
Issue: 4
Pages: 794-806
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[Journal Article] Characteristics of PPT1 and TPP1 enzymes in neuronal ceroid lipofuscinosis (NCL) 1 and 2 by dried blood spots (DBS) and leukocytes and their application to newborn screening.2018
Author(s)
Itagaki R, Endo M, Yanagisawa H, Hossain MA, Akiyama K, Yaginuma K, Miyajima T, Wu C, Iwamoto T, Igarashi J, Kobayashi Y, Tohyama J, Iwama K, Matsumoto N, Shintaku H, Eto Y.
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Journal Title
Mol Genet Metab.
Volume: S1096-7192(18)
Issue: 1
Pages: 30154-9
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[Journal Article] A case of new PCDH12 gene variants presented as dyskinetic cerebral palsy with epilepsy.2018
Author(s)
Suzuki-Muromoto S# (#: correspondence), Wakusawa K, Miyabayashi T, Sato R, Okubo Y, Endo W, Inui T, Togashi N, Kato A, Oba H, Nakashima M, Saitsu H, Matsumoto N, Haginoya K.
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Journal Title
J Hum Genet.
Volume: 63(6)
Issue: 6
Pages: 749-753
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[Journal Article] wo Japanese cases of epileptic encephalopathy associated with an FGF12 mutation.2018
Author(s)
Takeguchi R#, Haginoya K# (# denotes equal contribution), Uchiyama Y, Fujita A, Nagura M, Takeshita E*, Inui T, Okubo Y, Sato R, Miyabayashi T, Togashi N, Saito T, Nakagawa E, Sugai K, Nakashima M, Saitsu H, Matsumoto N, Sasaki M.
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Journal Title
Brain Dev.
Volume: 40(8)
Issue: 8
Pages: 728-732
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[Journal Article] Bilateral cerebellar cysts and cerebral white matter lesions with cortical dysgenesis: Expanding the phenotype of LAMB1 gene mutations.2018
Author(s)
*Okazaki T, Saito Y, Hayashida T, Akaboshi S, Miyake N, Matsumoto N, Kasagi N, Adachi K, Shinohara Y, Nanba E, Maegaki Y.
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Journal Title
Clin Genet.
Volume: 94(3-4)
Issue: 3-4
Pages: 391-392
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[Journal Article] Successful hemostatic management of major surgery for cervical spondylotic myelopathy in a patient with severe factor XI deficiency.2018
Author(s)
*Ogawa Y, Yanagisawa K, Uchiyama Y, Akashi N, Mieda T, Iizuka H, Inoue M, Shizuka R, Murakami M, Matsumoto N, Handa H.
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Journal Title
Int J Hematol.
Volume: 108(4)
Issue: 4
Pages: 443-446
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[Journal Article] GRIN2D variants in three cases of developmental and epileptic encephalopathy2018
Author(s)
Tsuchida Naomi、Hamada Keisuke、Shiina Masaaki、Kato Mitsuhiro、Kobayashi Yu、Tohyama Jun、Kimura Kazue、Hoshino Kyoko、Ganesan Vigneswari、Teik Keng W.、Nakashima Mitsuko、Mitsuhashi Satomi、Mizuguchi Takeshi、Takata Atsushi、Miyake Noriko、Saitsu Hirotomo、Ogata Kazuhiro、Miyatake Satoko、Matsumoto Naomichi
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Journal Title
Clinical Genetics
Volume: 94
Issue: 6
Pages: 538-547
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[Journal Article] PLPBP mutations cause variable phenotypes of developmental and epileptic encephalopathy.2018
Author(s)
Shiraku H#, Nakashima M#, Takeshita S# (# denotes equal contribution), Khoo CS, Haniffa M, Ch'ng GS, Takada K, Nakajima K, Ohta M, Okanishi T, Kanai S, Fujimoto A, Saitsu H, Matsumoto N*, Kato M* (*: co-correspondence).
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Journal Title
Epilepsia Open.
Volume: 3(4)
Issue: 4
Pages: 495-502
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[Journal Article] Screening of known disease genes in congenital scoliosis.2018
Author(s)
Takeda K, Kou I, Mizumoto S, Yamada S, Kawakami N, Nakajima M, Otomo N, Ogura Y, Miyake N, Matsumoto N, Kotani T, Sudo H, Yonezawa I, Uno K, Taneichi H, Watanabe K, Shigematsu H, Sugawara R, Taniguchi Y, Minami S, Nakamura M, Matsumoto M; Japan Early Onset Scoliosis Research Group, Watanabe K, Ikegawa S.
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Journal Title
Molecular Genetics & Genomic Medicine
Volume: -
Issue: 6
Pages: 966-974
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[Journal Article] SOFT syndrome in a patient from Chile2018
Author(s)
Saida Ken、Silva Sebastian、Solar Benjamin、Fujita Atsushi、Hamanaka Kohei、Mitsuhashi Satomi、Koshimizu Eriko、Mizuguchi Takeshi、Miyatake Satoko、Takata Atsushi、Miyake Noriko、Matsumoto Naomichi
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Journal Title
American Journal of Medical Genetics Part A
Volume: 179
Issue: 3
Pages: 338-340
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[Journal Article] Epileptic apnea in a patient with inherited glycosylphosphatidylinositol anchor deficiency and PIGT mutations.2018
Author(s)
Kohashi K, Ishiyama A*, Yuasa S, Tanaka T, Miya K, Adachi Y, Sato N, Saitsu H, Ohba C, Matsumoto N, Murakami Y, Kinoshita T, Sugai K, Sasaki M.
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Journal Title
Brain Dev
Volume: 40(1)
Issue: 1
Pages: 53-57
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[Journal Article] Heterozygous Mutations in OAS1 Cause Infantile-Onset Pulmonary Alveolar Proteinosis with Hypogammaglobulinemia.2018
Author(s)
Cho K, Yamada M, Agematsu K, Kanegane H, Miyake N, Ueki M, Akimoto T, Kobayashi N, Ikemoto S, Tanino M, Fujita A, Hayasaka I, Miyamoto S, Tanaka-Kubota M, Nakata K, Shiina M, Ogata K, Minakami H, Matsumoto N, Ariga T.
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Journal Title
Am J Hum Genet
Volume: 102
Issue: 3
Pages: 480-486
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NAID
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[Journal Article] Three patients with Schaaf-Yang syndrome exhibiting arthrogryposis and endocrinological abnormalities.2018
Author(s)
Enya T*, Okamoto N, Iba Y, Miyazawa T, Okada M, Ida S, Naruto T, Imoto I, Fujita A, Miyake N, Matsumoto N, Sugimoto K, Takemura T.
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Journal Title
Am J Med Genet A
Volume: 176(3)
Issue: 3
Pages: 707-711
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[Journal Article] Novel recessive mutations in MSTO1 cause cerebellar atrophy with pigmentary retinopathy.2018
Author(s)
Iwama K, Takaori T, Fukushima A, Tohyama J, Ishiyama A, Ohba C, Mitsuhashi S, Miyatake S, Takata A, Miyake N, Ito S, Saitsu H, Mizuguchi T, Matsumoto N*.
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Journal Title
J Hum Genet
Volume: 63(3)
Issue: 3
Pages: 263-270
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[Journal Article] A novel GFI1B mutation at the first zinc finger domain causes congenital macrothrombocytopenia2017
Author(s)
Uchiyama Y, Ogawa Y, Kunishima S, Shiina M, Nakashima M, Yanagisawa K, Yokohama A, Imagawa E, Miyatake S, Mizuguchi T, Takata A, Miyake N, Ogata K, Handa H, Matsumoto N
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Journal Title
British Journal of Haematology
Volume: 印刷中
Issue: 6
Pages: 843-847
DOI
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[Journal Article] A novel missense mutation affecting the same amino acid as the recurrent PACS1 mutation in Schuurs-Hoeijmakers syndrome2017
Author(s)
Miyake N, Ozasa S, Mabe H, Kimura S, Shiina M, Imagawa E, Miyatake S, Nakashima M, Mizuguchi T, Takata A, Ogata K, Matsumoto N
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Journal Title
Clinical Genetics
Volume: 93
Issue: 4
Pages: 929-930
DOI
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[Journal Article] MTCL1 plays an essential role in maintaining Purkinje neuron axon initial segment.2017
Author(s)
Satake T, Yamashita K, Hayashi K, Miyatake S, Tamura-Nakano M, Doi H, Furuta Y, Shioi G, Miura E, Takeo YH, Yoshida K, Yahikozawa H, Matsumoto N, Yuzaki M, Suzuki A.
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Journal Title
EMBOJ
Volume: 36
Issue: 9
Pages: 1227-1242
DOI
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[Journal Article] Mutations in genes encoding polycomb repressive complex 2 subunits cause Weaver syndrome2017
Author(s)
Eri Imagawa, Ken Higashimoto, Yasunari Sakai, Chikahiko Numakura, Nobuhiko Okamoto, Satoko Matsunaga, Akihide Ryo, Yoshinori Sato, Masafumi Sanefuji, Kenji Ihara, Yui Takada, Gen Nishimura, Hirotomo Saitsu, Takeshi Mizuguchi, Satoko Miyatake, Mitsuko Nakashima, Noriko Miyake, Hidenobu Soejima, Naomichi Matsumoto
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Journal Title
Human Mutation
Volume: 印刷中
Issue: 6
Pages: 637-648
DOI
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Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
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[Journal Article] ANKRD11 variants cause variable clinical features associated with KBG syndrome and Coffin-Siris-like syndrome.2017
Author(s)
Miyatake S, Okamoto N, Stark Z, Nabetani M, Tsurusaki Y, Nakashima M, Miyake N, Mizuguchi T, Ohtake A, Saitsu H, Matsumoto N.
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Journal Title
J Hum Genet.
Volume: 印刷中
Issue: 8
Pages: 741-746
DOI
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[Journal Article] An atypical case of SPG56/CYP2U1-related spastic paraplegia presenting with delayed myelination.2017
Author(s)
Minase G, Miyatake S, Nabatame S, Arai H, Koshimizu E, Mizuguchi T, Nakashima M, Miyake N, Saitsu H, Miyamoto T, Sengoku K, Matsumoto N.
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Journal Title
J Hum Genet.
Volume: 62
Issue: 11
Pages: 997-1000
DOI
Related Report
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[Journal Article] A patient with Muenke syndrome manifesting migrating neonatal seizures.2017
Author(s)
Okubo Y*, Kitamura T, Anzai M, Endo W, Inui T, Takezawa Y, Suzuki-Muromoto S, Miyabayashi T, Togashi N, Oba H, Saitsu H, Matsumoto N, Haginoya K.
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Journal Title
Brain Dev
Volume: 39(10)
Issue: 10
Pages: 873-876
DOI
Related Report
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[Journal Article] Equivalent missense variant in the FOXP2 and FOXP1 transcription factors causes distinct neurodevelopmental disorders.2017
Author(s)
Sollis E, Deriziotis P, Saitsu H, Miyake N, Matsumoto N, Hoffer MJV, Ruivenkamp CAL, Alders M, Okamoto N, Bijlsma EK, Plomp AS, Fisher SE.
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Journal Title
Hum Mutat
Volume: 38(11)
Issue: 11
Pages: 1542-1554
DOI
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Peer Reviewed / Int'l Joint Research
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[Journal Article] Identification of biallelic EXTL3 mutations in a novel type of spondylo-epi-metaphyseal dysplasia2017
Author(s)
*Long Guo, *Nursel H Elcioglu, *Shuji Mizumoto, Zheng Wang, Bilge Noyan, Hatice M Albayrak, Shuhei Yamada, Naomichi Matsumoto, Noriko Miyake, Gen Nishimura, Shiro Ikegawa (equal contribution)
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Journal Title
Journal of Human Genetics
Volume: -
Issue: 8
Pages: 797-801
DOI
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Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
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[Journal Article] Three cases of KCNT1 mutations: malignant migrating partial seizures in infancy with massive systemic to pulmonary collateral arteries.2017
Author(s)
*Kawasaki Y, Kuki I, Ehara E, Murakami Y, Okazaki S, Kawawaki H, Hara M, Watanabe Y, Kishimoto S, Suda K, Saitsu H, Matsumoto N.
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Journal Title
J Pediatr
Volume: 191
Pages: 270-274
DOI
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Peer Reviewed
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