Deciphering Origin and Establishment of Japonesians mainly based on genome sequence data

• Project Area: Deciphering Origin and Establishment of Japonesians mainly based on genome sequence data
• Project/Area Number: 18H05511
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Complex systems
• Research Institution: Hokkaido University
• Principal Investigator: 長田 直樹 北海道大学, 情報科学研究院, 准教授 (70416270)
• Co-Investigator(Kenkyū-buntansha): 五條堀 淳 総合研究大学院大学, 先導科学研究科, 講師 (00506800) ; 河合 洋介 国立研究開発法人国立国際医療研究センター, その他部局等, 副プロジェクト長 (30435515) ; 藤本 明洋 東京大学, 大学院医学系研究科(医学部), 教授 (30525853)
• Project Period (FY): 2018-06-29 – 2023-03-31
• Project Status: Granted (Fiscal Year 2022)
• Budget Amount: ¥49,140,000 (Direct Cost: ¥37,800,000、Indirect Cost: ¥11,340,000); Fiscal Year 2022: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000); Fiscal Year 2021: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000); Fiscal Year 2020: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000); Fiscal Year 2019: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000); Fiscal Year 2018: ¥10,660,000 (Direct Cost: ¥8,200,000、Indirect Cost: ¥2,460,000)
• Keywords: ゲノム / 進化 / 日本人 / 人口動態 / 集団遺伝学 / ヤポネシア人 / ゲノム配列

Outline of Annual Research Achievements

当初の計画に沿って研究を進行したが，その他の関連する研究も行った．ヤポネシア人ゲノムの解析については，東アジア人におけるアミラーゼ遺伝子のコピー数推定を行った．その際，コピー数推定のバラツキが少なくなるような手法を開発し，従来手法よりもよい精度で東アジア人集団のアミラーゼ遺伝子コピー数推定を行った．その結果，縄文人が現代東アジア人で典型的な8コピーのAMY1遺伝子をもっていることが示された．また，ハプロタイプ情報を用いてヤポネシア人と他の人類集団との分岐年代を推定した．その他，新規手法に基づいて同定されたマイクロサテライト配列の多型を用いて人類集団の解析を行い，従来手法よりもSNP解析に近い結果を得ることができた．さらに，9850人のヤポネシア人全ゲノムシークエンスデータの解析を行い，日本列島内での現代人の遺伝的構造を高解像度で示すことに成功した．他に，希少変異解析を用いて複数の縄文人個体ゲノムや弥生人ゲノムを解析し，別の手法を用いて解析を行った結果と比較した．
その他，マダガスカル産ハツカネズミの全ゲノム解析による渡来経路の推定，北海道産ヒグマの全ゲノム解析による集団動態の解析，日本列島におけるハツカネズミの亜種間交雑過程の全ゲノム規模での解析，ハイイロオオカミ，ニホンオオカミ，イヌなどのゲノム解析に関する研究など，ヤポネシア人に関する研究だけでなく，動植物のゲノム解析などについての解析を他研究班と共同で進めた．

Current Status of Research Progress

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

Reason

当初計画した内容について，論文での公表を含めて予定通りに進んでいる．また，他班との共同研究も順調に進行しており，おおむね順調に進展していると考えられる．

Strategy for Future Research Activity

昨年度に引き続き研究を行うが，令和4年度は5年間の研究期間の最終年となるため，これまでの成果をまとめ上げ，ヤポネシア人の歴史についての全体像を明らかにする．
(1)性染色体の分化パターンには一定の傾向がみられるものの，ヤポネシア人の歴史を考える場合においては，その統計的な検出力はそれほど高くはないということが明らかになった．この前提を踏まえたうえで，性染色体ゲノムデータに基づいたヤポネシア人の移住過程の解明を行う．最終年度は縄文人と弥生人の混合がゲノムの表現型にどのような影響を与えたのかについて詳細なレベルで調べていく．また，5年間で蓄積されたゲノムデータから，ヤポネシア人がどのように日本列島へ到達し，その後どのような歴史を経て現在の遺伝的特徴をもつに至ったのかについて，考古学や言語学のデータとも照らし合わせながら(2)複数の古代人ゲノムの解析を行い,希少変異などの情報を用いながら,その遺伝的特徴を明らかにする．(3)マイクロサテライト座位におけるゲノム多型データをもちいて，ヤポネシア人の詳細な遺伝構造を明らかする．(4)ハプロタイプ共有情報を用いて集団の分岐時間や移住の解析を行う手法についての検討を行う.複数の古代人,大量の現代人ゲノムについて手法を適用し,ヤポネシア人の歴史を明らかにしていく．以上の個別の目的に加え他の研究計画班,公募研究班との連携を広く進め，研究領域の発展に貢献する．動植物ゲノムなどの解析において進行中である他研究班との共同研究について，データ解析の結果をまとめ，公表へ向けて着実に研究を進めていく．

Research Products

• [Int'l Joint Research] University College Dublin(アイルランド)
• [Int'l Joint Research] Trinity Collage Dublin(アイルランド)
• [Journal Article] Phylogeographic study using nuclear genome sequences of <i>Asip</i> to infer the origins of ventral fur color variation in the house mouse <i>Mus musculus</i> (2021)
  • Author(s): Takeishi, T., Fujiwara, K., Osada, N., Mita, A., Takada, T., Shiroishi, T., and Suzuki, H.
  • Journal Title: Genes & Genetic Systems Volume: 96 Issue: 6 Pages: 271-284
  • DOI: 10.1266/ggs.21-00075
  • ISSN: 1341-7568, 1880-5779
  • Year and Date: 2021-12-01
  • Peer Reviewed / Open Access
• [Journal Article] Demographic history of the brown bear (Ursus artcos) on Hokkaido Island, Japan, based on whole-genomic sequence analysis. Genome Biology and Evolution (2021)
  • Author(s): Endo, Y., Osada, N., Mano, T., and Masuda, R.
  • Journal Title: Genome Biology and Evolution Volume: - Issue: 9
  • DOI: 10.1093/gbe/evab195
  • Peer Reviewed / Open Access
• [Journal Article] ヤポネシア人の人口・歴史推定 (2021)
  • Author(s): 長田直樹
  • Journal Title: メディカル・サイエンス・ダイジェスト Volume: 47 Pages: 476-478
• [Journal Article] Exploring models of human migration to the Japanese archipelago using genome-wide genetic data (2021)
  • Author(s): OSADA NAOKI、KAWAI YOSUKE
  • Journal Title: Anthropological Science Volume: 129 Issue: 1 Pages: 45-58
  • DOI: 10.1537/ase.201215
  • NAID: 130008030483
  • ISSN: 0918-7960, 1348-8570
  • Peer Reviewed / Open Access
• [Journal Article] Modern human DNA analyses with special reference to the inner dual-structure model of Yaponesian (2021)
  • Author(s): Jinam T. A., Kawai Y., and Saitou N.
  • Journal Title: Anthropological Science Volume: 129 Issue: 1 Pages: 3-11
  • DOI: 10.1537/ase.201217
  • NAID: 130008030443
  • ISSN: 0918-7960, 1348-8570
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Whole genome sequencing with long-reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer. (2021)
  • Author(s): Fujimoto A, Wong JH, Yoshii Y, Akiyama S, Tanaka A, Yagi H, Shigemizu D, Nakagawa H, Mizokami M, and Shimada M.
  • Journal Title: Genome Medicine Volume: 13 Issue: 1 Pages: 65-65
  • DOI: 10.1186/s13073-021-00883-1
  • Peer Reviewed / Open Access
• [Journal Article] Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression (2021)
  • Author(s): Ashouri Saeideh、Wong Jing Hao、Nakagawa Hidewaki、Shimada Mihoko、Tokunaga Katsushi、Fujimoto Akihiro
  • Journal Title: Human Genetics Volume: 140 Issue: 8 Pages: 1201-1216
  • DOI: 10.1007/s00439-021-02291-2
  • Peer Reviewed
• [Journal Article] Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences. (2021)
  • Author(s): Mizuno, F., Gojobori, J., Kumagai, M., Baba, H., Taniguchi, Y., Kondo, O., Matsushita, M., Matsushita, T., Matsuda, F., Higasa, K., Hayashi, M., Wang, L., Kurosaki, K. and Ueda, S.
  • Journal Title: Scientific Reports Volume: 11 Issue: 1 Pages: 1-11
  • DOI: 10.1038/s41598-021-91357-2
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] House mouse Mus musculus dispersal in East Eurasia inferred from 98 newly determined complete mitochondrial genome sequences. (2021)
  • Author(s): Li Y, Fujiwara K, Osada N, Kawai Y, Takada T, Kryukov AP, Abe K, Yonekawa H, Shiroishi T, Moriwaki K, Saitou N, Suzuki H
  • Journal Title: Heredity Volume: 126 Issue: 1 Pages: 132-147
  • DOI: 10.1038/s41437-020-00364-y
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Genome-wide SNP data of Izumo and Makurazaki populations support inner-dual structure model for origin of Yamato people (2021)
  • Author(s): Jinam Timothy、Kawai Yosuke、Kamatani Yoichiro、Sonoda Shunro、Makisumi Kanro、Sameshima Hideya、Tokunaga Katsushi、Saitou Naruya
  • Journal Title: Journal of Human Genetics Volume: - Issue: 7 Pages: 681-687
  • DOI: 10.1038/s10038-020-00898-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Testing sex-biased admixture origin of macaque species using autosomal and X-chromosomal genomic sequences (2020)
  • Author(s): Osada Naoki、Matsudaira Kazunari、Hamada Yuzuru、Malaivijitnond Suchinda
  • Journal Title: Genome Biology and Evolution Volume: 13 Pages: 1-14
  • DOI: 10.1093/gbe/evaa209
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of Characteristic Genomic Markers in Human Hepatoma HuH-7 and Huh7.5.1-8 Cell Lines (2020)
  • Author(s): Kawamoto M#, Yamaji T#, Saito K, Shirasago Y, Satomura K, Endo T, Fukasawa M, Hanada K, Osada N.
  • Journal Title: Front Genet Volume: 11 Pages: 546106-546106
  • DOI: 10.3389/fgene.2020.546106
  • Peer Reviewed / Open Access
• [Journal Article] Comparative characterization of flavivirus production in two cell lines: Human hepatoma-derived Huh7.5.1-8 and African green monkey kidney-derived Vero (2020)
  • Author(s): Kyoko Saito, Masayoshi Fukasawa, Yoshitaka Shirasago, Ryosuke Suzuki, Naoki Osada, Toshiyuki Yamaji, Takaji Wakita, Eiji Konishi, Kentaro Hanada
  • Journal Title: PLOS ONE Volume: 15 Issue: 4 Pages: e0232274-e0232274
  • DOI: 10.1371/journal.pone.0232274
  • Peer Reviewed / Open Access
• [Journal Article] Dysfunctional missense variant of OAT10/SLC22A13 decreases gout risk and serum uric acid levels. (2020)
  • Author(s): Higashino T, Morimoto K, Nakaoka H, Toyoda Y, Kawamura Y, Shimizu S, Nakamura T, Hosomichi K, Nakayama A, Ooyama K, Ooyama H, Shimizu T, Ueno M, Ito T, Tamura T, Naito M, Nakashima H, Kawaguchi M, Takao M, Kawai Y, Osada N, Ichida K, Yamamoto K, Suzuki H, Shinomiya N, Inoue I, Takada T, Matsuo H.
  • Journal Title: Ann Rheum Dis. Volume: 79(1) Issue: 1 Pages: 164-166
  • DOI: 10.1136/annrheumdis-2019-216044
  • Peer Reviewed / Open Access
• [Journal Article] Multiregional whole‐genome sequencing of hepatocellular carcinoma with nodule‐in‐nodule appearance reveals stepwise cancer evolution (2020)
  • Author(s): Takeda Haruhiko、Takai Atsushi、Kumagai Ken、Iguchi Eriko、Arasawa Soichi、Eso Yuji、Shimizu Takahiro、Ueda Yoshihide、Taura Kojiro、Uemoto Shinji、Kita Ryuichi、Haga Hironori、Marusawa Hiroyuki、Fujimoto Akihiro、Seno Hiroshi
  • Journal Title: The Journal of Pathology Volume: 252 Issue: 4 Pages: 398-410
  • DOI: 10.1002/path.5533
  • Peer Reviewed
• [Journal Article] Aberrant (pro)renin receptor expression induces genomic instability in pancreatic ductal adenocarcinoma through upregulation of SMARCA5/SNF2H (2020)
  • Author(s): Shibayama,Y., Takahashi, K., Yamaguchi, H., Yasuda, J., Yamazaki, D., Rahman, A., Fujimori, T., Fujisawa, Y., Takai, S., Furukawa, T., Nakagawa, T., Ohsaki, H., Kobara, H., Wong, J.H., Masaki, T., Yuzawa, Y., Kiyomoto, H., Yachida, S., Fujimoto, A., Nishiyama, A.
  • Journal Title: Communications Biology Volume: 3 Issue: 1 Pages: 724-724
  • DOI: 10.1038/s42003-020-01434-x
  • NAID: 130008001357
  • Peer Reviewed / Open Access
• [Journal Article] Whole genome sequencing analysis identifies recurrent structural alterations in esophageal squamous cell carcinoma (2020)
  • Author(s): Dutta Munmee、Nakagawa Hidewaki、Kato Hiroaki、Maejima Kazuhiro、Sasagawa Shota、Nakano Kaoru、Sasaki-Oku Aya、Fujimoto Akihiro、Mateos Ra?l Nicol?s、Patil Ashwini、Tanaka Hiroko、Miyano Satoru、Yasuda Takushi、Nakai Kenta、Fujita Masashi
  • Journal Title: PeerJ Volume: 8 Pages: e9294-e9294
  • DOI: 10.7717/peerj.9294
  • Peer Reviewed / Open Access
• [Journal Article] Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population (2020)
  • Author(s): Iwasaki Risa L.、Ishiya Koji、Kanzawa-Kiriyama Hideaki、Kawai Yosuke、Gojobori Jun、Satta Yoko
  • Journal Title: Genes Volume: 11 Issue: 7 Pages: 775-775
  • DOI: 10.3390/genes11070775
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally? (2020)
  • Author(s): Nishiyama Kumiko V.、Satta Yoko、Gojobori Jun
  • Journal Title: Genes Volume: 11 Issue: 6 Pages: 658-658
  • DOI: 10.3390/genes11060658
• [Journal Article] Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations. (2020)
  • Author(s): Fujita M, Yamaguchi R, Hasegawa T, Shimada S, Arihiro K, Hayashi S, Maejima K, Nakano K, Fujimoto A, Ono A, Aikata H, Ueno M, Hayami S, Tanaka H, Miyano S, Yamaue H, Chayama K, Kakimi K, Tanaka S, Imoto S, Nakagawa H.
  • Journal Title: EBioMedicine Volume: 53 Pages: 102659-102659
  • DOI: 10.1016/j.ebiom.2020.102659
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Rare allele sharing in the East Asian (2020)
  • Author(s): Gojobori, J
  • Journal Title: Archivio per l’Antropologia e la Etnologia Volume: CL
• [Journal Article] Comprehensive Analysis of Indels in Whole-genome Microsatellite Regions and Microsatellite Instability across 21 Cancer Types (2020)
  • Author(s): Fujimoto A*, Fujita M, Hasegawa T, Wong JH, Maejima K, Oku-Sasaki A, Nakano K, Shiraishi Y, Miyano S, Yamamoto G, Akagi K, Imoto S, and Nakagawa H
  • Journal Title: Genome Research Volume: 30 Issue: 3 Pages: 334-34
  • DOI: 10.1101/gr.255026.119
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Pan-cancer analysis of whole genomes (2020)
  • Author(s): The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
  • Journal Title: Nature Volume: 578 Issue: 7793 Pages: 82-93
  • DOI: 10.1038/s41586-020-1969-6
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Implications of HLA diversity among regions for bone marrow donor searches in Japan (2020)
  • Author(s): Hashimoto S, Nakajima F, Imanishi T, Kawai Y, Kato K, Kimura T, Miyata S, Takanashi M, Nishio M, Tokunaga K, Satake M
  • Journal Title: HLA Volume: in press Issue: 1 Pages: 24-42
  • DOI: 10.1111/tan.13881
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 港川人のミトコンドリア DNA全塩基配列からわかること (2020)
  • Author(s): 水野文月，五條堀淳
  • Journal Title: 学術の動向 Volume: 25 Pages: 2-2
  • NAID: 130007865037
• [Journal Article] eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA (2019)
  • Author(s): Mizuno Kei、Akamatsu Shusuke、Sumiyoshi Takayuki、Wong Jing Hao、Fujita Masashi et al.
  • Journal Title: Scientific Reports Volume: 9 Issue: 1 Pages: 15017-15017
  • DOI: 10.1038/s41598-019-51459-4
  • NAID: 120006734882
  • Peer Reviewed / Open Access
• [Journal Article] Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan (2019)
  • Author(s): Kanzawa-Kiriyama Hideaki、Jinam Timothy A.、Kawai Yosuke、Sato Takehiro、Hosomichi Kazuyoshi、Tajima Atsushi、Adachi Noboru、Matsumura Hirofumi、Kryukov Kirill、Saitou Naruya、Shinoda Ken-Ichi
  • Journal Title: Anthropological Science Volume: 127 Issue: 2 Pages: 83-108
  • DOI: 10.1537/ase.190415
  • NAID: 130007696474
  • ISSN: 0918-7960, 1348-8570
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A key metabolic gene for recurrent freshwater colonization and radiation in fishes (2019)
  • Author(s): Ishikawa Asano, Kabeya Naoki, Ikeya Koki, Kakioka Ryo, Cech Jennifer N., Osada Naoki, Leal Miguel C., Inoue Jun, Kume Manabu, Toyoda Atsushi, Tezuka Ayumi, Nagano Atsushi J., Yamasaki Yo Y., Suzuki Yuto, Kokita Tomoyuki, Takahashi Hiroshi et al.
  • Journal Title: Science Volume: 364 Issue: 6443 Pages: 886-889
  • DOI: 10.1126/science.aau5656
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Genetic diversity and population structure of Glossina morsitans morsitans in the active foci of human African trypanosomiasis in Zambia and Malawi (2019)
  • Author(s): Yukiko Nakamura, Junya Yamagishi, Kyoko Hayashida, Naoki Osada, Elisha Chatanga, Cornelius Mweempwa, Kalinga Chilongo, John Chisi, Jenelisa Musaya, Ryosuke Omori, Noboru Inoue, Boniface Namangala, Chihiro Sugimoto
  • Journal Title: PLoS Negl. Trop. Dis Volume: 13 Issue: 7 Pages: e0007568-e0007568
  • DOI: 10.1371/journal.pntd.0007568
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Achiasmy and sex chromosome evolution (2019)
  • Author(s): Kazuhiro Satomura, Naoki Osada, Toshinori Endo
  • Journal Title: Ecological Genetics and Genomics Volume: 13 Pages: 1000046-1000046
  • Peer Reviewed / Open Access
• [Journal Article] 日本人ゲノム解析において集団差をどう考えるか (2019)
  • Author(s): 河合洋介
  • Journal Title: IBD Research Volume: 13 Pages: 31-34
• [Journal Article] 東アジアの人々のゲノム多様性 (2019)
  • Author(s): 徳永勝士，河合洋介
  • Journal Title: 腎臓内科・泌尿器科 Volume: 10 Pages: 561-565
  • NAID: 40022102238
• [Journal Article] ヤポネシア人の歴史の解明が医学にもたらすもの (2019)
  • Author(s): 長田直樹
  • Journal Title: 実験医学 Volume: 37 Pages: 926-929
• [Journal Article] Clinical utility of androgen receptor gene aberrations in circulating cell-free DNA as a biomarker for treatment of castration-resistant prostate cancer (2019)
  • Author(s): Sumiyoshi Takayuki、Mizuno Kei、Yamasaki Toshinari、Miyazaki Yu、Makino Yuki、Okasho Kosuke、Li Xin、Utsunomiya Noriaki、Goto Takayuki、Kobayashi Takashi、Terada Naoki、Inoue Takahiro、Kamba Tomomi、Fujimoto Akihiro、Ogawa Osamu、Akamatsu Shusuke
  • Journal Title: Scientific Reports Volume: 9 Issue: 1 Pages: 4030-4030
  • DOI: 10.1038/s41598-019-40719-y
  • NAID: 120006709427
  • Peer Reviewed / Open Access
• [Journal Article] Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan (2019)
  • Author(s): Kanzawa-Kiriyama H, Jinam TA, Kawai Y, Sato T, Hosomichi K, Tajima A, Adachi N, Matsumura H, Kryukov K, Saitou N and Shinoda K
  • Journal Title: Anthropological Science Volume: -
  • NAID: 130007696474
  • Peer Reviewed
• [Journal Article] POGLUT1, the putative effector gene driven by rs2293370 in primary biliary cholangitis susceptibility locus chromosome 3q13.33 (2019)
  • Author(s): Hitomi, Y. Ueno, K. Kawai, Y. Nishida, N. , Umemura, T. et al
  • Journal Title: Sci Rep Volume: 9 Issue: 1 Pages: 102-102
  • DOI: 10.1038/s41598-018-36490-1
  • NAID: 120007179055
  • Peer Reviewed / Open Access
• [Journal Article] Novel endogenous simian retroviral integrations in Vero cells: implications for quality control of a human vaccine cell substrate (2018)
  • Author(s): Sakuma Chisato、Sekizuka Tsuyoshi、Kuroda Makoto、Kasai Fumio、Saito Kyoko、Ikeda Masaki、Yamaji Toshiyuki、Osada Naoki、Hanada Kentaro
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 644-644
  • DOI: 10.1038/s41598-017-18934-2
  • NAID: 120006401475
  • Peer Reviewed / Open Access
• [Journal Article] Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys (2018)
  • Author(s): Ikeda Masaki、Satomura Kazuhiro、Sekizuka Tsuyoshi、Hanada Kentaro、Endo Toshinori、Osada Naoki
  • Journal Title: American Journal of Primatology Volume: 80 Issue: 7
  • DOI: 10.1002/ajp.22882
  • NAID: 120006643589
  • Peer Reviewed
• [Journal Article] Whole Genome Sequencing of a Vietnamese Family from a Dioxin Contamination Hotspot Reveals Novel Variants in the Son with Undiagnosed Intellectual Disability (2018)
  • Author(s): Nguyen Dang、Nguyen Hai、Nguyen Thuy、Nguyen Thi、Nakano Kaoru、Maejima Kazuhiro、Sasaki-Oku Aya、Nguyen Van、Nguyen Duy、Le Bach、Wong Jing、Tsunoda Tatsuhiko、Nakagawa Hidewaki、Fujimoto Akihiro、Nong Van
  • Journal Title: International Journal of Environmental Research and Public Health Volume: 15 Issue: 12 Pages: 2629-2629
  • DOI: 10.3390/ijerph15122629
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis (2018)
  • Author(s): Shigemizu Daichi、Miya Fuyuki、Akiyama Shintaro、Okuda Shujiro、Boroevich Keith A、Fujimoto Akihiro、Nakagawa Hidewaki、Ozaki Kouichi、Niida Shumpei、Kanemura Yonehiro、Okamoto Nobuhiko、Saitoh Shinji、Kato Mitsuhiro、Yamasaki Mami、Matsunaga Tatsuo、Mutai Hideki、Kosaki Kenjiro、Tsunoda Tatsuhiko
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 5608-5608
  • DOI: 10.1038/s41598-018-23978-z
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Loss-of-function mutations in Zn-finger DNA-binding domain of <i>HNF4A</i> cause aberrant transcriptional regulation in liver cancer (2018)
  • Author(s): Taniguchi Hiroaki、Fujimoto Akihiro、Kono Hidetoshi、Furuta Mayuko、Fujita Masashi、Nakagawa Hidewaki
  • Journal Title: Oncotarget Volume: 9 Issue: 40 Pages: 26144-26156
  • DOI: 10.18632/oncotarget.25456
  • Peer Reviewed / Open Access
• [Journal Article] NFKB1 and MANBA Confer Disease Susceptibility to Primary Biliary Cholangitis via Independent Putative Primary Functional Variants. (2018)
  • Author(s): Hitomi Y, Nakatani K, Kojima K, Nishida N, Kawai Y, Kawashima M, Aiba Y, Nagasaki M, Nakamura M, Tokunaga K.
  • Journal Title: Cell Mol Gastroenterol Hepatol Volume: 7 Issue: 3 Pages: 515-532
  • DOI: 10.1016/j.jcmgh.2018.11.006
  • Peer Reviewed / Open Access
• [Journal Article] A Genome-wide Association Study Identifying RAP1A as a Novel Susceptibility Gene for Crohn’s Disease in Japanese Individuals (2018)
  • Author(s): Kakuta Yoichi、Kawai Yosuke、Naito Takeo、Hirano Atsushi、Umeno Junji、Fuyuno Yuta、Liu Zhenqiu、Li Dalin、Nakano Takeru、Izumiyama Yasuhiro、Ichikawa Ryo、Okamoto Daisuke、et al.
  • Journal Title: Journal of Crohn's and Colitis Volume: - Issue: 5 Pages: 2019-2019
  • DOI: 10.1093/ecco-jcc/jjy197
  • Peer Reviewed / Open Access
• [Journal Article] Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy (2018)
  • Author(s): Latt Khun Zaw、Honda Kenjiro、Thiri Myo、Hitomi Yuki、Omae Yosuke、Sawai Hiromi、Kawai Yosuke、Teraguchi Shunsuke、Ueno Kazuko、Nagasaki Masao、Mabuchi Akihiko、Kaga Hajime、Komatsuda Atsushi、Tokunaga Katsushi、Noiri Eisei
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 15576-15576
  • DOI: 10.1038/s41598-018-33612-7
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project (2018)
  • Author(s): Yasuda Jun、et al.,
  • Journal Title: BMC Genomics Volume: 19 Issue: 1 Pages: 551-551
  • DOI: 10.1186/s12864-018-4942-0
  • Peer Reviewed / Open Access
• [Journal Article] Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2,049 individuals (2018)
  • Author(s): Y Yamaguchi-Kabata, J Yasuda, O Tanabe, Y Suzuki, H Kawame, N Fuse, M Nagasaki, Y Kawai, K Kojima, F Katsuoka, S Saito, I Danjoh, I Motoike, R Yamashita, S Koshiba, D Saigusa, G Tamiya, S Kure, N Yaegashi, Y Kawaguchi, F Nagami, S Kuriyama, J Sugawara, N Minegishi, A Hozawa, T Takai-Igarashi, K Kinoshita, M Yamamoto.
  • Journal Title: Journal of Human Genetics. Volume: 63 Issue: 2 Pages: 213-230
  • DOI: 10.1038/s10038-017-0347-1
  • Peer Reviewed / Open Access
• [Journal Article] Involvement of chalcone reductase in the soybean isoflavone metabolon: identification of GmCHR5, which interacts with 2-hydroxyisoflavanone synthase (2018)
  • Author(s): Mameda Ryo、Waki Toshiyuki、Kawai Yosuke、Takahashi Seiji、Nakayama Toru
  • Journal Title: The Plant Journal Volume: 96 Issue: 1 Pages: 56-74
  • DOI: 10.1111/tpj.14014
  • Peer Reviewed
• [Journal Article] Strong Association of the HLA-DR/DQ Locus with Childhood Steroid-Sensitive Nephrotic Syndrome in the Japanese Population. (2018)
  • Author(s): Jia X, Horinouchi T, Hitomi Y, Shono A, Khor SS, Omae Y, Kojima K, Kawai Y, Nagasaki M, Kaku Y, Okamoto T, Ohwada Y, Ohta K, Okuda Y, Fujimaru R, Hatae K, Kumagai N, Sawanobori E, Nakazato H, Ohtsuka Y, Nakanishi K, Shima Y, Tanaka R, Ashida A, Kamei K, Ishikura K, Nozu K, Tokunaga K, Iijima K
  • Journal Title: J Am Soc Nephrol. Volume: 29 Issue: 8 Pages: 2189-2199
  • DOI: 10.1681/asn.2017080859
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] 進化遺伝学とがんゲノム解析 (2018)
  • Author(s): 藤本明洋
  • Journal Title: 実験医学 Volume: 増刊号 Pages: 105-109
• [Journal Article] ゲノムシークエンスデータの情報解析 (2018)
  • Author(s): 藤本明洋
  • Journal Title: 生物物理 Volume: 58 Pages: 001-003
  • NAID: 130007378613
• [Journal Article] 肝癌の全ゲノムシークエンス解析 (2018)
  • Author(s): 藤本明洋
  • Journal Title: 医学のあゆみ Volume: 8月4日号 Pages: 399-404
• [Presentation] 古代・現代人ゲノムデータをもとにしたヤポネシアへの人類移住経路の考察 (2021)
  • Author(s): 長田直樹
  • Organizer: 第75回日本人類学会
  • Invited
• [Presentation] 現代・古代人ゲノム情報を用いた日本列島への移住経路と混合様式の推定 (2021)
  • Author(s): 長田直樹
  • Organizer: 日本人類遺伝学会第67回大会
  • Invited
• [Presentation] 現代ヤマト人のゲノムから探るヤポネシア人成立の歴史 (2021)
  • Author(s): 河合洋介
  • Organizer: 日本人類遺伝学会第66回大会/第28回日本遺伝子診療学会大会シンポジウム
  • Invited
• [Presentation] ナショナルセンターバイオバンクネットワークにおける全ゲノムシークエンス解析の取り組み (2021)
  • Author(s): 河合洋介
  • Organizer: 日本人類遺伝学会第66回大会/第28回日本遺伝子診療学会大会シンポジウム
• [Presentation] ロングリードをもちいたゲノム構造解析 (2021)
  • Author(s): 藤本明洋
  • Organizer: 日本人類遺伝学会第66回大会/第28回日本遺伝子診療学会大会シンポジウム
  • Invited
• [Presentation] Comprehensive analysis of microsatellites polymorphism in the human population (2021)
  • Author(s): 郷地麗央、河合洋介、嶋多美穂子、藤本明洋
  • Organizer: 日本人類遺伝学会第66回大会/第28回日本遺伝子診療学会大会シンポジウム
• [Presentation] Development of a haplotype-resolved local assembly tool with nanopore data (2021)
  • Author(s): 池本滉、藤本明洋
  • Organizer: 日本人類遺伝学会第66回大会/第28回日本遺伝子診療学会大会シンポジウム
• [Presentation] The investigation of the sign of selection on genes associated with dyslexia of Chinese characters. (2021)
  • Author(s): Nishiyama, K., Satta, Y. & Gojobori, J.
  • Organizer: Cultural Evolution Society Conference
  • Int'l Joint Research
• [Presentation] 漢字の識字障害関連遺伝子群に対する自然選択の検定 (2021)
  • Author(s): 西山久美子, 颯田葉子, 五條堀淳
  • Organizer: 第75回 日本人類学会大会
• [Presentation] ヒト東アジア集団において識字障害関連遺伝子DCDC2上に見られる自然選択の痕跡について (2021)
  • Author(s): 西山久美子, 颯田葉子, 五條堀淳
  • Organizer: 日本進化学会第23回東京大会
• [Presentation] PCA-UMAPを用いた現代および古代東アジア人の集団構造解析 (2021)
  • Author(s): 久保俊平, 遠藤俊徳, 長田直樹
  • Organizer: 第23回日本進化学会大会
• [Presentation] 全ゲノム配列データを用いたユーラシア産ハツカネズミMus musculusの系統解析 (2021)
  • Author(s): 藤原一道, 河合洋介, 森脇和郎, 高田豊行, 城石俊彦, 斎藤成也, 鈴木仁, 長田直樹
  • Organizer: 第23回日本進化学会大会
• [Presentation] Whole genome sequencing with long-reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer (2021)
  • Author(s): 藤本明洋
  • Organizer: Genome Concept Centennial Conference
  • Int'l Joint Research / Invited
• [Presentation] Genome-wide genetic diversity of wild house mice across Eurasia (2021)
  • Author(s): 長田直樹
  • Organizer: Genome Concept Centennial Conference
  • Int'l Joint Research / Invited
• [Presentation] マカク属7種のゲノム解析による進化モデルの構築 (2020)
  • Author(s): 長田直樹，松平一成，濱田穣，Malaivijitnond Suchinda
  • Organizer: 第36回日本霊長類学会
• [Presentation] ゲノム配列データからヤポネシア人の起源について考える (2020)
  • Author(s): 長田直樹
  • Organizer: 第22回日本進化学会オンライン大会
• [Presentation] 長鎖シークエンス技術を用いた構造多型／変異の検出とそれらの起源の推定 (2020)
  • Author(s): 藤本明洋
  • Organizer: 日本人類学会
  • Invited
• [Presentation] Whole genome sequencing with long-reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer (2020)
  • Author(s): 藤本明洋
  • Organizer: 日本人類遺伝学会
  • Invited
• [Presentation] Rare allele sharing in Yaponesians and its surrounding populations (2020)
  • Author(s): 五條堀淳
  • Organizer: 第22回日本進化学会オンライン大会
  • Invited
• [Presentation] Demographic inference of human population from haplotype sharing information. The 2019 SMBE conference (2019)
  • Author(s): Yosuke Kawai
  • Organizer: SMBE 2019
  • Int'l Joint Research
• [Presentation] Analysis of Mutations and Protein Stability on Human Mitochondrial DNA Haplogroups (2019)
  • Author(s): Kazumichi Fujiwara, Toshinori Endo, Naoki Osada
  • Organizer: SMBE 2019
  • Int'l Joint Research
• [Presentation] ハプロタイプ共有長の分布から推定する東アジア人の集団史 (2019)
  • Author(s): 河合洋介
  • Organizer: 日本進化学会第21回大会
  • Invited
• [Presentation] Identification of structural variations and analysis of their functional roles (2019)
  • Author(s): 藤本明洋
  • Organizer: 日本進化学会第21回大会
  • Invited
• [Presentation] Genetic diversity of wild house mice (Mus musculus) using whole-genome sequences of multiple samples (2019)
  • Author(s): 藤原一道，長田直樹，鈴木仁
  • Organizer: 日本進化学会第21回大会
  • Invited
• [Presentation] The negative selection pressure on autosomal recessive congenital ichthoyosis is weaker in African population (2019)
  • Author(s): 東野俊英，長田直樹
  • Organizer: 日本進化学会第21回大会
• [Presentation] Temporal change of protein stability in human mitochondria during out-of-Africa migration (2019)
  • Author(s): 藤原一道，里村和浩，遠藤俊徳，長田直樹
  • Organizer: 日本進化学会第21回大会
• [Presentation] Identification of structural variations and analysis of their functional roles (2019)
  • Author(s): 藤本明洋
  • Organizer: 日本癌学会
  • Invited
• [Presentation] 長鎖シークエンス技術を用いた癌の全ゲノムシークエンス (2019)
  • Author(s): 藤本明洋
  • Organizer: 日本人類遺伝学会
• [Presentation] Population Genetics (2019)
  • Author(s): Akihiro Fujimoto
  • Organizer: InCoB
  • Int'l Joint Research / Invited
• [Presentation] Identification of structural variations and analysis of their functional roles (2019)
  • Author(s): Akihiro Fujimoto
  • Organizer: InCoB
  • Int'l Joint Research / Invited
• [Presentation] ミトコンドリア塩基配列から推定された日本人集団特異的な有効集団サイズの増加 (2019)
  • Author(s): 五條堀 淳，日笠 幸一郎，松田 文彦，石谷 孔司，水野 文月，熊谷 真彦，植田 信太郎
  • Organizer: 第73回日本人類学会大会
• [Presentation] ハツカネズミ（Mus musculus）亜種を用いた全ゲノム集団解析ハツカネズミ（Mus musculus）亜種を用いた全ゲノム集団解析 (2019)
  • Author(s): 藤原一道，河合洋介，斎藤成也，長田直樹，鈴木仁
  • Organizer: 第91回日本遺伝学会
• [Presentation] 構造異常／構造多型の検出と機能的意義の解析 (2019)
  • Author(s): 藤本明洋
  • Organizer: ナノポア現場の会
  • Invited
• [Presentation] 情報解析と人類遺伝学 (2019)
  • Author(s): 藤本明洋
  • Organizer: 遺伝統計学・夏の学校
  • Invited
• [Presentation] がんゲノム配列決定と今後の課題 -B型・C型肝炎に由来する肝癌の全ゲノム配列解析を例に- (2019)
  • Author(s): 藤本明洋
  • Organizer: 京大小児科血液腫瘍研究会
  • Invited
• [Presentation] 「港川人骨のミトコンドリア DNA 全塩基配列からわかること」 (2019)
  • Author(s): 五條堀淳，水野文月
  • Organizer: 日本学術会議シンポジウム「日本旧石器人研究の発展:沖縄の現場から」
  • Invited
• [Presentation] ヒトゲノムの多様性をどのように解析するのか (2019)
  • Author(s): 長田直樹
  • Organizer: BI人材育成講座
  • Invited
• [Presentation] ソフトウェア講習 (2019)
  • Author(s): 長田直樹
  • Organizer: 第3回木村資生記念進化学セミナー
  • Invited
• [Presentation] Big data in biology: perspectives of genomic diversity studies (2019)
  • Author(s): Naoki Osada
  • Organizer: Winter International Symposium on Big-Data, Cybersecurity and IoT
  • Int'l Joint Research / Invited
• [Presentation] 性による移住率の偏りをゲノムデータから推定する (2018)
  • Author(s): 長田直樹
  • Organizer: 第72回日本人類学会大会
  • Invited
• [Presentation] ミトコンドリアDNAハプログループに注目した，ヒトミトコンドリアタンパク質複合体IVにおける突然変異とタンパク質構造安定性に関する研究 (2018)
  • Author(s): 藤原一道，遠藤俊徳，長田直樹
  • Organizer: 第72回日本人類学会大会
• [Presentation] ミトコンドリアタンパク質複合体IVでの突然変異とそのタンパク質の構造安定性が与える影響について (2018)
  • Author(s): 藤原一道，遠藤俊徳，長田直樹
  • Organizer: 第90回日本遺伝学会大会
• [Presentation] 霊長類ミトコンドリア遺伝子における多重置換に対する自然選択 (2018)
  • Author(s): 里村和浩，長田直樹，遠藤俊徳
  • Organizer: 第90回日本遺伝学会大会
• [Presentation] Understanding the relationship among the structural and functional properties of amino acid changes to predict the effect of mutations on human beta globin gene (2018)
  • Author(s): Sangeetha Udani Ratnayake, Toshinori Endo, Naoki Osada
  • Organizer: 第90回日本遺伝学会大会
• [Presentation] Predicting disease causality of mutations in human beta globin gene (2018)
  • Author(s): Sangeetha Udani Ratnayake, Toshinori Endo, Naoki Osada
  • Organizer: SMBE2018
  • Int'l Joint Research
• [Presentation] Hybrid type of nuclear and plastid DNAs suggests the hypothesis for ancient propagation of American bottle gourd (Lagenaria siceraria) (2018)
  • Author(s): Dai Watabe, Hiroshi Yuasa, Naoki Osada, Kazuhiro Satomura, Toshinori endo
  • Organizer: SMBE2018
  • Int'l Joint Research
• [Presentation] Search for the factors related to HCV replication in the HuH-7 cell line lineages (2018)
  • Author(s): Masaki Kawamoto, Toshinori Endo, Masayoshi Fukasawa, Kentaro Hanada, Naoki Osada
  • Organizer: SMBE2018
  • Int'l Joint Research
• [Presentation] Compensatory back mutations in mitochondrial genome of primates (2018)
  • Author(s): Kazuhiro Satomura, Naoki Osada, Toshinori Endo
  • Organizer: SMBE2018
  • Int'l Joint Research
• [Presentation] 全ゲノム塩基配列を用いたヤポネシアとその周辺集団の解析 (2018)
  • Author(s): 五條堀淳
  • Organizer: 第72回日本人類学会大会
• [Presentation] Genome-wide genetic variation of people in Japan and its implication of demographic history (2018)
  • Author(s): Kawai Y, Mimori T, Hitomi Y, Khor SS, Gervais O, Nagasaki M and Tokunaga K
  • Organizer: SMBE2018
  • Int'l Joint Research
• [Presentation] Comprehensive Analysis of Indels in Whole-genome Microsatellite Regions and Microsatellite Instability across 21 Cancer Types (2018)
  • Author(s): 藤本明洋
  • Organizer: アメリカ人類遺伝学会
  • Int'l Joint Research
• [Presentation] Identification of structural variations and analysis of their functional roles (2018)
  • Author(s): 藤本明洋
  • Organizer: 日本分子生物学会
  • Invited
• [Presentation] ヒトのゲノム配列の解析と今後の課題；ゲノム解析の基礎、がんゲノム.研究、リキッドバイオプシーの個別化医療への応用 (2018)
  • Author(s): 藤本明洋
  • Organizer: 薬物動態談話会
  • Invited
• [Presentation] ヒト肝癌のゲノム異常の包括的解析と今後の課題 (2018)
  • Author(s): 藤本明洋
  • Organizer: 関西肝癌局所療法研究会
  • Invited
• [Book] 遺伝学の百科事典 (2022)
  • Author(s): 日本遺伝学会（編）
  • Total Pages: 690
  • Publisher: 丸善出版
  • ISBN: 9784621306604
• [Book] ヒトの分子遺伝学 (2021)
  • Author(s): 戸田 達史、井上 聡、松本 直通（編）
  • Total Pages: 904
  • Publisher: メディカル・サイエンス・インターナショナル
  • ISBN: 9784815730321
• [Book] ヒトゲノム事典 (2021)
  • Author(s): 井ノ上 逸朗, 今西 規, 河村 正二, 斎藤 成也, 颯田 葉子, 田嶋 敦（編）
  • Total Pages: 448
  • Publisher: 一色出版
  • ISBN: 9784910389127
• [Book] Evolution of the Human Genome II: Human Evolution Viewed from Genomes (Evolutionary Studies) (2021)
  • Author(s): Naruya Saitou (ed)
  • Total Pages: 268
  • Publisher: Springer
  • ISBN: 9784431569022
• [Book] 最新DNA研究が解き明かす。日本人の誕生 (2020)
  • Author(s): 斎藤成也、木村亮介、鈴木留美子、河合洋介、松波雅俊
  • Total Pages: 240
  • Publisher: 秀和システム
  • ISBN: 9784798060224
• [Book] 進化で読み解く バイオインフォマティクス入門 (2019)
  • Author(s): 長田 直樹
  • Total Pages: 232
  • Publisher: 森北出版
  • ISBN: 9784627261419
• [Remarks] ヤポネシアゲノム
  • URL: http://www.yaponesian.jp/
• [Funded Workshop] New development of human genome diversity studies (2019)