Establishment to differentiate an estimateing method using genome-wide repeat sequences between Japanese and human populations near Japan

• Project/Area Number: 17H04148
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Legal medicine
• Research Institution: Nagoya University
• Principal Investigator: Yamamoto Toshimichi 名古屋大学, 医学系研究科, 准教授 (50260592)
• Project Period (FY): 2017-04-01 – 2022-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥16,120,000 (Direct Cost: ¥12,400,000、Indirect Cost: ¥3,720,000); Fiscal Year 2021: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2020: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2019: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2018: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2017: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
• Keywords: 反復配列 / Alu配列 / Short tandem repeats / 日本人 / 韓族 / 漢中国人 / 識別法 / 漢民族 / Short Tandem Repeats

Outline of Final Research Achievements

Regarding Alu elements, a novel method to apply to search unknown them in human genome was established. However, it was proved difficult to make genome DNA appropriate size of fragmentation. Therefore, using the data of the Alu element positions obtained from whole genome sequence data in about 400 Japanese and 90 Korean, those with different between both populations and with more than 20 % of the frequencies in each population were extracted and evaluated. As a result, it was suggested that there were not so much Alu-Y subtypes as more descendant.
Alternatively, regarding STRs, we performed some population genetical analyses using the genotype data for 261 autosomal STRs from each 32 Japanese and Han-Chinese. Then, it was suggested it would be possible to differentiate statistically between both populations if we could select each a locus, which has high personal discriminating power and power of the differentiation between both populations. on each arm of each autosomal chromosome.

Academic Significance and Societal Importance of the Research Achievements

反復配列を利用した近縁ヒト集団の遺伝的区別（生物地理学的祖先系の推定）を目的として行った。その結果、日本人と韓国人をAlu配列により区別することは難しいことが判明したことの学術的意義は高い。
一方、日本人と漢中国人における261座位のSTRsの遺伝型データの統計・集団遺伝学的解析では、ほぼ常染色体の短腕・長腕に各1座位に相当する計44座位で、個人及び集団間でも識別力のあるSTRs座位により、その識別は可能であることが示唆されたことの学術的意義は高い。また、そのような約45座位による、２つの判定システムを構築すれば、その祖先推定の可能性が得られたことの社会的意義は非常に大きいと考えられる。

Research Products

• [Journal Article] Comparisons between Japanese and Han Chinese populations for 261 autosomal STR loci (2022)
  • Author(s): Toshimichi Yamamoto, Kentaro Doi, Ryutaro Fukami, Takashi Yoshimoto, Yujin Natori, Akira Ishii
  • Journal Title: Forensic Science International: Genetics Supplement Series Volume: 8 Pages: 117-119
  • DOI: 10.1016/j.fsigss.2022.10.003
  • Peer Reviewed
• [Journal Article] Next-generation genome sequencing of a matched normal-tumor pair from a patient with intractable gestational choriocarcinoma: A case report (2021)
  • Author(s): Niimi Kaoru, Yamamoto Eiko, Morita Sachi, Morikawa Maki, Hattori Hikaru, Hatakeyama Miki, Morita Mami, Nishino Kimihiro, Oda Yukari, Watanabe Eri, Yamamoto Toshimichi, Kajiyama Hiroaki, Kikkawa Fumitaka
  • Journal Title: Molecular and Clinical Oncology Volume: 15 Issue: 1 Pages: 143-143
  • DOI: 10.3892/mco.2021.2305
  • Peer Reviewed / Open Access
• [Journal Article] Short tandem repeat analysis to identify the causative pregnancy of high-risk gestational trophoblastic neoplasia: Molar versus nonmolar pregnancy and its relation to the outcome (2021)
  • Author(s): Nishino Kimihiro, Yamamoto Eiko, Oda Yukari, Watanabe Eri, Niimi Kaoru, Yamamoto Toshimichi, Kajiyama Hiroaki
  • Journal Title: Placenta Volume: 112 Pages: 28-35
  • DOI: 10.1016/j.placenta.2021.06.015
  • Peer Reviewed / Open Access
• [Journal Article] 日本人の全ゲノム塩基配列データからin silicoで得られたAlu配列挿入箇所の評価 (2020)
  • Author(s): 佐藤 史織，李 知娟，佐野 開人，吉本 高士，石井 晃，河合 洋介，徳永 勝士，山本敏充
  • Journal Title: DNA多型 Volume: 28 Pages: 125-128
• [Journal Article] Bayesian approach to discriminant problems for count data with application to multilocus short tandem repeat dataset (2020)
  • Author(s): Koji Tsukuda, Shuhei Mano, Toshimichi Yamamoto
  • Journal Title: Statistical Applications in Genetics and Molecular Biology Volume: - Issue: 2
  • DOI: 10.1515/sagmb-2018-0044
  • Peer Reviewed
• [Journal Article] エルサルバドルにおける17座位のY-STRs及びY-hgsの法科学的及び集団遺伝学的解析 (2019)
  • Author(s): 荒川智哉，吉本高士，佐藤史織，石井晃，山本敏充
  • Journal Title: DNA多型 Volume: 27 Pages: 177-180
• [Journal Article] Japaneseplex: A forensic SNP assay for identification of Japanese people using Japanese-specific alleles (2018)
  • Author(s): Isao Yuasa, Atsushi Akane, Toshimichi Yamamoto, Aya Matsusue, Minoru Endoh, Mayumi Nakagawa, Kazuo Umetsu, Takaki Ishikawa, Morio Iino
  • Journal Title: Legal Medicine Volume: 33 Pages: 17-22
  • DOI: 10.1016/j.legalmed.2018.04.008
  • Peer Reviewed
• [Journal Article] Analysis of mainland Japanese and Okinawan Japanese populations using the precision ID Ancestry Panel (2018)
  • Author(s): Hiroaki Nakanishi, Vania Pereira, Claus Boslashrsting, Toshimichi Yamamoto, Torben Tvedebrink, Masaaki Hara, Aya Takada, Kazuyuki Saito, Niels Morling
  • Journal Title: Forensic Science International: Genetics Volume: 33 Pages: 106-109
  • DOI: 10.1016/j.fsigen.2017.12.004
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] STR Genotyping from a Dry-Cleaned Skirt in a Sexual Assault Case (2018)
  • Author(s): Hisae Ogawa, Yuuji Hiroshige, Takashi Yoshimoto, Akira Ishii, Toshimichi Yamamoto
  • Journal Title: Journal of Forensic Sciences Volume: 63 Issue: 4 Pages: 1291-1297
  • DOI: 10.1111/1556-4029.13698
  • Peer Reviewed
• [Journal Article] エルサルバドルの少数民族ピピル族における15座位のSTR解析 (2018)
  • Author(s): 山本敏充，柘植雅大，小川久恵，吉本高士，石井晃
  • Journal Title: DNA多型 Volume: 27 Pages: 164-167
• [Journal Article] A human genotyping trial to estimate the post-feeding time from mosquito blood meals (2017)
  • Author(s): Yuuji Hiroshige, Masaaki Hara, Atsushi Nagai, Tomoyuki Hikitsuchi, Mitsuo Umeda, Yumi Kawajiri, Koji Nakayama, Koichi Suzuki, Aya Takada, Akira Ishii, Toshimichi Yamamoto
  • Journal Title: PLoS ONE Volume: 12 Issue: 6 Pages: e0179319-e0179319
  • DOI: 10.1371/journal.pone.0179319
  • Peer Reviewed / Open Access
• [Journal Article] インドネシアにおける15 STRsのアレル頻度分布及び世界中のヒト集団との集団遺伝学的解析 (2017)
  • Author(s): 山本敏充，浅井一，廣重優二，小川久恵，吉本高士，石井晃
  • Journal Title: DNA多型 Volume: 26 Pages: 138-142
• [Journal Article] 吸血した蚊からのY-STR型分析による個人識別 (2017)
  • Author(s): 永井淳，武内康雄，原正昭，髙田綾，廣重優二，小川久恵，石井晃，山本敏充，引土知幸，梅田光夫，川尻由美，中山幸治，鈴木廣一
  • Journal Title: DNA多型 Volume: 26 Pages: 131-134
• [Presentation] 常染色体上の261座位のSTRsデータにおける日本人と中国人の法科学・集団遺伝学的解析 (2023)
  • Author(s): 山本敏充、土井健太郎、吉本高士、名取雄人、石井晃
  • Organizer: 第107次日本法医学会学術全国集会
• [Presentation] Comparisons between Japanese and Han-Chinese populations in terms of 261 autosomal STR loci (2022)
  • Author(s): Toshimichi Yamamoto, Kentaro Doi, Ryutaro Fukami, Takashi Yoshimoto, Yujin Natori, Akira Ishii
  • Organizer: The 29th Congress of the International Society for Forensic Genetics (ISFG 2022)
  • Int'l Joint Research
• [Presentation] Y-STRsハプロタイプから日本人に由来する男性であることを推定した例 (2021)
  • Author(s): 山本敏充，吉本高士，名取雄人，安達登，石井晃
  • Organizer: 第105次日本法医学会学術全国集会
• [Presentation] 吸血した蚊からの吸血後の時間経過推定及びＳＴＲ型分析による個人識別（第２報） (2020)
  • Author(s): 山本敏充，佐藤史織，立元杏平，李知娟，吉本高士，原正昭，永井淳，引土知幸，川尻由美，石井晃
  • Organizer: 第104次日本法医学会学術全国集会
• [Presentation] 唾液斑の付着状況が問題となったDNA再鑑定例 (2020)
  • Author(s): 山本敏充，吉本高士，石井晃
  • Organizer: 第42回日本法医学会学術中部地方会
• [Presentation] Evaluation of Alu insertion positions observed in silico in Japanese whole genome sequencings (2019)
  • Author(s): Toshimichi Yamamoto, Kaito Sano, Ji yeon Lee, Shiori Sato, Takashi Yoshimoto, Akira Ishii, Yosuke Kawai, Katsushi Tokunaga
  • Organizer: International Society of Forensic Genetics (ISFG) 2019
  • Int'l Joint Research
• [Presentation] 日本人の全ゲノム塩基配列データからin silicoで得られたAlu配列挿入箇所の評価 (2019)
  • Author(s): 佐藤史織，李知娟，佐野開人，吉本高士，石井晃，河合洋介，徳永勝士，山本敏充
  • Organizer: 日本ＤＮＡ多型学会第28回学術集会
• [Presentation] Forensic and Population Genetic Analyses for 15 STR Loci among Three Regional Populations of Small Ethnic Group “Pipil” in El Salvador (2018)
  • Author(s): Toshimichi Yamamoto, Masahiro Tsuge, Takashi Yoshimoto, Akira Ishii
  • Organizer: International Society of Forensic Genetics-English Speaking Working Group (ISFG-ESWG) 2018
  • Int'l Joint Research
• [Presentation] エルサルバドルにおける17座位のY-STRs及びY-hgsの法科学的及び集団遺伝学的解析 (2018)
  • Author(s): 荒川智哉，吉本高士，佐藤史織，石井晃，山本敏充
  • Organizer: 日本ＤＮＡ多型学会第27回学術集会
• [Presentation] エルサルバドルの少数民族ピピル族における15座位のSTR解析 (2018)
  • Author(s): 山本敏充，柘植雅大，小川久恵，吉本高士，石井晃
  • Organizer: 日本ＤＮＡ多型学会第26回学術集会
• [Presentation] Ancestry analysis of mainland Japanese and Okinawa Japanese populations using the Precision ID Ancestry Panel (2017)
  • Author(s): Hiroaki Nakanishi, Vania Pereira, Claus Boslashrsting, Toshimichi Yamamoto, Torben Tvedebrink, Masaaki Hara, Aya Takada, Kazuyuki Saito, Niels Morling
  • Organizer: International Society of Forensic Genetics (ISFG) 2017
  • Int'l Joint Research
• [Presentation] A human genotyping trial to estimate the post-feeding time from mosquito blood meals (2017)
  • Author(s): Yuuji Hiroshige, Masaaki Hara, Atsushi Nagai, Tomoyuki Hikitsuchi, Mitsuo Umeda, Yumi Kawajiri, Koji Nakayama, Koichi Suzuki, Aya Takada, Akira Ishii, Toshimichi Yamamoto
  • Organizer: International Society of Forensic Genetics (ISFG) 2017
  • Int'l Joint Research
• [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
  • Total Pages: 448
  • Publisher: 一色出版
  • ISBN: 9784910389127